Hi Julie,
I noticed that you were running recon-all with ‘-parallel’ flag. It is causing
the error.
The process should work if you remove ‘-parallel’ from recon-all command.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Julie Ottoy
Sent: Tuesday, November 8, 2022 9:
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Thanks for the input.
I was thinking that maybe 7.X would generate better surfaces than 6.0, but all
our data is 1mm^3 so I don’t think we’d benefit much since we don’t use the
-hires flag in either 6.0 or 7.X
Would you agree?
Jim
From: freesurf
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I aim at FS-FAST preprocessing of rs-fMRI data and extracting timeseries from
Yeo's Networks.
1 - I won’t perform a seed based analysis.
2 - I want to exclude the five sets of nuisance variables in mkanalysis-sess.
Please could you check whet
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Preproc worked -- it seems it was an issue in setting up my freesurfer set
up file!
I am now running into an error with FSFAST functions that require MATLAB.
I downloaded MATLAB runtime using the command in freesurfer (fs_install_mcr
R2014b) which dow
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We are using the command:
mri_aparc2aseg --s bert --annot mpm.vpnl
on FS7.1.0 in linux. This creates the mpm.vpnl+aseg.mgz in the mri folder.
We are referring to the mpm.vpnl.annot.
A little bit more context is that we have ASL images, that we are t
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Hi Douglas,
If I want to obtain outputs similar to -contrasurfreg, is it correct to
execute the following commands?
surfreg --s subjid --t fsaverage_sym --lh --no-annot --o rh.sphere.reg
surfreg --s subjid --t fsaverage_sym --rh --no-annot --o lh.sph
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Hi,
Is there a specific pipeline for segmenting the cerebellum, cortical gray
and deep nuclei? Like the one for hippocampus and thalamus?
Best
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Freesurfer@nmr.mgh.harvard.edu
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Dear James and FreeSurfer experts,
for lobes average cortical thickness we use this solution
https://secure-web.cisco.com/12kn5RGwkDP8VJQa9PtCWSWT_3GfJlJYy06k6EpiyBm3DNksk5cBO1m_9Le5zbQFSumsT0NoxwNy2VNIh9LcoRkXkj5UlRW4ZVXK_mdgK-47PUJnpHKrnofShRBd4hn04wU
you should weight by the number of vertices in each roi
On 11/9/2022 8:01 AM, James Brown wrote:
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Dear Freesurfer experts,
We are new to Freesurfer. We appreciate your help & apologize if the
question is simple.
We need cortical thickness in lobes instead o
it would be helpful to see some images. Also send the log file
On 11/9/2022 6:47 AM, dimitra kokkinou wrote:
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Dear freesurfer experts,
I am analysing some MP2RAGE images on freesurfer and found an error I
am unable to correct.
After the recon-all finishe
I would weight by the number of vertices in each ROI
On 11/8/2022 12:20 PM, James Brown wrote:
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Dear Freesurfer experts,
I would like to know if this procedure is correct.
I have cortical thickness data from aparc+aseg for every ROI in DTK
atlas (i.e. outp
On 11/8/2022 11:27 AM, Addison, Reuben wrote:
Just as a quick verification and follow up using
1. Specifying the number of components eg. if I want 5 -nuisreg the
various components I want to regress out “-comp 6 – comp 7 comp 8
comp 9
not sure what you mean here. The format is -nu
The coords are in the surface structure, which you can get by running
mris_convert lh.white lh.white.asc (asc will be an ascii file) or by
loading into matlab with read_surf.m
The surface area is computed for white (?h.area) and pial
(?h.pial.area). These can be converted to mgz or nifti (mri_c
FS does not warp any images. No smoothing is ever applied.
On 11/7/2022 3:30 PM, Katrina Simon wrote:
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Hi, I have a dataset i have run with the default settings of
Freesurfer 6.0. A reviewer for a paper recently raised the question
"Were T1 images warped w
are you talking about the whole hippo seg? That will have some WM in it.
You can also try the hippo subfield segmentation which will give you a
more refined segmentation separating GM and WM.
On 11/7/2022 11:16 AM, Jun Yeon Won wrote:
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Dear Freesurfer expe
I think I took it out because it was a bad idea (can't really remember).
If you want to do cross-hemi analysis, better to use the xhemi tool
https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 11/7/2022 8:46 AM, Francois Tadel, Mr [Affiliate] wrote:
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>
> Hel
Hi Victor,
I'm trying to understand what you described, and re-produce it here. Which
.annot are you referring to? Also, can you provide the command sequences that
you used to generate mpm.vpnl+aseg.mgz?
Thanks.
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Zeng, Victor
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Dear Freesurfer experts,
We are new to Freesurfer. We appreciate your help & apologize if the
question is simple.
We need cortical thickness in lobes instead of parcellates. Is it correct
to take the average of the parcelates from the aparc+aseg.stats f
Hi Julie,
Thank you for using Freesurfer and bought the problem to our attention.
We are looking into the issue.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Julie Ottoy
Sent: Tuesday, November 8, 2022 9:27 AM
To: Freesurfer support list ; fsbuild
Subject: [Freesu
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Dear freesurfer experts,
I am analysing some MP2RAGE images on freesurfer and found an error I am unable
to correct.
After the recon-all finished successfully, I looked at the T1 and brainmask
images on freeview and I noticed a skullstripping error
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