<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Hi Mark,<br><br>You can load the 4D analyze file in 3D viewer and then save it in raw file format. Then you can load the raw file in DTI mapping.<br><br>Jun Yi Wang<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mark A. Pinsk <mpinsk@gmail.com><br><b><span style="font-weight: bold;">To:</span></b> "DTI Studio, ROI Editor, Landmarker Questions/Support" <mristudio-users@mristudio.org><br><b><span style="font-weight: bold;">Sent:</span></b> Wed, December 16, 2009 4:43:53 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [Mristudio-users] Using processed
data<br></font><br>
When I read in a 3D ANALYZE file using MRIView3D + Analyze file<br>format, all of the parameters are grayed out, and they read as<br>follows. This reads in the file successfully as far as I can tell.<br><br>Image Width: 96<br>Image Height: 128<br>Image Slices: 1 ??<br>Coronal / Ant-Pos<br>FOV: 96 x 128<br>Slice thickness: 1.1<br>Pixel Size: 0 x 0 ??<br># of Image-blocks: 1<br>Word (16 Bits).<br>Image File Format: Analyze<br>Image Sequence: in blocks.<br><br><br>On Wed, Dec 16, 2009 at 7:39 PM, Mark A. Pinsk <<a ymailto="mailto:mpinsk@gmail.com" href="mailto:mpinsk@gmail.com">mpinsk@gmail.com</a>> wrote:<br>> No luck. Let me outline my steps here:<br>><br>> 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0).<br>> The image dimensions are 96x128, 47 slices per volume.<br>> Slice orientation is Coronal. FOV is 96x128. Pixels are 1x1x1.1.<br>><br>> 2. I split the 4D NIFTI
file into 65 3D NIFTI files using this FSL command:<br>> fslsplit input.nii.gz<br>><br>> 3. I convert each of the 65 3D NIFTI files to ANALYZE format:<br>> fslchfiletype ANALYZE vol0000.nii.gz<br>> [..]<br>> fslchfiletype ANALYZE vol0064.nii.gz<br>><br>> 4. I am able to successfully import the ANALYZE files in MRIView3D by<br>> choosing Analyze format (but no luck with Raw format).<br>><br>> 5. I have no luck importing the ANALYZE files in DTI Mapping choosing<br>> Raw format. I get this message:<br>> "Number of files in this fold is less than expected: (Img_Slices*Img_Blocks).<br>><br>> Any suggestions? Thanks for all your help!<br>> Mark<br>><br>><br>><br>><br>> On Wed, Dec 16, 2009 at 1:34 PM, darshan pai <<a ymailto="mailto:darshanp20@yahoo.com" href="mailto:darshanp20@yahoo.com">darshanp20@yahoo.com</a>> wrote:<br>>> when you say a 4D file I assume that you have
a Analyze file with an entry on the number of volumes , Is it? . If it is then try to make it a 3D file with all the 65 slices added in the z direction and see if it helps..<br>>><br>>> Regards<br>>><br>>> Dp<br>>><br>>><br>>><br>>> ----- Original Message ----<br>>> From: Mark A. Pinsk <<a ymailto="mailto:mpinsk@gmail.com" href="mailto:mpinsk@gmail.com">mpinsk@gmail.com</a>><br>>> To: "DTI Studio, ROI Editor, Landmarker Questions/Support" <<a ymailto="mailto:mristudio-users@mristudio.org" href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a>><br>>> Sent: Wed, December 16, 2009 12:13:42 AM<br>>> Subject: Re: [Mristudio-users] Using processed data<br>>><br>>> Also, I should mention that the Analyze file loads just fine using<br>>> "MRI View3D" and "Analyze" file format.<br>>><br>>><br>>> On Wed, Dec 16, 2009 at
12:09 AM, Mark A. Pinsk <<a ymailto="mailto:mpinsk@gmail.com" href="mailto:mpinsk@gmail.com">mpinsk@gmail.com</a>> wrote:<br>>>> Thanks for your help, I'll do my best to answer them...<br>>>><br>>>> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm resolution):<br>>>><br>>>> Image Dimensions: 96 Width, 128 Height, 47 slices<br>>>> Slice Orientation: Axial<br>>>> Slice Sequencing: Inferior-Superior<br>>>> FOV: 96 Width, 128 Height, 1.1 Slice Thickness<br>>>> Pixel Size: 1.000 Width, 1.000 Height<br>>>> Slices to be processed: 0 to 46, All Slices<br>>>> Image Sequence: Gradient By Gradient<br>>>> b_Value: 1000<br>>>><br>>>> My gradient table has 65 entries. The first 5 entries are B0 images,<br>>>> the remaining 60 are for the 60 directions. There is no mean image at<br>>>> the end
of my data. I can discard 4 of the B0 images, but that does<br>>>> not seem to make a difference on my error message. I have several B0<br>>>> images in accord with recent work that suggests having a ratio of 6:1<br>>>> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage<br>>>> 2008).<br>>>><br>>>><br>>>><br>>>> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas <<a ymailto="mailto:grojasy@puc.cl" href="mailto:grojasy@puc.cl">grojasy@puc.cl</a>> wrote:<br>>>>> Hi Mark:<br>>>>><br>>>>> Many questions:<br>>>>><br>>>>> i) do you specify correctly the "image slices" quantity in "iamge dimension"<br>>>>> ?... that value is the quantitry of axial slices in each gradient<br>>>>> direction...<br>>>>><br>>>>> ii) and the "image width" and "image
