DWI dimension and atlas dimension

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Catherine Tang

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Sep 7, 2021, 11:16:49 PMSep 7
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Hi Frank,

Just want to do a quick double check - when I ran connectivity analyses, the command line says:
DWI dimension=(78,94,68)
NIFTI dimension=(157,189,136)
nifti loaded as multiple ROI file
looking for region label file
label file loaded:/usr/local/dsistudio/atlas/ICBM152/FreeSurferDKT.txt
NIFTI file has a different dimension from DWI.
loaded NIFTI file used as MNI space image.


I was wondering if I need to resample the atlas to the same dimension as the DWI or does DSI studio automatically take care of it?

Thanks!
Catherine

Frank Yeh

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Sep 8, 2021, 7:04:22 PMSep 8
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Hi Catherine,

    DSI Studio should be able to take care of it for more of the cases, but sometimes it may overkill.

    Whether we need to resample depends on how the images are saved and which reconstruction method you used for DWI. 

    Could you post the entire command line and also the full processing output? 

    I will help to check whether DSI Studio is working as expected.


Best,
Frank

    
 
Best regards,
Frank

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Catherine Tang

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Sep 8, 2021, 7:40:01 PMSep 8
to dsi-s...@googlegroups.com, Frank Yeh

HI Frank,

Thanks for offering to take a look at it! Below are the commands I used and I opted for QSDR for reconstruction.

#convert
dsi_studio --action=src --source=*.nii.gz --bval=bvals.txt --bvec=bvecs.txt --output=/results/19021B

#reconstruction
dsi_studio --action=rec --source=*src.gz --method=7 --param0=1.25 --check_btable=0 --output=/results/19021









#fiber tracking and conn matrix calc
dsi_studio --action=trk --source=*.fib.gz --parameter_id=c9A99193FF3B3513Fb803Fcb2041b4843A08601dcaCDCC4C3Ec --connectivity=/usr/local/dsistudio/atlas/ICBM152/ the atlas nii.gz (i used both freesurferdkt and the schaefer 400 attached in a link).

I also attached the links to the processing results.

Thanks a lot!
Catherine





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Frank Yeh

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Sep 9, 2021, 10:41:21 AMSep 9
to Catherine Tang, dsi-s...@googlegroups.com
All looks good to me.
You don't have to resample the Schaefer 400.
Frank
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