Hi again, My apologies for the barrage of emails! I was able to do mri_segstats on V1 labels for pial_lgi using the following:
mri_segstats --label-thresh .5 --slabel $s lh $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats However, now I'm having trouble with bringing all of the data into one table using aparcstats2table. I found online how to get the data for aparc annotation ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033069.html) and tried to adapt to the labels. Here is what I've tried: aparcstats2table --subjects BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 --hemi lh --meas thickness --parc V1.thresh.label.LGI --tablefile lh.V1.thresh.label.LGI.txt I get the following output when I do this: SUBJECTS_DIR : /Applications/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File "/Applications/freesurfer/bin/aparcstats2table", line 371, in <module> parc_measure_map = parsed.parse(options.meas) File "/Applications/freesurfer/bin/fsutils.py", line 207, in parse val = float(strlist[self.measure_column_map[measure]]) ValueError: could not convert string to float: Seg0000 I've attached an example of the file created during mri_segstats in case that helps. Thanks! Krista On Wed, Mar 5, 2014 at 1:21 PM, krista kelly <krista.kell...@gmail.com>wrote: > Perfect, it works thanks! > > > On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> sorry, it is --slabel >> btw, there is documentation. If you run it without options it gives you a >> list of arguments as well as examples >> doug >> >> On 03/05/2014 11:32 AM, krista kelly wrote: >> >>> Thanks Doug, but when I try this I get the following error: Option >>> --label unknown >>> >>> >>> On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve < >>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> >>> try >>> mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i >>> $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats >>> >>> On 03/05/2014 11:15 AM, krista kelly wrote: >>> > Hello, >>> > >>> > I would like to extract the pial_lgi data from Freesurfer's >>> V1.thresh >>> > labels but can't quite figure it out. I've tried adapting the >>> commands >>> > from the LGI Freesurfer tutorial as such: >>> > >>> > mri_segstats --label-thresh BV20 lh V1.thresh.label --i >>> > $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats >>> > >>> > I've also tried >>> > >>> > mris_anatomical_stats -l lh.V1.thresh.label -f >>> > BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi >>> > >>> > but I've had no luck with either. >>> > >>> > I would appreciate any help! >>> > >>> > Thanks, >>> > Krista >>> > >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer@nmr.mgh.harvard.edu >>> <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> >>> Phone Number: 617-724-2358 <tel:617-724-2358> >>> Fax: 617-726-7422 <tel:617-726-7422> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> <http://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 <mailto:freesur...@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. >>> >>> >>> >> -- >> 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/ >> >> >
lh.V1.thresh.label.LGI.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.
