Hi Alan - All the "set ..." commands for tracula need to be in a
configuration file. You then pass that configuration file as an argument
to the "-c" option of trac-all. See tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps,
a.y
On Fri, 2 Aug 2013, Alan Francis wrote:
Hi Anastasia and others:
I have been trying to run Trac all on five brains. It keeps giving me the
error message:
ERROR: run list is longer than subject list
My run list is equal to the subject list: Here is the environment:
Thanks for your help,
Alan
Martinos Center for Biomedical Imaging
__________________________________________________________________
-------- freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer/stable5_3_0/
FSFAST_HOME /usr/local/freesurfer/stable5_3_0//fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /usr/local/freesurfer/stable5_3_0//subjects
MNI_DIR /usr/local/freesurfer/stable5_3_0//mni
FSL_DIR /usr/pubsw/packages/fsl/current
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : setenv SUBJECTS_DIR /autofs/space/d
dali_001/ dali_002/ dali_003/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : setenv
SUBJECTS_DIR/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set dtroot = /autofs/space/d
dali_001/ dali_002/ dali_003/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set dtroot
=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set subjlist = (101/ 102/ 103/ 104/ 105/)
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set dcmroot = /autofs/space/d
dali_001/ dali_002/ dali_003/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set dcmroot
=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set dcmlist
=(101/Diffusion_Recons/20080424_182054563000-000012-000001DTIValeras012a001.
nii \
?102/Diffusion_Recons/20080911_101015358000-000010-000001DIFFUSIONHighResval
erabi1002s010a001.nii \
?103/Diffusion_Recons/20080911_140753578000-000010-000001DIFFUSIONHighResval
eraBI1003s010a001.nii \
?104/Diffusion_Recons/20080915_160812745000-000010-000001DIFFUSIONHighResVal
eraBI104s010a001.nii \
?105/Diffusion_Recons/20080917_190940899000-000016-000001DIFFUSIONHighResVal
eraBI105s016a001.nii \
? )
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set runlist = (101/ 102/ 103/ 104/
bem/ mri/ stats/ touch/
Diffusion_Recons/ scripts/ surf/ trash/
label/ src/ tmp/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set runlist = (101/ 102/ 103/ 104/ 105/)
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set bvecfile = /autofs/space/dbvecs.txt
dali_001/ dali_002/ dali_003/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set bvecfile
=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs/bvecs.txt
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set bvalfile
=/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs/bvals.txt
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set doeddy = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set dorotbvecs = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set usemaskanat = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set thrbet = 0.3
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set doregflt = 0
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set doregbbr = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set doregmni = 1
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set doregcvs = 0
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set cvstemp = cvs_avg35
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set cvstempdir = $FREESURFER_HOME/subjects
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set pathlist = ( lh.cst_AS rh.cst_AS \
? lh.ilf_AS rh.ilf_AS \
? lh.unc_AS rh.unc_AS \
? fmajor_PP fminor_PP \
? lh.atr_PP rh.atr_PP \
? lh.cab_PP rh.cab_PP \
? lh.ccg_PP rh.ccg_PP \
? lh.slfp_PP rh.slfp_PP \
? lh.slft_PP rh.slft_PP )
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : trac-all -prep -c /autofs/space/d
dali_001/ dali_002/ dali_003/
csh::alanf@dali[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_
recons] : trac-all -prep
-c/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_r
econs/
ERROR: run list is longer than subject list
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