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, Tommiraij@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)". 1. Does "targ=mid" implicate that the target, within each run, is the image half way through the run?Yes2. 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. dougThanks, 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
-- 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