use asegstats2table (I know, it's confusing:) doug
On 03/05/2014 01:42 PM, krista kelly wrote: > 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 > <mailto: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 <mailto: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> > <mailto: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> > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > > <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:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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. > > > > -- > 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/ > > > -- 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
