From leiwang1 at northwestern.edu Fri Jan 20 16:24:07 2017 From: leiwang1 at northwestern.edu (Lei Wang) Date: Fri, 20 Jan 2017 21:24:07 +0000 Subject: [Mristudio-users] postdoc position Message-ID: A postdoc position is available immediately in the Neuroimaging and Applied Computational Anatomy Lab, Department of Psychiatry and Behavioral Sciences at the Northwestern University Feinberg School of Medicine. Our laboratory aims to develop multidimensional and multimodal neuroimaging biomarkers using the tools of computational anatomy. Working with collaborators from engineering, mathematics, psychology and clinical specialties, our research is focused on the following major areas: automated pipelines for mapping of brain structures using MRI, development of complex neuroimaging biomarkers, clinical applications in dementia, psychosis, mood disorders and genetics, neuroinformatics, and neuroimaging of animal models. This position is initially limited to two years with the possibility of extension. It will be partially funded by an ongoing NIH study (PI Greg Miller, PhD) of the relationship between socioeconomic status and maturation patterns in the corticolimbic and corticostriatal circuitries of school-age youths. The successful applicant will work primarily on DTI analysis, along with T1, and resting-state fMRI analysis in this and various other clinical populations with a particularly emphasis on multimodal approaches. The position will be integrated closely with the existing collaborative environment. Additionally, supervision of graduate and medical students will be required. Candidates should hold a Ph.D. in neuroscience, psychology, engineering or related fields. A strong publication record and background on structural neuroimaging research should be demonstrated. Experience with fMRI analysis is highly desirable. Applicants should have strong analytical skills and experience with existing tools for large-scale analysis of neuroimaging data (i.e., FreeSurfer, 3D Slicer, SPM, FSL, AFNI, etc.). Proficiency in relevant programming languages (e.g. MATLAB, Python) and statistical analysis (R, SAS, SPSS) is required. Working experience in epidemiological research or large-scale clinical studies is highly desirable. The successful candidate must be capable of working independently and taking initiatives. The candidate is expected to be a team-player with excellent communication and writing skills. Please send a letter of research interest, CV, and names of 3 references to Dr. Lei Wang (leiwang1 at northwestern.edu). Northwestern University is an Equal Opportunity, Affirmative Action Employer of all protected classes, including veterans and individuals with disabilities. Women and minorities are encouraged to apply. Hiring is contingent upon eligibility to work in the United States. --Lei -- Lei Wang, Ph.D. ----------------------------------------------------------------- Northwestern University Feinberg School of Medicine Departments of Psychiatry and Behavioral Sciences and Radiology 710 N. Lake Shore Drive, Abbott Hall 1322 Chicago, IL 60611 Tel. office: 312-503-3983 Fax: 312-503-0527 Email: leiwang1 at northwestern.edu URL: http://niacal.northwestern.edu ----------------------------------------------------------------- [fsm-signature] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 3247 bytes Desc: image001.gif URL: From liup1985 at 126.com Mon Feb 6 21:51:52 2017 From: liup1985 at 126.com (liup1985) Date: Tue, 7 Feb 2017 10:51:52 +0800 (CST) Subject: [Mristudio-users] postdoc position In-Reply-To: References: Message-ID: <7ebec004.2658.15a167c0c3f.Coremail.liup1985@126.com> thank you for your invitation .I'm just a beginner of this technology.And I would like to know can we use DTI Studio to calculate the volume of the optic nerves,especially for the intraobital segment. I would appreciate it if you could give me an answer. At 2017-01-21 05:24:07, "Lei Wang" wrote: A postdoc position is available immediately in the Neuroimaging and Applied Computational Anatomy Lab, Department of Psychiatry and Behavioral Sciences at the Northwestern University Feinberg School of Medicine. Our laboratory aims to develop multidimensional and multimodal neuroimaging biomarkers using the tools of computational anatomy. Working with collaborators from engineering, mathematics, psychology and clinical specialties, our research is focused on the following major areas: automated pipelines for mapping of brain structures using MRI, development of complex neuroimaging biomarkers, clinical applications in dementia, psychosis, mood disorders and genetics, neuroinformatics, and neuroimaging of animal models. This position is initially limited to two years with the possibility of extension. It will be partially funded by an ongoing NIH study (PI Greg Miller, PhD) of the relationship between socioeconomic status and maturation patterns in the corticolimbic and corticostriatal circuitries of school-age youths. The successful applicant will work primarily on DTI analysis, along with T1, and resting-state fMRI analysis in this and various other clinical populations with a particularly emphasis on multimodal approaches. The position will be integrated closely with the existing collaborative environment. Additionally, supervision of graduate and medical students will be required. Candidates should hold a Ph.D. in neuroscience, psychology, engineering or related fields. A strong publication record and background on structural neuroimaging research should be demonstrated. Experience