Hi,
This all looks correct.
However, be aware that a significant result obtained from the average of several quantities does not necessarily imply that any one of the quantities on its own need by significant. What you get may well indicate this. However, there is also quite a difference in the way that FIRST extracts volumes and how SIENAX does. I would also run a VBM analysis to see what that shows, in order to help you understand what is going on.
All the best,
Mark
> On 18 Dec 2017, at 23:02, Mohammad Aboulwafa <[log in to unmask]> wrote:
>
> 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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