Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Re: [Freesurfer] Freesurfer on WSL2/Ubuntu 20: Could not connect to any X display
by fsbuild 02 May '22

02 May '22

External Email - Use Caution Hello Maaike, If you have not already done so, I would try, $ export DISPLAY=:0.0 See if you get the same IP address you used below from the ip route command.  If you don’t see the ip command is installed with, $ which ip/bin/ip … then sudo (or as root) to install it by doing, $ sudo apt install iproute2 … when done you should see $ which ip/bin/ip Then see what you get for an IP address with the command below.  Just as an example let’s say the result was 172.40.20.10 $ ip route|awk '/^default/{print $3}'172.40.20.10 If you get a different IP address as the result from the ip command compared to the IP address you already tried setting in DISPLAY, then try setting DISPLAY with the above address - appending :0.0 to it, e.g., using my pretend IP address result, $ export DISPLAY=172.40.20.10:0.0 If this does not work with Xming, then try using MobaXterm.  Some people have found MobaXTerm to be more reliable and easier to setup compared to Xming. https://secure-web.cisco.com/1PqVMG91VpcP_-hOrawBKaVjEi3Gmb_gU5j7isLHOirjuO… FYI, if you are OK with running Freesurfer 7.2.0, then if you have not already done so, I would suggest you try installing and running the Ubuntu 18 Freesurfer debian package on Ubuntu 20. … download from,https://secure-web.cisco.com/1rvaTELxM79WMd_dCOCgo8HxuoY20rI0XiWNF-o3o… … then to install$ sudo apt install ./freesurfer_7.2.0_amd64.deb - R. On May 2, 2022, at 15:32, Maaike Oosterling <maaikeoosterling(a)hotmail.com> wrote:        External Email - Use Caution        Hello everyone,As I currently do not have any access to university servers, I am trying to install Freesurfer on my own personal Windows laptop, mostly just to experiment in between doing actual studies.I followed the FS7_wsl_ubuntu guide, running it on WSL2/Ubuntu 20 and as I am not really that good with computers at all, I was already impressed with myself I got this far... until I hit the error predicted in the guide. I followed the guide's steps to edit $DISPLAY and I have also edited the Xming X0.hosts file to represent my own localhostmaaikeo@LAPTOP-EA4GL46K:/mnt/c/Program Files (x86)/Xming$ cat X0.hostslocalhost172.27.128.1maaikeo@LAPTOP-EA4GL46K:~ echo $DISPLAY172.27.128.1:0Yet I am still getting the same error as before (although I feel the 'No protocol specified' is new....)maaikeo@LAPTOP-EA4GL46K:~$ freeviewNo protocol specifiedQXcbConnection: Could not connect to display 172.27.128.1:0Could not connect to any X display.I've looked all over and have found numerous threads that slightly relate to this issue, but none of the fixes listed there. I have double checked my Xming install and it is definitely running in the background.. Is there anything I might have missed? Or is this an indicator that my laptop is just not up for the task?Thanks in advance!Maaike Oosterling_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Average subject and head size
by Sébastien Daligault 02 May '22

02 May '22

External Email - Use Caution Hi support, I have a naive question about the make_average_subject function. I want to average MRIs to create a template. This process uses the talairach transformation to average in a common space. Once averaged, is the MRI still in this space or is there an inverse transformation to return to a real size? (which would be the average size of talairach boxes). Thank you in advance for your answer. Sebastien

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Freesurfer on WSL2/Ubuntu 20: Could not connect to any X display
by Maaike Oosterling 02 May '22

02 May '22

External Email - Use Caution Hello everyone, As I currently do not have any access to university servers, I am trying to install Freesurfer on my own personal Windows laptop, mostly just to experiment in between doing actual studies. I followed the FS7_wsl_ubuntu guide, running it on WSL2/Ubuntu 20 and as I am not really that good with computers at all, I was already impressed with myself I got this far... until I hit the error predicted in the guide. I followed the guide's steps to edit $DISPLAY and I have also edited the Xming X0.hosts file to represent my own localhost maaikeo@LAPTOP-EA4GL46K:/mnt/c/Program Files (x86)/Xming$ cat X0.hosts localhost 172.27.128.1 maaikeo@LAPTOP-EA4GL46K:~ echo $DISPLAY 172.27.128.1:0 Yet I am still getting the same error as before (although I feel the 'No protocol specified' is new...) maaikeo@LAPTOP-EA4GL46K:~$ freeview No protocol specified QXcbConnection: Could not connect to display 172.27.128.1:0 Could not connect to any X display. I've looked all over and have found numerous threads that slightly relate to this issue, but none of the fixes listed there. I have double checked my Xming install and it is definitely running in the background.. Is there anything I might have missed? Or is this an indicator that my laptop is just not up for the task? Thanks in advance! Maaike Oosterling

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error for qdec
by Chen ZY 02 May '22

