Hi Corinna,
you need a single folder with all subjects and all time point:
so the subjects directory will look like:
me1
me2
me3
you1
you2
...
You can create such a folder and insert symbolic links to the original
subject folders if you want to keep your structure.
Then create the base in this folder for each subject and then the
longitudinals. You either need to path this folder via the environment
variable SUBJECTS_DIR, or on the command line to recon-all via the -sd
switch.
Also, the -tp <stpid> needs only the subject time point id. So in my
example above this would be:
recon-all -base me -tp me1 -tp me2 -tp me3 -all
it will create the directory 'me'. Don't pass full pathnames or even a
file name (you passed the norm.mgz).
Best, Martin
On Tue, 2012-05-15 at 09:54 -0400, Corinna Bauer wrote:
> 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 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
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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