Freesurfer July 2021

freesurfer@nmr.mgh.harvard.edu

91 participants
121 discussions

Re: [Freesurfer] Announcing FreeSurfer version 7.2
by fsbuild 20 Jul '21

20 Jul '21

External Email - Use Caution Hello Kiyotaka, You may not need to be concerned about that warning.  You can suppress it by setting the following in your shell environment. $ export NO_MINC=1 For Ubuntu linux, if you have sudo/root/admin privileges, then you could try running the installer file instead of using the tar file, i.e., $ sudo apt-get install ./freesurfer_7.2.0_amd64.deb - R. On Jul 19, 2021, at 21:08, Kiyotaka Nemoto <kiyotaka(a)nemotos.net> wrote:        External Email - Use Caution        Dear Doug,Thank you for the announcement of 7.2..0 update.I updated using freesurfer-linux-ubuntu18_amd64.tar.gz and noticed that the 'mni' directory is missing.As a result, now the shell shows warning about MNI=====-------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210714-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /usr/local/freesurfer/7.2.0FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /home/username/freesurfer/7.2.0/subjectsWARNING: MINC_BIN_DIR not defined.         'nu_correct' and other MINC tools         are used by some Freesurfer utilities.         Set NO_MINC to suppress this warning.WARNING: MINC_LIB_DIR not defined.         Some Freesurfer utilities rely on the         MINC toolkit libraries.         Set NO_MINC to suppress this warning.FSL_DIR           /usr/local/fsl=====Is it intended?Best regards,KiyotakaOn Tue, Jul 20, 2021 at 7:45 AM Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:We are  please to announce version 7.2. Mostly bug fixes and behind-the-scenes enhancements. But there are a few new goodies and one new "known issue" about defacing. Check outMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1b5VnwKaEKBSNi_MClrmr5mhsgtZpYrCJb2i3C… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1oN1v-0nlD3KNrEKeGheMD9zX46y7ILMiD9UbG… 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1L2nd_LrPOTdd2iOpi_WzkxLoF2dsLhVQ2K1inK…;. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.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. -- Kiyotaka Nemoto, M..D., Ph.D.Associate ProfessorDepartment of PsychiatryDivision of Clinical Medicine, Faculty of MedicineUniversity of Tsukuba1-1-1Tennodai Tsukuba, Ibaraki 305-8575, JapanE-mail: kiyotaka@nemotos.net_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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MNI to RAS conversion
by Bronwyn Overs 20 Jul '21

20 Jul '21

External Email - Use Caution Dear Mailing List, I have a set of MNI coordinates (from SPM2) that I need to visualise relative to the Desikan-Killiany Atlas parcellation. However, I'm unsure how to convert these coordinates so that I can load up Freeview and visualise their location in RAS. I took at look at the 'Co-ordinate Systems' wiki ( [ https://secure-web.cisco.com/1sbzzg5doGPykSwEzV3LinGmIIvWDNkgsNwyHDKOFsZ45-… | https://secure-web.cisco.com/1sbzzg5doGPykSwEzV3LinGmIIvWDNkgsNwyHDKOFsZ45-… ] ), but was unable to determine how this could be done. The coordinates I need to convert are x = − 31, y = 25, z = − 7 and x = 41, y = 25, z = − 9 . Any assistance you can provide would be much appreciated. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://secure-web.cisco.com/1XfLgNltTMcAj2hlB2lDXpneNH0BEKa7I3JWAe0V_YjLyyl… | neura.edu.au ] [ https://secure-web.cisco.com/1-OSuRhzQFyIpveSl9n2IYWwim3153jvTfOp0oP1NoQ9i8… | Twitter ] | [ https://secure-web.cisco.com/1zhTUDQgzdpMvHMPZJABMqxDyMdkh6R-Adj3u1S_KK6RNO… | Facebook ] | [ http://secure-web.cisco.com/1eRxCu2OH0byg9xiwEv_GHTtEbivbUdVd52g3sB-lt6fa9S… | Subscribe ]

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Claustrum segmentation
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 19 Jul '21

19 Jul '21

External Email - Use Caution ?Hi all, I was wondering if any of you guys have had experience wanting to segment the claustrum in 3T scans. It is a label that is found in Freesurfer, but isn't reported in the stats. Is that something that Freesurfer hopes to develop. Or is there some sort of toolbox that works well that can also segment it? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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recon all parallel
by Amar Shukla 19 Jul '21

