[Freesurfer] mri_synthmorph

2023-05-15 Thread Nadia Kane 
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Hi,
I tried using mri_synthmorph in FreeSurfer on synthetic mouse brain data,
but my output moved image is just black pixels.

Thanks,
Nadia

Nadia Kane

Junior Imaging Specialist

University Imaging Centers | University of Minnesota
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[Freesurfer] mri_synthmorph

2023-09-01 Thread John Anderson 
External Email - Use Caution

Dear Freesurfer experts,
I processed DTI data using dt_recon, and I want to register FA images to
the standard MNI152 space. However, after running the command
mri_synthmorph fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz,

the registration is not accurate. I'm not sure what I've done wrong. Thank
you for any guidance.

sincerely
J
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Re: [Freesurfer] mri_synthmorph

2023-05-15 Thread Douglas N. Greve 
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try fixing your qform first

On 5/15/2023 3:28 PM, Nadia Kane wrote:


External Email - Use Caution

Hi,
I tried using mri_synthmorph in FreeSurfer on synthetic mouse brain 
data, but my output moved image is just black pixels.


Thanks,
Nadia



  Nadia Kane

Junior Imaging Specialist

University Imaging Centers | University of Minnesota

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Re: [Freesurfer] mri_synthmorph

2023-09-01 Thread Hoffmann, Malte,PhD 
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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: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of John Anderson 

Sent: Friday, September 1, 2023 12:45
To: Freesurfer support list
Subject: [Freesurfer] mri_synthmorph

External Email - Use Caution

Dear Freesurfer experts,
I processed DTI data using dt_recon, and I want to register FA images to the 
standard MNI152 space. However, after running the command
mri_synthmorph fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz,

the registration is not accurate. I'm not sure what I've done wrong. Thank you 
for any guidance.

sincerely
J


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Re: [Freesurfer] mri_synthmorph

2023-09-01 Thread John Anderson 
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Dear Malte
Thank you so much. I've tried both rigid and affine transformations, and
I've attached a snapshot that shows how the CC doesn't fully overlap with
the template. I'm using a high-quality DTI image and am wondering if
incorporating a T1 image would help improve the registration. I'm not sure
how to apply a two-step registration, if that's even possible, using
mri_synthmorph. Thanks for your guidance.

Best,
John

On Fri, Sep 1, 2023 at 1:27 PM Hoffmann, Malte,PhD <
mhoffm...@mgh.harvard.edu> wrote:

> 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: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of John Anderson <
> jb19790...@gmail.com>
> Sent: Friday, September 1, 2023 12:45
> To: Freesurfer support list
> Subject: [Freesurfer] mri_synthmorph
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
> I processed DTI data using dt_recon, and I want to register FA images to
> the standard MNI152 space. However, after running the command
> mri_synthmorph fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz,
>
> the registration is not accurate. I'm not sure what I've done wrong. Thank
> you for any guidance.
>
> sincerely
> J
>
>
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Re: [Freesurfer] mri_synthmorph

2023-09-01 Thread Hoffmann, Malte,PhD 
External Email - Use Caution

You could try affine first and initialize the deformable registration with 
that. Something like:

mri_synthmorph -m affine fa.nii.gz template.nii.gz -t affine.txt
mri_synthmorph -m deform -i affine.txt fa.nii.gz template.nii.gz -o 
fa_in_MNI.nii.gz

Alternatively, assuming your T1 is aligned with the FA map, you can run the 
above on the T1, save the warp with `-t warp.nii.gz` in the second call, and 
apply it to the FA map:

mri_warp_convert -g t1.nii.gz --inras warp.nii.gz --outm3z warp.m3z
mri_convert -at warp.m3z fa.nii.gz fa_in_MNI.nii.gz


From: John Anderson 
Sent: Friday, September 1, 2023 13:43
To: Freesurfer support list; Hoffmann, Malte,PhD
Subject: Re: [Freesurfer] mri_synthmorph

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Dear Malte
Thank you so much. I've tried both rigid and affine transformations, and I've 
attached a snapshot that shows how the CC doesn't fully overlap with the 
template. I'm using a high-quality DTI image and am wondering if incorporating 
a T1 image would help improve the registration. I'm not sure how to apply a 
two-step registration, if that's even possible, using mri_synthmorph. Thanks 
for your guidance.

Best,
John

On Fri, Sep 1, 2023 at 1:27 PM Hoffmann, Malte,PhD 
mailto:mhoffm...@mgh.harvard.edu>> wrote:
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: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of John Anderson mailto:jb19790...@gmail.com>>
Sent: Friday, September 1, 2023 12:45
To: Freesurfer support list
Subject: [Freesurfer] mri_synthmorph

External Email - Use Caution

Dear Freesurfer experts,
I processed DTI data using dt_recon, and I want to register FA images to the 
standard MNI152 space. However, after running the command
mri_synthmorph fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz,

the registration is not accurate. I'm not sure what I've done wrong. Thank you 
for any guidance.

sincerely
J


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Re: [Freesurfer] mri_synthmorph

2024-04-11 Thread Hoffmann, Malte,PhD 
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 

Sent: Thursday, April 11, 2024 16:21
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_synthmorph

External Email - Use Caution

Hi,

I am developping a Nextflow DSL2 module through nf-core for registration using 
mri_synthmorph, through the dockerised version:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://hub.docker.com/r/freesurfer/synthmorph<https://secure-web.cisco.com/1F0tLsgl5mSp6FHNJceZtb0_zJW26GZiSS0O_W7cYXg5eO4k5Y4IO_yTbNoM7nfomidDPGAXjnzDCPm1UkTtOSiMK4V-oxH_U0ANMcn0FaJWjIAMW5hs8czh3EagsX2LcanlrE3nXRXmRcgiSes0j0Cfn1CkR7VUMV8nkYvpgECTfe6Nmm0VmloYUv0dk-GakSQqBqy0mJcLZ2swdnvwcb73E8jMH85qEMn4ERtLq_NApLHeeeMXvaDLoQC3b-rj2RfwLGFbrRHPt9SF_aBgFjut9dHd7vvdkVZhJEMQ6ttbyU_40e3K2YlcWllOCb1fM/https%3A%2F%2Fhub.docker.com%2Fr%2Ffreesurfer%2Fsynthmorph>

Here is a couple of screenshots showing the ressource consumption of my 
computer and through Docker.

I don't have any issue running it locally, but there seems to be an issue 
through my container which is set at 16 core at 24 GB. Does anyone have any 
insight on how to troubleshoot this?

Thank you!


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