Hi Nawaf - The first error occured much earlier in the log file. Your gradient table file could not be found. Did you set the bvecfile variable in your configuration file?
a.y
On Fri, 29 Mar 2013, Nawaf Yassi wrote:
Hi Anastasia Thanks for your reply Here is the file attached (I have replaced the subject's name with 'AAAAA' for anonymity) Regards Nawaf
On 29/03/13 2:17 AM, "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu wrote:
Hi Nawaf - Can you please send your trac-all.log? It's possible that the
problem started at an earlier step.
Thanks, a.y
On Thu, 28 Mar 2013, Nawaf
Yassi wrote:
Dear mailing list
I am encountering an error at the trac-all path stage of a tracula analysis (the first two stages on trac-all seem to have run ok) with the appropriate outputs. I am getting the error ³Segmentation fault² (core dumped) very early on after the dmri_paths command is run (see below). Can anyone help?
I am using freesurfer 5.2 and FSL 5.0.2.1 (linux) Regards Nawaf ATTACHED: ERROR MESSAGE + config file below
=========================================================
[nyassi@bee1 scripts]$ trac-all -path -c dmrirc_single_subject Too many )'s. INFO: SUBJECTS_DIR is
/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer
INFO: Diffusion root is
/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer5.2 trac-paths -c/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /scripts/ dmrirc.local -log/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C 01/scripts/ trac-all.log -cmd/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C 01/scripts/ trac-all.cmd #-------------------------------------
/usr/local/freesurfer5.2/bin/trac-paths
#------------------------------------- #@# Path reconstruction Thu Mar 28 10:01:34 EST 2013 rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .cst_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .cst_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .ilf_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .ilf_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .unc_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .unc_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/fm ajor_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/fm inor_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .atr_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .atr_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .ccg_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .ccg_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .cab_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .cab_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .slfp_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .slfp_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .slft_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .slft_PP_avg33_mni_bbr /usr/local/freesurfer5.2/bin/dmri_paths --outdir/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurf er/C01/dpath/lh
.cst_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis /C01_freesurfer/C01/dpath/rh
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ajor_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis /C01_freesurfer/C01/dpath/fm
inor_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis /C01_freesurfer/C01/dpath/lh
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ni/rh.atr_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re covery/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re covery/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re covery/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.cab_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re covery/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.cab_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-R ecovery/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec overy/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-R ecovery/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec overy/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-R ecovery/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.slft_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec overy/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-R ecovery/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.slft_PP_avg33_mni_bbr_fsnnids_all --lprior/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurf er/C01/dlabel/m
ni/lh.cst_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.cst_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove ry/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.cst_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.cst_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove ry/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.ilf_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.ilf_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove ry/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.ilf_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.ilf_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove ry/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.unc_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.unc_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove ry/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.unc_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.unc_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove ry/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/fmajor_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/fmajor_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove ry/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/fminor_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/fminor_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove ry/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.atr_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.atr_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove ry/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.atr_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.atr_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove ry/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.ccg_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.ccg_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove ry/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.ccg_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.ccg_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove ry/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.cab_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.cab_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove ry/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.cab_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco very/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.cab_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove ry/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.slfp_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec overy/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.slfp_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recov ery/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.slfp_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec overy/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.slfp_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recov ery/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.slft_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec overy/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/lh.slft_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recov ery/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.slft_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec overy/C01/Analysis/C01_freesurfer/C01/dlabel/m
ni/rh.slft_PP_avg33_mni_bbr_fsids_all --seg/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/ C01/dlabel/m ni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 --sdp/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/ C01/dlabel/d
iff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d
iff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt Segmentation fault (core dumped) foreach: No match.
==============================================================================
================================================
[nyassi@bee1 scripts]$ cat dmrirc_single_subject # # dmrirc.example # # This file contains commands that will be run by trac-all before an analysis. # It is used to set all parameters needed for the analysis. # # Remove a parameter from your dmrirc file if you want use the default value. # Parameters that don't have default values must be specified. # # Any other commands that you might want to run before an analysis can be added # to this file. #
# Original Author: Anastasia Yendiki # CVS Revision Info: # $Author: ayendiki $ # $Date: 2013/02/16 22:49:06 $ # $Revision: 1.3.2.4 $
# # Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
# # Terms and conditions for use, reproduction, distribution and contribution # are found in the 'FreeSurfer Software License Agreement' contained # in the file 'LICENSE' found in the FreeSurfer distribution, and here: # # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense # # Reporting: freesurfer@nmr.mgh.harvard.edu # #
# FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR
/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/>
# Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR #
# Subject IDs # set subjlist = (C01)
# In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects #
# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format # but then bvecfile, bvalfile, and nb0 must be specified (see below) # set dcmroot =
/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/DICOMS/raw_dti/HURLE_LISA
set dcmlist = (IM-0001-0001.dcm)
# Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format, one row for each volume in the diffusion data set # Default: Read from DICOM header
# # set bvecfile = /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/bvecs.txt
# Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # Single-column format, one value for each volume in the diffusion data set> # Default: Read from DICOM header # # set bvalfile = /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/bvals.txt
# Number of low-b images # Must be specified if inputs are not DICOM # Default: Read from DICOM header # set nb0 = 0
# Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1
# Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm)
# Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1.dcm)
# Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # # set echospacing = 0.7
# Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1
# Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 1
# Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.3
# Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0
# Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1
# Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1
# MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # # set mnitemp = /path/to/mni_template.nii.gz
# Perform registration of T1 to CVS template? # Default: 0 (no) # set doregcvs = 0
# CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # # set cvstemp = donald
# Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # # set cvstempdir = /path/to/cvs/atlases/of/ducks
# Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1
# Paths to reconstruct # Default: All paths in the atlas # # set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \
lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \
lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP )
# Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths #
# set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)
# List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # # set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt
# Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2
# Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # # set nburnin = 200
# Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 5000 # # set nsample = 7500
# Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # # set nkeep = 5
# Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # # set reinit = 0
The
information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
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freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki