Hi Simon - You are correct, this was a bug specific only to running the -stat part of trac-all with the CVS template. Your work-around was correct. I've fixed the bug so that, as of the next version, the configuration as shown in the sample config file should work with the -stat part as well. Thanks for catching that!

Best,
a.y

On Fri, 30 Oct 2015, Simon Jones wrote:


Dear Tracula developers,

 

I posted a problem with tracula when I ran

trac-all -stat -c  dmrirc_ind_mni_cvs_all_stats.all

 

I receive this error message

 

Loading output reference volume from

/home/spj24/app/freesurfer/subjects/cvs_avg35

 

corRead(): can't open file

/home/spj24/app/freesurfer/subjects/cvs_avg35/COR-.info

 

ERROR: Could not read /home/spj24/app/freesurfer/subjects/cvs_avg35

There is no file called COR-.info in the directory

/home/spj24/app/freesurfer/subjects/cvs_avg35/

 

I have now changed the lines in the configuration file

 

set doregcvs = 1

 

# CVS template subject ID

# Only used if doregcvs = 1

# Default: cvs_avg35

#

#set cvstemp = donald

set cvstemp = cvs_avg35

 

set cvstempdir = $FREESURFER_HOME/subjects

 

to

 

set doregcvs = 1

set cvstemp = cvs_avg35/mri/brainmask.mgz

set cvstempdir = $FREESURFER_HOME/subjects

 

i.e. explicitly pointing to an image in the cvs_avg35 directory and the stats 
seem to complete without error.

 

Is that the right thing to do?

 

Thanks for your help,

 

Simon

 

 

 


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