Hi Martin, I think this is what you're looking for. If not, let me know.
recon-all -base 137_S_0158_template -tp /Applications/freesurfer/subjects/corinna/ADNI/BL/137_S_0158/mri/norm.mgz -tp /Applications/freesurfer/subjects/corinna/ADNI/12mos/137_S_0158/mri/norm.mgz -tp /Applications/freesurfer/subjects/corinna/ADNI/24mos/137_S_0158/mri/norm.mgz -tp /Applications/freesurfer/subjects/corinna/ADNI/36mos/137_S_0158/mri/norm.mgz -all
So it will create this for each of the subjects. There are folders for each time point and then the subjects within those folders.
Corinna
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 http://ebrcb-dhcp-240-126.bumc.bu.edu 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 http://ebrcb-dhcp-240-126.bumc.bu.edu 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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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