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 <mreu...@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 <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 <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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