Right, one more thing. add --excludeid 0 On 03/05/2014 05:59 PM, krista kelly wrote: > Thanks Doug! That fixed it. But now I have two numbers in each file, > which do I use (see also attached file)? > > ColHeaders Index SegId NVertices Area_mm2 StructName > Mean > StdDev Min Max Range > 1 0 124241 81007.3 Seg0000 2.7306 0.6613 1.4985 > 4.4779 2.9795 > 2 1 3540 2225.6 Seg0001 2.4966 0.3254 2.0502 3.0296 > 0.9794 > > > > > > > > > > > > > > On Wed, Mar 5, 2014 at 5:07 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > Sorry, I gave you some bad advice. Only use --label-thresh with > labels that have a statistic that is non-zero (this is the last > column of the label file). Eg, in lh.V1.thresh.label, the stat is > always 0 (but it is non-zero in lh.V1.label). The stat is the > probability that the vertex is in the label, so you can choose the > threshold based on that. The lh.V1.thresh.label is for when the > stat is the max for V1 relative to the other labels (eg, V2). If > you select thresh=.5, you may miss places where V1 is the most > likely but still less than .5. I would probably use > lh.V1.thresh.label (and then do not spec --label-thresh) > > doug > > > > On 03/05/2014 03:40 PM, krista kelly wrote: > > Thanks Doug! I did that and it worked, but now here's another > problem: the values that I obtained for V1, V2, and cortex for > each subject are all the same. For example, BV20 left > hemisphere values for V1, V2, and cortex are all 2.7241 (same > thing happens for the right hemisphere). Maybe I can tell you > what I did step by step to see if you can find where I went > wrong. > > First, I did a for loop to run mri_segstats for each > participant for each label per hemisphere (here is an example > of V1): > > foreach s (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 MB19 MB20) <<hit enter>> > 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 <<hit enter>> > end <<hit enter>> > > for left V2 I ran: > > foreach s (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 MB19 MB20) <<hit enter>> > mri_segstats --label-thresh .5 --slabel $s lh > $SUBJECTS_DIR/$s/label/lh.V2.thresh.label --i > $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum > $SUBJECTS_DIR/$s/stats/lh.V2.thresh.label.LGI.stats <<hit enter>> > end <<hit enter>> > > and for left cortex I ran: > foreach s (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 MB19 MB20) <<hit enter>> > mri_segstats --label-thresh .5 --slabel $s lh > $SUBJECTS_DIR/$s/label/lh.cortex --i > $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum > $SUBJECTS_DIR/$s/stats/lh.cortex.LGI.stats > end <<hit enter>> > > > This is where the problem must be occurring since all files > created during these commands show the same files per > hemisphere. I've attached three files created during > mri_segstats (left V1, V2, cortex.stats) for one participant. > I've also attached files created during asegstats2table to > show how all values are the same for each label for all > participants (V1, V2, cortex.LGI.txt). > > If anyone has any insight into the problem, that would be great! > > Best, > Krista > > > On Wed, Mar 5, 2014 at 1:54 PM, 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: > > > 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> > <mailto:krista.kell...@gmail.com > <mailto:krista.kell...@gmail.com>> > <mailto:krista.kell...@gmail.com > <mailto:krista.kell...@gmail.com> > > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto: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>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto: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>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto: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>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto: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>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel: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>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > <tel: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> > > <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> > > <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>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto: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>> > <tel: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>> <tel: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> > > <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> > > <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 <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/ > > > > -- > 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
