Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg - Freesurfer

28 Sep 2023


      External Email - Use Caution
&nbsp;
Thanks for reporting this.&nbsp; This posting indicates there is a difference in defining that for arm64 compared to intel architectures,&nbsp;&nbsp;https://secure-web.cisco.com/1FTmSa1QjGMsQB8Xf5Zs5AKj4Xk9F312HcVmOIIHIT5kDUD...
We will look into it along with producing an updated arm64 build.&nbsp; You could try making the change described in the posting in the SynthSeg code if you like.
You will not encounter that error in any existing/previous release, 7.4.1 ... 7.3.2 as you are using a new arm64 development build which is post the 7.4.1 release.
- R.
On 9/28/23 07:20, Conrad, Julian (Julian.Conrad@medma.uni-heidelberg.de) wrote:
Hello again FreeSurfer Developers,
&nbsp;
I'm attempting to&nbsp;do a surface reconstruction from a GRE magnitude image using recon-all-clinical.sh
As was stated before, there seem to be issues with the current Mac processors.
so I downloaded the dev version (https://secure-web.cisco.com/1k8eRfZmZxutbzTfMi5opOvIJvAU3A9yjOgbNxek0vGGGW2...)
 as was suggested by your team. Now it started to run. But I got this error:
&nbsp;
File 
"/Applications/freesurfer/dev/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/numpy/__init__.py",
 line 320, in __getattr__
&nbsp; &nbsp; raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'float128'
Error in SynthSeg
&nbsp;
(see also attached recon log)
&nbsp;
My numpy version is 1.26, python 3.9.6
&nbsp;
I tried to change the float specifications using this but this did not do the job
https://secure-web.cisco.com/1Nw2CoSnBRIpwTK-GWDBJpxLeD53b5CAywKvOfsawRYQsCt...
&nbsp;
Do you have an idea how to fix this?
&nbsp;
Will this also occur if I opted for freesurfer 7.3.2? I am a little hesitant do install the older version just yet..
&nbsp;
Best regards,
Julian
&nbsp;
&nbsp;
Mit freundlichen Grüßen
&nbsp;
Dr. med. Julian Conrad
&nbsp;
&nbsp;
&nbsp;
Oberarzt&nbsp;| senior physician
Sektion Neurodegeneration&nbsp;| Division of Neurodegeneration
Neurologische Klinik&nbsp;| Department of Neurology
Universitätsmedizin Mannheim&nbsp;| University Medicine Mannheim
Medizinische Fakultät Mannheim&nbsp;| Medical Faculty Mannheim
Universität Heidelberg| Heidelberg University
Theodor-Kutzer-Ufer 1 - 3
D-68167 Mannheim
Tel.&nbsp;&nbsp;+49 621 383-9025
E-Mail:&nbsp;julian.conrad@umm.de
https://secure-web.cisco.com/1Ys12d1Q7EjaOXQJ3u43f5YMcfnSzuXxz579PUioZIBnkdj...
&nbsp;
Universitätsklinikum Mannheim GmbH
Geschäftsführer: Freddy Bergmann, Prof. Dr. med. Hans-Jürgen Hennes&nbsp;|&nbsp;Aufsichtsratsvorsitzender:
 Dr. Peter Kurz
Handelsregister-Nr. 7331 Mannheim | Sitz und Gerichtsstand: Mannheim
&nbsp;
Medizinische Fakultät Mannheim der Universität Heidelberg
Dekan: Prof. Dr. med. Sergij Goerdt
----------
Diese 
E-Mail enthält möglicherweise vertrauliche und/oder rechtlich geschützte
 Informationen. Wenn Sie nicht der richtige Adressat sind oder diese 
E-Mail irrtümlich erhalten haben, informieren
 Sie bitte sofort den Absender und löschen Sie diese Mail. Das 
unerlaubte Kopieren sowie die unbefugte Weitergabe dieser Mail ist nicht
 gestattet.
Universitätsmedizin Mannheim
universitär - modern – menschlich
&nbsp;
&nbsp;
Von: fsbuild &lt;fsbuild@contbay.com&gt;
Datum: Mittwoch, 27. September 2023 um 00:55
An: "freesurfer@nmr.mgh.harvard.edu" &lt;freesurfer@nmr.mgh.harvard.edu&gt;
Cc: "Conrad, Julian" &lt;Julian.Conrad@medma.uni-heidelberg.de&gt;
Betreff: Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg
&nbsp;
&nbsp;
Besides
 patching the python distribution, another option available now is the 
development arm64 build for silicon Macs with an M1, M2 processor. &nbsp;But 
this is not a release
 build and so has not been tested like a stable release. &nbsp;The dev builds
 are currently ~3 months post the 7.4.1 release from back in June of 
this. year.&nbsp; We’d be happy to hear how it goes if you try it. &nbsp;The 
download links are below.
&nbsp;
- R.
https://secure-web.cisco.com/1k8eRfZmZxutbzTfMi5opOvIJvAU3A9yjOgbNxek0vGGGW2...
https://secure-web.cisco.com/1ISJip9DWoHbMeApDNRqD9f2lcyluijXFKQrQuGiqB8rzpI...
&nbsp;
&nbsp;
On Sep 26, 2023, at 18:01, Sorby-Adams, Annabel &lt;ASORBY-ADAMS@mgh.harvard.edu&gt; wrote:
&nbsp;
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
&nbsp;
Hi Julian,
&nbsp;
I
 have managed to run recon-all on my Apple M1 macOS Ventura using the 
7.3.2 version of Freesurfer. It does not work on 7.4.2 or dev versions, 
however. These instructions were posted
 in a previous correspondence from fsbuild, but reposting here for 
anyone else having the same issue:
&nbsp;
&nbsp;
You may not be able to run these commands without sudo/admin permissions on your machine.
