In a first moment, I run:
fsl5.0-run_first_all -i C1_007_crop_restore_flirted.nii.gz
-o C1_007 -s L_Hipp,R_Hipp,L_Amyg,R_Amyg
I got the following outputs:
1. all_fast_firstseg
2. all_fast_origsegs
3. vtk files for every structure selected
4. .bvars files for every structure selected
5. no .nii.gz for every structure selected
Problem 1: Fine! I thought, what I inspected firstseg and origsegs files before taking into account only the fast_origsegs (following Mark instructions in the fsl list forum regarding the use of firstseg files in order to calculate my interested volumes because those files are boundary corrected. The surprise I got was that origsegs files only contained the R_Hippocampus....and firstseg only contained left and right hippocampus...what about my amygdalal???? ...and also appeared a number (i.e: 1448) after finishing the command line....
Then I chose to run:
fsl5.0-run_first_all -i C1_007_crop_restore_flirted.nii.gz
-o C1_007 -s in order to get the volume of all structures and run the script kindly provided by Mark:
im=YOUR_IMAGE_NAME_firstseg.nii.gz
maxn=`fslstats $im -P 100`
fslstats $im -h $maxn | grep [1-9] | sed -n '2,$p'
Taking into account spaces, commas and not just cut and paste....
I got only the following outputs:
1. vtk files for all the deep gm structures
2. .bvars files for all structure selected
3. nii.gz files for all the deep gm structures
Nothing about: firstseg or origseg files????
I am just interested in R and L Hippocampus and R and L Amygdala...but it seems that something is not working.
When I type: cat *.logs/*.e* It appears the following message:
rosalia@rosalia-PORTEGE-Z930:~/Desktop/PPMI/45/FIRST$ cat *.logs/*.e*
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
/usr/share/fsl/5.0/bin/first_boundary_corr: 194: shift: can't shift that many
rosalia@rosalia-PORTEGE-Z930:~/Desktop/PPMI/45/FIRST$