Re: [Freesurfer] mri_average vs mri_concat

2016-11-07 Thread Douglas N Greve
I did not see binary values. The values were 255 in the mnc volume. The caveat here is that I can only read it in using FS, so if there is something burried in the FS code that causes the values to change from 1 to 255, I might not see it. Is there a minc viewer you can use to resolve this? O

Re: [Freesurfer] mri_average vs mri_concat

2016-11-07 Thread Douglas N Greve
It looks like the input has values of 255 and 0, not 1 and 0. How do you verify that the values are 0 and 1? On 11/07/2016 03:43 PM, Trisanna Sprung-Much wrote: > Hi Doug > > I have uploaded the label_aalf.mnc and testsurfaceoverlay.mgz > > Here is an example of the mri_vol2surf that I use > > *

Re: [Freesurfer] mri_average vs mri_concat

2016-11-01 Thread Douglas N Greve
Can you send me the mri_concat command and also upload the input files to our filedrop? https://gate.nmr.mgh.harvard.edu/filedrop2 On 11/01/2016 02:31 PM, Trisanna Sprung-Much wrote: > Does anyone know who wrote the script for mri_concat? I would really > like to get this figured out. > > thank

Re: [Freesurfer] mri_average vs mri_concat

2016-11-01 Thread Trisanna Sprung-Much
Does anyone know who wrote the script for mri_concat? I would really like to get this figured out. thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Oct 21, 2016 at 12:13 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wr

Re: [Freesurfer] mri_average vs mri_concat

2016-10-21 Thread Trisanna Sprung-Much
thanks Bruce - I had indeed used this months ago but at the workshop this semester Doug had suggested mri_concat as it is a newer command and also doesn't blur the data. I am just having problems creating percentage values with mri_concat. *Would you know why mri_vol2surf is taking a binary minc f

Re: [Freesurfer] mri_average vs mri_concat

2016-10-21 Thread Bruce Fischl
Hi Trisanna not sure about mri_concat, but mri_average -noconform -p ... should do the trick cheers Bruce On Wed, 19 Oct 2016, Trisanna Sprung-Much wrote: Something weird is happening with mri_vol2surf - even though the data looks great, the values are odd which carries over when I try to a

Re: [Freesurfer] mri_average vs mri_concat

2016-10-19 Thread Trisanna Sprung-Much
Something weird is happening with mri_vol2surf - even though the data looks great, the values are odd which carries over when I try to average with mri_concat. I would just like to get percentage values with mri_concat. thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in

Re: [Freesurfer] mri_average vs mri_concat

2016-10-12 Thread Douglas N Greve
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 st

Re: [Freesurfer] mri_average vs mri_concat

2016-10-11 Thread Trisanna Sprung-Much
Hi Doug Any thoughts on this? Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Thu, Oct 6, 2016 at 10:37 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > Hi Doug > > So the pixel values are 0 and 1 *in the original .mnc*. I

Re: [Freesurfer] mri_average vs mri_concat

2016-10-06 Thread Trisanna Sprung-Much
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

Re: [Freesurfer] mri_average vs mri_concat

2016-10-06 Thread Douglas Greve
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,

Re: [Freesurfer] mri_average vs mri_concat

2016-10-06 Thread Trisanna Sprung-Much
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 wrote: > what is a labeled vertex? What file format? mgz? annot? > > > On 10/05/2016 05:03 PM, Trisanna Sprung-Much wrot

Re: [Freesurfer] mri_average vs mri_concat

2016-10-05 Thread Douglas N Greve
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 cre

Re: [Freesurfer] mri_average vs mri_concat

2016-10-05 Thread Trisanna Sprung-Much
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

Re: [Freesurfer] mri_average vs mri_concat

2016-10-05 Thread Douglas N Greve
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,

Re: [Freesurfer] mri_average vs mri_concat

2016-10-05 Thread Douglas N Greve
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 Fre