Thank you, I think it worked. I've attached the file again. There was one error message in the terminal output though:
atlas_icv (eTIV) = 1287829 mm^3 (det: 1.512705 ) /nobackup/etsch2/kids/prepost-61kids//ZF1K.base/mri/aseg.presurf.mgz doesn't exist, using old naming conventions Is that something to worry about? ----- Ursprüngliche Mail ----- Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 17:34:06 Betreff: Re: [Freesurfer] extract area.pial stats It either has to be in your path or you need to supply the full path when running it, like this $SUBJECTS_DIR/mris_anatomical_stats-doug On 02/08/2017 11:27 AM, Clara Kühn wrote: > I'm so sorry, I don't know anything about programming... > I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug > and tried to run the whole thing again like this: > > mris_anatomical_stats-doug -mgz -cortex > $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f > $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a > $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c > $SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial > > but then I got this error: > > bash: mris_anatomical_stats-doug: command not found > > > > ----- Ursprüngliche Mail ----- > Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Mittwoch, 8. Februar 2017 17:08:26 > Betreff: Re: [Freesurfer] extract area.pial stats > > You don't need to open it. Just download it and put it in your path. You > may want to call it something slightly differnt so that you don't > confuse it with the v5.3 version > > > On 02/08/2017 10:53 AM, Clara Kühn wrote: >> thanks. What kind of format is it? How do I open it? >> >> Cheers >> Clara >> >> ----- Ursprüngliche Mail ----- >> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> >> An: freesurfer@nmr.mgh.harvard.edu >> Gesendet: Mittwoch, 8. Februar 2017 16:43:47 >> Betreff: Re: [Freesurfer] extract area.pial stats >> >> Try this version (same as version 6) >> >> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats >> >> >> >> On 02/08/2017 04:55 AM, Clara Kühn wrote: >>> Hi Doug, >>> >>> thanks for your reply. I tried it out and attached the lh.aparc.pial.stats >>> file for you to take a look at. As far as I can tell it's still reporting >>> the white surface area. Or am I reading it wrong? >>> >>> Cheers Clara >>> >>> ----- Ursprüngliche Mail ----- >>> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> >>> An: freesurfer@nmr.mgh.harvard.edu >>> Gesendet: Mittwoch, 8. Februar 2017 00:15:22 >>> Betreff: Re: [Freesurfer] extract area.pial stats >>> >>> try >>> >>> cd $SUBJECTS_DIR/subject/surf >>> >>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f >>> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c >>> ../label/aparc.annot.ctab subject lh pial >>> >>> >>> On 2/7/17 4:48 AM, Clara Kühn wrote: >>>> Dear FreeSurfer experts, >>>> >>>> I'm trying to extract a total Pial Surface Area like it is extracted for >>>> White Surface Area in the ?h.aparc.stats file. I have tried this command >>>> but it doesn't seem to include Pial Surface Area: >>>> >>>> mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f >>>> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial >>>> >>>> How could I extract the total Pial Surface Area for each participant? >>>> >>>> Thank you for you help! >>>> Clara >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> _______________________________________________ >>> 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. >>> >>> >>> _______________________________________________ >>> 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
lh.aparc.pial.stats
Description: Binary data
_______________________________________________ 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.
