[Freesurfer] mri_vol2surf; --projfrac-avg and --projfrac-max

[Horn, Mitchell Jacob]

Dear FS Experts,

When using --projfrac-max or --projfrac-avg, how is the “min” component 
defined? If I specify:

--projfrac-max -2 1 0.1

Is the min (-2) simply 2x the thickness at each vertex below/inside the GM/WM 
boundary?

Thanks in advance!
Mitch
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Re: [Freesurfer] Freesurfer/6.0.0 license

[fsbuild]

External Email - Use Caution

Hello We,
This page lists how to install Freesurfer 6 including an example command you 
can run under “Test Your 
Installation”,https://secure-web.cisco.com/1uXKYTRtJ7KhSIT5Y6Hfq8w0uybgogtKWPLL3rpSfWGi4b2gCt0B4RH9j0zQJTkXCafjzMIpo-ZAMuJj4RlDCRz8EQ5ru2236uOeO1xE2gdCPNZMYGPZNUkNNi_2z1MtA5JIn9czNkdIJak3Mm9BKA_jh9c6J8mYREIIBzzM4L6aFRi8kSBaYYeozATUi4zg0j_g3q26vB3Uyy4jsEzZ0MPFNwsvFIQiadSCHxv3UiIQW-XpHOngQlEDP7UnD0jNkHe0ZIvujPiJfZysx7IX_ow/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel6downloads
You could verify the example command works.

The message about glibc being newer than version 2.15 may be from the 
mris_make_surfaces binary which I see included in the git FastSurfer project 
tree.

You can tell what version of glibc your system is running with the command,
$ ldd —version
Did you try moving aside your current freesurfer license.txt file and 
downloading a new one ?
- R.

On Mar 10, 2021, at 11:18, Wei Shao ws...@research.baycrest.org 
wrote:External Email - Use 
CautionHello, Freesurfer 
expertsI have used Freesurfer/6.0.0 in order to run FastSurferMailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1uv_m5A81P_awQBoh7PdUD3ZAFlDqMHUr1T3d1fOB7k47WiJu6Oo_GouBKIUZRFb0HzQrTShUGuz8DA1Cr9cb-hS5RvCY4TsjPjG93wIm_OiJFhShMVYyIJZC8Y6Nw43d4CmJGq77R9QJM2G-cnGrB8Avsi9GUESvSZFS7WMlx143nzQHkrfJxel8aDUoE7EfY78hm8BTpAOzZM9Pl5y_kyiBumJFWtwvLdbBo_HmZYkBy_MJrMsJ1JK7I7MBvDFfNk5NZ6kxAIWUGvk6i__QUw/https%3A%2F%2Fgithub.com%2FDeep-MI%2FFastSurfe.%C2%A0And
 copy the latest license.txt into the Freesurfer/6.0.0 home directory.Here is 
the problem every time I run FastSurfer, The attachment is the full 
logGNU libc version: 2.17ERROR: Systems running GNU glibc version greater 
than 2.15 require a newly formatted license file (it's free). 
Please download a new one from the following page:MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttp://secure-web.cisco.com/1WwX4YlDWG6EL7gxi6Tpv0IB2qmcgFkC4lwQmcFKbRCbmjWGFoLrMfsJDqkmpcVn4n1nHyalsCzrvvi8ycE7NsjnU4Dizx887XdLeNS7nYu2LEhHCpIVBPdmeFPQU3EYOvwyTcq7qg05QJD3HEWGsKHUUOxNOe3DMA3jYmzO4pvE9O0f2TUl2_2GhYBQCnd8AUacwi8F4sFPXg4QCL1ROxy5IQrvNctONaWMB1uj1onRvoC1eZ2-YPqx0CgHgMjRGhlrrWXKd_3zzoJBVOgsTvA/http%3A%2F%2Fsurfer.nmr..mgh.harvard.edu%2Fregistration.html%C2%A0Could
 you give me some suggestions? 
ThanksBest,Weslurm-45540976.out___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] make_average_subject error

[Jordan Mullins]

