[Mristudio-users] Using processed data

Wed Dec 16 19:57:13 EST 2009

Hi Gonzalo,

Yes, I tried that first after your suggestions yesterday:
4D NIFTI to 4D ANALYZE:
fslchfiletype ANALYZE input.nii.gz

And I get the same error about less than expected number of files,
even though it's only one img/hdr pair in that folder.

Somebody else next suggested going to 65 3D Analyze files instead of a
single 4D Analyze file.  That also did not work.

Sorry this is turning out to be so difficult!   I wonder where I went wrong....

On Wed, Dec 16, 2009 at 7:51 PM, Gonzalo Rojas <grojasy at puc.cl> wrote:
> Hi Mark:
>
>  I read your e-mail, but why you convert the 4D NIFTI to 3D NIFTI ?... you
> must convert the 4D NIFTI to 4D ANALYZE... no 3D... you must read the 4D
> ANLYZE in DTI mapping using RAW format, but you must specify coronal as the
> "slice orientation"...
>
>  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 21:39, Mark A. Pinsk escribió:
>>
>> 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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>>>>>
>>>>
>>>
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>