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Dear Malte,
I am currently utilizing the Docker version of SynthMorph 2 for MNI space normalization and have encountered a technical issue I hope you can assist me with. Below, I have detailed the command line used in my attempt:
(GBM) chang@chang-System-Product-Name:~/projects$ synthmorph -t post_004_M_to_F.lta -T post_004_F_to_M.lta -o post_004_syn_MNI.nii.gz -O post_004_syn_nat.nii.gz post_004_T1_nat_filled_synthsr.nii.gz wmni_icbm152_t1_tal_nlin_asym_09c_strip.nii
I am operating SynthMorph version 2, which is sourced from Docker Hub under the FreeSurfer user. The Docker container is managed using /usr/bin/docker, and I have configured the /mnt directory in the image to bind to the SUBJECTS_DIR at /home/chang/projects. The command executed was as follows:
Running SynthMorph version 2 from https://secure-web.cisco.com/1Y50YTxjgoN3UdzsNhDlXNbHmFHe5Kd4HWQ6MprgqaoItzh... Using /usr/bin/docker to manage containers Will bind /mnt in image to SUBJECTS_DIR="/home/chang/projects" Command: docker run --rm -v /home/chang/projects:/mnt -t -u 1000:1000 freesurfer/synthmorph:2 SynthMorph arguments: -t post_004_M_to_F.lta -T post_004_F_to_M.lta -o post_004_syn_MNI.nii.gz -O post_004_syn_nat.nii.gz post_004_T1_nat_filled_synthsr.nii.gz wmni_icbm152_t1_tal_nlin_asym_09c_strip.nii Traceback (most recent call last): File "/freesurfer/mri_synthmorph", line 608, in <module> out.save(arg.trans) File "/freesurfer/env/lib/python3.11/site-packages/surfa/core/framed.py", line 279, in save save_framed_array(self, filename, fmt=fmt) File "/freesurfer/env/lib/python3.11/site-packages/surfa/io/framed.py", line 137, in save_framed_array raise ValueError(f'cannot determine file format from extension for {filename}') ValueError: cannot determine file format from extension for post_004_M_to_F.lta
Upon changing the file format from .lta to .nii.gz, the command executed successfully. However, this adjustment presents a new challenge as I am unable to use mri_convert to apply the transformation to another NIfTI file.
Could you provide any insights or suggestions on how to resolve these issues? Specifically, I need guidance on saving in the .lta format and applying transformations using mri_convert.
Thank you in advance for your assistance.
Best regards,
-Edward 引述 "Hoffmann, Malte,PhD" MHOFFMANN@MGH.HARVARD.EDU:
The displacement field stored will be the same, so I would say the file format shouldn't really matter. Malte
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Antoine Royer Antoine.Royer@usherbrooke.ca Sent: Saturday, May 4, 2024 15:06 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Understanding registration with mri_synthmorph
External Email - Use CautionThanks Malte!
Would you recommend anything between saving deform transforms generated from synthmorph, between .mgz or .nii.gz? Which in my case, are expected to be passed onto mri_warp_convert for itk conversion. I'm running numerous tests trying to find dissimilarities between the two approach, trying to determine which will be better for me.
Any insight? ________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Antoine Royer Antoine.Royer@usherbrooke.ca Envoyé : 20 avril 2024 13:52 À : freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] Understanding registration with mri_synthmorph
External Email - Use CautionThank you very much!! ________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu de la part de Hoffmann, Malte,PhD MHOFFMANN@mgh.harvard.edu Envoyé : 20 avril 2024 11:16 À : freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Objet : 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 saves these with surfa, which insists on the .lta suffix.
Similarly, we recently added code to save warp files in .mgz format, which is more similar to NIfTI and less clunky than .m3z (surfa might not let you save warps with NIfTI extension just yet). Until the next FS release, I would recommend using SynthMorph from the Docker Hub.
In any case, the warps store shifts in physical RAS space: your `mri_warp_convert` call looks correct, and `antsApplyTransforms -v -d 3 -i [moving] -r [fixed] -t ants_warp.nii.gz -o out.nii.gz` should produce an image identical to "warped.nii.gz".
Malte
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Antoine Royer Antoine.Royer@usherbrooke.ca Sent: Friday, April 19, 2024 16:08 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Understanding registration with mri_synthmorph
External Email - Use CautionHi all!
I am working on implementing some freesurfer synth tools into a larger diffusion processing pipeline. Doing so, I would like to use mri_synthmorph to generate a transform and then pass it downstream. FIrstly, I use the dockerized synthmorph version, which seems to present discrepancies in its behaviour vs local testing:
Can someone explain the expected output format of freesurfer transforms? When used within docker, I must define affine transforms as .lta and deform transforms as .mgz, otherwise: "ValueError: cannot determine file format from extension for test__init_warp.txt"; while when using mri_synthform from my local freesurfer installation, it doesn't seem like an issue. While I expected .m3z to be the expected output. 2. Here is the sequence of functions I use. My objective is to pass down the resulting transform (affine initialization + deform warp) downstream my pipeline for further registration using ANTs (antsApplyTransforms). I tested and it seems to work, but i would appreciate an opinion. Does the --insrcgeom parameter fixes everything for me?
*Initialization + registration (freesurfer): * mri_synthmorph -m affine -t <init.lta> [moving] [fixed]
mri_synthmorph -m deform -t <freesurfer_warp.mgz> -o <warped.nii.gz> -i <init.txt> [moving] [fixed]
Convert warp from freesurfer (RAS) to ANTs (LPS) using freesurfer warp_convert: mri_warp_convert -g [moving] --inras <freesurfer_warp.mgz> --outlps <ants_warp.nii.gz>
Thank you very much!
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