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
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
>
> *
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
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
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
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
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
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
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
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
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,
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
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
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
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,
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
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