Hmmm, I don't know what could be going on. Can you send the command line 
and all terminal output?


On 10/06/2016 10:37 PM, Trisanna Sprung-Much wrote:
> 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 <mailto: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 <mailto: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>
>>         <mailto: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>>
>>         >     <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:
>>         >     >
>>         >     >     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>>
>>         >     >     <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
>>         <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
>>         <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>>
>>         >     <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>>
>>         >     >   
>>          <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
>>         <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
>>         <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>>
>>         >     >   
>>          <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/
>>         <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/
>>         <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>>
>>         >     <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
>>         <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
>>         <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>>
>>         >     >     <http://www.partners.org/complianceline
>>         <http://www.partners.org/complianceline>
>>         >     <http://www.partners.org/complianceline
>>         <http://www.partners.org/complianceline>>> . If the e-mail
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>>         >     > _______________________________________________
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>>         <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>>
>>         >
>>         >
>>         >
>>         >
>>         > _______________________________________________
>>         > 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:Freesurfer@nmr.mgh.harvard.edu>
>>         https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>         <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>>
>>
>>
>>     _______________________________________________
>>     Freesurfer mailing list
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>>     <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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>     information in this e-mail is intended only for the person to whom
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-- 
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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
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