The functional stream changed a lot from version 4 to version 5. The commands and workflow are very different now
On 03/04/2016 04:31 PM, Ji Won Bang wrote: > Dear. Freesurfer experts. > > Hi. How are you? > > It might be very naive question. > > When using version 4.5.0 I used the command: > mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd > bold_retino > > However under the version 5.3.0, mkbrainmask-sess does not have -funcstem. > > May I use -maskstem instead of -funcstem? > > If so, after that, I tried: > inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd > bold_retino > > However, it complains that: > ERROR: cannot find > /home/jbang/Projects/replay/epi/replay06/bold_retino/masks/brain > You may need to run preproc-sess or mkbrainmask-sess to create a brain > mask > > Could you please help? > > Thank you very much. > > Best, > Ji Won > > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
