Hi Bruce, Oh yes, I see that now! And the problem is that FS looks for the FSGDF under SUBJECTS_DIR//space/emc1/3/data/TOP/Analysis_lmr/, but SUBJECTS_DIR and Analysis_lmr are both in the same directory, i.e. /space/emc1/3/data/TOP. I thought that by giving the full path to the FSGDF I had taken care of that: make_average_subject --fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest
Is there a way around that, or do I have to put the FSGDF inside the SUBJECTS_DIR? The reason I would like to keep them separate is that lab techs are doing scan workups inside the SUBJECTS_DIR, and I don't want to create new directories and files inside there all the time. I guess this is a general question, is it possible to run make_average_subject, mris_preproc and surf2surf and get the FSGDF from a dir that is not a subdirectory of the subjectsdir, and also write the output to that dir? It seems if you give the full path, FS assumes that it should be added to the path of the subjects dir.
Thank you! Lars
Hi Lars,
it looks like no input subjects are defined.
Bruce On Wed, 27 Jun 2007, Lars M. Rimol wrote:
Hi, Trying to run make_average_subject but getting an error message. Any idea what may be wrong?
Thank you! Lars M. Rimol
make_average_surface --fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest $Id: make_average_surface,v 1.27.2.2 2006/06/09 15:46:28 nicks Exp $ Wed Jun 27 18:06:43 PDT 2007 /space/emc1/3/data/TOP/Analysis_lmr setenv SUBJECTS_DIR /space/emc1/3/data/TOP/Containers output sdir is /space/emc1/3/data/TOP/Containers uid=7266(lmr) gid=7266(lmr) groups=7266(lmr),7450(topproj) context=user_u:system_r:unconfined_t ==================== make_average_surface ==================== input subjects: output subject: /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest mri_add_xform_to_header -c auto
Lars,
From looking at the make_average_surface script (which is a text file),
it appears that it reads the argument for --fsgd <arg> directly, and does not prepend SUBJECTS_DIR. Can you append the --debug option to make_average_surface to verify this? The --debug option will dump the details of the --fsgd <arg> portion of the script.
Nick
On Thu, 2007-06-28 at 20:12 +0200, Lars M. Rimol wrote:
Hi Bruce, Oh yes, I see that now! And the problem is that FS looks for the FSGDF under SUBJECTS_DIR//space/emc1/3/data/TOP/Analysis_lmr/, but SUBJECTS_DIR and Analysis_lmr are both in the same directory, i.e. /space/emc1/3/data/TOP. I thought that by giving the full path to the FSGDF I had taken care of that: make_average_subject -- fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf -- out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest
Is there a way around that, or do I have to put the FSGDF inside the SUBJECTS_DIR? The reason I would like to keep them separate is that lab techs are doing scan workups inside the SUBJECTS_DIR, and I don't want to create new directories and files inside there all the time.
I guess this is a general question, is it possible to run make_average_subject, mris_preproc and surf2surf and get the FSGDF from a dir that is not a subdirectory of the subjectsdir, and also write the output to that dir? It seems if you give the full path, FS assumes that it should be added to the path of the subjects dir.
Thank you! Lars
Hi Lars,
it looks like no input subjects are defined.
Bruce On Wed, 27 Jun 2007, Lars M. Rimol wrote:
Hi, Trying to run make_average_subject but getting an error message. Any
idea
what may be wrong?
Thank you! Lars M. Rimol
make_average_surface --fsgd /space/emc1/3/data/TOP/Analysis_lmr/TOPtest.fsgdf --out /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest $Id: make_average_surface,v 1.27.2.2 2006/06/09 15:46:28 nicks Exp
$
Wed Jun 27 18:06:43 PDT 2007 /space/emc1/3/data/TOP/Analysis_lmr setenv SUBJECTS_DIR /space/emc1/3/data/TOP/Containers output sdir is /space/emc1/3/data/TOP/Containers uid=7266(lmr) gid=7266(lmr) groups=7266(lmr),7450(topproj) context=user_u:system_r:unconfined_t ==================== make_average_surface ==================== input subjects: output subject: /space/emc1/3/data/TOP/Analysis_lmr/average_TOPtest mri_add_xform_to_header -c auto
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