The "wrong" is that you did not give any "estimate command" to fslstats. "l" and "u" flags only thresholds the image, but the "v" or "V" would instruct fslstats to actually estimate the volume.
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide#Volumetric_Analysis: fslstats output_name_all_fast_firstseg -l 16.5 -u 17.5 -V

Vale,

Auer, Tibor M.D. Ph.D.
MRC Cognition and Brain Sciences Unit
15 Chaucer Road
Cambridge
CB2 7EF
United Kingdom
Phone/Work: +44-(0)1223-273613
Mail: [log in to unmask]

________________________________________
Feladó: FSL - FMRIB's Software Library [[log in to unmask]] ; meghatalmazó: wolf zinke [[log in to unmask]]
Küldve: 2016. május 20. 19:10
Címzett: [log in to unmask]
Tárgy: Re: [FSL] Something is wrong with FIRST analysis

i will be busy the next couple of hours but come back to you as soon as i can.

On 5/20/16 12:33 PM, Rosalia Dacosta Aguayo wrote:
There is something I must be missing because when I try to calculate the volume of the Amygdala, that does not appear in my firstseg file....it does not calculate anything!!!

To calculate the volume of the left Amygdala...label 18...and following instructions in the web....nothing appears!

rosalia@rosalia-PORTEGE-Z930:~$ cd /home/rosalia/Desktop/PPMI/45/FIRST
rosalia@rosalia-PORTEGE-Z930:~/Desktop/PPMI/45/FIRST$ fslstats C1_007_all_fast_firstseg.nii.gz -l 17.5 -u 18.5
rosalia@rosalia-PORTEGE-Z930:~/Desktop/PPMI/45/FIRST$

I do not know where is the problem...

Rosalia

2016-05-20 18:14 GMT+02:00 Rosalia Dacosta Aguayo <<mailto:[log in to unmask]>[log in to unmask]<mailto:[log in to unmask]>>:

Now I have run:

rosalia@rosalia-PORTEGE-Z930:~$ cd /home/rosalia/Desktop/PPMI/45/FIRST
rosalia@rosalia-PORTEGE-Z930:~/Desktop/PPMI/45/FIRST$ 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
8966....what this number means?
rosalia@rosalia-PORTEGE-Z930:~/Desktop/PPMI/45/FIRST$

And about the outputs:

1, all_fast_firstseg (only with the R and L Hippocampus...but nothing about my desired Amygdala)
2. all_fast_origsegs (only left Hippocampus...)
3. vtk files for every structure selected
4. .bvars files for every structure selected
5. no .nii.gz for every structure selected

Regarding errors:

rosalia@rosalia-PORTEGE-Z930:~/Desktop/PPMI/45/FIRST$ cat *.logs/*.e*
rosalia@rosalia-PORTEGE-Z930:~/Desktop/PPMI/45/FIRST$

There are NO errors....I do not know what more can I do...I am trying not to use an atlas template because my T1 images are not as good as for this kind of analysis....

Some help with this problem would be very appreciate

Kind regards,

Rosalia

2016-05-20 17:46 GMT+02:00 Rosalia Dacosta Aguayo <[log in to unmask]<mailto:[log in to unmask]>>:

Dear Mark, Anderson and FSL team,

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