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Dear experts,
We are working with a large MRI dataset (FLAIR, T1) and we are performing
recon-all based on the 3D T1. At the end, no error is detected but the
visualization of the pial, white and inflated surfaces in freeview is somehow
bad as you c
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These are the same ROIs, just labeled differently by me late at night. They
are all normalized by the ICV. Just didn't add the N next to the ROI in a
different row.
Good point. I am not correcting for gradient distortions. Will do.
Many thanks
AJ
If they are not part of the T1w series, then you can delete them (but
then they should not have caused the error). If they are part of the
series, then they are probably corrupted or perhaps the output of a very
aggressive anonymization.
On 11/25/2021 8:40 AM, Alison McDonnell wrote:
Are you correcting for gradient distortion? That could easily make 2%.
It looks like you used different ROIs in your comparisons.
On 11/28/2021 10:14 PM, AJ wrote:
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Many thanks for this. My experience so far with SAMSEG,
SynthSeg---small sample so far. A
This is a bug. I've put a new version of mri_annotation2label here:
https://gate.nmr.mgh.harvard.edu/safelinks/greve/
username 'guest'
password 'collab'
copy it into $FREESUFER/bin (after making a copy of the one that is there).
On 11/22/2021 12:23 PM, Dr. Cornelius Kronlage wrote:
> Ex
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Many thanks for this. My experience so far with SAMSEG, SynthSeg---small
sample so far. All images were obtained 3DT1 isomeric voxel. Just wanted
to see how the two pipelines would compare.
2 subjects who went on 6 different clinical scanners, GE or
That will work; it may be clearer to use mris_fwhm, eg,
mris_fwhm --smooth-only --s sub-0006 --hemi lh --fwhm 5 --cortex --i
input --o output
On 11/26/2021 6:48 AM, Mason Wells wrote:
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Hi Experts,
This question may have been addressed elsewhereon the lis
For volumes, load labels using the "Load ROI..." under the File menu
For surfaces, use the "Load" button in the "Label" section
On 11/23/2021 2:44 PM, Shapiro, Noah Lorenz wrote:
Hello,
I am very new to FreeSurfer, and I was going through the tutorials and
bumped into difficulties when loading
Just add -cw256 to the recon-all command line
On 11/23/2021 8:34 AM, Alison McDonnell wrote:
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Hi Tim,
I looked at orig.mgz and it seemed fine and could see the whole head.
i dont know what is meant by the flag -cw256 error. I am taking over a
project from
Can you send some pictures?
On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:
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Hi,
I am editing subjects for a research project. After reconstruction,
some parts of the brain are not included in the segmentation. Often,
some parts of the temporal lobe and the
Yes, but if there is an anat2orig2diff.bbr.lta file, use that instead
On 11/22/2021 12:48 PM, Zeng, Qi wrote:
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Sorry for the trouble, I seemed to find the registration matrix
located in xfms/anatorig2diff.bbr.dat. Is that one correct?
Best,
Jackie
On M
I noticed that you are explicitly setting the mask and funcstem in
mkanalysis-sess. Is there a reason for that? Also, I'd set -poly to 5.
On 11/21/2021 1:11 PM, Hiersche, Kelly J. wrote:
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Hello FreeSurfer Developers,
First, I am new to using Freesurfer, so
I see what you mean, though I don't think either one look that great.
The first thing to do is to backup and look at the registration to
fsaverage_sym by mapping the lh and rh curv to lh.fsaverage_sym and see
if the curv patterns match up with those in fsaverage_sym and to each
other (use mris_
That is a label atlas; you cannot run that through FS. You will need a
t1-weighted image to use as input to recon-all to start.
On 11/19/2021 1:59 PM, Flanagan, Shawn D wrote:
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Hello,
I would like to use the Brainnectome atlas for cortical thickness
analy
Also samseg, see https://pubmed.ncbi.nlm.nih.gov/33940143/
On 11/26/2021 11:16 AM, Fischl, Bruce wrote:
Hi AJ
you might try SynthSeg, as that is one of the advantages of it - it
isn't biased towards any particular MRI sequence
cheers
Bruce
Sure. I should add that because the method is sequence agnostic doesn’t mean
the results won’t be biased by differences in contrast in the input sequence.
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of AJ
Sent: Saturday, November 27, 2021 11:03 PM
To: Freesurfer support list
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