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Hi Edward,

From my understanding, since you do not specify the registration model (the "-m" parameter), it assumes "-m joint", which outputs .nii.gz or .mgz; this explains your error message. You can use the "-m affine" parameter to allow "-t affine_transform.lta" and then pass it through mri_convert -at [...]. 

or alternatively, use the intermediate mri_warp_convert :

  1. synthmorph -m joint (or two steps affine-deform) -t [warp.mgz]
  2. mri_warp_convert --invox [warp.mgz] --outm3z [warp.m3z]
  3. mri_convert -at [warp.m3z] <invol> <outvol>


Hope this helps a bit.
De : freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> de la part de r04458005@ntu.edu.tw <r04458005@ntu.edu.tw>
Envoyé : 5 mai 2024 02:44
À : Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Objet : Re: [Freesurfer] Understanding registration with mri_synthmorph
 
        External Email - Use Caution       

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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-web.cisco.com%2F1Y50YTxjgoN3UdzsNhDlXNbHmFHe5Kd4HWQ6MprgqaoItzhB7TZmJmrIoLkJKt3ZcnxvmxQUCnzv0Ap54dPOiDj2bMrNyNviTT7u-iprCKXdd11a7u1TumyNiecgn-kIF08bq2J7o7t0DbgWCOgcKVJJwLfzPInBor5l_Kfc5YYoNiW8lQHAAd3KGfsRAUHv0xLTgnUfOJGRhYceU2dsqu147IhG86SLsIwt89lx7FO9S6wCrvGMs8Ab1pnP-qbpXhfFTgbH075lCeO3du_1FzBvQFtzy2Mmodedib9_BbIRvaJnEcIYy4uZin-h-B_V0%2Fhttps%253A%252F%252Fhub.docker.com%252Fu%252Ffreesurfer&data=05%7C02%7Croya2118%40usherbrooke.ca%7C7a15aa77a7144e56d0a308dc6cceda20%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C638504882887527789%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=tS2AqH%2Bh8EBtIU7cIeJ3QgDmLaVaYeXjsjnQgP0Q93I%3D&reserved=0
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 Caution
>
> Thanks 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 Caution
>
> Thank 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 Caution
>
> Hi 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:
>
>
>   1.
> 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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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=05%7C02%7Croya2118%40usherbrooke.ca%7C7a15aa77a7144e56d0a308dc6cceda20%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C638504882887582436%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=cnx8M8in%2BMM%2Fx0RDhBgNDFR2mQqwT2lJniYjCfqxysw%3D&reserved=0
The information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline&data=05%7C02%7Croya2118%40usherbrooke.ca%7C7a15aa77a7144e56d0a308dc6cceda20%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C638504882887586238%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=3TLLuBSubG3j9Uk2Pu7H%2BZtMY0WwH1OnAB7QW%2BO577E%3D&reserved=0 <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline&data=05%7C02%7Croya2118%40usherbrooke.ca%7C7a15aa77a7144e56d0a308dc6cceda20%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C638504882887589729%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=JdT1JAMQ1KyOURPg9jbQj2yGefuxQW51BpmLgqS6K0o%3D&reserved=0> .
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