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 <corinna...@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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