with fMRI analysis is highly desirable. Applicants should have strong analytical skills and experience with existing tools for large-scale analysis of neuroimaging data (i.e., FreeSurfer, 3D Slicer, SPM, FSL, AFNI, etc.). Proficiency in relevant programming languages (e.g. MATLAB, Python) and statistical analysis (R, SAS, SPSS) is required. Working experience in epidemiological research or large-scale clinical studies is highly desirable. The successful candidate must be capable of working independently and taking initiatives. The candidate is expected to be a team-player with excellent communication and writing skills. Please send a letter of research interest, CV, and names of 3 references to Dr. Lei Wang (leiwang1 at northwestern.edu). Northwestern University is an Equal Opportunity, Affirmative Action Employer of all protected classes, including veterans and individuals with disabilities. Women and minorities are encouraged to apply. Hiring is contingent upon eligibility to work in the United States. --Lei -- Lei Wang, Ph.D. ----------------------------------------------------------------- Northwestern UniversityFeinberg School of Medicine Departments of Psychiatry and Behavioral Sciences and Radiology 710 N. Lake Shore Drive, Abbott Hall 1322 Chicago, IL 60611 Tel. office: 312-503-3983 Fax: 312-503-0527 Email: leiwang1 at northwestern.edu URL: http://niacal.northwestern.edu ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 3247 bytes Desc: not available URL: From shaimaa96 at hotmail.com Sun Mar 26 14:05:03 2017 From: shaimaa96 at hotmail.com (Shaimaa Abdelsattar) Date: Sun, 26 Mar 2017 18:05:03 +0000 Subject: [Mristudio-users] Head Motion issue Message-ID: Hello, There are papers in the literature discussing the effect of head motion on DTI analysis as it can induce spurious differences among groups. I would like to ask if this motion is still a concern even after eddy current correction and registration into b0 image using AIR tool in DTI studio for tractography. Thank you in advance Dr.Shaimaa Mohammad, MD Sent from my iPad From mmclane1 at jhmi.edu Mon Mar 27 08:56:54 2017 From: mmclane1 at jhmi.edu (Michael McLane) Date: Mon, 27 Mar 2017 12:56:54 +0000 Subject: [Mristudio-users] MRI - Head Motion issue In-Reply-To: References: Message-ID: <1490619413906.25060@jhmi.edu> FYI - ? ________________________________________ From: mristudio-users on behalf of Shaimaa Abdelsattar Sent: Sunday, March 26, 2017 2:05 PM To: MRI Studio Subject: [Mristudio-users] Head Motion issue Hello, There are papers in the literature discussing the effect of head motion on DTI analysis as it can induce spurious differences among groups. I would like to ask if this motion is still a concern even after eddy current correction and registration into b0 image using AIR tool in DTI studio for tractography. Thank you in advance Dr.Shaimaa Mohammad, MD Sent from my iPad _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org From smoriw at gmail.com Mon Mar 27 10:39:23 2017 From: smoriw at gmail.com (Susumu Mori) Date: Mon, 27 Mar 2017 10:39:23 -0400 Subject: [Mristudio-users] Head Motion issue In-Reply-To: References: Message-ID: Yes, motion always degrades MR images. It's not just DTI, but DTI is one of the most susceptible.If data degrade in the time domain, there is only so much you can do in postprocessing, which is always "after the fact" remedy. 1> Any MR image degrades if the subject moves more than 1 pixel during the scan (I mean "DURING" the scan, not in between the scan). This is a macroscopic motion in the order of 1-2mm or more. It is not a DTI specific issue. During one phase encoding to the next phase encoding, if the subject moved more than 1 voxel, the fourier transform won't work. When we talk about motion-correction for DTI, this type of motion correction is not included. This effect is more severe for 3D T1 scans which usually take 2-5 min for one image, during which the subject could move. For DTI, we consider this effect is much less because we usually use a single-shot EPI, which takes only less than a second. To correct this motion, we need a real-time motion monitoring, which usually involves external motion tracker or extra imaging schemes, but we assume this problem is negligible for DTI. 2> There are true-3D MRI and multi-slice 3D MRI approaches. T1 is usually the former and T2 and DTI are usually the latter. The former suffers more of the #1 problem. The latter has it's own problem; between-slice misalignment within one 3D volume. As I mentioned in #1, one 2D DWI is taken within less than a second. However, to obtain a whole 3D volume with multi-slice acquisitions, I believe it takes 10-15 s. Any macroscopic motion (>1-2mm) during this time period would cause among-2D-slice misalignment within a 3D volume. In DTI motion correction, this type of misalignment is NOT corrected while this problem does happen. To correct this problem, a real-time motion tracker and real-time FOV alignment DURING the data acquisition is needed. And even with such a method, it may be difficult to eliminate the problem completely. There are some technique already presented but the important point is, this problem cannot be corrected after the scan, just like the problem #1. 