Dear Mark, Anderson and FSL team,

I am running FIRST following carefully the web: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide

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$


And also, before of this it appears the following message too (that did not appear with the first option):

rosalia@rosalia-PORTEGE-Z930:~$ cd /home/rosalia/Desktop/PPMI/45/FIRST
rosalia@rosalia-PORTEGE-Z930:~/Desktop/PPMI/45/FIRST$ fsl5.0-run_first_all C1_007_crop_restore_flirted -o C1_007
 /usr/share/fsl/5.0/bin/run_first_all: 284: [: thresh: unexpected operator
/usr/share/fsl/5.0/bin/run_first_all: 292: [: -gt: unexpected operator


I will go on trying...but no idea about what is happening and I would really appreciate your always helpful advices...

Kind regards,

Rosalia