First scan is 005_IHD_1
Second scan is 005_IHD_1_post These were in $SUBJECTS / ihd I moved them into $SUBJECTS (i.e. no subfolder within $SUBJECTS folder). I am following this; https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongProcessing FsTutorial/LongProcessing - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongProcessing> surfer.nmr.mgh.harvard.edu Processing your data consists of three steps: First, run all your data independently (we also say cross sectionally) using "recon-all -all" (i.e. all time points for ... I ran a normal recon all on both scans first. I then ran this command: recon-all -base 005_IHD_1_base-tp 005_IHD_1 -tp 005_IHD_1_post -all and all seemed well. I then tried to run this command. recon-all -long <tpNid> <templateID> -all This is how I entered the command: recon-all -long 005_IHD_1 005_IHD_1_base -all It resulted in errors...here is the last bit of the error log: Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 writing to /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/rawavg.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/orig.mgz /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Mar 30 14:31:07 EDT 2017 /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri cp /usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm /usr/local/freesurfer/subjects/005_IHD_1.long.005_IHD_1_base/mri/transforms/talairach.auto.xfm cp: cannot stat '/usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm': No such file or directory Linux bjmatush-System-Product-Name 4.4.0-51-generic #72~14.04.1-Ubuntu SMP Thu Nov 24 19:22:30 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 005_IHD_1.long.005_IHD_1_base exited with ERRORS at Thu Mar 30 14:31:07 EDT 2017 What went wrong?
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