3> Motion correction between 3D volumes. This is a problem common to all quantitative MRIs that require calculation using multiple 3D MRI data, like DTI, fMRI, quantitative T2 map, etc. What is specific to this group is the mis-alignment among 3D data. Here we assume that each 3D data is free from #1 and #2 problems and therefore each data are not degraded. This is one of the motion corrections we routinely do for DTI and all other quantitative MRI. This method is well established and we can expect the errors are minimized. Of course, this correction can introduce resolution degradation but we usually ignore it. 4> Image distortion correction. There are B0 susceptibility and eddy-current distortion, while the former is common to all EPI-based acquisition (DTI, fMRI, etc) and the latter is specific to DWI. These corrections are approximation at best but they do substantially reduce the error. So, it is a good idea to do it. The degradation by eddy current can especially be bad in old days and the correction schemes helped us a lot. B0 problem does not degrade DTI data because all DWIs and b0 are deformed in the same way, but it can cause some interpretation errors of the data. Morphologic results (like volumes) could be inaccurate without correction, although, we can't expect perfect correction by postprocessing regardless of the method we use because sometimes the degradation occurs in the time domain (can't retrieve in the spatial domain anymore). 5> motion-caused phase error and intensity drop. This is DWI specific. Microscopic motion (like brain pulsation) less than one pixel (<1-2mm) causes signal drop IF it happens during a pair of diffusion-weighting gradients. Because our brains are constantly moving, this is an significant issue. The higher the b-value, more problem we have. Thus, HARDI-type scans with higher b-values suffer more. Once this happens, the only thing we can do is to discard the image or affected pixels. Many DTI postprocessing software has pixel-rejection programs. This is again, an after-the-fact remedy, not a fundamental solution. Even if it works perfectly, we suffer from loss of data points. For example, if we acquire 30 DWIs and 3 of them are badly affected and removed, we loose SNR. For high-b-value scans with poor SNR, I'm not sure how you can reliably detect affected voxels or images. I believe there are some papers discussing about it. So, overall, you can see that the motion problems for DTI (and MRI) are not solved but many software tries to reduce it. As some of the issues are inherent to MRI, which is one of the slowest imaging techniques, we can't dismiss MRI entirely due to its sensitivity to motions. We always need to be careful when we interpret the data, especially when you suspect that the patient group may have more motion-related problems. Otherwise, we would end up in using MRI and sophisticated analysis only to say, "patients moved more." On Sun, Mar 26, 2017 at 2:05 PM, Shaimaa Abdelsattar wrote: > Hello, > There are papers in the literature discussing the effect of head motion on > DTI analysis as it can induce spurious differences among groups. I would > like to ask if this motion is still a concern even after eddy current > correction and registration into b0 image using AIR tool in DTI studio for > tractography. > Thank you in advance > Dr.Shaimaa Mohammad, MD > > Sent from my iPad > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe@ > mristudio.org > -------------- next part -------------- An HTML attachment was scrubbed... URL: From shaimaa96 at hotmail.com Tue Mar 28 09:06:51 2017 From: shaimaa96 at hotmail.com (Shaimaa Abdelsattar) Date: Tue, 28 Mar 2017 13:06:51 +0000 Subject: [Mristudio-users] Head Motion issue In-Reply-To: References: , Message-ID: Thank you very much for your reply, so movement is inevitable problem that can't be completely solved by AIR. Is there a way to know objectively the degree of motion in each dti study, eg. Motion index calculation (may be implemented with AIR), in order to perform group comparison, taking in concideration this motion index Shaimaa Sent from my ASUS -------- Original Message -------- From:Susumu Mori Sent:Mon, 27 Mar 2017 16:48:04 +0200 To:"DTI Studio, ROI Editor, DiffeoMap Questions/Support" Subject:Re: [Mristudio-users] Head Motion issue Yes, motion always degrades MR images. It's not just DTI, but DTI is one of the most susceptible.If data degrade in the time domain, there is only so much you can do in postprocessing, which is always "after the fact" remedy. 1> Any MR image degrades if the subject moves more than 1 pixel during the scan (I mean "DURING" the scan, not in between the scan). This is a macroscopic motion in the order of 1-2mm or more. It is not a DTI specific issue. During one phase encoding to the next phase encoding, if the subject moved more than 1 voxel, the fourier transform won't work. When we talk about motion-correction for DTI, this type of motion correction is not included. This effect is more severe for 3D T1 scans which usually take 2-5 min for one image, during which the subject could move. For DTI, we consider this effect is much less because we usually use a single-shot EPI, which takes only less than a second. To correct this motion, we need a real-time motion monitoring, which usually involves external motion tracker or extra imaging schemes, but we assume this problem is negligible for DTI. 2> There are true-3D MRI and multi-slice 3D MRI approaches. T1 is usually the former and T2 and DTI are usually the latter. The former suffers more of the #1 problem. The latter has it's own problem; between-slice misalignment within one 3D volume. As I mentioned in #1, one 2D DWI is taken within less than a second. However, to obtain a whole 3D volume with multi-slice acquisitions, I believe it takes 10-15 s. Any macroscopic motion (>1-2mm) during this time period would cause among-2D-slice misalignment within a 3D volume. In DTI motion correction, this type of misalignment is NOT corrected while this problem does happen. To correct this problem, a real-time motion tracker and real-time FOV alignment DURING the data acquisition is needed. And even with such a method, it may be difficult to eliminate the problem completely. There are some technique already presented but the important point is, this problem cannot be corrected after the scan, just like the problem #1. 