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
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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:
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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
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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
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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
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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
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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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Dear James and FreeSurfer experts,
for lobes average cortical thickness we use this solution
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
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
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.
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
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
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
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
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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>
>
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
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:
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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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