External Email - Use Caution

Hello,

I am trying to create an average subject from a set of subjects, but keep
getting an error that says "mghRead(mri/norm.mgz, -1): could not open
file". I've read that several others have solved this issue by installing
the patch available at
http://secure-web.cisco.com/1holHARxUGo27ZLvlj5vX0sbezsRgmRaNdE1T-Z728EASqGjdSamQfU6_udvX8lNDAGu6fMmZJqlcAAuJtuijJsAYfi7M55moSpWy1McHpeqmMGAqqWT-7M-IStYk9Qs2pOnTfoJznpdLsEgVASogVifdHzPfK1t3pQowp_WCXSDaaHhTDzz7qCl-DUbTHTPKKgBhR1NruBOW9_7sIsS86UbWXqE7CaL5hUOQNwrRGh4iX37y5CgC4I9HuJDYQNG_3fPAfLJmyVuWMB5QC4E_jw/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F6.0.0-patch%2F.
 I did
this, but continue to get the same error. I'm working with Freesurver
Version 6.0.0 and MacOS Big Sur Version 11.2.3. I've attached the
recon-all.log below, but please let me know if you need additional
information.

Any insight on this would be appreciated! Thank you!

Jordan

-- 
*Jordan L. Mullins, B.A.*
Doctoral Student, Department of Psychology
University of California, Riverside
http://secure-web.cisco.com/1mshZJHsrG2WjtWWNRNV7vunyA6LicMMo4DqXl-CgSaJWwHVpzdDUXsf8sRfvrwwkKf_KCQA4CYMRZs_am6IcPJO32Jd2eKl8shUDgQlOekTOscmE92Qtz70DWtJSOKxC8By5T4JuwEig2QC0e1ectPTPZjOGXa_t8ycn5bPjuoIWCqI8uXn86bmPqLVHkPzX-YRnSkCSbiIVsQ8zLNZ4ZNr58YvZl22BNeoGzuyye1eQfd_y4ENFJHQxgCNS7c9JXTBAX_N76Z_PQM9TFwvJPA/http%3A%2F%2Fucrkindlab.com


recon-all.log
Description: Binary data
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[Freesurfer] Flip image (resize)

[Ramesh Babu]

External Email - Use Caution

Dear Experts,

The fMRI data, when viewed in SPM, some images have 3x3x4 voxel dimensions
and some images have -3x3x4. Should I flip the image (using resize option)
so that all images will have the same dimensions? or Should I leave it
without flipping?

Please give your suggestions.

Regards
Ramesh
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[Freesurfer] Freesurfer/6.0.0 license

[Wei Shao]

External Email - Use Caution

Hello, Freesurfer experts

I have used Freesurfer/6.0.0 in order to run FastSurfer
https://secure-web.cisco.com/12C5JQprff2Y8YL4t7AWGn9XhCzBPeQ7qRNQPcetjS7kldVEPElI-HBY4lvBwmcGWPng5XPsW7emsFxfyef1JeRdMP7sMkqWm7IEO8tzrW7UTSYMJ2MDjJp2w0ehQ5L6Q9P17wvylT89WxIKeMCuTG7ndT3RxP_jRXk3OAv6k6O6D9RBTWOLzwuG1y0KsdVkt8CzkthsjFeGjk0_5IlubjtGznNBOu28M6FPwj5vM4wVgQLK3ySliEXORgtU0qduGLINjgj7iMOr5iIZ_UYLA-A/https%3A%2F%2Fgithub.com%2FDeep-MI%2FFastSurfe.

And copy the latest license.txt into the Freesurfer/6.0.0 home directory.

Here is the problem every time I run  FastSurfer,  The attachment is the
full log

GNU libc version: 2.17
ERROR: Systems running GNU glibc version greater than 2.15
  require a newly formatted license file (it's free). Please
  download a new one from the following page:
  
http://secure-web.cisco.com/1K8wEaOjxHfI-SY43wEEp8bk2OLIpUlwQ6KolO1v5nULkvtq_K7eZ-3gSs__1C9lpsxqWwwuRd02IvR0cY5m-wN5Y1_dzXHJ1omDX27wOuKpaBiusuVYnvOG1DhMC_YvtSaLVKO3OsN_8l7RuV56Kg5IKuHEZxXES_0NLgJ1MY8NvLeeX75ZEgXBWGixgRBKkuwO3iIbAckCU2HLFdIBj_iN-v9yB0QcC6WAi3g__WBftAwNzt-iaywPtiWdXpSaooUjQqycGmnnmvq5zdUdFZg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html

 Could you give me some suggestions? Thanks

Best,
We


slurm-45540976.out
Description: Binary data
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[Freesurfer] Absolute volume difference between Freesurfer 6.0 and 7.1

[Lee, Sang Hoon]

External Email - Use Caution

I recently installed version 7.1, and I compared absolute volumes with version 
6.0, and I realized that there are some significant differences in some brain 
structures (e.g. Hippocampus and amygdala).  In some cases, the differences are 
more than 7%-14%.
I understand that I should not be mixing the version when I process my 
datasets, but can you let me know what the main reason for the differences is, 
and how much should I expect?

thank you.
Sang
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Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Iglesias Gonzalez, Juan E.]