3> Motion correction between 3D volumes. This is a problem common to all quantitative MRIs that require calculation using multiple 3D MRI data, like DTI, fMRI, quantitative T2 map, etc. What is specific to this group is the mis-alignment among 3D data. Here we assume that each 3D data is free from #1 and #2 problems and therefore each data are not degraded. This is one of the motion corrections we routinely do for DTI and all other quantitative MRI. This method is well established and we can expect the errors are minimized. Of course, this correction can introduce resolution degradation but we usually ignore it. 4> Image distortion correction. There are B0 susceptibility and eddy-current distortion, while the former is common to all EPI-based acquisition (DTI, fMRI, etc) and the latter is specific to DWI. These corrections are approximation at best but they do substantially reduce the error. So, it is a good idea to do it. The degradation by eddy current can especially be bad in old days and the correction schemes helped us a lot. B0 problem does not degrade DTI data because all DWIs and b0 are deformed in the same way, but it can cause some interpretation errors of the data. Morphologic results (like volumes) could be inaccurate without correction, although, we can't expect perfect correction by postprocessing regardless of the method we use because sometimes the degradation occurs in the time domain (can't retrieve in the spatial domain anymore). 5> motion-caused phase error and intensity drop. This is DWI specific. Microscopic motion (like brain pulsation) less than one pixel (<1-2mm) causes signal drop IF it happens during a pair of diffusion-weighting gradients. Because our brains are constantly moving, this is an significant issue. The higher the b-value, more problem we have. Thus, HARDI-type scans with higher b-values suffer more. Once this happens, the only thing we can do is to discard the image or affected pixels. Many DTI postprocessing software has pixel-rejection programs. This is again, an after-the-fact remedy, not a fundamental solution. Even if it works perfectly, we suffer from loss of data points. For example, if we acquire 30 DWIs and 3 of them are badly affected and removed, we loose SNR. For high-b-value scans with poor SNR, I'm not sure how you can reliably detect affected voxels or images. I believe there are some papers discussing about it. So, overall, you can see that the motion problems for DTI (and MRI) are not solved but many software tries to reduce it. As some of the issues are inherent to MRI, which is one of the slowest imaging techniques, we can't dismiss MRI entirely due to its sensitivity to motions. We always need to be careful when we interpret the data, especially when you suspect that the patient group may have more motion-related problems. Otherwise, we would end up in using MRI and sophisticated analysis only to say, "patients moved more." On Sun, Mar 26, 2017 at 2:05 PM, Shaimaa Abdelsattar > wrote: Hello, There are papers in the literature discussing the effect of head motion on DTI analysis as it can induce spurious differences among groups. I would like to ask if this motion is still a concern even after eddy current correction and registration into b0 image using AIR tool in DTI studio for tractography. Thank you in advance Dr.Shaimaa Mohammad, MD Sent from my iPad _______________________________________________ mristudio-users mailing list mristudio-users at mristudio.org http://lists.mristudio.org/mailman/listinfo/ Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From susumu at mri.jhu.edu Tue Mar 28 09:40:45 2017 From: susumu at mri.jhu.edu (susumu mori) Date: Tue, 28 Mar 2017 09:40:45 -0400 Subject: [Mristudio-users] Head Motion issue In-Reply-To: References: Message-ID: The short answer is, unfortunately, "difficult" and "you need to rely on your eyeballs", but there are some metrics you can use as a not perfect but somewhat reliable tool. Here is why; 1: As simple as linear co-registration of 3D volumes by AIR or eddy current corrections, in the end of the day, you use your eyeballs to see if it works well or not. You may think, "but there must be a way to monitor the goodness of registration or correction quantitatively." Yes, such metric exists and all registration programs have their own functions to monitor the goodness of registration. Registration algorithms try to maximize their goodness functions while moving and deforming the target images. The goodness function is as simple as subtraction of target and template images and minimizes the subtraction errors. However, we all know that registration algorithms are not perfect and in the end of the day, we use our eyeballs to see if it is working. If we have a good metric that can substitute this eye inspection, or as good as our eyes, we would have used such a function in the registration algorithms to begin with. 2: Having said that, there are several