[Mristudio-users] Using processed data

Mark A. Pinsk mpinsk at gmail.com
Wed Dec 16 20:00:13 EST 2009 

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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