Hi Doug So the pixel values are 0 and 1 *in the original .mnc*. It seems that after performing mri_vol2surf they become 0 and 255, and stay this way after mri_surf2surf as well. So, why would mri_vol2surf be changing the values?
Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Thu, Oct 6, 2016 at 11:30 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > What are the pixel values in the mgz file? They should be binary, ie, 1=in > a label, 0 = out of label > > On 10/6/16 10:22 AM, Trisanna Sprung-Much wrote: > > 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 <gr...@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 >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 >> > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> > <mailto:gr...@nmr.mgh.harvard.edu >> > <mailto:gr...@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 >> > > 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 >> > <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/ >> > <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 >> > <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>> >> > > >> > > >> > > 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 >> > <http://www.partners.org/complianceline> >> > > <http://www.partners.org/complianceline >> > <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 >> > <mailto:Freesurfer@nmr.mgh.harvard.edu> >> > > 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 >> > 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 >> > <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/ >> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.har >> vard.edu> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > <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 > listfreesur...@nmr.mgh.harvard.eduhttps://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. > >
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