objective metrics you can use to infer the goodness of your data and registration results. First, you can monitor how many voxels you needed to move 3D images to register them. Second, you can monitor the results of the goodness functions. Third, if your software has automated pixel rejection, you can monitor how many pixels were rejected. These metrics are not perfect. For example, there are papers describing how many voxels AIR needed to move images for registration and use the metrics (such as translational and rotational motions) to report the patient motions. This is a good attempt but not perfect because it assumes that AIR (or any registration software) works perfectly, extracting accurate information about the motion. However, in reality, if the subject moved too much, AIR may not work and sometimes it gives up, reporting 0 motion. If the 3D images are corrupted, there is no point of doing cross-3D registration to begin with. If you know these limitations of such metrics, they should give you a good guidance about the quality of the data. In DtiStudio and MRICloud, there is a very comprehensive reports about the metrics mentioned above. As a matter of fact, it may be too comprehensive with a flood of numbers. We tried to create a wrapper software that summarize and visualize the reports, but haven't completed the work. If anybody is interested in pursuing this topic based on the quantitative reporting of DtiStudio/MRICloud, please contact Yue and ask for the wrapper software. I assume that other well-regarded software such as RESTORE also has similar reporting, but I'm not sure. On Tue, Mar 28, 2017 at 9:06 AM, Shaimaa Abdelsattar wrote: > Thank you very much for your reply, so movement is inevitable problem that > can't be completely solved by AIR. > Is there a way to know objectively the degree of motion in each dti study, > eg. Motion index calculation (may be implemented with AIR), in order to > perform group comparison, taking in concideration this motion index > > Shaimaa > > Sent from my ASUS > > -------- Original Message -------- > From:Susumu Mori > Sent:Mon, 27 Mar 2017 16:48:04 +0200 > To:"DTI Studio, ROI Editor, DiffeoMap Questions/Support" > Subject:Re: [Mristudio-users] Head Motion issue > > Yes, motion always degrades MR images. It's not just DTI, but DTI is one > of the most susceptible.If data degrade in the time domain, there is only > so much you can do in postprocessing, which is always "after the fact" > remedy. > > 1> Any MR image degrades if the subject moves more than 1 pixel during the > scan (I mean "DURING" the scan, not in between the scan). This is a > macroscopic motion in the order of 1-2mm or more. It is not a DTI specific > issue. During one phase encoding to the next phase encoding, if the subject > moved more than 1 voxel, the fourier transform won't work. When we talk > about motion-correction for DTI, this type of motion correction is not > included. This effect is more severe for 3D T1 scans which usually take 2-5 > min for one image, during which the subject could move. For DTI, we > consider this effect is much less because we usually use a single-shot EPI, > which takes only less than a second. To correct this motion, we need a > real-time motion monitoring, which usually involves external motion tracker > or extra imaging schemes, but we assume this problem is negligible for DTI. > > 2> There are true-3D MRI and multi-slice 3D MRI approaches. T1 is usually > the former and T2 and DTI are usually the latter. The former suffers more > of the #1 problem. The latter has it's own problem; between-slice > misalignment within one 3D volume. As I mentioned in #1, one 2D DWI is > taken within less than a second. However, to obtain a whole 3D volume with > multi-slice acquisitions, I believe it takes 10-15 s. Any macroscopic > motion (>1-2mm) during this time period would cause among-2D-slice > misalignment within a 3D volume. In DTI motion correction, this type of > misalignment is NOT corrected while this problem does happen. To correct > this problem, a real-time motion tracker and real-time FOV alignment DURING > the data acquisition is needed. And even with such a method, it may be > difficult to eliminate the problem completely. There are some technique > already presented but the important point is, this problem cannot be > corrected after the scan, just like the problem #1. > > 3> Motion correction between 3D volumes. This is a problem common to all > quantitative MRIs that require calculation using multiple 3D MRI data, like > DTI, fMRI, quantitative T2 map, etc. What is specific to this group is the > mis-alignment among 3D data. Here we assume that each 3D data is free from > #1 and #2 problems and therefore each data are not degraded. This is one of > the motion corrections we routinely do for DTI and all other quantitative > MRI. This method is well established and we can expect the errors are > minimized. Of course, this correction can introduce resolution degradation > but we usually ignore it. > > 4> Image distortion correction. There are B0 susceptibility and > eddy-current distortion, while the former is common to all EPI-based > acquisition (DTI, fMRI, etc) and the latter is specific to DWI. These > corrections are approximation at best but they do substantially reduce the > error. So, it is a good idea to do it. The degradation by eddy current can > especially be bad in old days and the correction schemes helped us a lot. > B0 problem does not degrade DTI data because all DWIs and