Overlays in .mgz format using mri_vol2surf
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Oct 5, 2016 at 5:56 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
what is a labeled vertex? What file format? mgz? annot?
On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrote:
the source files are labelled vertices from 20 subjects:
-T1s were labelled using an MNI software -Surfaces were created in FreeSurfer and surface overlays of the labels were created using mri_vol2surf -Surface overlays were registered to fsaverage using mri_surf2surf and then averaged to create a probability map, originally using "mri_average"
So, essentially the overlays are binary files of my labels I believe
- I can send one over if you wish.
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Oct 5, 2016 at 4:52 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what are the source files ("all files"). What data type, value range, where did they come from? On 10/05/2016 04:48 PM, Trisanna Sprung-Much wrote: > Hi Doug > > So, of course now it works without --keep-filetype... :p it looks > pretty much the same was when I use --keep-filetype. > > However, the values of Min and Max are still odd (out of 256) - see > snapshot > > Trisanna > > > > > > -- > Ph.D. Candidate > McGill University > Integrated Program in Neuroscience > Psychology > > > On Wed, Oct 5, 2016 at 4:23 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Depending upon the type of the data, the --keep-datatype may mess > things > up quite a bit. What happens if you don't include that? It will not > create an annotation. maybe you mean some other file type? > > > On 10/05/2016 02:36 PM, Trisanna Sprung-Much wrote: > > > > Hi Doug > > > > I spoke with you at the Freesurfer tutorial last week about using > > mri_average to average my sulcal labels and get a probability map on > > fsaverage. You had suggested using "mri_concat" instead, which is a > > newer command. So, I performed the following command: > > > > *mri_concat all files --o output.mgz --mean --keep-datatype* > > > > I had to put --keep-datatype or else it tried to create an annot > file. > > > > This worked just fine. > > > > My question then is concerning *the min and max values *when this > > average is overlayed in Freeview. See the snapshot attached. The > > values seem to be based on 256 instead of percentage and this is > what > > happens when I used "mri_average" without specifying the "-p". Is > > there a way to illustrate the values in percentage in a similar way > > with mri_concat? > > > > Many thanks! > > > > Trisanna > > > > > > -- > > Ph.D. Candidate > > McGill University > > Integrated Program in Neuroscience > > Psychology > > > > > > > > _______________________________________________ > > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> > <https://gate.nmr.mgh.harvard.edu/filedrop2 <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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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/
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