Thanks for your help! I'd like to run mkbrainmask-sess & inorm-sess under version 5.3.0
What I used to run are: mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd bold_retino However, since version 5.3.0 changed a lot, I tried: mkbrainmask-sess -s $SUBJECT -df sessdirfile -fsd bold_retino inorm-sess -s $SUBJECT -motioncor -df sessdirfile -fsd bold_retino It gives me an error: ERROR: could not determine file for /home/jbang/Projects/replay/epi/replay06/bold_retino/023/fmc ERROR: inorm failed Which part am I doing wrong? Thank you so much. Best, Ji Won 2016-03-04 17:13 GMT-05:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > 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. > >
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