Hi Pablo
why are you listing fsaverage as the subject you are processing? The error
says you are runing:
recon-all -s fsaverage
which is not what you want.
cheers
Bruce
On Sat, 9 May 2015, pablo najt wrote:
Hello I guess my message got lost in the long mailing list. If anyone is
able to advice on the message I will be grateful to you.
Thanks
Pablo
____________________________________________________________________________
From: pablon...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Thu, 7 May 2015 16:37:29 +0000
Subject: [Freesurfer] Error #@# MotionCor
Dear FS experts,
I am processing my subjects with a foreach batch as below.
foreach I (*)
echo $i
recon-all -subjd $i -all
end
I run this in four parallel terminals and save output in 4 different
folders. Once they are finshed I moved all output to a main output folder
and process a new batch of subjects.
The recon-all.log reads "finished without error" but at the end of each of
the batches I get the following error. Should I'll be warring about this?
For further reference I am attaching the recon-all.log file. But as I said I
cannot find anything wrong with it.
Thanks,
Pablo
#--------------------------------------------
#@# MotionCor Sat May 2 07:48:28 IST 2015
ERROR: no run data found in
/media/OS/ENIGMA_Genetic_Risk/output_batch4/fsaverage/mri. Make sure to
have a volume called 001.mgz in
/media/OS/ENIGMA_Genetic_Risk/output_batch4/fsaverage/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Linux dara-Precision 3.0.0-21-generic #35-Ubuntu SMP Fri May 25 17:57:41 UTC
2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s fsaverage exited with ERRORS at Sat May 2 07:48:28 IST 2015
For more details, see the log
file/media/OS/ENIGMA_Genetic_Risk/output_batch4/fsaverage/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
lh.EC_average
ERROR: you do not have write permission to
/media/OS/ENIGMA_Genetic_Risk/output_batch4/lh.EC_average
rh.EC_average
ERROR: you do not have write permission to
/media/OS/ENIGMA_Genetic_Risk/output_batch4/rh.EC_average
dara-Precision:/media/OS/ENIGMA_Genetic_Risk/output_batch4>
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