02 May '22

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to use qdec tool, but I received the following error when I type qdec in the terminal: developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ qdec Tcl_Init error: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 /usr/local/freesurfer/7.2.0/lib/tcl8.4 /usr/local/freesurfer/lib/tcl8.4 /usr/local/freesurfer/7.2.0/library /usr/local/freesurfer/library /usr/local/freesurfer/tcl8.4.6/library /usr/local/tcl8.4.6/library /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Error initializing Tcl. I would be appreciated if you can help me solve this problem. Thank you very much! Regrads, ZYC

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Issue with FDR-correction
by Tsiknia, Amaryllis 02 May '22

02 May '22

External Email - Use Caution Dear Freesurfer experts, I want to apply FDR correction to a sig.mgh map I have loaded onto tksurfer, but noticed that the FDR-correction is inconsistent. When I load multiple sig.mgh overlays on tksurfer and then apply FDR correction on all layers I get the following sig.mgh map for the measure I am interested in. [cid:ee22d887-18db-45c4-86b4-134b66ce7b6c] Whereas when I load just the overlay that I am interested in and apply FDR correction to that one layer, I get this FDR-corrected map: [cid:5df909c9-469d-490c-8af6-47cfdb74cd5c] Is there any reason why the two FDR corrected maps are expected to differ? Any insight would be much appreciated. Best, Amaryllis

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whole brain volume measures from SynthSeg+ ??
by jason.millward＠mdc-berlin.de 02 May '22

02 May '22

External Email - Use Caution Hello! I am using SynthSeg (SynthSeg+), and so far testing this on my own data is going well. A question I have for the forum is whether it is possible to get additional measures, such as whole brain volume and total intracranial volume. Both of these (and others) are available from FreeSurfer, but do not seem to be included in the SynthSeg output. I see a discussion thread from a few months ago referring to SamSeg, but I would really prefer to get this from SynthSeg, if possible – it runs much faster, and we are already implementing it These whole brain measures are very important to our work, since we are measuring relative changes in patients over time, and need to normalize the volumes. Is there any way to get this directly from SynthSeg+? Any help is appreciated! Best regards, Jason Millward.

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Re: [Freesurfer] FreeSurfer Ubuntu VirtualBox
by fsbuild 02 May '22

02 May '22

External Email - Use Caution Already replied to your email. - R. On May 1, 2022, at 14:51, Joanna L Eckhardt <jeckhardt(a)health.ucsd.edu> wrote:        External Email - Use Caution        Hello,I apologize if this is a repeat email (I had issues with my email on the subscribing list). I earlier received the password to open the 7Zip file on windows so that I can use FreeSurfer Ubuntu VM, but I received the following error codes shown below when using the passcode : ! C:\Users\joeck\Downloads\FS_7_2_0_ubuntu_18_04_06.ova.7z: Checksum error in the encrypted file C:\Users\joeck\Downloads\FS_7_2_0_ubuntu_18_04_06.ova.7z. Corrupt file or wrong password.Is there an alternative way to open these files? Thank you for your assistance!Joanna--Joanna EckhardtNeurosciences Graduate ProgramUniversity of California, San Diego_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeSurfer Ubuntu VirtualBox
by Joanna L Eckhardt 01 May '22

01 May '22

External Email - Use Caution Hello, I apologize if this is a repeat email (I had issues with my email on the subscribing list). I earlier received the password to open the 7Zip file on windows so that I can use FreeSurfer Ubuntu VM, but I received the following error codes shown below when using the passcode : ! C:\Users\joeck\Downloads\FS_7_2_0_ubuntu_18_04_06.ova.7z: Checksum error in the encrypted file C:\Users\joeck\Downloads\FS_7_2_0_ubuntu_18_04_06.ova.7z. Corrupt file or wrong password. Is there an alternative way to open these files? Thank you for your assistance! Joanna -- Joanna Eckhardt Neurosciences Graduate Program University of California, San Diego

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Re: [Freesurfer] Request for passcode
by fsbuild 30 Apr '22

30 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 30, 2022, at 03:29, Katrine Sand Andersen <katrine.sand(a)psy.ku.dk> wrote:        External Email - Use Caution        Hi, I am installing Freesurfer. Is it possible to get the passcode for the Ubuntu virtual box? Best, Katrine SandPhD fellowAuthorised psychologist University of CopenhagenDepartment of Psychology Øster Farimagsgade 2A1353 København K DIR +45 35 32 51 95Employee profile <image001.png>  How we protect personal data    _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Call for papers for the 5th international workshop on machine learning in clinical neuroimaging
by MLCN Workshop 30 Apr '22

