Hi there,
I am trying to run reg-feat2anat and having a bit of an odd problem. It runs but doesn't produce a anat2exf.register.dat. If I look at the anat2exf.register.dat.fslregister.log file I see right at the beginning it fail with:
/data/results/genDIS mri_convert ERROR: could not determine file for /data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR: /data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii mri_convert ERROR: could not determine file for /data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR: /data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
type mri_convert -u for usage
This is running on a SGE cluster using Ubuntu 12.04.1, FreeSurfer 5.3 and FSL 5.0.4 which made me think it is is similar to Sal's problem recently. So I added "set fsvol = brainmask" and that seems to have fixed it. Is there a different fix I can make to solve this?
Cheers,
-Morgan
Hi Morgan that is odd. I think Doug is traveling which may slow down his normal rapid response time. Bruce
On Sat, 27 Jul 2013, Morgan Hough wrote:
Hi there,
I am trying to run reg-feat2anat and having a bit of an odd problem. It runs but doesn't produce a anat2exf.register.dat. If I look at the anat2exf.register.dat.fslregister.log file I see right at the beginning it fail with:
/data/results/genDIS mri_convert ERROR: could not determine file for
/data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR: /data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii
mri_convert ERROR: could not determine file for /data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR: /data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
type mri_convert -u for usage
This is running on a SGE cluster using Ubuntu 12.04.1, FreeSurfer 5.3 and FSL 5.0.4 which made me think it is is similar to Sal's problem recently. So I added "set fsvol = brainmask" and that seems to have fixed it. Is there a different fix I can make to solve this?
Cheers,
-Morgan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Morgan, this is a problem with newer versions of csh -- they changed the way that errors are reported. Try using this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat
doug
On 7/28/13 10:00 AM, Bruce Fischl wrote:
Hi Morgan that is odd. I think Doug is traveling which may slow down his normal rapid response time. Bruce
On Sat, 27 Jul 2013, Morgan Hough wrote:
Hi there,
I am trying to run reg-feat2anat and having a bit of an odd problem. It runs but doesn't produce a anat2exf.register.dat. If I look at the anat2exf.register.dat.fslregister.log file I see right at the beginning it fail with:
/data/results/genDIS mri_convert ERROR: could not determine file for
/data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR: /data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii
mri_convert ERROR: could not determine file for /data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR: /data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
type mri_convert -u for usage
This is running on a SGE cluster using Ubuntu 12.04.1, FreeSurfer 5.3 and FSL 5.0.4 which made me think it is is similar to Sal's problem recently. So I added "set fsvol = brainmask" and that seems to have fixed it. Is there a different fix I can make to solve this?
Cheers,
-Morgan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Can you make that file available again? I am having a similar issue....
Thanks,
Emily
On Mon, Jul 29, 2013 at 11:13 AM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Hi Morgan, this is a problem with newer versions of csh -- they changed the way that errors are reported. Try using this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat
doug
On 7/28/13 10:00 AM, Bruce Fischl wrote:
Hi Morgan that is odd. I think Doug is traveling which may slow down his normal rapid response time. Bruce
On Sat, 27 Jul 2013, Morgan Hough wrote:
Hi there,
I am trying to run reg-feat2anat and having a bit of an odd problem. It
runs but doesn't produce a anat2exf.register.dat. If I look at the anat2exf.register.dat.fslregister.log file I see right at the beginning it fail with:
/data/results/genDIS mri_convert ERROR: could not determine file for
/data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR:
/data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii
mri_convert ERROR: could not determine file for
/data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR: /data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
type mri_convert -u for usage
This is running on a SGE cluster using Ubuntu 12.04.1, FreeSurfer 5.3
and FSL 5.0.4 which made me think it is is similar to Sal's problem recently. So I added "set fsvol = brainmask" and that seems to have fixed it. Is there a different fix I can make to solve this?
Cheers,
-Morgan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
(my trouble is with fslregister-sess though)
On Thu, Sep 26, 2013 at 11:25 PM, Emily Ward amyunimus@gmail.com wrote:
Hi Doug,
Can you make that file available again? I am having a similar issue....
Thanks,
Emily
On Mon, Jul 29, 2013 at 11:13 AM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Morgan, this is a problem with newer versions of csh -- they changed the way that errors are reported. Try using this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat
doug
On 7/28/13 10:00 AM, Bruce Fischl wrote:
Hi Morgan that is odd. I think Doug is traveling which may slow down his normal rapid response time. Bruce
On Sat, 27 Jul 2013, Morgan Hough wrote:
Hi there,
I am trying to run reg-feat2anat and having a bit of an odd problem.
It runs but doesn't produce a anat2exf.register.dat. If I look at the anat2exf.register.dat.fslregister.log file I see right at the beginning it fail with:
/data/results/genDIS mri_convert ERROR: could not determine file for
/data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR:
/data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii
mri_convert ERROR: could not determine file for
/data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR: /data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
type mri_convert -u for usage
This is running on a SGE cluster using Ubuntu 12.04.1, FreeSurfer 5.3
and FSL 5.0.4 which made me think it is is similar to Sal's problem recently. So I added "set fsvol = brainmask" and that seems to have fixed it. Is there a different fix I can make to solve this?
Cheers,
-Morgan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas Greve -
Emily Ward -
Morgan Hough