1) Download the&nbsp;tensorflow-2.4.1-py3-none-any..whl from,
MailScanner
 has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://drive.google.com/file/d/15Qeve5FIA137KON67ehKIOyXy1N0PbAC/view?usp=s...
2) Check the download is OK with the md5 command in the terminal window,
$ md5&nbsp;tensorflow-2.4.1-py3-none-any.whl
MD5 (tensorflow-2.4.1-py3-none-any.whl) = fab44de8702faf65e17a22d706a525a4
DO NOT PROCEED UNTIL YOU GET THE ABOVE OUTPUT FROM the md5 command.
3) Setup the Freesurfer 7.3.2 environment (shown here as installed via 
..pkg file under /Applications) and verify the path to fspython is from 
the 7.3.2 release,
$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-darwin-macOS-7.3.2-20220803-878457d --------
.... environment variable settings output ...
$ which fspython
/Applications/freesurfer/7.3.2/bin/fspython
4) Uninstall the existing&nbsp;tensorflow&nbsp;package with,
$ sudo $FREESURFER_HOME/python/bin/python3 -m pip uninstall&nbsp;tensorflow
.... apart from any warnings you should see the output ...
Successfully uninstalled&nbsp;tensorflow-2.4.1
5) Install the package downloaded above.&nbsp; This command assumes the package is in the current directory where the command is run.
$ sudo -H $FREESURFER_HOME/python/bin/python3 -m pip install ./tensorflow-2..4.1-py3-none-any.whl
.... apart from warnings and output about requirements (which should all be satisfied) ...
.... you should see&nbsp;tensorflow&nbsp;was updated .....
Successfully installed&nbsp;tensorflow-2.4.1
CHECK THE UPDATE:
$ which fspython
/Applications/freesurfer/7.3.2/bin/fspython
$ fspython
&gt;&gt;&gt; import sys, os
&gt;&gt;&gt; import&nbsp;tensorflow
&gt;&gt;&gt;
You should see the prompt return to "&gt;&gt;&gt;" after the import of&nbsp;tensorflow&nbsp;with no errors reported.&nbsp; Hit Ctrl-D to escape the python
 session.&nbsp; The update should now be complete.
&nbsp;
Once you have done this you should be able to run recon-all via 7.3.2. Hope this works!
Annabel
&nbsp;
From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu &lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt;
 on behalf of Iglesias Gonzalez, Juan E. &lt;JIGLESIASGONZALEZ@mgh.harvard.edu&gt;
Date:&nbsp;Tuesday, 26 September 2023 at 17:35
To:&nbsp;Freesurfer support list &lt;freesurfer@nmr.mgh.harvard.edu&gt;
Subject:&nbsp;Re: [Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Dear Julian,
I believe this is a problem with
 SynthSeg not being compatible with the new microprocessor in MAC 
computers. Our software engineers are looking into solutions to this.
Sorry for the inconvenience,
Eugenio
&nbsp;
--
Juan Eugenio Iglesias
http://secure-web.cisco.com/15K8tGUf8tZtMuq_5Nf3tfTFHYuzBUKgcIyghX2882Gja50a...
&nbsp;
From:&nbsp;freesurfer-bounces@nmr.mgh..harvard.edu &lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt;
 on behalf of Conrad, Julian &lt;Julian.Conrad@medma.uni-heidelberg.de&gt;
Date:&nbsp;Tuesday, September 26, 2023 at 4:38 PM
To:&nbsp;freesurfer@nmr.mgh.harvard.edu &lt;freesurfer@nmr.mgh.harvard.edu&gt;
Subject:&nbsp;[Freesurfer] Recon-all-clinical error: Illegal instruction Error in SynthSeg
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Hello FreeSurfer Developers,
&nbsp;
I'm attempting to &nbsp;do a surface reconstruction from a GRE magnitude image using recon-all-clinical.sh
When I am running the pipeline, I get the following error:
&nbsp;
Illegal instruction
Error in SynthSeg
&nbsp;
neuroadmin@medma0236
 ~ % recon-all-clinical.sh 
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii
 RC026_sub-010_ses-mri01
 8 
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer
#--------------------------------------------
#@# recon-all-clinical Di 26 Sep 2023 21:53:31 CEST
&nbsp;
mri_convert
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer/RC026_sub-010_ses-mri01/mri/native.mgz&nbsp;
reading from /Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/RC026_sub-10_ses-mri01_part-mag.nii...
TR=49.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.997386, 0.00125151, 0.0722456)
j_ras = (2.37011e-10, 0.99985, -0.0173204)
k_ras = (-0.0722564, 0.0172751, 0.997236)
writing
 to 
/Users/neuroadmin/Daten/UMM/ALS/Nifti/RC026_sub-010/ses-mri01/anat/freesurfer/RC026_sub-010_ses-mri01/mri/native.mgz...
&nbsp;
Illegal instruction&nbsp;
Error in SynthSeg
&nbsp;
1) FreeSurfer version: freesurfer-macOS-darwin_x86_64-7.4.1
2) Platform: MacOS X Darwin
&nbsp;
Hope this information is sufficient and there is an easy solution.
Best regards,
Julian
&nbsp;
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1WzT07ap5K7I2AhkWT_MIV_xAyZTUYP9UShEb3DDRK757O3...