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Sorry I did not see your reply (having issues getting notifications from the freesurfer list). The error seemed to be an issue with the version I was using, which wasn't reading the subject list correctly. Wanted to make sure I posted a solution. Thank you for your help! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298
On Thu, Aug 8, 2019 at 9:07 AM Daniel Callow ddcc2442@gmail.com wrote:
Hello,
When trying to run TRACULA on my data I keep getting the following error.
domainname: Command not found.
INFO: SUBJECTS_DIR is /Volumes/DANIEL/freesurfer_Tracy
INFO: Diffusion root is /Volumes/DANIEL/dti_Tracy/trac
Actual FREESURFER_HOME /Applications/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20190326-01e71dc
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Applications/freesurfer Previous: /Applications/freesurfer_dev/Volumes/DANIEL/trac-all -c /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/dmrirc.local -log /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/trac-all.log -cmd /Volumes/DANIEL/dti_Tracy/trac/HMN002/scripts/trac-all.cmd
domainname: Command not found.
ERROR: run list is longer than subject list
I have never had this issue before and have tried multiple options for the run list from () to (1 2 3) to include a number for every subject. However, I always get this error.
I wonder if there is some issue with the formatting this go around that could be causing the issue but I can't find it.
Below is what I have for the initial part of my dmrirc folder.
*# FreeSurfer SUBJECTS_DIR*
*# T1 images and FreeSurfer segmentations are expected to be found here*
*# *
setenv SUBJECTS_DIR /Volumes/DANIEL/freesurfer_Tracy/
*# Output directory where trac-all results will be saved*
*# Default: Same as SUBJECTS_DIR*
*#*
set dtroot = /Volumes/DANIEL/dti_Tracy/trac
*# Subject IDs (one per time point per subject)*
*#*
set subjlist = (HMN002 HMN003 HMN005 HMN006 HMN007 HMN011 HMN014 HMN018 HMN020 HMN021 HMN022 HMN025 HMN029 HMN035 HMN037 HMN039 HMN045 HMN050 HMN055 HMN057 HMN060 HMN064 HMN065 HMN069 HMN072 HMN073 HMN079 HMN085 HMN087 HMN088 HMN095 HMN097 HMN098 HMN099 HMN101 HMN102 HMN103 HMN105 HMN108 HMN110 HMN112 HMN113 HMN115 HMN118 HMN120 HMN121 HMN123 HMN135 HMN141 HMN144 HMN152 HMN156 HMN160 HMN163 HMN175 HMN180 HMN186 HMN187 HMN189 HMN190 HMN191 HMN193 HMN195 HMN196 HMN200 HMN201)
*# Longitudinal base template subject IDs (one for each time point above)*
*#*
set baselist = ()
*# In case you want to analyze only Huey and Louie*
*# Default: Run analysis on all time points and subjects*
*#1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66*
set runlist = ()
*# Input diffusion DICOMs (file names relative to dcmroot)*
*# If original DICOMs don't exist, these can be in other image format*
*# but then the gradient table and b-value table must be specified (see below)*
*#*
set dcmroot = /Volumes/DANIEL/Tracy/HMN_W1
set dcmlist = ( HMN002/image000001.dcm HMN003/image000001.dcm HMN005/image000001.dcm HMN006/image000001.dcm HMN007/image000001.dcm HMN011/image000001.dcm HMN014/image000001.dcm HMN018/image000001.dcm HMN020/image000001.dcm HMN021/image000001.dcm HMN022/image000001.dcm HMN025/image000001.dcm HMN029/image000001.dcm HMN035/image000001.dcm HMN037/image000001.dcm HMN039/image000001.dcm HMN045/image000001.dcm HMN050/image000001.dcm HMN055/image000001.dcm HMN057/image000001.dcm HMN060/image000001.dcm HMN064/image000001.dcm HMN065/image000001.dcm HMN069/image000001.dcm HMN072/image000001.dcm HMN073/image000001.dcm HMN079/image000001.dcm HMN085/image000001.dcm HMN087/image000001.dcm HMN088/image000001.dcm HMN095/image000001.dcm HMN097/image000001.dcm HMN098/image000001.dcm HMN099/image000001.dcm HMN101/image000001.dcm HMN102/image000001.dcm HMN103/image000001.dcm HMN105/image000001.dcm HMN108/image000001.dcm HMN110/image000001.dcm HMN112/image000001.dcm HMN113/image000001.dcm HMN115/image000001.dcm HMN118/image000001.dcm HMN120/image000001.dcm HMN121/image000001.dcm HMN123/image000001.dcm HMN135/image000001.dcm HMN141/image000001.dcm HMN144/image000001.dcm HMN152/image000001.dcm HMN156/image000001.dcm HMN160/image000001.dcm HMN163/image000001.dcm HMN175/image000001.dcm HMN180/image000001.dcm HMN186/image000001.dcm HMN187/image000001.dcm HMN189/image000001.dcm HMN190/image000001.dcm HMN191/image000001.dcm HMN193/image000001.dcm HMN195/image000001.dcm HMN196/image000001.dcm HMN200/image000001.dcm HMN201/image000001.dc)
Any help debugging the issue would be greatly appreciated!
*Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298