[Mristudio-users] Using processed data

Thu Dec 17 10:13:07 EST 2009

Hi Mark:

   If you want, you could send me the images to test it with 
DTI-Studio... it is better to send me the 4D Nifti, and the DICOM 
original ones...  you could use www.senduit.com...

   Sincerely,

Gonzalo Rojas Costa
Department of Radiology
Las Condes Clinic
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl

El 17-12-2009 0:40, Mark A. Pinsk escribió:
> Still no luck.  In the DTI Mapping parameters window, there is no
> lower left field for the number "65" to appear.  I only see that in
> the MRIView3D parameters window.
>
> I am beginning to wonder if I'm having a more low-level problem?  I'm
> running the latest DTI-Studio 3.0.1 beta x64 on Windows 7 64bit.   I
> also tried DTI-Studio 3.0.1 beta x86.
>
> Anyone interested in having a copy of my 4D Nifti file and seeing if
> they can import it?
>
> thanks
> Mark
>
>
>
> On Wed, Dec 16, 2009 at 8:46 PM, susumu mori<susumu at mri.jhu.edu>  wrote:
>> Hi Mark,
>>
>> Please try Philips REC format. This is a 4D raw format with integer. For
>> both "raw" and "Philips REC", DtiStudio expect you to have 4D raw
>> (no-header) file, not a bunch of 3D files. In your case, you need a single
>> raw file that contains all 65 volume data (65 x 96 x 128 x 47) in one file.
>>
>> For this conversion, you can read 4D Nifty or 4D analyze (depending on the
>> version of DtiStudio) by MriView3D and save all the images at once as a
>> "raw" format. Then, the images are ready for DtiMapping. In DtiMapping, as I
>> mentioned, open it as Philips REC. In the opening window, specify;
>>
>> 96x128x47
>>
>> Then you should get "65" as the number of the 3D images correctly calculated
>> from the file size at the left bottom of the window. Also choose
>> gradient-by-gradient for the order of the file. If you have a correct table
>> with 65 lines, you should not get the error message.
>>
>> If you have the 4D analyze file, the *.img file of the Analyze format can
>> also be directly read as "Philips REC". However, you have to be careful
>> because if the Analyze is in Neurology convention (default setup) and read
>> the *.img as "Philips REC", the images may be inverted because DtiStudio
>> uses Radiology convention.
>>
>> I hope it helps.
>>
>> Susumu
>>
>>
>>
>> On Wed, Dec 16, 2009 at 7:39 PM, Mark A. Pinsk<mpinsk at gmail.com>  wrote:
>>>
>>> No luck.  Let me outline my steps here:
>>>
>>> 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0).
>>> The image dimensions are 96x128, 47 slices per volume.
>>> Slice orientation is Coronal.  FOV is 96x128.  Pixels are 1x1x1.1.
>>>
>>> 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL
>>> command:
>>> fslsplit input.nii.gz
>>>
>>> 3. I convert each of the 65 3D NIFTI files to ANALYZE format:
>>> fslchfiletype ANALYZE vol0000.nii.gz
>>> [..]
>>> fslchfiletype ANALYZE vol0064.nii.gz
>>>
>>> 4. I am able to successfully import the ANALYZE files in MRIView3D by
>>> choosing Analyze format (but no luck with Raw format).
>>>
>>> 5. I have no luck importing the ANALYZE files in DTI Mapping choosing
>>> Raw format.  I get this message:
>>> "Number of files in this fold is less than expected:
>>> (Img_Slices*Img_Blocks).
>>>
>>> Any suggestions?  Thanks for all your help!
>>> Mark
>>>
>>>
>>>
>>>
>>> On Wed, Dec 16, 2009 at 1:34 PM, darshan pai<darshanp20 at yahoo.com>  wrote:
>>>> 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..
>>>>
>>>> Regards
>>>>
>>>> Dp
>>>>
>>>>
>>>>
>>>> ----- Original Message ----
>>>> From: Mark A. Pinsk<mpinsk at gmail.com>
>>>> To: "DTI Studio, ROI Editor, Landmarker Questions/Support"
>>>> <mristudio-users at mristudio.org>
>>>> Sent: Wed, December 16, 2009 12:13:42 AM
>>>> Subject: Re: [Mristudio-users] Using processed data
>>>>
>>>> Also, I should mention that the Analyze file loads just fine using
>>>> "MRI View3D" and "Analyze" file format.
>>>>
>>>>
>>>> On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk<mpinsk at gmail.com>
>>>> wrote:
>>>>> Thanks for your help, I'll do my best to answer them...
>>>>>
>>>>> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm
>>>>> resolution):
>>>>>
>>>>> Image Dimensions: 96 Width, 128 Height, 47 slices
>>>>> Slice Orientation: Axial
>>>>> Slice Sequencing: Inferior-Superior
>>>>> FOV: 96 Width, 128 Height, 1.1 Slice Thickness
>>>>> Pixel Size: 1.000 Width, 1.000 Height
>>>>> Slices to be processed: 0 to 46, All Slices
>>>>> Image Sequence: Gradient By Gradient
