Does this file exist?
$FREESURFER_HOME/subjects/fsaverage/label/lh.BA1_exvivo.label
If not, what version of FS are you using?
On 08/24/2016 08:14 PM, Elpiniki Andrew wrote:
Thankyou! It worked when I removed the trailing “ / “. However after it finished running, I received this error:
ERROR reading /usr/local/DTI_processed_data/freesurfer_data_dir/fsaverage/label/lh.BA1_exvivo.label
Because the “lh.BA1_exvivo.label” file for some reason, when I checked, was not in my subjects_dir.
What should I do?
Thankyou very much!
Elpiniki
Douglas N Greve https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22 Mon, 22 Aug 2016 13:12:24 -0700 https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20160822
Nothing looks suspicious. Try setting
setenv SUBJECTS_DIR /usr/local/DTI_processed_data/freesurfer_data_dir
ie, removing the trailing "/"
On 08/22/2016 02:12 AM, Elpiniki Andrew wrote:
Hello Freesurfer experts,
I'm having a bit of difficulty running the recon-all command. I
recently downloaded Freesurfer version 6.0.
The command that I'm running is:
recon-all -all -s $name -hippocampal-subfields-T1
However I keep receiving this error:
If: Expression Syntax
I've attached the output using the -debug flag.
I'm using Linux ( centos6.3). Not sure if this is related but I
initially had an issue with recon-all stopped with an error when I
first ran the same dataset. There was an error in the log file " too
many levels of symbolic links".
So, I created a new subjects directory and created a symlink to the
fsaverage dir as per the instructions on the freesurfer wiki page.
Thankyou very much in advance for your time and efforts!
Kind regards,
Elpiniki
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