30 Apr '22

External Email - Use Caution Dear Colleagues, Please find below the call for papers for the International Workshop of Machine Learning in Clinical Neuroimaging (MLCN) which is held on *the 18th of September 2022 at MICCAI 2022, Singapore*. We welcome contributions to novel machine learning methods and their applications to clinical neuroimaging data. The submission deadline is *25 June 2022*, and all MLCN accepted papers will be eligible for the best paper award of 500 USD. Top accepted papers will be invited to submit an extended version to the MELBA journal. For more information, please visit https://secure-web.cisco.com/1Fj8iLHdu4VLOETa8o2c0ylx17UB3PQp-WKfayO6j5XSuP… Best wishes, The MLCN 2022 steering and organizing committees Christos Davatzikos, Andre Marquand, Jonas Richiardi, Emma Robinson Ahmed Abdulkadir, Nicha C. Dvornek, Mohamad Habes, Seyed Mostafa Kia, Vinod Kumar, Thomas Wolfers *Call for Papers* The International Workshop of Machine Learning in Clinical Neuroimaging (MLCN 2022 <https://secure-web.cisco.com/1B1YWxb-pPXy0e9h8uURMg1bMuCXV3MXCGrqE4pCYthutX…>), a satellite event of MICCAI (MICCAI 2022 <https://secure-web.cisco.com/1Sffs0qU73EnPz7M23Eu9zW55ekCOl5-KN_SWwvJK7BHHq…>), calls for original papers in the field of clinical neuroimaging data analysis with machine learning. The two tracks of the workshop include methodological innovations as well as clinical applications. This highly interdisciplinary topic provides an excellent platform to connect researchers of varying disciplines and to collectively advance the field in multiple directions. In the *machine learning* track, we seek novel contributions that address current methodological gaps in analyzing high-dimensional, longitudinal, and heterogeneous clinical neuroscientific data using stable, scalable, and interpretable machine learning models. Topics of interest include but are not limited to: · Big data · Spatio-temporal brain data analysis · Structural data analysis · Graph theory and complex network analysis · Longitudinal data analysis · Model stability and interpretability · Model scalability in large neuroimaging datasets · Multi-source data integration and multi-view learning · Multi-site data analysis, from preprocessing to modeling · Domain adaptation, data harmonization, and transfer learning in neuroimaging · Unsupervised methods for stratifying brain disorders · Deep learning in clinical neuroimaging · Model uncertainty in clinical predictions · … In the *clinical neuroimaging *track*,* the applications of existing machine learning algorithms are evaluated to move towards precision medicine for complex brain disorders. The discovery of biological markers in medicine is an important challenge across different fields and various experimental procedures and designs are used to detect biological signatures that can be utilized for improvement in diagnostic, treatment, or for other beneficial ends. However, for most complex brain disorders, we do not have reliable biomarkers today. The application of advanced machine learning methods may help to reach this goal. Therefore, we invite the community to submit conference contributions on machine learning approaches with the goal to improve our understanding of complex brain disorders, moving the field closer to precision medicine. Topics of interest include but are not limited to: · Biomarker discovery · Refinement of nosology and diagnostics · Biological validation of clinical syndromes · Treatment outcome prediction · Course prediction · Analysis of wearable sensors · Neurogenetics and brain imaging genetics · Mechanistic modeling · Brain aging · The presentation of clinical neuroimaging databases to stimulate developments in machine learning · … ------------------------------ *Submission Process:* The workshop seeks high-quality, original, and unpublished work that addresses one or more challenges described above. Papers should be submitted electronically in Springer Lecture Notes in Computer Science (LCNS) style (see this link <https://secure-web.cisco.com/1x4sFG0et25l4buDNOLJ4VAhZNyqwuQsbQHKG7FuvJSgzH…> for detailed author guidelines) using the CMT system here <https://secure-web.cisco.com/1PEufL2yn6FIE1GnKz6bmX7m_2F03ZU-8ROdw448s2t3bb…>. The page limit is 8-pages (text, figures, and tables) plus up to 2-pages of references. We review the submissions in a double-blind process. Please make sure that your submission is anonymous. Accepted papers will be published in a joint proceeding with the MICCAI 2022 conference. ------------------------------ *MLCN Special Issue at the MELBA journal:* We will invite the top accepted papers to submit an extended version of their contribution to the MLCN special issue at the Journal of Machine Learning for Biomedical Imaging (MELBA) <https://secure-web.cisco.com/1LI6kPOlmJuM3jc0wntNJ8rEV1ad3v3NyKxy37DtmnrSqg…>. The invited papers will go through an independent review process by the journal. *Error! Filename not specified.* <https://secure-web.cisco.com/1LI6kPOlmJuM3jc0wntNJ8rEV1ad3v3NyKxy37DtmnrSqg…> ------------------------------ *Donders Best Paper Award:* The MLCN’s best paper award is sponsored by Donders Institute <https://secure-web.cisco.com/1ZxIhrR9AWXisP_yTr74CQc-owmRP8MxehA2MSEZAAaJ4f…>. All MLCN accepted papers will be eligible for the best paper award. The recipient of the award will be chosen by the MLCN scientific committee based on the scientific quality, novelty, and clarity of contributions. The winner will be announced at the end of the workshop and will receive a 500 USD honorarium. ------------------------------ *Important Dates:* · Paper submission deadline: June 25, 2022 · Notification of Acceptance: July 23, 2022 · Camera-ready Submission: Aug 6, 2022 · