Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Visualization of FreeSurfer overlays in the HCP format
by Katsumi, Yuta 18 Jun '20

18 Jun '20

Dear FreeSurfer community, I would like to be able to display OVERLAY files generated in FreeSurfer on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team states in their documentation (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersF…) that any surfaces to be converted to fs_LR need to be in .gii first, but I know mris_convert doesn’t take overlay files as input. It would be great if you could please let me know how I might be able to achieve this task. Thanks, Yuta

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Re: [Freesurfer] VM ubuntu developer password
by fsbuild 18 Jun '20

18 Jun '20

External Email - Use Caution Ok Cyrus - I have just sent it to your email. - R. Sarosh, Cyrus June 18, 2020 at 16:02         External Email - Use Caution         I have also just ran into this issue. Can someone send me the password as well? Thansk, Cyrus Cyrus Sarosh Research Area Specialist Intermediate Department of Radiology Functional Neuroimaging, Cognitive and Mobility Laboratory Domino’s Farms  Lobby B Suite 1200 24 Frank Lloyd Wright Dr  PO BOX 362 Ann Arbor, MI 48106 t: 734-998-4790 f: 734-998-8403 From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of FAIRS Amie <amie.FAIRS(a)univ-amu.fr> Sent: Thursday, June 18, 2020 1:43 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] VM ubuntu developer password   External Email - Use Caution         External Email - Use Caution         Hello everyone,   I have been sent the VM ubuntu password. But in case this is useful for others – at least on my laptop the ubuntu distribution is using a US/international QWERTY keyboard. My laptop has an AZERTY keyboard (French) and so I had some problems with the password being rejected. In case future VM users encounter errors entering the password, you may need to switch keyboard layout..   Thank you to the people who sent me the password so speedily!   Best,   Amie   ------------------   Dr. Amie Fairs Post-doctorant Aix-Marseille Université Laboratoire Parole et Langage (LPL) | CNRS UMR 7309 | 5 Avenue Pasteur | 13100 Aix-en-Provence Email : amie.fairs(a)univ-amu.fr   While I may send this email outside of typical working hours, I have no expectation to receive an email outside of your typical hours..   From: fsbuild <fsbuild(a)contbay.com> Sent: 18 June 2020 19:24 To: freesurfer(a)nmr.mgh.harvard.edu Cc: FAIRS Amie <amie.FAIRS(a)univ-amu.fr> Subject: Re: [Freesurfer] VM ubuntu developer password   Hello Amie,   I have just sent the password to your private email.   - R.   ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer FAIRS Amie June 18, 2020 at 13:43         External Email - Use Caution         Hello everyone,   I have been sent the VM ubuntu password. But in case this is useful for others – at least on my laptop the ubuntu distribution is using a US/international QWERTY keyboard. My laptop has an AZERTY keyboard (French) and so I had some problems with the password being rejected. In case future VM users encounter errors entering the password, you may need to switch keyboard layout.   Thank you to the people who sent me the password so speedily!   Best,   Amie   ------------------   Dr. Amie Fairs Post-doctorant Aix-Marseille Université Laboratoire Parole et Langage (LPL) | CNRS UMR 7309 | 5 Avenue Pasteur | 13100 Aix-en-Provence Email : amie.fairs(a)univ-amu.fr   While I may send this email outside of typical working hours, I have no expectation to receive an email outside of your typical hours.   From: fsbuild <fsbuild(a)contbay.com> Sent: 18 June 2020 19:24 To: freesurfer(a)nmr.mgh.harvard.edu Cc: FAIRS Amie <amie.FAIRS(a)univ-amu.fr> Subject: Re: [Freesurfer] VM ubuntu developer password   Hello Amie,   I have just sent the password to your private email.   - R.   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer fsbuild June 18, 2020 at 13:24         External Email - Use Caution        Hello Amie, I have just sent the password to your private email. - R. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] VM ubuntu developer password
by fsbuild 18 Jun '20

18 Jun '20

External Email - Use Caution Hello Amie, I have just sent the password to your private email. - R. On Jun 18, 2020, at 08:57, FAIRS Amie <amie.FAIRS(a)univ-amu.fr> wrote:        External Email - Use Caution        Dear Freesurfer mailing list, I have just downloaded the virtual machine + ubuntu package, as outlined on the website when running a VM in windows. However, ubuntu is asking for a developer password to open within the VM. I see on the help page (on the website) that the log in ID could be in the README doc, but I can’t actually get the VM open to get there. Does anyone know the password so I can set up the VM and get started with freesurfer? Thanks so much in advance! Best, Amie ------------------  Dr. Amie FairsPost-doctorantAix-Marseille UniversitéLaboratoire Parole et Langage (LPL) | CNRS UMR 7309 | 5 Avenue Pasteur | 13100 Aix-en-ProvenceEmail : amie.fairs@univ-amu.fr While I may send this email outside of typical working hours, I have no expectation to receive an email outside of your typical hours. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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recon-all for macaque brain
by Minqing Jiang 18 Jun '20

18 Jun '20

External Email - Use Caution Hi there, I'm running freesurfer to analyze macaque brain. Since the monkey brain is much smaller than human brain. We use 0.5*05* 05mm to scan the monkey brain. Is there anyway I can avoid downsampling the scan resolution to 1*1*1mm by recon-all? Thank you so much. Please allow me to apologize if I ask a naive question. bests, Minqing

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Bbregister misalignment
by Mason Wells 18 Jun '20