b0 are deformed > in the same way, but it can cause some interpretation errors of the data. > Morphologic results (like volumes) could be inaccurate without correction, > although, we can't expect perfect correction by postprocessing regardless > of the method we use because sometimes the degradation occurs in the time > domain (can't retrieve in the spatial domain anymore). > > 5> motion-caused phase error and intensity drop. This is DWI specific. > Microscopic motion (like brain pulsation) less than one pixel (<1-2mm) > causes signal drop IF it happens during a pair of diffusion-weighting > gradients. Because our brains are constantly moving, this is an significant > issue. The higher the b-value, more problem we have. Thus, HARDI-type scans > with higher b-values suffer more. Once this happens, the only thing we can > do is to discard the image or affected pixels. Many DTI postprocessing > software has pixel-rejection programs. This is again, an after-the-fact > remedy, not a fundamental solution. Even if it works perfectly, we suffer > from loss of data points. For example, if we acquire 30 DWIs and 3 of them > are badly affected and removed, we loose SNR. For high-b-value scans with > poor SNR, I'm not sure how you can reliably detect affected voxels or > images. I believe there are some papers discussing about it. > > So, overall, you can see that the motion problems for DTI (and MRI) are > not solved but many software tries to reduce it. > > As some of the issues are inherent to MRI, which is one of the slowest > imaging techniques, we can't dismiss MRI entirely due to its sensitivity to > motions. We always need to be careful when we interpret the data, > especially when you suspect that the patient group may have more > motion-related problems. Otherwise, we would end up in using MRI and > sophisticated analysis only to say, "patients moved more." > > > > On Sun, Mar 26, 2017 at 2:05 PM, Shaimaa Abdelsattar < > shaimaa96 at hotmail.com> wrote: > >> Hello, >> There are papers in the literature discussing the effect of head motion >> on DTI analysis as it can induce spurious differences among groups. I would >> like to ask if this motion is still a concern even after eddy current >> correction and registration into b0 image using AIR tool in DTI studio for >> tractography. >> Thank you in advance >> Dr.Shaimaa Mohammad, MD >> >> Sent from my iPad >> _______________________________________________ >> mristudio-users mailing list >> mristudio-users at mristudio.org >> http://lists.mristudio.org/mailman/listinfo/ >> Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mr >> istudio.org >> > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe@ > mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From acerniyazi at gmail.com Fri Mar 31 03:11:40 2017 From: acerniyazi at gmail.com (Niyazi Acer) Date: Fri, 31 Mar 2017 10:11:40 +0300 Subject: [Mristudio-users] Mricloud DTI multiatlas segmentation Message-ID: Hello I am MriCloud user and I am happy to use this web site. but I have a question. I sent data for DTI-multiatlas segmentation. But I dont have any result altough it passed two days. I zipped below files and uploaded your web site. 1) b0 image (subjectname_b0.img, subjectname_b0.hdr) 2) Mean diffusion weighted images (subjectname_dwi.img, subjectname_dwi.hdr) 3) Tensor file (subjectname_tensor.dat), Why did I fail? Please Could you give me answer for reason? Best -- Niyazi Acer, phD, email:acerniyazi at gmail.com Erciyes Universitesi Tip Fakultesi Anatomi Anabilim Dali Kayseri, Turkiye -------------- next part -------------- An HTML attachment was scrubbed... URL: From shaimaa96 at hotmail.com Mon May 15 01:29:34 2017 From: shaimaa96 at hotmail.com (Shaimaa Abdelsattar) Date: Mon, 15 May 2017 05:29:34 +0000 Subject: [Mristudio-users] error message Message-ID: Dear experts, this error message appeared after downloading DTI studio and running it for the first time. what does this error message mean? "C:\Users\user\Download\DtiStudio-latest-x64.exe The application has failed to start because its side-by-side configuration is incorrect. Please see the application event log or use the command-line sxstrace.exe tool for more detail. regards Shaimaa -------------- next part -------------- An HTML attachment was scrubbed... URL: From engmohamedelnagar93 at gmail.com Mon May 15 06:33:07 2017 From: engmohamedelnagar93 at gmail.com (Mohamed elnagar) Date: Mon, 15 May 2017 13:33:07 +0300 Subject: [Mristudio-users] error message In-Reply-To: References: Message-ID: Dear Shaimaa, hope i can help, what's your system is x64 or x86? Try installing the latest version of Microsoft visual c++, regards On Mon, May 15, 2017 at 8:29 AM, Shaimaa Abdelsattar wrote: > Dear experts, > > this error message appeared after downloading DTI studio and running it > for the first time. what does this error message mean? > > > "C:\Users\user\Download\DtiStudio-latest-x64.exe > > The application has failed to start because its side-by-side configuration > is incorrect. Please see the application event log or use the command-line > sxstrace.exe tool for more detail. > > > regards > > Shaimaa > > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe@ > mristudio.