This is all with ‘recon-all -parallel’
Thanks,
Mitch
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Huang, Yujing
Sent: Friday, February 23, 2024 2:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline
Do you run ‘recon-all
Do you run ‘recon-all -parallel’ or ‘recon-all –threads ’?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Horn, Mitchell Jacob
Sent: Friday, February 23, 2024 12:28 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] consistency in recon-all parallel pipeline
Bottom line is
you can run recon-all on the mni152 to get the aparc+aseg.mgz, then take
the temporal lobe from that
On 2/23/2024 11:29 AM, Camargo, Aldo wrote:
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Hi there,
I would like to know where I can find a mask in MNI space for the
temporal lobe.
Thanks a lot in
Just sample the activation onto the full surface (eg, --surf white
--projfrac 0.5), then just load it as an overlay when you view the patch
in freeview
On 2/22/2024 12:18 PM, Atena Akbari wrote:
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Hello Freesurfer team,
I have flattened the occipital
You can run mri_vol2surf to sample the ROI onto the surface, eg,
mri_vol2surf --regheader subject --mov yourROI.mgz --projfrac-max 0 1 .1
--hemi lh --o lh.yourROI.mgz
yourROI.mgz should be voxel-for-voxel aligned with the orig.mgz
View your sample with
tksurferfv subject lh inflated -aparc -ov
Can you include the full terminal output for one of the mris_preproc
commands that is failing?
On 2/22/2024 7:12 AM, Asuka Toyofuku wrote:
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Dear Freesurfer experts,
I have issues with creating a custom registration template. (I'm
following this
Do you see a subject/stats/lh.w-g.pct.stats file?
You can use asegstats2table to compile this across subjects. Run it with
-help to get more info
On 2/22/2024 3:26 AM, ERNEST KISSI wrote:
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I processed several items of data. And I have rh.w-g.pct file in
Yes, you just have to make sure the input and seg volumes are in voxel
for voxel alignment
On 2/21/2024 4:30 AM, ERNEST KISSI wrote:
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Hello freesurfer Team,
I have the grey matter segmentation from FSL and I have freesurfer
recon-all output but the
In what context? For fMRI, it is the signal change divided by the signal
mean (x100%)
On 2/20/2024 6:43 PM, Tina Zahrie wrote:
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Hi all,
How is the percent signal change calculated within a ROI? What is the
formula for it?
Thanks,
Tina
I'm not sure what you are looking for as it is just the equation of a
gaussian. The PSF is given as the full-width-half-max. This is converted
to a std dev with
gstd = fwhm/sqrt(log(256.0))
On 2/18/2024 7:03 AM, Federica Di Antonio wrote:
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Dear experts,
Bottom line is that when I run any FreeSurfer version 7+ in parallel on COS8 I
get different results each time.
Thanks,
Mitch
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Friday, February 23, 2024 11:03 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re:
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Dear Freesurfer Developers,
I installed Freesurfer 6.0.0 fresh on a Macbook Pro (2021) with M1 chip running
macOS Monterey 12.5.
I tried to run recon-all on both on the bert data shipped with freesurfer and
my own brain data in .nii.gz format
I cannot reproduce this locally. If you still want help, attach logs.
You can also try running it with -debug as the first option and capture
the copious terminal output.
On 2/6/2024 8:39 AM, Huang, Yujing wrote:
Not sure where this happened. Does it produce any log files that you
can
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Hi there,
I would like to know where I can find a mask in MNI space for the temporal lobe.
Thanks a lot in advance for your help,
Aldo Camargo
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Sorry, don't know what VLSM is. Can you elaborate?
On 2/6/2024 3:19 PM, Martin Juneja wrote:
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Dear FreeSurfer community and experts,
I would greatly appreciate any help/response with the following.
Thanks.
-- Forwarded message -
From:
On 2/6/2024 2:01 PM, Sarah Skinner wrote:
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Question 1 - We found a few voxels that are labeled as the right
choroid-plexus, but it is nowhere near the rest of the structure. See
attached image. Is this a problem? If yes, what is the best way to fix
If you look in the recon-all.log file (or recon-all.cmd file), you will
find the command that creates the wmparc.mgz. You can adapt it to use
the DKT
On 2/6/2024 6:53 AM, Hamied Haroon wrote:
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Hello Freesurfer Gurus,
Is it possible to obtain “wmparc”
The TkR vox2ras will never have direction cosine info. The -conform-dc
will keep the original DC in the "conformed" volume (eg, orig.mgz vs
rawavg.mgz)
On 1/11/2024 3:22 PM, Dipterix Wang wrote:
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I tried `--conform-dc` and the flag was not recognized.
Hi Lauri, that command does look right (and no need to worry about that
warning). The projfrac is the projection fraction. This is the distance
away from the white surface that fMRI will be sampled relative to the
thickness at that location. So a value of 0.5 means to sample in the
middle of
So, is the bottom line that when you run 7.4.1 on COS8 in parallel that
you get (slightly) different results each time?
On 2/2/2024 11:20 AM, Horn, Mitchell Jacob wrote:
Hi FS Devs,
I’m experiencing unreproducible thickness results when running any 7+
version with parallelization enabled.
Hi, no snapshots were attached.
On 2/1/2024 6:02 AM, Luisa Klahn wrote:
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Hello!
I am processing structural data from a 3T scanner using Freesurfer
version 7.3.2. For some subjects, the grey matter looks very thin, and
the white matter looks overestimated.
Are you saying that synthseg itself is generating the wrong seg or that
something is going wrong further downstream? The recon-all stream with
synthseg is not a supported pipeline at the moment. For the standard
stream, can you send the full recon-all.log file?
On 1/29/2024 2:04 PM, Maya
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