19 Jul '21

External Email - Use Caution Dear All, Actually I am trying to run multiple subjects using parallel commands . So I am trying to run multiple .nii files in the current directory. Subject folder has been created for each file I can sinstructions in ee in the back end. but when i see in the terminal there is no response and the cursor is blinking. i am running this command ls *.nii | parallel --jobs 8 recon-all -s {.} -i {} -all -qcache 1) I want to know if it is running parallely , or if it shows any further instructions in the terminal. 2) So please tell me if I am doing it correctly. I am adding the screen shots -- With Regards, Amar Shukla Assistant Professor, M tech AI ANN(2014-2016), Centre Of Information Technology, UPES Contact :+91 897 977 8016

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Regarding recon-all
by Amar Shukla 19 Jul '21

19 Jul '21

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Joining Hippocampal files
by Gregorio Borghi 19 Jul '21

19 Jul '21

External Email - Use Caution Dear sir/madam, After the segmentation I obtained the hippocampal segmented file for each hemisphere. Since I want to use them as mask for my functional scans, I wanted to join the the 2 hemisphere files together (otherwise I would obtain a different Multiple comparison computation), but when i tried doing that in FSL (fslmaths) the 2 files were joined but in very different spatial configuration. Is there a way to join the 2 hemisphere file in Freesurfer? -- Kind regards, Gregorio

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Drawing ROIs
by Akkoyunlu, Beyza 19 Jul '21

19 Jul '21

External Email - Use Caution Dear FS experts, I am planning to extract early visual region ROIs from my retinotopy scan. Is it possible group vertices according to radian values? (Like it is done in functional scans, filling an area according to the threshold). Or is there any common practice for delineating? Kind regards, Beyza

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Obtaining single file from segmented images
by Gregorio Borghi 19 Jul '21

19 Jul '21

External Email - Use Caution Dear sir/madam, I have successfully segmented my participants' hippocampus thanks to "segmentHA_T2.sh" command, which provided me both right and left hippocampal segmented files. However, I was wondering if it is possible to obtain single files for each of the hippocampal subfields (e.g. CA1 and CA3) since I would like to use those files as masks and I need them to be distinguishable. Thanks in advance. -- Kind regards, Gregorio

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Developer password
by Clemens M 19 Jul '21

19 Jul '21

External Email - Use Caution Dear Freesurfer Team, I am currently setting up freesurfer using the Ubuntu VM but I can't log in because I don't have the developer password. Would it be possible to provide me with the password? Thank you! Best, Clemens

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Re: [Freesurfer] FreeView issue!
by fsbuild 18 Jul '21

18 Jul '21

External Email - Use Caution Something is probably not right trying to launch the window since it works to run the binary and produce the help output. You can check the following command produces no output, $ otool -L /Applications/freesurfer/7.1.1/Freeview.app/Contents/MacOS/freeview | grep not If Xquartz is installed, then you should be able to run the following and see a clock, $ /opt/X11/bin/xclock If the above work, then reproduce the segfault and the system should display a window with the crash report.  You should be able to select all the crash report text and paste it into an email to send along. - R. Sahil Bajaj (sahil.brain(a)gmail.com) July 16, 2021 at 20:35 Yes, actually I have the environment already set up, please see below: When I open the terminal I get: Last login: Fri Jul 16 16:46:38 on ttys000-------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.1.1FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.1.1/subjectsMNI_DIR           /Applications/freesurfer/7.1.1/mniFSL_DIR           /usr/local/fsl The default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`. For more details, please visit https://secure-web.cisco.com/1TfCfDsXw-5fFic1YizTPgQdjE3Hh6816iInHxunF-GQ7d…. When I type freeview, I get: BT136080:~ bajsah$ freeview  /Applications/freesurfer/7.1.1/bin/freeview: line 2:  8086 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" When I type which freeview and --help, I get: BT136080:~ bajsah$ which freeview /Applications/freesurfer/7.1.1/bin/freeview BT136080:~ bajsah$ freeview --helpUsage: freeview [OPTION <ARGUMENT:SUB-OPTION>]... Volume and surface viewer and editor for freesurfer.-v, --volume <FILE>....        Load one or multiple volume files. Available sub-options are: ....... Screenshot for the above stuff is attached below: fsbuild (fsbuild(a)contbay.com) July 16, 2021 at 19:49         External Email - Use Caution        Just wondering if you already tried using bash to setup the environment.  - R. %] bashbash-3.2$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1bash-3..2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.1.1FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.1.1/subjects bash-3.2$ which freeview/Applications/freesurfer/7.1.1/bin/freeviewbash-3.2$ freeview --help. . . output deleted . . .. . . if that succeeds then see if freeview will open an empty window . . .bash-3.2$ freeview _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1KOnAxva0ve197uUFRuTjWFDKKOkH2SFWFFJhzgpM0ly-9…

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Freesurfer July 2021