External Email - Use Caution 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 *ddcc2...@gmail.com <ddcc2...@gmail.com>* 443-254-6298
On Thu, Aug 8, 2019 at 9:07 AM Daniel Callow <ddcc2...@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 > *ddcc2...@gmail.com <ddcc2...@gmail.com>* > 443-254-6298 >
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