Re: [Freesurfer] Installing Two Versions of FreeSurfer on One System at the Same Time

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

Re: [Freesurfer] mri_synthmorph

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

Re: [Freesurfer] mri_synthmorph

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

Re: [Freesurfer] Longitudinal Freesurfer in the presence of large tissue defects

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

Re: [Freesurfer] Longitudinal Freesurfer in the presence of large tissue defects

: 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

Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

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

Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

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? > > __

Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

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

Re: [Freesurfer] mri_synthmorph

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

Re: [Freesurfer] Understanding registration with mri_synthmorph

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

Re: [Freesurfer] Understanding registration with mri_synthmorph

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,

Re: [Freesurfer] Incoporating synthstrip and synthseg into recon-all

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

Re: [Freesurfer] Incoporating synthstrip and synthseg into recon-all

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

Re: [Freesurfer] Use synthetic in recon-all pipeline

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

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

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

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

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

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file

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

Re: [Freesurfer] mri_synthmorph regularisation

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

Re: [Freesurfer] FS version 8-beta

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

Re: [Freesurfer] needed: tools to work with synthmorph deformations in ANTS and FSL pipelines.

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

Re: [Freesurfer] synthmorph for functional registration?

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

Re: [Freesurfer] needed: tools to work with synthmorph deformations in ANTS and FSL pipelines.

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

Re: [Freesurfer] Issues with FS 7.3 skull stripping but NOT mri_synthstrip

Hi Carly, SynthStrip has been included since FreeSurfer 7.3 but not as the default skull-stripping method before the 8.0 beta release. You can explicitly enable it by adding the `-synthstrip` flag to your recon-all command and setting the environment variable FS_ALLOW_DEEP to 1. Details can be