[Mristudio-users] Using processed data

Wed Dec 16 19:43:53 EST 2009

When I read in a 3D ANALYZE file using MRIView3D + Analyze file
format, all of the parameters are grayed out, and they read as
follows.  This reads in the file successfully as far as I can tell.

Image Width: 96
Image Height: 128
Image Slices: 1  ??
Coronal / Ant-Pos
FOV: 96 x 128
Slice thickness: 1.1
Pixel Size: 0 x 0  ??
# of Image-blocks: 1
Word (16 Bits).
Image File Format: Analyze
Image Sequence: in blocks.

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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>>>
>>
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>