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_recons/
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_recons/
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_recons/
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_101015358000-000010-000001DIFFUSIONHighResvalerabi1002s010a001.nii \
? 103/Diffusion_Recons/20080911_140753578000-000010-000001DIFFUSIONHighResvaleraBI1003s010a001.nii \
? 104/Diffusion_Recons/20080915_160812745000-000010-000001DIFFUSIONHighResValeraBI104s010a001.nii \
? 105/Diffusion_Recons/20080917_190940899000-000016-000001DIFFUSIONHighResValeraBI105s016a001.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_recons/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_recons/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_recons/

ERROR: run list is longer than subject list