height" in "image dimension" ?... did<br>>>>> you checked that values ?...<br>>>>><br>>>>> ii) in "lice orientation" did you specify "axial" ?..<br>>>>><br>>>>> iii) and in "Voxel Size", "Field of View-width" and "Field of View-Heigth"<br>>>>> did you specifiy the FOV value correctly ?...<br>>>>><br>>>>> iv) you could check the previos values looking at "Pixel Size-Width" and<br>>>>> "Pixel Size-Height"...<br>>>>><br>>>>> v) in "Slices to be processed" it must appears 0-(image slices-1)<br>>>>><br>>>>> vi) in gradient table you must put the 61 (0-60) directions... in your 4D<br>>>>> analyze file is included the "mean" of all the 60 directions at the end of<br>>>>> the file ?... if it is, you must put "100,100,100" as the last gradient<br>>>>> direction to skip that
image in the computation...<br>>>>><br>>>>> vii) in "Image secuence" you must select "Gradient by Gradient" option...<br>>>>><br>>>>> viii) in "Raw-BIN Files folder you must specify the IMG file of the Analyze<br>>>>> pair...<br>>>>><br>>>>> ix) why you have 5 b0 volumes ?... to compute tractography, you must have<br>>>>> only one b0 volume... you must put "100,100,100" in "Gradient Table" for<br>>>>> each of the 4 b0 slices to skipt them...<br>>>>><br>>>>> Sincerely,<br>>>>><br>>>>><br>>>>> Gonzalo Rojas Costa<br>>>>> Department of Radiology<br>>>>> Las Condes Clinic<br>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile.<br>>>>> Tel: 56-2-2105170<br>>>>> Cel: 56-9-97771785<br>>>>> <a target="_blank"
href="http://www.clc.cl">www.clc.cl</a><br>>>>><br>>>>> El 16-12-2009 1:07, Mark A. Pinsk escribió:<br>>>>>><br>>>>>> Thanks !<br>>>>>><br>>>>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested.<br>>>>>><br>>>>>> I attempt to read it in as RAW, but it seems to get stuck...<br>>>>>><br>>>>>> I specify the file in the Raw-BIN Files Folder field, but I get this<br>>>>>> message:<br>>>>>> "Number of files in this fold is less than expected:<br>>>>>> (Img_Slices*Img_Blocks)."<br>>>>>><br>>>>>> I only have a single .img/.hdr pair in my folder since it is a 4D file<br>>>>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)).<br>>>>>><br>>>>>> Sorry, any help would be
greatly appreciated.<br>>>>>> Thanks<br>>>>>> Mark<br>>>>>><br>>>>>><br>>>>>><br>>>>>><br>>>>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas<<a ymailto="mailto:grojasy@puc.cl" href="mailto:grojasy@puc.cl">grojasy@puc.cl</a>> wrote:<br>>>>>>><br>>>>>>> Hi Mark:<br>>>>>>><br>>>>>>> Yes... you could do all the processing that you mentioned (in FSL), and<br>>>>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... you<br>>>>>>> must<br>>>>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file as<br>>>>>>> a<br>>>>>>> RAW data file format in DTI-STUDIO...<br>>>>>>><br>>>>>>>
Sincerely,<br>>>>>>><br>>>>>>><br>>>>>>> Gonzalo Rojas Costa<br>>>>>>> Department of Radiology<br>>>>>>> Las Condes Clinic<br>>>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile.<br>>>>>>> Tel: 56-2-2105170<br>>>>>>> Cel: 56-9-97771785<br><span>>>>>>> <a target="_blank" href="http://www.clc.cl">www.clc.cl</a></span><br>>>>>>><br>>>>>>> El 15-12-2009 23:37, Mark A. Pinsk escribió:<br>>>>>>>><br>>>>>>>> Hi, someone asked this a while ago in the archives but I didn't see a<br>>>>>>>> reply. Can I use data that I've processed in FSL (eddy current<br>>>>>>>> correction, motion correction, and field map-based undistortion) and<br>>>>>>>> bring it
into dti-studio? The data is in one large 4D nifti file. I<br>>>>>>>> don't see where I can do this, is it not possible?<br>>>>>>>><br>>>>>>>> thanks<br>>>>>>>> mark<br>>>>>>>> _______________________________________________<br>>>>>>>> Mristudio-users mailing list<br>>>>>>>> <a ymailto="mailto:Mristudio-users@mristudio.org" href="mailto:Mristudio-users@mristudio.org">Mristudio-users@mristudio.org</a><br><span>>>>>>>> <a target="_blank" href="http://lists.mristudio.org/mailman/listinfo/">http://lists.mristudio.org/mailman/listinfo/</a></span><br>>>>>>>> Unsubscribe, send a blank email to:<br>>>>>>>> <a ymailto="mailto:Mristudio-users-unsubscribe@mristudio.org"
href="mailto:Mristudio-users-unsubscribe@mristudio.org">Mristudio-users-unsubscribe@mristudio.org</a><br>>>>>>>><br>>>>>>><br>>>>>><br>>>>>> _______________________________________________<br>>>>>> Mristudio-users mailing list<br>>>>>> <a ymailto="mailto:Mristudio-users@mristudio.org" href="mailto:Mristudio-users@mristudio.org">Mristudio-users@mristudio.org</a><br>>>>>> <a href="http://lists.mristudio.org/mailman/listinfo/" target="_blank">http://lists.mristudio.org/mailman/listinfo/</a><br>>>>>> Unsubscribe, send a blank email to:<br>>>>>> <a ymailto="mailto:Mristudio-users-unsubscribe@mristudio.org" href="mailto:Mristudio-users-unsubscribe@mristudio.org">Mristudio-users-unsubscribe@mristudio.org</a><br>>>>>><br>>>>><br>>>><br>>><br>>>
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