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Dear Freesurfer team,
I have a question about the inconsistency between the vertex read from
read_surf and vertex shown in Freeview.
I have a volume from the hippocampal subfield pipeline and I converted it to
surface mesh using
mri_tessellate mri/lh
On 3/21/2021 3:33 PM, Adam Li wrote:
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Hi,
I am a bit noob on FreeSurfer and coordinate systems and I had a few
questions. I am wondering if I have the |T1.mgz| file of FreeSurfer
after running recon-all and this is the 256^3 image re-scaled and
re-orien
Look in recon-all.log to find the command that creates the wmparc.mgz.
Run that command changing the aparc annot to your annot and the output
to a new file name. Look in wmparc.stats; at the top will be an
mri_segstats command line. Copy that command line changing the file
names as needed.
On
On 3/22/2021 2:56 PM, Jones, Richard wrote:
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>
> A couple of questions:-
> 1) Do you experience similar variability with the T2 and FLAIR options or is
> FLAIR more variable due to it's generally lower SNR?
I have not run it enough to really say. I would t
Do you want to do it on a voxel-wise (map) basis? I guess you could just run
mri_concat subj1/lesionmap.mni152.mgz subj2/lesionmap.mni152.mgz ...
subjN/lesionmap.mni152.mgz --o stack.lesionmaps.mgz
Then run a voxel-wise GLM on the stack. This tricky. You'll probably
want to smooth it some (mri_f
Can you send the recon-all.log file?
On 3/23/2021 3:31 PM, Taylor, Lisa Marie wrote:
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Hi,
This is the first time I have encountered this problem. I have a
participant that has been through recon all, but when trying to create
PET masks, the error that co
On 3/23/2021 4:54 PM, Devavrat Vartak wrote:
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Hello freesurfer experts,
I am using mri_label2vol to convert my surface drawn label (of
functional activity) to functional space (nifti) for more analysis (prf).
When I open the label file in text editor -
It looks like something is wrong with your input. For starters, the
voxel size looks huge. Run
mri_info subject/mri/orig/001.mgz
and send the result
On 3/23/2021 10:54 PM, Harkey, Thomas Jarrott wrote:
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Hello,
My name is Thomas Harkey and I am conducting r
On 3/24/2021 5:11 PM, Blanpain, Lou wrote:
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Hello,
I had the following 2 general questions regarding Freesurfer:
1. Is there an extensive list of anatomical labels for each atlas
used? For instance, what are all
The surface coordinates are in "tkregister" coordinates whereas freeview
is giving you scanner coordinates.
See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems for how
to convert between them
On 3/25/2021 7:14 AM, Shizuka Hayashi wrote:
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Dear F
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Hi there
I’d like to know if it is possible to create an average volume and average
surface of several subjects without having to incorporate the Talairach
transform and no transform at all.
Thank you,
Trisanna Sprung-Much
Research Associate
McGill
Sure, I guess you can just run mri_average. I think also if you specify the
file name for the transform as identity.nofile to any binary that takes an lta
file, the code will internally create an identity transform.
I won’t look pretty though….
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harv
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Thanks Bruce for your speedy response.
I am dealing with chimp scans and therefore am trying to avoid anything to do
with Talairach. The surfaces have reconstructed pretty nicely using recon-all,
but I’d like to create an average surface now.
I will
If you don't have a transform, how will you align the subjects into a
common space?
On 3/25/2021 10:19 AM, Trisanna Sprung-Much wrote:
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Hi there
I’d like to know if it is possible to create an average volume and
avera
You can just use the identity matrix. The white and pial surfaces will
be bogus (probably the inflated too), but the atlas created from it will
be valid
On 3/25/2021 11:17 AM, Trisanna Sprung-Much wrote:
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Thanks Bruce
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Hi Doug
The scans were registered (6 parameter) to a common chimp template prior to
input to recon-all. The surfaces have reconstructed nicely and match the input
volumes.
I would now like to create an average surface from these surfaces that are “in
If you have the transform in the form of an LTA file, I think all you
need to do is put it in the subject/mri/transforms folder, then spec
--xfrom your.lta when running make_average_subject
On 3/25/2021 11:33 AM, Trisanna Sprung-Much wrote:
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Extern
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Ah, neat! Ok, will give this a go!
Thanks a bunch
Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--
From: on behalf of "Douglas N. Greve"
Reply-To: Freesurfer support list
Date: Thursday, March 25, 2021 at 11:
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Hello,
I’ve run both longitudinal and cross-sectional TRACULA pipelines on the same
dataset, and I’ve found surprisingly low correlations of FA measurements for
several tracts (as low as r= .1 in some cases). Which measurement should be
considered m
Hi Carissa - Any QA issues aside, the first reason for a difference that I can
think of is that the same % threshold for the tract probability distribution
(e.g., 20% of the max) would not be equivalent between cross and long streams.
In the long stream I'd expect the distributions to be tighter
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Douglas,
Thank you for your help. I have pasted the result below.
Volume information for 2020-24axialScalarvolumeall/mri/orig/001.mgz
type: MGH
dimensions: 384 x 384 x 25
voxel sizes: 0.598958, 0.598958, 1.00
type: SHORT
That is an axial scan that only covers 25mm of the brain
inferior-superior. This is not whole brain coverage, which is causing
the problem
On 3/25/2021 9:07 PM, Harkey, Thomas Jarrott wrote:
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Douglas,
Thank you for your help. I have pasted the result below
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Hello, Fs
I saw an article that gave the Dice coefficient and ACC of Freesurfer's
automatic segmentation, so I am curious, can Fs automatically divide it into 32
regions?___
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