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
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-------- 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
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
freesurfer@nmr.mgh.harvard.edu
-
Alan Francis -
Anastasia Yendiki