Yeah, I was thinking that might be easier. On my previous run (the one that has a fmc.mcdat file) I re-ran the script calling for fmcpr.mcdat instead of fmc.mcdat. The results changed quite a bit (average displacement being .11mm rather than .16mm). How does per-run vs. per-session motion calculation differ?
Thanks for your advice! Anais ________________________________________ From: [email protected] [[email protected]] on behalf of Douglas N Greve [[email protected]] Sent: Friday, July 10, 2015 11:57 AM To: [email protected] Subject: Re: [Freesurfer] fmc.mcdat file missing you probably did use -per-session at some point, or maybe it was from a pre-version-5 run. Why not just point your displacement script at the fmcpr.dat? It is a lot easier than re-running all the preprocessing (which would also needlessly take up a lot of space) On 07/10/2015 11:52 AM, Rodriguez-Thompson, Anais wrote: > Hi Doug, > > There is an fmcpr.mcdat file. However we use fmc.mcdat in a script that > calculates average displacement during each run. I will run the commands > again using -per-session, thanks! > > Do you know why our other runs would have a fmc.mcdat but not these? We've > never run our commands using -per-session before. > > Thanks, > Anais > ________________________________________ > From: [email protected] > [[email protected]] on behalf of Douglas N Greve > [[email protected]] > Sent: Friday, July 10, 2015 11:24 AM > To: [email protected] > Subject: Re: [Freesurfer] fmc.mcdat file missing > > Is there an fmcpr.mcdat file? That is the one produced with using > -per-run (fmc.mcdat is for -per-session) > > On 07/10/2015 11:16 AM, Rodriguez-Thompson, Anais wrote: >> Hi Freesurfer experts, >> >> Currently I'm having issues generating a fmc.mcdat file for one of my >> subjects. We had previously unpacked and preprocessed a resting run for >> NNC0101 (/cluster/roffman/users/Stable5_PerRun/NNC0101/resting/004), which >> does have this file. I just recently unpacked two more resting runs (021 and >> 022), which do not have this file despite pre-processing the runs. I have a >> file called fmcpr.mcdat, but not fmc.mcdat. >> >> These are the commands I ran (working in 5.3): >> >> recon-all -autorecon-all -s NNC0101 >> preproc-sess -s NNC0101 -d $SUBJECTS_DIR -fsd resting -fwhm 5 -per-run >> register-sess -s NNC0101 -d $SUBJECTS_DIR -per-run -fsd resting >> >> I also ran a mc-sess command to try to generate this file (although I think >> it usually is generated during preproc-sess): >> >> mc-sess -s NNC0101 -d $SUBJECTS_DIR -fsd resting -per-run >> >> Do you know why I'm missing this file and how I can generate it? >> >> Thanks for your help! >> >> Anais >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > 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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] 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.
