[Mristudio-users] Using processed data

[Gonzalo Rojas]

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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