Dear FSL
I am comparing two different groups (ethnically) and each group was scanned on a different 1.5 T scanner (3D T1)
one group has a significantly lower SIENAX brain volume, the only significant difference was in fraction was the Grey matter fraction
As I wanted to investigate which part exactly of grey matter is involved..but neither the cortical fraction (Peripheral grey), and subcortical structures (using FIRST) was significantly different.
Is there a technical error in my analysis here is my script loop:
#MPR.nii.gz is my initial 3D T1 volume
fslreorient2std MPR MPR
robustfov -i MPR -r MPR -m T1_roi2nonroi.mat
fslview MPR
#check your cropping
first_flirt MPR T1_biascorr_to_std_sub
mkdir first_results
run_first_all -i MPR -o first_results/T1_first -a T1_biascorr_to_std_sub.mat
cp -r first_results/T1_first_all_fast_firstseg.nii.gz T1_subcort_seg.nii.gz
sienax MPR -r
cd first_results
echo "Left Thalamus" `fslstats T1_first_all_fast_firstseg.nii.gz -l 9.5 -u 10.5 -V` >> Subcortical_Volumes.log
echo "Left Caudate" `fslstats T1_first_all_fast_firstseg.nii.gz -l 10.5 -u 11.5 -V` >> Subcortical_Volumes.log
echo "Left Putamen" `fslstats T1_first_all_fast_firstseg.nii.gz -l 11.5 -u 12.5 -V` >> Subcortical_Volumes.log
echo "Left Pallidum" `fslstats T1_first_all_fast_firstseg.nii.gz -l 12.5 -u 13.5 -V` >> Subcortical_Volumes.log
echo "Left Hippocampus" `fslstats T1_first_all_fast_firstseg.nii.gz -l 16.5 -u 17.5 -V` >> Subcortical_Volumes.log
echo "Left Amygdala" `fslstats T1_first_all_fast_firstseg.nii.gz -l 17.5 -u 18.5 -V` >> Subcortical_Volumes.log
echo "Left Accumbens-area" `fslstats T1_first_all_fast_firstseg.nii.gz -l 25.5 -u 26.5 -V` >> Subcortical_Volumes.log
echo "Right Thalamus" `fslstats T1_first_all_fast_firstseg.nii.gz -l 48.5 -u 49.5 -V` >> Subcortical_Volumes.log
echo "Right Caudate" `fslstats T1_first_all_fast_firstseg.nii.gz -l 49.5 -u 50.5 -V` >> Subcortical_Volumes.log
echo "Right Putamen" `fslstats T1_first_all_fast_firstseg.nii.gz -l 50.5 -u 51.5 -V` >> Subcortical_Volumes.log
echo "Right Pallidum" `fslstats T1_first_all_fast_firstseg.nii.gz -l 51.5 -u 52.5 -V` >> Subcortical_Volumes.log
echo "Right Hippocampus" `fslstats T1_first_all_fast_firstseg.nii.gz -l 52.5 -u 53.5 -V` >> Subcortical_Volumes.log
echo "Right Amygdala" `fslstats T1_first_all_fast_firstseg.nii.gz -l 53.5 -u 54.5 -V` >> Subcortical_Volumes.log
echo "Right Accumbens-area" `fslstats T1_first_all_fast_firstseg.nii.gz -l 57.5 -u 58.5 -V` >> Subcortical_Volumes.log
echo "Brainstem" `fslstats T1_first_all_fast_firstseg.nii.gz -l 15.5 -u 16.5 -V` >> Subcortical_Volumes.log
cd ..
Kind Regards
Wafa
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