The `--inmgzwarp` flag likely didn't make it into the 7.4.1 release in June
2023, as the commit adding it was made in July 2023:
https://github.com/freesurfer/freesurfer/commit/2014205c296dca5a1a2715b6b9b6d73fc553a514.
You are correct that SynthMorph warps are both in MGZWARP format and RAS
disp
We haven't explored this yet, but I'd be curious to know as well.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Josh
Sent: Friday, December 13, 2024 00:12
To: Freesurfer support list
Subject: [Freesurfer] synthmorph for functional registrati
Hi Josh,
Thank you for your interest in SynthMorph. FreeSurfer includes the tool
`mri_warp_convert` for converting between deformation field formats.
To convert to LPS displacements (ITK/ANTs format), you can use the following
command:
mri_warp_convert --inmgzwarp synthmorph.nii.gz --outitk an
Hi Martin,
In addition to the --gpu=all or 0 flag for Docker, you'll need to include the
-g flag for SynthMorph to enable the GPU. You can choose the device by setting
CUDA_VISIBLE_DEVICES; SynthMorph will default to 0. Affine registration should
require at least 16 GB of device memory, and the
Hi Simon,
The SynthMorph version in FreeSurfer 7.4.1 only supports a fixed regularization
value of 1. For more adjustable regularization via the `-r` flag (and improved
registration overall), I recommend the latest SynthMorph from the Docker Hub.
We distribute a script that supports Docker, Pod
a file are attached
Thank you!
Noga
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Hoffmann, Malte,PhD
Sent: Wednesday, October 9, 2024 17:07
To: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta
ask.nii.gz is not generated
Thanks,
Noga
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Hoffmann, Malte,PhD
Sent: Wednesday, October 9, 2024 03:22
To: Freesurfer support list
Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta
Hi Noga,
Could you elaborate on the issue you're experiencing with the LTA and send an
example?
Thanks,
Malte
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
noga.ker...@campus.technion.ac.il
Sent: Tuesday, October 8, 2024 05:06
To: Freesur
ure, sorry.
From: Dan Levitas
Sent: Friday, June 7, 2024 15:13
To: Freesurfer support list
Cc: Hoffmann, Malte,PhD
Subject: Re: [Freesurfer] Incoporating synthstrip and synthseg into recon-all
External Email - Use Caution
To update my progress, I m
Hi Dan,
I'm afraid these options aren't currently easy to find as they are being parsed
by scripts/rca-config. You can find a set of recon-all options along with a
description in distribution/etc/recon-config.yaml [1].
To pass additional options to SynthStrip, you'll need to specify an expert
nvoyé : 20 avril 2024 13:52
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] Understanding registration with mri_synthmorph
External Email - Use Caution
Thank you very much!!
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part de Hoffmann,
Hi Antoine,
Thanks for reaching out. Unless you're using a dev build of FreeSurfer,
mri_synthmorph may lag behind the dockerized version, which is likely why you
see a different behavior. For affine transforms, we switched to LTA format to
track the source and target spaces. SynthMorph now save
Hi Antoine,
I would guess this is a memory issue. You could try allocating more and/or look
at the exit code. I believe 137 would indicate that Python ran out of memory.
Malte
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Antoine Royer
Se
y artifact in the registered images.
Could you possibly shed light on the nature of this anomaly?
Thanks in advance.
Warm regards,
Edward
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Hoffmann, Malte,PhD
Sent: Saturday, April 6, 2024 1:04 AM
To: Freesurfer
tive approach within
FreeSurfer that you might recommend for achieving this objective.
Thanks in advance!
Best regards,
Edward
Sent from my iPad
> On Apr 5, 2024, at 9:57 AM, Hoffmann, Malte,PhD
> wrote:
>
> What are you trying to achieve?
>
> __
What are you trying to achieve?
From: Iglesias Gonzalez, Juan E.
Sent: Thursday, April 4, 2024 09:02
To: Freesurfer support list
Cc: Hoffmann, Malte,PhD
Subject: Re: [Freesurfer] Easyreg > cortical parcels missingafter
SynthSegw
: Hoffmann, Malte,PhD
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Longitudinal Freesurfer in the presence of large
tissue defects
External Email - Use Caution
Hi Malte,
Thanks for the response, it’s encouraging to hear you think the longitudinal
pipeline will still
Hi Philip,
The deformable template was most beneficial when differences between time
points (TPs) were largest. While this is perhaps not surprising, it meant that
the long registration time of 8h/TP in the abstract was not time well spent
since we were already certain of group differences.
We
From: John Anderson
Sent: Friday, September 1, 2023 13:43
To: Freesurfer support list; Hoffmann, Malte,PhD
Subject: Re: [Freesurfer] mri_synthmorph
External Email - Use Caution
Dear Malte
Thank you so much. I've tried both rigid and a
External Email - Use Caution
Hi John,
Currently, the default transformation model is "deform". Could you check if
"affine" yields a better result?
mri_synthmorph -m affine fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz
Cheers,
Malte
From
strip
similar to what the current watershed algorithm does. Whether the -T2 option
would still help remains to be seen...
Cheers,
Malte
From: Greve, Douglas N.,Ph.D.
Sent: Tuesday, June 20, 2023 09:36
To: freesurfer@nmr.mgh.harvard.edu; Hoffmann, Malte,PhD
Su
Hi Maedeh,
Instead of changing your .bashrc, you can just execute the following lines when
you want to switch versions (or place them into a bash script that you load
with "source your_script").
export FREESURFER_HOME=/path/to/your/desired/freesurfer/directory
source $FREESURFER_HOME/SetUpFreeS
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