Recon-all ceases working after mri_nu_correct.mni ... - Freesurfer

9 Sep 2013


      Dear FreeSurfer community,
My recon-all commands have stopped working, when previously they (usually) completed just fine. I am not sure at what level the problem is at.
I'm working off the Jalapeno cluster at FMRIB, where FreeSurfer is centrally installed. I run a configuration script to get started  (. $FREESURFER_HOME/SetUpFreeSurfer.sh) and then define my subjects directory (SUBJECTS_DIR=~/scratch/my_fs_subjects). I then run recon-all commands e.g.
fsl_sub -q verylong.q recon-all -s SubjectXXX -i T1_biascorr.nii.gz -all
This previously worked. I now within minutes get a log file with no obvious error message, but which ends
#--------------------------------------------
#@# Talairach Wed Aug 28 15:38:06 BST 2013
/home/fs0/amyb/scratch/Enigma_bipolar/FSURFER_OUTPUT/BF_subject10/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux jalapeno04.fmrib.ox.ac.uk 2.6.32-358.14.1.el6.x86_64 #1 SMP Mon Jun 17 15:54:20 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s SubjectXXX exited with ERRORS at Wed Aug 28 15:38:13 BST 2013
We are using FreeSurfer version 5.3.0. After reading some of the archive I've checked that nu_correct is indeed stored in the freesurfer directory mni/bin/nu_correct.
Any tips?
Thanks and warm regards,
Amy
Dr.  Amy Bilderbeck
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of ye tian
Sent: 09 August 2013 21:05
To: Douglas N Greve
Cc: Freesurfer
Subject: Re: [Freesurfer] Qdec and one discrete variable
Dear Doug,
Thank you very much!
Sincerely,
Ye
On Thu, Aug 8, 2013 at 4:46 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
Try adding a carriage return after TM
doug
On 08/08/2013 05:30 PM, ye tian wrote:
Dear Doug,
It is a mac. I made the meditation.levels file using emacs.
emacs meditation.levels --> type "Normal" (level1) --> hit enter --> type "TM" (level2) --> save file
Thank you very much!
Sincerely,
Ye
On Thu, Aug 8, 2013 at 4:22 PM, Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu>> wrote:
How did you create the levels file? Eg, did you use a windows
    computer?
    Or did you use msword or some other word processor. If not, can
    you send
    the levels file?
    On 08/08/2013 03:49 PM, ye tian wrote:
    > Dear freesurfers,
    >
    > I am experimenting qdec with one of my discrete variables. Besides
    > qdec.table.dat file, I do have a .levels file with the two levels of
    > the variable (say level1 and level2). However, I keep getting the
    > following error message:
    >
    > Reading discrete factor levels from config file
    > /$SUBJECTS_DIR/qdec/meditation.levels
    >         level1
    > done.
    > ERROR: /$SUBJECTS_DIR/qdec/meditation.levels is invalid. Must
    have at
    > least two levels.
    > Error loading the data table.
    >
    > Is there something that I have missed in the declaration of the
    variable?
    >
    > Thank you very much!
    >
    > Sincerely,
    > Ye
    >
    >
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--
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
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