>>>>> b_Value: 1000
>>>>>
>>>>> My gradient table has 65 entries.  The first 5 entries are B0 images,
>>>>> the remaining 60 are for the 60 directions.  There is no mean image at
>>>>> the end of my data.   I can discard 4 of the B0 images, but that does
>>>>> not seem to make a difference on my error message.  I have several B0
>>>>> images in accord with recent work that suggests having a ratio of 6:1
>>>>> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage
>>>>> 2008).
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas<grojasy at puc.cl>  wrote:
>>>>>> Hi Mark:
>>>>>>
>>>>>>   Many questions:
>>>>>>
>>>>>> i) do you specify correctly the "image slices" quantity in "iamge
>>>>>> dimension"
>>>>>> ?... that value is the quantitry of axial slices in each gradient
>>>>>> direction...
>>>>>>
>>>>>> ii) and the "image width" and "image height" in "image dimension" ?...
>>>>>> did
>>>>>> you checked that values ?...
>>>>>>
>>>>>> ii) in "lice orientation" did you specify "axial" ?..
>>>>>>
>>>>>> iii) and in "Voxel Size", "Field of View-width" and "Field of
>>>>>> View-Heigth"
>>>>>> did you specifiy the FOV value correctly ?...
>>>>>>
>>>>>> iv) you could check the previos values looking at "Pixel Size-Width"
>>>>>> and
>>>>>> "Pixel Size-Height"...
>>>>>>
>>>>>> v) in "Slices to be processed" it must appears 0-(image slices-1)
>>>>>>
>>>>>> vi) in gradient table you must put the 61 (0-60) directions... in your
>>>>>> 4D
>>>>>> analyze file is included the "mean" of all the 60 directions at the
>>>>>> end of
>>>>>> the file ?... if it is, you must put "100,100,100" as the last
>>>>>> gradient
>>>>>> direction to skip that image in the computation...
>>>>>>
>>>>>> vii) in "Image secuence" you must select "Gradient by Gradient"
>>>>>> option...
>>>>>>
>>>>>> viii) in "Raw-BIN Files folder you must specify the IMG file of the
>>>>>> Analyze
>>>>>> pair...
>>>>>>
>>>>>> ix) why you have 5 b0 volumes ?... to compute tractography, you must
>>>>>> have
>>>>>> only one b0 volume... you must put "100,100,100" in "Gradient Table"
>>>>>> for
>>>>>> each of the 4 b0 slices to skipt them...
>>>>>>
>>>>>>   Sincerely,
>>>>>>
>>>>>>
>>>>>> Gonzalo Rojas Costa
>>>>>> Department of Radiology
>>>>>> Las Condes Clinic
>>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile.
>>>>>> Tel: 56-2-2105170
>>>>>> Cel: 56-9-97771785
>>>>>> www.clc.cl
>>>>>>
>>>>>> El 16-12-2009 1:07, Mark A. Pinsk escribió:
>>>>>>>
>>>>>>> Thanks !
>>>>>>>
>>>>>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested.
>>>>>>>
>>>>>>> I attempt to read it in as RAW, but it seems to get stuck...
>>>>>>>
>>>>>>> I specify the file in the Raw-BIN Files Folder field, but I get this
>>>>>>> message:
>>>>>>> "Number of files in this fold is less than expected:
>>>>>>> (Img_Slices*Img_Blocks)."
>>>>>>>
>>>>>>> I only have a single .img/.hdr pair in my folder since it is a 4D
>>>>>>> file
>>>>>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)).
>>>>>>>
>>>>>>> Sorry, any help would be greatly appreciated.
>>>>>>> Thanks
>>>>>>> Mark
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas<grojasy at puc.cl>
>>>>>>>   wrote:
>>>>>>>>
>>>>>>>> Hi Mark:
>>>>>>>>
>>>>>>>>   Yes... you could do all the processing that you mentioned (in FSL),
>>>>>>>> and
>>>>>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ...
>>>>>>>> you
>>>>>>>> must
>>>>>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D
>>>>>>>> file as
>>>>>>>> a
>>>>>>>> RAW data file format in DTI-STUDIO...
>>>>>>>>
>>>>>>>>   Sincerely,
>>>>>>>>
>>>>>>>>
>>>>>>>> Gonzalo Rojas Costa
>>>>>>>> Department of Radiology
>>>>>>>> Las Condes Clinic
>>>>>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile.
>>>>>>>> Tel: 56-2-2105170
>>>>>>>> Cel: 56-9-97771785
>>>>>>>> www.clc.cl
>>>>>>>>
>>>>>>>> El 15-12-2009 23:37, Mark A. Pinsk escribió:
>>>>>>>>>
>>>>>>>>> Hi, someone asked this a while ago in the archives but I didn't see
>>>>>>>>> a
>>>>>>>>> reply.   Can I use data that I've processed in FSL (eddy current
>>>>>>>>> correction, motion correction, and field map-based undistortion)
>>>>>>>>> and
>>>>>>>>> bring it into dti-studio?   The data is in one large 4D nifti file.
>>>>>>>>>   I
>>>>>>>>> don't see where I can do this, is it not possible?
>>>>>>>>>
>>>>>>>>> thanks
>>>>>>>>> mark
>>>>>>>>> _______________________________________________
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>>>>>>>
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