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CoBrALab / quarantine

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FSL_First #21

Closed Princess-of-the-lab closed 9 years ago

Princess-of-the-lab commented 9 years ago

Hi, I wanted to run fsl-first on 4 subjects. I ran the following command on them 

kubste@cicws29:/data/chamal/projects/steph/try-fsl/SUBJECTS$ run_first_all -i subj1.nii -o subj1_L_caud -s L_Caud

and got an output that I did not expected subj1_L_caud.com. As the fsl-userguide tells you, I should be getting files that end with nii.gz (userguide: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST/UserGuide). Looking at the .com file revealed that it looks for a model, that it cant find:

kubste@cicws29:/data/chamal/projects/steph/try-fsl/SUBJECTS$ /opt/quarantine/FSL/5.0.7/build/usr/share/fsl/5.0/bin/run_first -i subj1 -t subj1_to_std_sub.mat -n 30 -o subj1_L_caud-L_Caud_first -m /opt/quarantine/FSL/5.0.7/build/usr/share/fsl/5.0/data/first/models_336_bin/intref_thal/L_Caud.bmv -intref /opt/quarantine/FSL/5.0.7/build/usr/share/fsl/5.0/data/first/models_336_bin/05mm/L_Thal_05mm.bmv
linear transformation matrix file not found
kubste@cicws29:/data/chamal/projects/steph/try-fsl/SUBJECTS$ ls /opt/quarantine/FSL/5.0.7/build/usr/share/fsl/5.0/data/first/models_336_bin/intref_thal/L_Caud.bmv
ls: cannot access /opt/quarantine/FSL/5.0.7/build/usr/share/fsl/5.0/data/first/models_336_bin/intref_thal/L_Caud.bmv: No such file or directory

also looking at the log files seemed like a module cant be found: /bin/sh: error importing function definition for BASH_FUNC_module%%' /opt/quarantine/FSL/5.0.7/build/usr/share/fsl/5.0/bin/flirt: /lib/libc.so.6: versionGLIBC_2.14' not found (required by /opt/quarantine/FSL/5.0.7/build/usr/share/fsl/5.0/bin/flirt)

while running run_first_all I had the following module loaded: 1) quarantine 2) gcc/4.1.2 3) FSL/5.0.7

Many Thanks!

gdevenyi commented 9 years ago

Please try FSL/5.0.7-full.

Also please remember to unload gcc, it is only needed for CIVET and may break other things