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From xli16 at jhmi.edu Mon May 15 10:07:48 2017 From: xli16 at jhmi.edu (Xin Li) Date: Mon, 15 May 2017 14:07:48 +0000 Subject: [Mristudio-users] error message In-Reply-To: References: Message-ID: <1494857278767.20034@jhmi.edu> Hi Shaimaa, DTIStudio is the Microsoft Visual Studio application. The Microsoft Visual Studio Redistribution package needs to be installed on the machine before the MRI Studio applications. Please download vcredist_x64.exe at https://www.mristudio.org/wiki/installation and run it before you run DtiStudio. Xin ________________________________ From: mristudio-users on behalf of Shaimaa Abdelsattar Sent: Monday, May 15, 2017 1:29 AM To: MRI Studio Subject: [Mristudio-users] error message Dear experts, this error message appeared after downloading DTI studio and running it for the first time. what does this error message mean? "C:\Users\user\Download\DtiStudio-latest-x64.exe The application has failed to start because its side-by-side configuration is incorrect. Please see the application event log or use the command-line sxstrace.exe tool for more detail. regards Shaimaa -------------- next part -------------- An HTML attachment was scrubbed... URL: From shaimaa96 at hotmail.com Mon May 15 13:53:58 2017 From: shaimaa96 at hotmail.com (Shaimaa Abdelsattar) Date: Mon, 15 May 2017 17:53:58 +0000 Subject: [Mristudio-users] error message In-Reply-To: <1494857278767.20034@jhmi.edu> References: , <1494857278767.20034@jhmi.edu> Message-ID: Thank you very much, it worked -------- Original Message -------- From:Xin Li Sent:Mon, 15 May 2017 16:09:21 +0200 To:"DTI Studio, ROI Editor, DiffeoMap Questions/Support" Subject:Re: [Mristudio-users] error message Hi Shaimaa, DTIStudio is the Microsoft Visual Studio application. The Microsoft Visual Studio Redistribution package needs to be installed on the machine before the MRI Studio applications. Please download vcredist_x64.exe at https://www.mristudio.org/wiki/installation and run it before you run DtiStudio. Xin ________________________________ From: mristudio-users on behalf of Shaimaa Abdelsattar Sent: Monday, May 15, 2017 1:29 AM To: MRI Studio Subject: [Mristudio-users] error message Dear experts, this error message appeared after downloading DTI studio and running it for the first time. what does this error message mean? "C:\Users\user\Download\DtiStudio-latest-x64.exe The application has failed to start because its side-by-side configuration is incorrect. Please see the application event log or use the command-line sxstrace.exe tool for more detail. regards Shaimaa -------------- next part -------------- An HTML attachment was scrubbed... URL: From PLIN at augusta.edu Fri May 19 11:11:51 2017 From: PLIN at augusta.edu (Lin, Ping-Chang) Date: Fri, 19 May 2017 15:11:51 +0000 Subject: [Mristudio-users] [EXTERNAL] [Announcements] MRICloud tutorial on April 10-12 In-Reply-To: <1490624785457.12362@jhmi.edu> References: <1490624785457.12362@jhmi.edu> Message-ID: Dear Xin, I am so excited that you and your colleague built up this MRI analysis platform. Unfortunately, I am not in Baltimore Metro anymore (I have moved south to Georgia one and a half years back) and wouldn?t and won?t be able to attend any tutorial held on Hopkins campus. Is it possible that you can provide any material such as ppt slices or pdf files for the tutorial? I really appreciate your help. Best, Ping-Chang Ping-Chang Lin, Ph.D. Research Scientist 1410 Laney Walker Blvd. CN-3124A Georgia Cancer Center Augusta University Augusta, GA 30912 phone: 706-723-4613 email: plin at augusta.edu From: announcements [mailto:announcements-bounces at mristudio.org] On Behalf Of Xin Li Sent: Monday, March 27, 2017 10:26 AM To: announcements at mristudio.org Subject: [EXTERNAL] [Announcements] MRICloud tutorial on April 10-12 This is an external email. Use caution responding, opening attachments and following links. Hello, We plan to give a MRICloud tutorial from April 10 to 12. MriCloud is our new cloud platform designed for automated image analysis. It has unique features focusing on anatomical segmentation and integration of multiple MRI results. The tutorial is a three-day session including image analysis for T1-based morphology, DTI analysis, rs-fMRI analysis, and ASL analysis. The tentative schedule is; Monday (April 10): 10am-11am: Introduction 11am-12pm: T1 multi-atlas segmentation: theory 12:50pm-13:50pm: Research topic I: Application of Segmentation-based analysis for AD 14pm-15pm: Hands-on: T1-based segmentation procedure step-by-step. Tuesday (April 11): 10am-11am: Hands-on: DTI analysis 11am-12pm: Hands-on: rs-fMRI analysis 13pm-14pm: Hands-on: ASL analysis 14pm-15pm: Research topic II: Integrative analysis of T1, DTI, and rs-fMRI 15pm-16pm: Discussion Wednesday (April 12): 10am-12am: Introduction to R 13pm-14pm: Application of R to MriCloud results:T1-based volumetric analysis 14pm-15pm: Application of R to MriCloud results:Functional connectivity analysis The tutorial will be hosted in Johns Hopkins University School of Medicine. The location is: Room G03 on April 10-11, Room G07 on April 12 Miller Research Building 733 North Broadway, Baltimore, MD 21205 The attachment is the campus map. As usual, the tutorial is free, but you are expected to bring your own laptop and cover all the travel expense by yourself. Please make sure to register yourself at www.mricloud.org. We will provide sample data but you are welcome to bring your own data in DICOM format (not from PACS but from scanners). Please follow the instructions at https://www.mristudio.org/wiki/mricloud to download the sample data and install the softwares. If you would like to attend this tutorial, please send me an email. Xin? -------------- next part -------------- An HTML attachment was scrubbed... URL: From xli16 