I’m trying to write a script (.sh) to preprocess some brain MRI (T1 and FLAIR). First and second steps (convert dicom to nifti and N4bias correction) are done, now I want to segment the T1 image using SPM and the white matter hyperintensities of FLAIR images using the Lesion Segmentation Toolbox (LPA) also from SPM, but I don’t know how to do it from the terminal (in other words, how to add this step to my script).
Also, because I have several images in the same folder, the script needs to match just the T1 and FLAIR images I want to segment for every subject
My folders look like:
So, the match would be something like
folder/*/preprocessing/*T1.nii ffor the T1 images and
folder/*/preprocessing/*FLAIR.nii for FLAIR images
I hope you can help me.
SPM person, so my response might not be the most accurate/helpful.
However, IIRC you can call
matlab and thus
SPM functions via
.sh scripts. I think there might be different options to do that:
- you create a
matlab script/function that runs the commands you want (for an example check this section of Andy Jahn’s great “Brain Book”) and call that via the
matlab -nodesktop -nosplash -r "segment_T1_FLAIR"
- call each
spm script/function via the
matlab -nodesktop -nosplash -r "function1(argument1,argument2);exit"
matlab -nodesktop -nosplash -r "function2(argument1);exit"
(check this stackoverflow thread for details)
I guess the precise implementation depends on your
setup (local machine, HPC, etc.) and how you want to define
for-loops et al. . If you’re up for it, you could share a toy version of your script so that folks can provide more precise help (I hope other folks with more experience wrt this will reply as well).
HTH, cheers, Peer
Thank you @PeerHerholz , I’ll have a look at these recommendations. For now I have nothing in matlab, the first two steps were done with MRtrix. I’ll try a first attempt and see what can I do (I’m a beginner so this have been a bit difficult but exciting hehe). Thanks again.