Re: [Freesurfer] samseg error: illegal hardware instructions

2023-01-20 Thread fsbuild 
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Hello Jacky,
You can try the procedure listed below, which was posted to the list around 
Dec. 12th. It might work for 7.3.1 release, though I have only tried it 
on the 7.3.2 release. If it does not work for you on 7.3.1, then I would 
download and install 7.3.2.

- R.
- - - - - -
If you are running the Freesurfer 7.3.2 release on an Apple Silicon machine 
(M1/M2 processor) with MacOS BigSur (11.X) or Monterey (12.X) AND have seen the 
error message "illegal hardware instruction", then please read following.The 
"illegal hardware instruction" error can occur when running commands such as 
samseg and mri_synthseg. This update is not necessary if your normal 
workflow does not include commands that produce this error.Please note the 
update should not be applied if:- Your Mac has an Intel processor.- Your Apple 
silicon machine (M1/M2 processor) is running a version of Freesurfer that is 
not the 7.3.2 release, e.g., a more recent development build.UPDATE 
PROCEDURE:You may not be able to run these commands without sudo/admin 
permissions on your machine.1) Download the tensorflow-2.4.1-py3-none-any.whl 
from,https://secure-web.cisco.com/1RlFRGxkPg7szXjSO-DV1PYt0XDgmWYUHtCxw8UNiebJydPDcf72nwsFHbwo6ziEWVfEglI-hwu7xCz3VYhRyaLa0bN5H6f2dUKMC6GfgB6ehEwFWPyV8ie_rJkewI-afQ_5JqEsoB2z57IhFbKagpgCQt6WeXz8gcVNbGQobh4b7SNUUbobw9dE5rkEr4-dMX6qKawEnHZhoWteyWuzqV4GG7wziFAB_9Jfr_W5PBVTaCfHTUNCsesg54JdY8UE_-2vDVJ-yvGEQIIz8rpU-GduVyjmWMD4a_hgGZ9w4iiaZZU99vnFuUplHIlMbh6OkbQ2Mn0KhCY57QlJDVCu4r3Quo7NuRvuH9XpOB9uJV1Q/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F15Qeve5FIA137KON67ehKIOyXy1N0PbAC%2Fview%3Fusp%3Dshare_link2)
 Check the download is OK with the md5 command in the terminal window,$ md5 
tensorflow-2.4.1-py3-none-any.whlMD5 (tensorflow-2.4.1-py3-none-any.whl) = 
fab44de8702faf65e17a22d706a525a4DO 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/fspython4) Uninstall the existing 
tensorflow package with,$ sudo $FREESURFER_HOME/python/bin/python3 -m pip 
uninstall tensorflow... apart from any warnings you should see the output 
...Successfully uninstalled tensorflow-2.4.15) Install the package downloaded 
above.. This command assumes the package is in the current directory 
where the command is run.$ sudo -H $FREESURFER_HOME/python/bin/python3 -m pip 
install ./tensorflow-2.4.1-py3-none-any.whl... apart from warnings and output 
about requirements (which should all be satisfied) .. you should see 
tensorflow was updated Successfully installed tensorflow-2.4.1CHECK THE 
UPDATE:$ which fspython/Applications/freesurfer/7.3.2/bin/fspython$ 
fspython import sys, os import 
tensorflowYou should see the prompt return to "" after 
the import of tensorflow with no errors reported. Hit Ctrl-D to escape 
the python session. The update should now be complete.

On Jan 20, 2023, at 05:16, Jacky Lee cyle...@gmail.com 
wrote:External Email - Use 
CautionHi FreeSurfer 
developers,I was trying to do lesion segmentation and calculation with 
FreeSurfer samseg function on my MS subjects as described 
here:MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1QPXcpu2aaMG6bcv5GooTisWdsTr3IYiqIFeaddLicp9JO9uP7D8fQeGipN3nu_O8d371ADwdlhoPmcGrQzucvTuvB5fhttSJ56dI8bnL90pWP0q6NZ2Kbasm49Jcz6NqIbShiq92lJbgRRL_hahEisIEhD-jqjmKiCYxCoiepuQBIULxoK44piixRASopUot_LoyqSYHwfdIBBo-PQhbjexwqKzuTS5tQEgBaC0nTC_rlPEJxXf_jsvyMlKJF2FOYvc3be9QJWYXo6l3BGZyTFfNCs7HG_3MVo4Glv3xqCWgY4iAlPMPNanQmJ7RHuM-6PKeNUaOSUFQM9FcW3CFe3UIqrn8wOu-45fSqpL5o7U/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSamsegI
 have performed coregistration and reformatting of my FLAIR image. I proceeded 
to run_samseg as follows:run_samseg --input 105_t1.nii 105_flairRegT1.nii 
--pallidum-separate --lesion --lesion-mask-pattern 0 1 --output 
samsegoutputThen I encountered this error:zsh: illegal hardware 
instructionrun_samseg --input 105_t1.nii 105_flairRegT1.nii 
--pallidum-separate --lesion1) FreeSurfer 
version:freesurfer-darwin-macOS-7.3.1-20220723-115e4662) Platform: 
macOS Ventura 13.1 (22c65) [Apple M1 macbook pro]Please help looking into it. 
ThanksJacky___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] samseg error: illegal hardware instructions

2023-01-20 Thread Jacky Lee 
External Email - Use Caution

Hi FreeSurfer developers,

I was trying to do lesion segmentation and calculation with FreeSurfer
samseg function on my MS subjects as described here:
https://secure-web.cisco.com/1zAsxk4FzHM5NR_SkitDdzHN3p9YF3oxn6CN---kSGPRsxsLrR96AiAnRJ4jOBVfwNnpls2HBOrLcACGlWeNk4ubbyOH3Yuaqai3T0d3m4Iut9_4u8SzhDHocmEUJ8tdwp6EojeFiGOrG71KL54fAn0cI9eBZB1kt0P6vR2JKJhf0n68xeKDqi5UWhEWLOavmBVKfeBTCCQ4tGTjTIkWZXVjJc-DZGzZhYWJqJLl1tez1958L02hE1RHGxCaPKOo3Y3escE9xPJz-k5p7RgcXuxuUBYLUVXyJ-5p3sRLDyJsnW86ClfYyW-X3Zq-mpOzK5KkuHHviCN-Z_wtEBOUebA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSamseg

I have performed coregistration and reformatting of my FLAIR image. I
proceeded to run_samseg as follows: run_samseg --input 105_t1.nii
105_flairRegT1.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1
--output samsegoutput

Then I encountered this error: zsh: illegal hardware instruction  run_samseg
--input 105_t1.nii 105_flairRegT1.nii --pallidum-separate --lesion

1) FreeSurfer version: freesurfer-darwin-macOS-7.3.1-20220723-115e466
2) Platform: macOS Ventura 13.1 (22c65) [Apple M1 macbook pro]

Please help looking into it. Thanks

Jacky
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