at jhmi.edu Fri May 19 11:32:33 2017 From: xli16 at jhmi.edu (Xin Li) Date: Fri, 19 May 2017 15:32:33 +0000 Subject: [Mristudio-users] [EXTERNAL] [Announcements] MRICloud tutorial on April 10-12 In-Reply-To: References: <1490624785457.12362@jhmi.edu>, Message-ID: <1495207975989.46229@jhmi.edu> Hi Ping-Chang, The online manual is available at https://braingps.anatomyworks.org/ Xin ________________________________ From: Lin, Ping-Chang Sent: Friday, May 19, 2017 11:11 AM To: Xin Li Cc: DTI Studio, ROI Editor, DiffeoMap Questions/Support Subject: RE: [EXTERNAL] [Announcements] MRICloud tutorial on April 10-12 Dear Xin, I am so excited that you and your colleague built up this MRI analysis platform. Unfortunately, I am not in Baltimore Metro anymore (I have moved south to Georgia one and a half years back) and wouldn't and won't be able to attend any tutorial held on Hopkins campus. Is it possible that you can provide any material such as ppt slices or pdf files for the tutorial? I really appreciate your help. Best, Ping-Chang Ping-Chang Lin, Ph.D. Research Scientist 1410 Laney Walker Blvd. CN-3124A Georgia Cancer Center Augusta University Augusta, GA 30912 phone: 706-723-4613 email: plin at augusta.edu From: announcements [mailto:announcements-bounces at mristudio.org] On Behalf Of Xin Li Sent: Monday, March 27, 2017 10:26 AM To: announcements at mristudio.org Subject: [EXTERNAL] [Announcements] MRICloud tutorial on April 10-12 This is an external email. Use caution responding, opening attachments and following links. Hello, We plan to give a MRICloud tutorial from April 10 to 12. MriCloud is our new cloud platform designed for automated image analysis. It has unique features focusing on anatomical segmentation and integration of multiple MRI results. The tutorial is a three-day session including image analysis for T1-based morphology, DTI analysis, rs-fMRI analysis, and ASL analysis. The tentative schedule is; Monday (April 10): 10am-11am: Introduction 11am-12pm: T1 multi-atlas segmentation: theory 12:50pm-13:50pm: Research topic I: Application of Segmentation-based analysis for AD 14pm-15pm: Hands-on: T1-based segmentation procedure step-by-step. Tuesday (April 11): 10am-11am: Hands-on: DTI analysis 11am-12pm: Hands-on: rs-fMRI analysis 13pm-14pm: Hands-on: ASL analysis 14pm-15pm: Research topic II: Integrative analysis of T1, DTI, and rs-fMRI 15pm-16pm: Discussion Wednesday (April 12): 10am-12am: Introduction to R 13pm-14pm: Application of R to MriCloud results:T1-based volumetric analysis 14pm-15pm: Application of R to MriCloud results:Functional connectivity analysis The tutorial will be hosted in Johns Hopkins University School of Medicine. The location is: Room G03 on April 10-11, Room G07 on April 12 Miller Research Building 733 North Broadway, Baltimore, MD 21205 The attachment is the campus map. As usual, the tutorial is free, but you are expected to bring your own laptop and cover all the travel expense by yourself. Please make sure to register yourself at www.mricloud.org. We will provide sample data but you are welcome to bring your own data in DICOM format (not from PACS but from scanners). Please follow the instructions at https://www.mristudio.org/wiki/mricloud to download the sample data and install the softwares. If you would like to attend this tutorial, please send me an email. Xin? -------------- next part -------------- An HTML attachment was scrubbed... URL: From bakk.hbg at googlemail.com Mon Mar 27 10:13:43 2017 From: bakk.hbg at googlemail.com (Barbara Kreilkamp) Date: Mon, 27 Mar 2017 14:13:43 -0000 Subject: [MRIStudio-users] [Mristudio-users] MRI - Head Motion issue In-Reply-To: <1490619413906.25060@jhmi.edu> References: <1490619413906.25060@jhmi.edu> Message-ID: Dear Dr Mohammad, This paper you are referring to (Yendiki et al. 2013 neuroimage) reports on the methods used to correct for motion and the spurious group differences present even when accounting for motion with special correction tools. If there are differences in motion between groups that you are comparing, then yes, motion can be have confounding effects on your results even if they have been 'corrected'. This is because motion always also means loss of information (e.g. slice dropout etc.) which cannot be easily mitigated. FSL and Freesurfer (Tracula) offer tools to extract motion parameters for individual subjects so you can compare gross motion across groups and account for it in your analysis. It's always a great idea to visually check your unprocessed DTI data as well for any signal loss etc. Best wishes, Barbara On 27/03/2017 14:56, Michael McLane wrote: > FYI - ? > ________________________________________ > From: mristudio-users on behalf of Shaimaa Abdelsattar > Sent: Sunday, March 26, 2017 2:05 PM > To: MRI Studio > Subject: [Mristudio-users] Head Motion issue > > Hello, > There are papers in the literature discussing the effect of head motion on DTI analysis as it can induce spurious differences among groups. I would like to ask if this motion is still a concern even after eddy current correction and registration into b0 image using AIR tool in DTI studio for tractography. > Thank you in advance > Dr.Shaimaa Mohammad, MD > > Sent from my iPad > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org > > _______________________________________________ > mristudio-users mailing list > mristudio-users at mristudio.org > http://lists.mristudio.org/mailman/listinfo/ > Unsubscribe, send a blank email to: mristudio-users-unsubscribe at mristudio.org