Hi Joel
there is internal code for this where we create a spatial lookup/hash
table and use it to find the closest vertex, but it is just a set of c
functions.
cheers
Bruce
On Tue, 4 Sep 2018, Bruss, Joel E wrote:
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Ah, that makes sense.
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Ah, that makes sense. Short of calculating a Euclidean distance between every
surface RAS and my point I'd like on the surface, then grabbing the one with
the shortest distance, is there a function/utility in FreeSurfer that will
generate the
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Hi Martin/Doug:
Still looking for an answer. Could not find a way to list the percentage change
values for each subject in a tabular form.
Thanks,
Anwar
On 2018-08-30, 12:15 PM, "Shatil, Anwar Shahadat"
wrote:
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> There is no linear transformation between the two. Vertex coordinate is
> equal to surfaceRAS when the point that you have selected is actually one
> of the vertices on the chosen surface. However, if the point is not on the
> surface, it finds the
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Hello Freesurfer experts,
When I exported the Destrieux and Desikian-Killiany volume values from
Freesurfer to SPSS I obtained "strange" eTIV values with 16 digits as
follows:
101,632,104,008.
134,253,072,953.
155,967,056,944.
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Close, but still not what I'm looking for. I start with orig.mgz file and have
RAS. I can convert that to voxel coordinates. I can then convert that to
TkReg RAS/SurfaceRAS coordinates, but what I'm looking for is the Vertex
coordinate. For
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Hi Joel,
you need to find the corresponding voxel ( using ras2vox transformation
matrix) and then apply your vox2ras-tkr matrix to it. it would give you the
tkrRAS coordinate.
cheers,
Ehsan.
On Tue, Sep 4, 2018 at 12:40 PM Bruss, Joel E wrote:
>
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Hello,
I'm extracting some stats from recon-all but noticed that it would stop running
in the middle (error message: end: Not in while/foreach) . Any suggestions on
how I could solve this problem would be greatly appreciated! Thank you so much
in
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If I load, say, orig.mgz and lh.pial, in FreeView and lay my cursor on a point,
I can see RAS (and surfaceRAS) as well as TKReg RAS (orig) coordinates.
Following the steps laid out on the CoordinateSystems web page I can convert
back and forth
Unfortunately, the disk that hosts the ftp data has died, so resolving this
might take a bit longer than expected. The new disk should be repopulated
within the next few days. Sorry about that everyone.
Best,
Andrew
On 9/3/18, 11:24 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
I'm not sure what this is referring to, but you should be very careful
flipping images. If you want to compare left and right, then use the
xhemi tool https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 9/4/18 10:41 AM, Martin Reuter wrote:
Hi Xiaoyu,
please keep the previous conversation as
what is your mris_convert command line?
On 9/3/18 4:10 PM, M. Jordan wrote:
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Hello,
I have a CT NIFTI coregistered to the MRI NIFTI used for reconAll.
When I export the .pial files to .vtk using mris_convert, they are
shifted with respect to the MRI. Is
Hi Xiaoyu,
please keep the previous conversation as inline citation below so I know what
we discussed before.
What I mean is to process every subject only once and not twice (with flipped
images, if that is what you did?).
Then run xhemi analysis on the subject-level. Invert the sign of
Hi Dani,
the regular FreeSurfer stream samples everything to 1mm isotropic. This is of
course problematic, if you have one group scanned at 1mm and the other at a
different resolution (as group differences could be affected by the different
resolutions). You would never know how much of what
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Hi,
I'm tyring to transform a bunch of MNI coordinates to subject's space using
mri_cvs_register and applyMorph. I have run the mri_cvs_register but
could'nt find detailed description of applyMorph. I appreciate any input
on what command should be
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Dear FreeSurfer experts,
Which tools would you recommend to compute quality metrics for FreeSurfer 6
output?
I would like to complement visual QC of the FreeSurfer segmentation output for
structural images with automated metrics, e.g., outlier
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