alright. Thank you so much! ----- Ursprüngliche Mail ----- Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 17:45:38 Betreff: Re: [Freesurfer] extract area.pial stats
No. The program is from version 6 so it is expecting v6 naming conventions On 02/08/2017 11:38 AM, Clara Kühn wrote: > 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 > > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
