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Thanks for the reply Doug.
I'm looking for the same number of verts as the *subject* - maybe it's
as simple as I should be registering the subjects *to* the FS average
subject? But the problem is that I want the points in subject space,
not average
Ian, it seems like you want two different things. When you run
mri_surf2surf, it gives you an output that has the same number of
vertices as the target which would allow you to do the one-to-one
comparison that you want to do. But at the same time, there seems to be
a problem with having the sa
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Thanks Tim.
I'd like a set of points on the surface to compare across subjects,
where there are the same number of points for each subject and they're
roughly in the same "physiological position" on each subject. So again,
if on my atlas I have a p
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I'm just going to try this again, but this time with a different command:
mris_apply_reg --src-xyz
/usr/local/freesurfer/subjects/fsaverage/surf/lh.white --trg
/home/ian/lh_reg.white --streg
/usr/local/freesurfer/subjects/fsaverage/surf/lh.sphere.re
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The registration registers the meshes, but it does not alter the number of
vertices in them. There is no 1-to-1 correspondence between the vertices of the
2 meshes.
May I ask why you need this? What do you want to achieve?
Tim
> On May 11, 2020 at
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I don't see how it's possible I got a comparable list of points when the
input was in the order of 300k verts, and the ouput was 180k verts - I
would need the number of output verts to be exactly the same as the
number of input verts.
On 07/05/2020
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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 07/05/2020 19:02, Douglas N. Greve wrote:
It comes down to how you want to define "roughly in the same place".
Does this mean an affin
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 07/05/2020 19:02, Douglas N. Greve wrot
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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 same place as the nth
point in brain B - so I'd like to have an agreed upon set of vertices
(the source brain's vertices) translated t
It comes down to how you want to define "roughly in the same place".
Does 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 ac
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:
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Ok, thanks Doug, but I'm looking to get the positions of the source
vertexes on the target brain, not the tar
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Ok, thanks Doug, but I'm looking to get the positions of the source
vertexes on the target brain, not the target subject's vertices...
On 06/05/2020 23:07, Douglas N. Greve wrote:
That looks like it could be right. It has 102,020 vertices, which
shou
That looks like it could be right. It has 102,020 vertices, which 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.
W
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FSLInfo attached, thanks Bruce.
When trying to run freeview I get "freeview.bin: error while loading
shared libraries: libpng12.so.0: cannot open shared object file: No such
file or directory" - do I need to add /usr/local/freesurfer/lib/* to
path o
sorry, I'm going to defer to Doug on surf2surf
On Wed, 6 May 2020, Ian
Hardingham wrote:
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Thanks Bruce.
So a reminder I'm calling:
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white --trgsubject
fs_target --tval-xyz {input_dir}/T1_ni
hmm, that is not an icosahedral surface, which should have 160K vertices.
Can you check your input surface? You'll also need to fix your freeview
problem, but someone else will have to help you with that
On Wed, 6 May
2020, Ian Hardingham wrote:
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can you run mris_info on the output surfcae? And maybe send a freeview
snapshot of it (in 3d rendering mode)
On Wed, 6 May 2020, Ian wrote:
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Thanks Tim and Doug.
I have the files generating and loading properly now, but I'm not convinced
it's giving the o
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Thanks Tim and Doug.
I have the files generating and loading properly now, but I'm not
convinced it's giving the output I'm looking for.
I am trying to convert the "fsaverage" subject's surface coordinates to
my own subject's surface space.
FSave
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Just a note: there should be no need to convert to gifti, nibabel can read the
FreeSurer binary surface format directly with
`nibabel.freesurfer.io.read_geometry()`.
The docs are here:
https://nipy.org/nibabel/reference/nibabel.freesurfer.html#nibab
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Thank you both.
I've made edits and these are the current commands:
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz
--trgsurfval {output_dir}/registered_lh.white
mri_surf2
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It would appear not, as I'm getting an error on my pial output files but
not my white ones. Here are my commands:
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white
--trgsubject fs_target --trgsurfval ./registered_lh.white --trg_type w
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Thanks Bruce, extremely helpful.
Can I just check that the "w" format is what is used by both the
lh/rh.pial and the lh/rh.white files? I only ask because my surf2surf
command outputs the exact output filename if the end is ".white", but if
it's ".
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Bruce, I've read the docs on mri_surf2surf - I wish to get surface files
out (again, lh.pial, rh.pial, lh.white, and rh.white) rather than values
for something such as thickness - is there an option for mri_surf2surf
to allow this?
On 05/05/2020 14:
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 --srcsubject
Don't specify a --trg_type. But add --tval-xyz
mris_apply_reg will do the same thing, 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
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 would appear not, as I'm getting an error on my pial output files but not
my white ones. Here
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 Hardingham wrote:
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Bruce, I've read the docs on mri_surf2surf - I wish to get surface files out
(again, lh.pial, rh
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Hi Freesurfers.
I have a subject S with recon-all having been run on it.
I have the subject-specific surface files /surf/lh.pial, rh.pial,
lh.white, and rh.white.
I would like an Atlas's lh.pial, rh.pial, lh.white, and rh.white in
subject space.
Hi Ian
you can use mri_surf2surf to map surfaces between subjects, but our atlas
isn't really a surface. You can use the surfaces in the fsaverage dir, but
they are meant for visualization and are much smoother than individuals
cheers
Bruce
On Tue, 5 May
2020, Ian wrote:
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