ong to the 3rd ventricle.
>
> I hope that is what you were asking?
>
> Tim
>
>> On June 17, 2020 at 11:41 AM Ian Hardingham wrote:
>>
>>
>> External Email - Use Caution
>>
>> Are the ventricles currently in V6 Surf directory as a set of vertices,
>
of the various Ventricles. Are they
included in the freesurfer segmentation images with a specific code?
If not, what approach would you use?
Thanks,
Ian
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https
. Greve wrote:
Yes, I put a linux version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids
On 6/16/2020 10:32 AM, Ian Hardingham wrote:
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Is this only in FSL 7 Doug? I can't find it in 6.
On 16/06/2020 14:59, Douglas N. Greve wrote:
Try
External Email - Use Caution
Thank you so much Doug.
Ian
On 16/06/2020 15:44, Douglas N. Greve wrote:
Yes, I put a linux version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids
On 6/16/2020 10:32 AM, Ian Hardingham wrote:
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looking to find the center of the various Ventricles. Are they
included in the freesurfer segmentation images with a specific code?
If not, what approach would you use?
Thanks,
Ian
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performed to an "average" subject on a sphere. Can you please
tell me
which subject this is? Is it SUBJECTS_DIR/fsaverage? If so, what is
SUBJECTS_DIR/fsaverage/lh.sphere.reg a registration to? If not,
where can I
find the subject that recon-all registers to?
Thanks,
Ia
't have my head around
just yet - thank you for your patience.
Ian
On 07/05/2020 22:45, Douglas N. Greve wrote:
Isn't that what you got from the mri_surf2surf command?
On 5/7/2020 3:08 PM, Ian Hardingham wrote:
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22:45, Douglas N. Greve wrote:
Isn't that what you got from the mri_surf2surf command?
On 5/7/2020 3:08 PM, Ian Hardingham wrote:
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Thanks Doug - yes, I'd like the vertex coordinates in the same format
as the local subject surface files are in.
On 07/05
this mean an affine (12dof) transform? And what information do
you want? An XYZ coordinate?
On 5/7/2020 11:06 AM, Ian Hardingham wrote:
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I'd like to get a set of points to compare across several brains, so
that the nth point in brain A is in roughly the
to positions on the target
brain (which may well not be vertices in the target geometry.)
On 07/05/2020 15:59, Douglas N. Greve wrote:
I don't understand. What is the difference between the target brain
and the target subject's vertices?
On 5/7/2020 2:17 AM, Ian Hardingham wrote
should be the number of vertices in the target subject (and is in the
typical range for an individual subject)
On 5/6/2020 10:21 AM, Ian Hardingham wrote:
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FSLInfo attached, thanks Bruce.
When trying to run freeview I get "freeview.bin: error while lo
e:
You should load the surfaces in FV. If it load in FV ok but
nibable is
crashing, you should contact them.
On 5/5/2020 1:05 PM, Ian Hardingham wrote:
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Thank you both.
I've made edits and these are the current commands:
mri_surf2surf --hemi lh
, but the interface might be a
little easier
On 5/5/2020 12:49 PM, Bruce Fischl wrote:
no definitely not "w" format, which we don't use for anything
anymore. YOu should use tval-xyz also I think
On Tue, 5 May 2020, Ian Hardingham wrote:
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It wo
--srcsubject fsaverage --sval-xyz pial
--trgsubject fs_target --trgsurfval ./registered_rh.pial --trg_type w
The white calls output seems to be fine, but the pial ones aren't. I
somewhat naively trued trg_type pial but that wasn't correct.
On 05/05/2020 17:33, Ian Hardingham wrote:
Thanks Bruce
", but if
it's ".pial" it outputs ".pial.w", which I find a little curious.
Ian
On 05/05/2020 16:34, Bruce Fischl wrote:
yes, check out options like:
--sval-xyz
if you need further help though I'll have to defer to Doug :)
Bruce
On Tue, 5 May 2020, Ian Hardingha
.
Any helpers on how to achieve this?
Thanks,
Ian
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Morning Freesurfers.
Can you describe how the FS stat Total cortical gray matter volume is
calculated from the files in the freesurfer subject directory? Is there
an mgz file where each voxel has an estimated percentage grey matter
here as the
nu_correct, built from:
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