Re: [Freesurfer] FreeSurfer atlas and statistics question

[Huang, Yujing]

Hi Jacob,

I hope this page will provide some information you are looking for - 
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation

BA/BA.thresh stats are computed with annotations created from a set of labels 
included in Freesurfer.

I think by default Freesurfer uses ?h.aparc.annot (Desikan-Killiany cortical 
atlas) to compute the stats.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Levman, Jacob
Sent: Friday, January 20, 2023 9:27 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FreeSurfer atlas and statistics question

To whom it may concern among FreeSurfer staff,

My colleagues and I have performed an analysis with FreeSurfer that is under 
peer review. The reviewer has asked that we detail each atlas relied upon and 
connect that with each of the statistics that we relied upon in our analysis.

The statistics that we relied upon were the .stats data from each of the 
following: aparc, aparc.DKTatlas40, aparc.a2009s, BA, BA.thresh, w-g.pct, curv, 
entorhinal_exvivo, wmparc, aseg.

Obviously we use the Desikan-Killiany-Tourville atlas (and aparc.DKTatlas40 
statistics were extracted from that atlas).
I know there are other atlases, such as the Destrieux atlas, etc., but I'm not 
certain which of the above codes were extracted from Destrieux, and which ones 
were extracted from other atlases (and the names of those other atlases).

We ran a recon-all command for this study, but we only used the statistics 
outlined above (aparc, aparc.DKTatlas40, etc.). We need a list of all atlases 
supported with recon-all, and which ones were relied upon to generate each of 
the statistics codes in the above list.

Perhaps there is a complete list on a website somewhere of all the atlases and 
which of these .stats codes came from which atlas, but my searches online have 
not revealed the appropriate website. Could someone answer this question, or 
direct me to a complete website with all these details?

Thanks so much for your assistance!

Jacob
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Re: [Freesurfer] samseg error: illegal hardware instructions

[fsbuild]

External Email - Use Caution

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] FSL on recon-all

[Aaron Tanenbaum]

External Email - Use Caution

Hello FreeSurfers,
I just need to know if the FSL is used in the recon-all scripts. Basically
if FSL_DIR is different will the recon-all produce different values.
Thank you
Aaron.
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Re: [Freesurfer] mri_glmfit

[Huang, Yujing]

Hi James,

Did mri_annotation2label commands create lh.lobes.annot and rh.lobes.annot in 
fsaverage/labels directory?

They are annot files. You can use mri_annotation2label to break them into label 
files.

Best,

Yujing




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of James Brown
Sent: Thursday, January 19, 2023 7:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_glmfit


External Email - Use Caution
Dear FS experts,
I am working on a surface based analysis using FS 7.1.1 and I would like to run 
mri_glmfit between two groups using the flag "--label" to restrict analysis 
within lobes.

I ran these commands on fsaverage

mri_annotation2label --subject fsaverage --hemi lh --lobesStrict lobes
mri_annotation2label --subject fsaverage --hemi rh --lobesStrict lobes

This created annotation files within the "labels"  folder of fsaverage, then I 
ran mri_glmfit using the flag --label lh.lobes from fsaverage

I got this error message
mri_glmfit: could not scan # of lines from label file

I am ot sure what I am doing wrong. Thanks for guidance

James
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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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] FreeSurfer atlas and statistics question

[Levman, Jacob]

To whom it may concern among FreeSurfer staff,

My colleagues and I have performed an analysis with FreeSurfer that is under 
peer review. The reviewer has asked that we detail each atlas relied upon and 
connect that with each of the statistics that we relied upon in our analysis.

The statistics that we relied upon were the .stats data from each of the 
following: aparc, aparc.DKTatlas40, aparc.a2009s, BA, BA.thresh, w-g.pct, curv, 
entorhinal_exvivo, wmparc, aseg.

Obviously we use the Desikan-Killiany-Tourville atlas (and aparc.DKTatlas40 
statistics were extracted from that atlas).
I know there are other atlases, such as the Destrieux atlas, etc., but I'm not 
certain which of the above codes were extracted from Destrieux, and which ones 
were extracted from other atlases (and the names of those other atlases).

We ran a recon-all command for this study, but we only used the statistics 
outlined above (aparc, aparc.DKTatlas40, etc.). We need a list of all atlases 
supported with recon-all, and which ones were relied upon to generate each of 
the statistics codes in the above list.

Perhaps there is a complete list on a website somewhere of all the atlases and 
which of these .stats codes came from which atlas, but my searches online have 
not revealed the appropriate website. Could someone answer this question, or 
direct me to a complete website with all these details?

Thanks so much for your assistance!

Jacob
___
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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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] samseg error: illegal hardware instructions

[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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continue communication over unencrypted e-mail, please notify the sender of 
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