Dropbox is fine.
Cheers,
/E


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of "Gronow, Franziska" 

Reply-To: Freesurfer support list 
Date: Wednesday, March 10, 2021 at 05:31
To: "'freesurfer@nmr.mgh.harvard.edu'" 
Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus 
mis-segmentation?


External Email - Use Caution
Dear Eugenio,

thanks for your response. I wasn’t sure whether .mgz files contain patient 
information so I had to clarify that. It would be great if you could take a 
look on the affected cases. I could send you norm.mgz files of one or more 
subjects. Can I send them directly via email or do you prefer dropbox?
Thanks again!

Best regards, Franziska


--



Message: 17

Date: Tue, 23 Feb 2021 16:20:43 +

From: "Iglesias Gonzalez, Juan E." 

Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus 
mis-segmentation?

To: Freesurfer support list 

Message-ID: <1f81bc20-3ba0-4a5b-b507-13eed2bee...@mgh.harvard.edu>

Content-Type: text/plain; charset="utf-8"



Sure! The more slices the better __

Maybe it would be possible to share norm.mgz (which is skull stripped and thus 
deidentified) and the segmentation? Or maybe even crop norm.mgz around the 
thalami with Freeview?

Cheers,

/E





Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com







?On 2/23/21, 11:00, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Gronow, Franziska"  wrote:



External Email - Use Caution



Dear Eugenio,



thank you for your response. Unfortunately it is not possible to share the 
whole subject. Would it be helpful to send you more screenshots of all three 
views (coronal, sagittal, axial) with different mask opacities?



Kind regards,

Franziska

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[Freesurfer] Absolute volume difference between Freesurfer 6.0 and 7.1

[Lee, Sang Hoon]

External Email - Use Caution

I recently installed version 7.1, and I compared absolute volumes with version 
6.0, and I realized that there are some significant differences in some brain 
structures (e.g. Hippocampus and amygdala).  In some cases, the differences are 
more than 7%-14%.
I understand that I should not be mixing the version when I process my 
datasets, but can you let me know what the main reason for the differences is, 
and how much should I expect?

thank you.
Sang
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Re: [Freesurfer] Matlab version 2012b installation problem

[Georgia Kapizioni]

External Email - Use CautionHello Andrew, Thank you once again for your help and apologies for writing one more time, but it seems that Freesurfer cannot detect/recognise Matlab. When I tried to ran local gyrification index for one participant, I got the following error:recon-all -s HD01 -localGISubject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96cCurrent Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96cINFO: SUBJECTS_DIR is /Users/georgina/Downloads/HDfActual FREESURFER_HOME /Applications/freesurfer-rw-rw-r--  1 georgina  staff  1188013 Mar 10 13:20 /Users/georgina/Downloads/HDf/HD01/scripts/recon-all.logDarwin Georgias-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64/Users/georgina/Downloads/HDf/HD01/surf##@# Local Gyrification Index lh Wed Mar 10 13:24:00 EET 2021\n mris_compute_lgi --i lh.pial \nERROR: Matlab is required to run mris_compute_lgi!Darwin Georgias-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64recon-all -s HD01 exited with ERRORS at Wed Mar 10 13:24:00 EET 2021Attached please also find the recon-all.error. When I go to Freesurfer directory and type: ls -l $FREESURFER_HOME/bin/fs_install_mcrThe output is: -rw-r--r--  1 root  wheel  2010 Mar  6 12:03 /Applications/freesurfer/bin/fs_install_mcrDo you have any idea about what went wrong?Thank you once more time.Best,Georgia

