On Mon, May 14, 2012 at 10:29 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:

Hi corinna,
Can you send the corresponding call to recon-all that your script generates?

Best Martin

On May 14, 2012, at 18:27, Corinna Bauer <corinnab83@gmail.com> wrote:

Hello all,
I am trying to create a template for longitudinal processing and am running into some problems generating the file. I have many subjects so I am running a batch script. I am using version 5.1.0

Any suggestions?

Thanks!
Corinna

Here is my script:
#!/bin/tcsh
setenv FREESURFER_HOME /Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh
setenv SUBJECTS_DIR /Applications/freesurfer/subjects/corinna/ADNI/template

set subjects=`cat $1`

foreach subject ($subjects)

    echo "-------------------- Processing $subject -------------------------"
    set subj_dir=/Applications/freesurfer/subjects/corinna/ADNI/
    set template=/Applications/freesurfer/subjects/corinna/ADNI/template/${subject}_template/mri
    set tp_BLmos=/Applications/freesurfer/subjects/corinna/ADNI/BL/${subject}/mri/norm.mgz
    set tp_12mos=/Applications/freesurfer/subjects/corinna/ADNI/12mos/${subject}/mri/norm.mgz
    set tp_24mos=/Applications/freesurfer/subjects/corinna/ADNI/24mos/${subject}/mri/norm.mgz
       set tp_36mos=/Applications/freesurfer/subjects/corinna/ADNI/36mos/${subject}/mri/norm.mgz
    #set nu_mgz=${subj_dir}/mri/nu.mgz

    recon-all -base ${subject}_template -tp ${tp_BLmos} -tp ${tp_12mos} -tp ${tp_24mos} -tp ${tp_36mos} -all

end

Here is my output:
-------------------- Processing 137_S_0631 -------------------------
Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/corinna/ADNI/template
Actual FREESURFER_HOME /Applications/freesurfer
Darwin ebrcb-dhcp-240-126.bumc.bu.edu 10.4.2 Darwin Kernel Version 10.4.2: Tue Jul 27 21:17:17 PDT 2010; root:xnu-1504.7.60~1/RELEASE_X86_64 x86_64
#--------------------------------------------
#@# Longitudinal Base Subject Creation Mon May 14 18:21:23 EDT 2012
/Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template
\n mri_robust_template --mov /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz --lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta --template /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/norm_template.mgz --average 1 --sat 4.685 \n
$Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $

--mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume.
--mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume.
--mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume.
--mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume.
    Total: 4 input volumes
--lta: Will output LTA transforms
--template: Using /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/norm_template.mgz as template output volume.
--average: Using method 1 for template computation.
--sat: Using saturation 4.685 in M-estimator!
reading source '/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz'...
mghRead(/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz, -1): could not open file
MultiRegistration::loadMovables: could not open input volume /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz.

Darwin ebrcb-dhcp-240-126.bumc.bu.edu 10.4.2 Darwin Kernel Version 10.4.2: Tue Jul 27 21:17:17 PDT 2010; root:xnu-1504.7.60~1/RELEASE_X86_64 x86_64

recon-all -s 137_S_0631_template exited with ERRORS at Mon May 14 18:21:23 EDT 2012

For more details, see the log file /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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