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I have 40 scans.

when I do a head -n4 02102-L_Accu_first.bvars on just 1 scan
I get this:
this is a bvars file
/usr/share/fsl/5.0/data/first/models_336_bin/L_Accu_bin.bmv
NumberOfSubjects 1
02102robBRAVO_restore 336 [u&�{j�� "P=�q��}��>~�V� �?nX

once I've concatenated all my *L_Accu_first.bvars

concat L-Accu_first.bvars *L_Accu_first.bvars

I run head -n4 L-Accu_first.bvars
I get this:

This is a bvars file

NumberOfSubjects 1
3541460

Then I run:
first_utils --vertexAnalysis --usebvars -i R-Thal_first.bvars -d design.mat -o shape_analysis/R-Thal --useReconMNI --surfaceout

and I get the error message
Warning: does not exist. Attempting to switch to: /usr/share/fsl/5.0
Not a vtk file (error in line 1).
Not a vtk file (error in line 1).

I've read in the archives that I'm supposed to put in the 2nd line of my concat bars file:

/usr/share/fsl/5.0

however, I'm unable to open my bvars file in gedit. it must be too large because it just keeps crashing.

I'm on Ubuntu and have 32G RAM. my fsl install is located in /usr/share/fsl/5.0

1) is the missing fsl line in my concat bvars file my problem?

2) how can I edit the file?

thanks so much, Sophie

Sophie Josee Lafaille, B.Sc. M.Sc.
Research Coordinator
Research Imaging Centre
Room B67, 250 College Street
Centre for Addiction and Mental Health
416-535-8501 ext. 34594

Fax: 416-979-4656