[Mristudio-users] Using processed data
Mark A. Pinsk
mpinsk at gmail.com
Wed Dec 16 20:02:49 EST 2009
And the original 4D Nifti follow reads as follows, in comparison:
fslinfo data.nii
data_type FLOAT32
dim1 96
dim2 128
dim3 47
dim4 65
datatype 16
pixdim1 1.0000000000
pixdim2 1.0000000000
pixdim3 1.1000000238
pixdim4 1.0000000000
cal_max 3154.5610
cal_min -1285.1160
file_type NIFTI-1+
On Wed, Dec 16, 2009 at 8:00 PM, Mark A. Pinsk <mpinsk at gmail.com> wrote:
> A report of my 4D Analyze header reads as follows. Can anyone spot
> anything strange?
>
> fslinfo data.hdr
>
> data_type
> dim1 96
> dim2 128
> dim3 47
> dim4 65
> datatype 16
> pixdim1 -1.0000000000
> pixdim2 1.0000000000
> pixdim3 1.1000000238
> pixdim4 1.0000000000
> cal_max 3154.5610
> cal_min -1285.1160
> glmax 0
> glmin 0
> origin1 51
> origin2 66
> origin3 9
> file_type ANALYZE-7.5
>
>
>
> On Wed, Dec 16, 2009 at 7:57 PM, Mark A. Pinsk <mpinsk at gmail.com> wrote:
>> 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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