Hi Doug,
The issue is motion correction in FS-FAST. The environment is nmr-dev-env.
mc-sess flag -perrun is documented like this: "MC each run separately (targ=mid)".
1. Does "targ=mid" implicate that the target, within each run, is the image half way through the run?
2. Does this equal to using the mc-sess -rlf runlistfile flag, and changing the contents of the runlistfile to match each of the run numbers, one at a time?
Thanks,
Tommi
--- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
raij@nmr.mgh.harvard.edu
raij@nmr.mgh.harvard.edu wrote:
Hi Doug,
The issue is motion correction in FS-FAST. The environment is nmr-dev-env.
mc-sess flag -perrun is documented like this: "MC each run separately (targ=mid)".
- Does "targ=mid" implicate that the target, within each run, is the
image half way through the run?
Yes
- Does this equal to using the mc-sess -rlf runlistfile flag, and
changing the contents of the runlistfile to match each of the run numbers, one at a time?
Almost. Method #2 will use the first image instead of the middle image.
doug
Thanks,
Tommi
Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
raij@nmr.mgh.harvard.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
mc-sess with -perrun failed with the output: targstem: Undefined variable.
*** Bug report: ***
on machine ai
source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri
cd /space/cognito/5/users/raij/avml_fmri_mcseparately/avml19_session_BRISI13_ISI1TR_BERT
which mc-sess /usr/local/freesurfer/dev/fsfast/bin/mc-sess
mc-sess -sf sessid -df sesspar -perrun
Logfile is /autofs/space/cognito_005/users/raij/avml_fmri_mcseparately/avml19_session_BRISI13_ISI1TR_BERT/log/mc-avml19_session_BRISI13_ISI1TR_BERT-bold.log ------------------------------------------- /autofs/space/cognito_005/users/raij/avml_fmri_mcseparately/avml19_session_BRISI13_ISI1TR_BERT RunList: 004 005 006 targstem: Undefined variable.
Notice that I am using the building 120 "cognito" installation where: /usr/local/feeesurfer = /space/cognito/24/opt/freesurfer/centos4.0
Bests,
Tommi
raij@nmr.mgh.harvard.edu wrote:
Hi Doug,
The issue is motion correction in FS-FAST. The environment is nmr-dev-env.
mc-sess flag -perrun is documented like this: "MC each run separately (targ=mid)".
- Does "targ=mid" implicate that the target, within each run, is the
image half way through the run?
Yes
- Does this equal to using the mc-sess -rlf runlistfile flag, and
changing the contents of the runlistfile to match each of the run numbers, one at a time?
Almost. Method #2 will use the first image instead of the middle image.
doug
Thanks,
Tommi
Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
raij@nmr.mgh.harvard.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
OK, I think this is fixed. Fixed version will be live tomorrow. If you need it before then (or just want to test it), use:
/space/greve/1/users/greve/freesurfer/fsfast/bin/mc-sess
doug
raij@nmr.mgh.harvard.edu wrote:
mc-sess with -perrun failed with the output: targstem: Undefined variable.
*** Bug report: ***
on machine ai
source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri
cd /space/cognito/5/users/raij/avml_fmri_mcseparately/avml19_session_BRISI13_ISI1TR_BERT
which mc-sess /usr/local/freesurfer/dev/fsfast/bin/mc-sess
mc-sess -sf sessid -df sesspar -perrun
Logfile is /autofs/space/cognito_005/users/raij/avml_fmri_mcseparately/avml19_session_BRISI13_ISI1TR_BERT/log/mc-avml19_session_BRISI13_ISI1TR_BERT-bold.log
/autofs/space/cognito_005/users/raij/avml_fmri_mcseparately/avml19_session_BRISI13_ISI1TR_BERT RunList: 004 005 006 targstem: Undefined variable.
Notice that I am using the building 120 "cognito" installation where: /usr/local/feeesurfer = /space/cognito/24/opt/freesurfer/centos4.0
Bests,
Tommi
raij@nmr.mgh.harvard.edu wrote:
Hi Doug,
The issue is motion correction in FS-FAST. The environment is nmr-dev-env.
mc-sess flag -perrun is documented like this: "MC each run separately (targ=mid)".
- Does "targ=mid" implicate that the target, within each run, is the
image half way through the run?
Yes
- Does this equal to using the mc-sess -rlf runlistfile flag, and
changing the contents of the runlistfile to match each of the run numbers, one at a time?
Almost. Method #2 will use the first image instead of the middle image.
doug
Thanks,
Tommi
Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
raij@nmr.mgh.harvard.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
raij＠nmr.mgh.harvard.edu