recon-all.error
Description: Binary data
On 1 Mar 2021, at 5:57 PM, Georgia Kapizioni  wrote:Hello Andrew,Thank you so much for your response.Here is the output when running the command you suggested:Georgias-MacBook-Pro:~ georgina$ curl MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr -o fs_install_mcr  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current                                 Dload  Upload   Total   Spent    Left  Speed100  2010  100  2010    0     0   8170      0 --:--:-- --:--:-- --:--:--  8137(base) Georgias-MacBook-Pro:~ georgina$ ls fs_install_mcrfs_install_mcrI assume, it didn’t download it, right?GeorgiaOn 26 Feb 2021, at 8:03 PM, Georgia Kapizioni  wrote:Hello Andrew,Please accept my apologies for such a detailed response, I had a health issue, and I was just able to test what you suggested.When I use the wget command, again I have an error: -bash: wget: command not foundAny ideas on how to overcome this issue?Thank you once again,Best,Georgia On 9 Feb 2021, at 5:49 PM, Georgia Kapizioni  wrote:Hello Andrew,Thank you for your response!The output of the first command (meaning sudo cd $FREESURFER_HOME/bin && curl MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr -o fs_install_mcr && chmod +x) was: % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current                                 Dload  Upload   Total   Spent    Left  Speed100  2010  100  2010    0     0   5275      0 --:--:-- --:--:-- --:--:--  5261usage:	chmod [-fhv] [-R [-H | -L | -P]] [-a | +a | =a  [i][# [ n]]] mode|entry file ...	chmod [-fhv] [-R [-H | -L | -P]] [-E | -C | -N | -i | -I] file …However, when I type: ls -l $FREESURFER_HOME/bin/fs_install_mcr as you suggested, it appears ls: /Applications/freesurfer/bin/fs_install_mcr: No such file or directoryWhen I type again fs_install_mcr while being in Freesurfer/bin path again fs_install_mcr: command not found appears.Any idea what went wrong?Thanks once again,Best,GeorgiaOn 9 Feb 2021, at 1:05 AM, Georgia Kapizioni  wrote:Dear Freesurfer experts, I am trying to install Matlab version 2012b but a message appears: command not found. Firstly, I ran: sudo cd $FREESURFER_HOME/bin && curl MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr -o fs_install_mcr && chmod +x Then I typed: fs_install_mcr R2012b and I receive: command not found. My FS version is 6 and I have already install Matlab2016_b on my Mac. Could you please help me resolve this issue? Thank you in advance,Georgia___
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[Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Gronow, Franziska]

External Email - Use Caution

Dear Eugenio,

thanks for your response. I wasn't sure whether .mgz files contain patient 
information so I had to clarify that. It would be great if you could take a 
look on the affected cases. I could send you norm.mgz files of one or more 
subjects. Can I send them directly via email or do you prefer dropbox?
Thanks again!

Best regards, Franziska


--



Message: 17

Date: Tue, 23 Feb 2021 16:20:43 +

From: "Iglesias Gonzalez, Juan E." 

Subject: Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus 
mis-segmentation?

To: Freesurfer support list 

Message-ID: <1f81bc20-3ba0-4a5b-b507-13eed2bee...@mgh.harvard.edu>

Content-Type: text/plain; charset="utf-8"



Sure! The more slices the better __

Maybe it would be possible to share norm.mgz (which is skull stripped and thus 
deidentified) and the segmentation? Or maybe even crop norm.mgz around the 
thalami with Freeview?

Cheers,

/E





Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://secure-web.cisco.com/11XaMU-QoiZKnXiNuQPJicEtr4gYDxjHq1ZrbybgK3HfB2JNtRZNtkp7LR4JPl6-pJz7sJHs8M-kH8Ci1A2-q8tJMtyChK6Wqv1wSkgzw8cY2K8Au4uGqJYiUxurISKRuzojPPxghTgD1R_HeBZly0U4i-PoeTS1vwrz2qscnBKCg5bK0kZFv8yRqQgUqkhE0YMCxqMENl9178aKiHu_OjKnJ4r1DFuB193GIpdgcoVjT8aVsbV7dt5DelQ47g1joONClSugcb-lAudzsb0y5lQ/http%3A%2F%2Fwww.jeiglesias.com







?On 2/23/21, 11:00, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Gronow, Franziska"  wrote:



External Email - Use Caution



Dear Eugenio,



thank you for your response. Unfortunately it is not possible to share the 
whole subject. Would it be helpful to send you more screenshots of all three 
views (coronal, sagittal, axial) with different mask opacities?



Kind regards,

Franziska

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