[Mristudio-users] Using processed data

[Mark A. Pinsk]

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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>