So the result of step 4 looks ok on the volume but not on the surface?
How are you putting the volume-based ROI back on the surface? This is
tricky because now it will be a 1mm thin label. You should use
mri_vol2surf for this, maybe selecting the --projfrac-max to make sure
that it grabs the
Doug-
Any further thoughts on this?
On 10/05/2016 04:47 PM, Joel Bruss wrote:
> Doug-
>
> I'm sooo close but something isn't right. I've run:
>
> 1)mri_vol2sur to sampel the ROI in subA surface space
>
> 2) mri_cor2label to convert it to a label
>
> 3) mri_label2lable to push it to subB
>
> 4)
mri_label2vol will transfer it into the volume, no need for surf2vol
On 10/04/2016 03:54 PM, Joel Bruss wrote:
> Doug (Bruce and Trisanna)-
>
> Thank you all for your help. I do, indeed, have a volume, then label,
> and see now how to load and view this properly. I've gotten through the
>
Doug (Bruce and Trisanna)-
Thank you all for your help. I do, indeed, have a volume, then label,
and see now how to load and view this properly. I've gotten through the
"label2label" step and now have a label (from subA) in subB space. If
I now want to back-project this label to subB's input
The rh.roiS.mgh file is a surface overlay (ie, one value per vertex),
not a surface itself (which would have a list of vertices, the XYZ for
each, and neighborhood relations). When you loaded rh.roiS.mgh as a
surface overlay, did you change the threshold to be 0.5? The default is
2, and if
Hi Joel
can you include the entire thread when responding? Usually overlay is a
suboption in freeview. So it would probably be something like:
freeview -f lh.inflated:overlay=lh.overlay.mgz
cheers
Bruce
On Tue, 4 Oct
2016, Joel Bruss wrote:
> .mgz format made no difference. I see no
.mgz format made no difference. I see no option for "overlay" in
freeview., I only get that option with tksurfer. The image is blank
when loaded as a volume in freeview. It loads forever when I try to
load it as a surface (I just get the 0-100% progress bar conintually
loading with no end). If
I think it might have to do with the format of your output file - perhaps
try .mgz? This is what I used.
Then open the surface and use the "overlay" option to overlay your ROI as a
surface overlay.
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On
Sorry, it sent before I finished. I'll try this again.
On 09/30/2016 02:00 PM, Douglas N Greve wrote:
> First, bring up the ROI on the volume along with the surface in the
> volume. You can do this with FreeView. Make sure that the ROI intersects
> the surface.
Yes, this looks fine
> Then run
Doug-
I'm really sorry to keep pestering you about this but I just can't seem
to get this to work. See my replies below:
On 09/30/2016 02:00 PM, Douglas N Greve wrote:
> First, bring up the ROI on the volume along with the surface in the
> volume. You can do this with FreeView. Make sure that
Thanks a lot. I'll try this out.
On 09/30/2016 02:00 PM, Douglas N Greve wrote:
> First, bring up the ROI on the volume along with the surface in the
> volume. You can do this with FreeView. Make sure that the ROI intersects
> the surface. Then run mri_vol2surf so sample the binary ROI volume
First, bring up the ROI on the volume along with the surface in the
volume. You can do this with FreeView. Make sure that the ROI intersects
the surface. Then run mri_vol2surf so sample the binary ROI volume onto
the surface. You can view the ROI on the surface by loading it as an
overlay.
Ah, I see. The ROI will be subject-dependent (I want to do this for
multiple subjects) but the majority, if not all, should be cortical.
Any help you'd be willing to provide would be much appreciated.
On 09/29/2016 11:31 AM, Douglas N Greve wrote:
> The way you have it configured now, this is a
The way you have it configured now, this is a volume-based ROI, so you
need to use the volume-based reg method. This will map between the two
subjects using the affine (12 dof) talairach registration which will not
be as accurate as the surface-based registration. If this is a cortical
ROI, I
Another bump.
On 09/21/2016 04:18 PM, Joel Bruss wrote:
> I have two subjects, subA and subB. subA has a binary ROI mask, native
> space, that I'd like to place in subB's native space. Both subjects have
> been run through all stages of recon, edited, etc. Is there a better or
> easier way to
Anyone have any thoughts on this?
On 09/21/2016 04:18 PM, Joel Bruss wrote:
> I have two subjects, subA and subB. subA has a binary ROI mask, native
> space, that I'd like to place in subB's native space. Both subjects have
> been run through all stages of recon, edited, etc. Is there a better
I have two subjects, subA and subB. subA has a binary ROI mask, native
space, that I'd like to place in subB's native space. Both subjects have
been run through all stages of recon, edited, etc. Is there a better or
easier way to achieve this than what I've run?:
#Resample the native space
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