External Email - Use Caution
Hi there,
I am looking for instructions on how to create/edit my own labels directly on
surfaces using the latest version of Freesurfer/Freeview but I cannot seem to
find this documentation. My understanding is that an annotation file has
multiple l
External Email - Use Caution
Hi there
As a follow-up to my earlier email, I figured it out. I can create 1 label in
an annotation and simply have to assign an "index" value before saving.
Could you please confirm that this is the best way to go about create a new
label on a sur
If you just need one label you can create a label instead of annotations. You
can click “Path/Custom Fill” icon on the left panel, draw a closed path and use
custom fill tool to draw a label. Just like in TkSurfer if you have used it
before.
[cid:15CC1D35-3F5C-4946-A2BE-C6B73EBEC9EF@lan]
On J
External Email - Use Caution
Hi Ruopeng
This makes a lot more sense! And I figured out how to erase parts and add parts
to the same label.
Many thanks!
Trisanna Sprung-Much, PhD
McGill University
Montreal Neurological Institute
--
From: on behalf of "Wang, Ruopeng"
Reply-T
Hi Pietro,
I’m not familiar with AnatomiCuts so I can’t answer that part of your question.
For visualizing tracts, freeview can load .trk files generated by TrackVis/DTK.
They do not support embedded colors. It can also load tract volumes in 4D mgz
format, which do support embedded colors.
Bes
External Email - Use Caution
Hello FreeSurfer Experts,
If I need to manually edit both the brainmask.mgz and the wm.mgz in a
FreeSurfer, what are the recommended flags when rerunning recon-all with the
edits (-all, -autorecon2, etc)? Or is it recommended to run an edited volume
Dear all,
We’re seeking to hire a postdoc at the Martinos to work on a cool new project
involving human brains, 3D shape scanning with infrared, registration, and
machine learning. Essentially, all the good stuff.
More information here:
https://scholar.harvard.edu/iglesias/jobs
https://scholar.ha
That’s right. The .trk files generated by AnatomiCuts have a color tag saved in
a private location in the header, as I remember now. I think it is only
effective when loaded as tract cluster. Are you going to write .trk files by
yourself? If so I can point you to where to write the color bytes i
External Email - Use Caution
Thank you Doug!
I have another question related to voxel size.
In the GTM PVC pipeline, the gtm.stats.dat file also outputs the NVoxels.
However, is there a way to easily retrieve the volume (instead of NVoxels)
for each ROI within the gtm.stats file?
External Email - Use Caution
Hi Ruopeng,
thanks for the reply.
Actually, I’m not really interested in using AnatomiCuts, but since I tried it
I wanted to signal the error.
Concerning the embedded colors in FreeView, I was thinking they were value
inserted as `data_per_streamli
External Email - Use Caution
Yes it would be helpful. I usually Dipy interface to write .trk, and thus
adding a field to the header should be a simple operation.
However, I was aiming at coloring each streamline diffferently with some random
picked color. I guess it is not possib
External Email - Use Caution
Hello! I'm experiencing an error while I try to use recon-all in a T1 MRI
image, the following error message appears:
"[...]
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading mri_src fr
12 matches
Mail list logo
