Hello,
I am looking to get a bit of guidance on how to generate a grey matter mask using SSwarper. I have never used this program before but one of my lab mates has used it for some issues she was having with her data. I am attaching the script used below for reference.
I have been reading as much documentation that I can find but as a novice am confused about a few things. First, when you run SSwarper on a subject do I need to input any specific command for it to produce a GM mask in the output? I have looked in my labmates outputs and cant seem to find any file that would correspond to such a thing.
Second, can this mask be used during for a single participants processing to restrict analysis to the GM only? Or is that only done during group analysis?
Finally, can a single mask generated from SSwarper be used for group analysis considering its warped to a specific template or would I still want to average each subjects together to try and create a better fit?
I know these are likely pretty basic questions but I would love to hear what someone has to say and it would help me greatly. Thanks very much.
Austin

#tcsh syntax

setenv OMP_NUM_THREADS 8


echo parameter 1 is $1
set subj = $1 

set indir     = /space/kmsyn03/projects/MGH_alc/Stroop/individual/$subj/Afni
set template  = /space/kmsyn03/projects/MGH_alc/Stroop/individual/$subj/Afni/MNI152_2009_template_SSW.nii.gz
set anat = /space/kmsyn03/projects/MGH_alc/Stroop/individual/$subj/Afni/{$subj}_anat2.nii
set odir = /space/kmsyn03/projects/MGH_alc/Stroop/individual/$subj/Afni/SSwarperTEST
 
    @SSwarper                     \
        -input  ${anat}           \
        -base   ${template}       \
        -subid  ${subj}           \
        -odir   ${odir}		  \

Edited 1 time(s). Last edit at 05/05/2021 09:05AM by ptaylor.