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Some commands such as mri_synthsr in previous releases, e.g., 7.4.1, use
code built with Intel processor specific instructions that cannot run on an arm
processor, i.e., there is not full backwards binary compatibility in that case
using the Rosetta
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Hello FreeSurfer developers,
I am trying to use mri_synthsr to improve the quality of clinical scans, but
this is the error I encountered:
Illegal instruction: 4
(I followed the instructions on SynthSR page, using mri_synthsr --i input.nii
--o outp
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Hi,
I'm using SynthSR on a sample of high-resolution T1 scans, however, I
noticed the dimensions are changed in between. For example, the original T1
is 176x256x256, but the SynthSRed version has a dimension of 176x257x257.
Can we resample this to the
unstable and not an official release.
Best,
Jackson
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Martin Juneja
Sent: Wednesday, February 7, 2024 5:05 PM
To: Iglesias Gonzalez, Juan E. ; Freesurfer
support list
Subject: [Freesurfer] Synthsr command
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The python distribution in the 7.4.1 release cannot run all the python based
tools on a Silicon Mac (M1, M2, M3 chip) because at that time we did not have a
python distribution that was completely compatible with the arm64 architecture.
We currently h
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Dear Juan and FreeSurfer developers,
I am trying to run the *mri_synthsr *command on a MacPro M2 Max chip (OS
13.6.4) - but somehow, I am getting the following error when I try to run
this command. I am using FreeSurfer's 7.4.1 version.
*Illegal instr
, January 4, 2024 at 4:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] SynthSR for T2-weighted images
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Hello Eugenio,
I wanted to inquire whether you have plans to create a tool for synthesizing
T2-weighted low-field MRI images similar to SynthSR
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Hello Eugenio,
I wanted to inquire whether you have plans to create a tool for synthesizing
T2-weighted low-field MRI images similar to SynthSR, which was developed for
T1-weighted images.
I'm in need of synthesizing T2-weighted images for Hyperfine
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] SynthSR Freesurfer Development Version Apple M1/2
Chip Compatability
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Thank you so much,
I previously used the workaround to uninstall and reinstall tensorflow that was
posted on the forum on 12th December 2022 for
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Thank you so much,
I previously used the workaround to uninstall and reinstall tensorflow that was
posted on the forum on 12th December 2022 for 7.3.2. This workaround worked for
the development version also this evening, but several tools are failin
On 12/15/2022 2:00 AM, Yoonho Hwang wrote:
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Dear FS developers,
Hi, I'm Yoonho.
I know that new features, such as SynthSeg, SynthStrip,
segment_subfields (beta version), etc, based on deep learning have
been added after the FreeSurfer 7.3.2.
Here I have
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Dear FS developers,
Hi, I'm Yoonho.
I know that new features, such as SynthSeg, SynthStrip, segment_subfields
(beta version), etc, based on deep learning have been added after the
FreeSurfer 7.3.2.
Here I have questions (I read papers related to SynthS
Dear FreeSurfers,
I have been trying to get SynthSR up and running and have come to the
realisation there is a conflict with the current tools and the new apple chips
(macOS Monterey, Apple M1 chip, 16GB).
I have tried the workaround via this thread on the mailing list to no avail
(https://www
Dear AJ,
Thanks for the interest in our tool.
Answers inline
Can SynthSR be used on MRI scans of subjects with T2 lesions, such as MS?
Yes!
If yes, is their a way to save the masks of lesions that were Inpainted or
their volume?
Nope, sorry.
For the output files, what are their image parameters
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Can SynthSR be used on MRI scans of subjects with T2 lesions, such as MS?
If yes, is their a way to save the masks of lesions that were Inpainted or
their volume?
For the output files, what are their image parameters such as TR, TE, TI?
Thank you,
A
ecific TF package can be installed
from? Best,Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Abdelkarim, Ahmed
<a.ka...@ucl.ac.uk>Date: Tuesday, July 12, 2022 at 9:29
AMTo: freesurfer@nmr.mgh.harvard.edu
<freesurfer@n
, July 12, 2022 at 9:29 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] SynthSR: Illegal Hardware Instruction
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Hello
I have an issue getting SynthSR working with FreeSurfer dev.
I have MacBook Pro with apple M1 chip and MacOS Monterey.
In bash terminal
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Hello Ahmed,
This
can result from how the code was compiled and/or optimized for older
versions of MacOS - which may not translate well to running on newer
versions of MacOS. In your case, the the Mac is also running the
Rosetta environment to tran
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Hello
I have an issue getting SynthSR working with FreeSurfer dev.
I have MacBook Pro with apple M1 chip and MacOS Monterey.
In bash terminal, after setting up FreeSurfer, and running the SynthSR command,
I get this error ‘’Illegal instruction: 4’’.
H
>
>> Hi AJ
>>
>> you might try SynthSeg, as that is one of the advantages of it - it isn't
>> biased towards any particular MRI sequence
>>
>> cheers
>> Bruce
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harva
rfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of AJ
<mailto:ajcns1...@gmail.com>
*Sent:* Thursday, November 25, 2021 9:00 PM
*To:* Freesurfer support list
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] SynthSR
particular MRI sequence
>
> cheers
> Bruce
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>
> on behalf of AJ
>
> *Sent:* Thursday, November 25, 2021 9:00 PM
> *To:* Freesurfer support list
>
> *Subject:* [Freesurfer] SynthSR
>
>
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of AJ
*Sent:* Thursday, November 25, 2021 9:00 PM
*To:* Freesurfer support list
*Subject:* [Freesurfer] SynthSR
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Hi,
Could synthetic MRIs generated by the SynthSR scri
urfer support list
Subject: [Freesurfer] SynthSR
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Hi,
Could synthetic MRIs generated by the SynthSR script be potentially used to
harmonize T1w weighted images acquired on different scanners? Then used
harmonized images for volumetric analyses?
Many than
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Hi,
Could synthetic MRIs generated by the SynthSR script be potentially used to
harmonize T1w weighted images acquired on different scanners? Then used
harmonized images for volumetric analyses?
Many thanks
AJ
__
Nice catch, Gonzalo.
mri_SynthSR was replaced by SynthSR.
Rob / Andrew: do you know when the Ubuntu version will be updated?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
On Oct 18, 2021, at 07:09, Castro Leal, Gonzal
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Dear Freesrufer Developer,
I have noticed that the ubuntu edition has not been updated since 05/10 (dd/mm)
and the issue with the synthsr tool is later to that. However, there is a
python script named mri_SynthSR that on the centos version is synthsr
Dear Gonzalo,
I’m incredibly sorry for the inconvenience but SynthSR is indeed broken right
now. It should be fixed in 1-2 days; please try downloading the development
version next week and it should all be fine!
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (
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Hello FreeSurfer,
I am trying to run the following comand:
:~$ synthsr --i $SUBJECTS_DIR/super_resolve/ --o $SUBJECTS_DIR/super_resolved/
--ct --threads 4 --cpu
synthsr: command not found
Is this due to the synthsr being broken or with my installat
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