18 Jun '20

External Email - Use Caution Hi Experts, I posted earlier, but I believe my message has not been posted due to the size of attachments so I’ve removed them. I am using bbregister to align functional data to anatomical space. I have been using the bbregister command with a combination of different flags. However, there appears to be varying levels of poor registration. The first command I used included flags for a whole brain ref image and the --init-header flag. This leads to a misalignment. bbregister --s PPT_1x --feat /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat/ --int Data/PMA_retinoScans/PPT_1x/WholeEPI.nii.gz --init-header I then removed the –int (whole brain reg image) flag. Again the registration is massively misaligned. bbregister --s PPT_1x --feat /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat --init-header I then removed the –init-header flag. Again poor registration. Then I removed both flags. This was the best registration, but even this still looks a little bit off to me. You can see that around the occipital lobe (reg3 attached), there white matter isn't aligned very well. bbregister --s PPT_1x --feat /Data/PPT_1x/run1_pre_processed_functional.feat/ Can anyone give me any advice on this? I really am unsure as to which why these flags failed to aid registration. I have 3 other participants from a different dataset for which the bbregister pointing to the feat directory and the –init-header flag worked perfectly. Have I missed an important step that could explain why no combination seems to register the data correctly? Any advice would be great. Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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Freeview - Load custom overlay from terminal
by Loucao, Ricardo 18 Jun '20

18 Jun '20

External Email - Use Caution Dear FS experts, I’m trying to load a surface with a custom overlay directly from the terminal using the sub-option “overlay_custom” but it returns “Unrecognized sub-option flag ‘overlay_custom’”. I checked the source code on GitHub and found the flag to be present and implemented. I also built the freeview app from the GitHub (as it could be that my version did not have that sub-option) but I got the same return message. Upon inspecting the code further, I figured the way this flag works is via quadruplets of the form “val, r, g, b”. However, I also noticed that this return message comes when the overlay_custom sub-option is empty (freeview/MainWindow.cpp: line 3484). It seems to me like I might be using the flag improperly. Here’s an example of how I am using it: “:overlay_custom=0.85,255,0,0,0.875,0,255,255,0.90,0,0,255” Do you have any hints for me on how to deal with this? Thank you very much in advance! Best regards, Ricardo ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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VM ubuntu developer password
by FAIRS Amie 18 Jun '20

18 Jun '20

External Email - Use Caution Dear Freesurfer mailing list, I have just downloaded the virtual machine + ubuntu package, as outlined on the website when running a VM in windows. However, ubuntu is asking for a developer password to open within the VM. I see on the help page (on the website) that the log in ID could be in the README doc, but I can't actually get the VM open to get there. Does anyone know the password so I can set up the VM and get started with freesurfer? Thanks so much in advance! Best, Amie ------------------ Dr. Amie Fairs Post-doctorant Aix-Marseille Université Laboratoire Parole et Langage (LPL) | CNRS UMR 7309 | 5 Avenue Pasteur | 13100 Aix-en-Provence Email : amie.fairs(a)univ-amu.fr<mailto:amie.fairs@univ-amu.fr> While I may send this email outside of typical working hours, I have no expectation to receive an email outside of your typical hours.

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Correcting recon-all output (missing parts in pial surface)
by Michael 17 Jun '20

17 Jun '20

External Email - Use Caution Hello, I ran recon-all on a post-surgery MRI scan. Because of the resection area FreeSurfer did not include certain parts which should be included. What is the correct way of correcting this? I thought about editing the wm.mgz file by adding missing white matter using a brush value of 255 and erase white matter with a value of 1. Followed by re-creating the surfaces using: recon-all -autorecon2-wm -autorecon3 -subjid ... Thank you very much. Best Regards, Michael [image: fs.png]

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version 7 docker container
by David Pagliaccio 17 Jun '20

17 Jun '20

External Email - Use Caution Hello I was wondering if Freesurfer version 7 will be released as a container on docker hub?

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Re: [Freesurfer] Freesurfer license file error
by Hoopes, Andrew 17 Jun '20

17 Jun '20

Hi Mason, My guess is that freesurfer is still grabbing the initial license. Have you been sure to remove the original one? It might be hiding as a .license file Best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1(a)cardiff.ac.uk> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, June 17, 2020 at 5:34 AM To: "freesurfer-bounces(a)nmr.mgh.harvard.edu" <freesurfer-bounces(a)nmr.mgh.harvard.edu>, FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Freesurfer license file error External Email - Use Caution Hi Expets, I am trying to work with the Ciftify package, a great tool for converting non-HCP data into cifti format. I am running the following docker command. However, I get an error with the return code 255 sudo docker run --entrypoint ciftify_recon_all -ti --rm -v /home/masontwells/Documents/Data/freesurfer/subjects:/data:ro -v /home/masontwells/Documents/Ciftify/HCP/outputs:/out tigrlab/fmriprep_ciftify:1.1.8-2.1.1 --surf-reg FS --fs-subjects-dir /data --ciftify-work-dir /out PPT_1x cmd: mri_convert /data/PPT_1x/mri/T1.mgz /out/PPT_1x/T1w/T1w.nii.gz Failed with returncode 255 At the bottom of the ciftify recon-all log it says the below. However, I downloaded the license as advised, placed it in the correct directory (usr/local/freesurfer). I have also added the path to the license to my bashrc. Have you seen this type of error before? GNU libc version: 2.23 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://surfer.nmr.mgh.harvard.edu/registration.html -------------------------------------------------------------------------- Cheers, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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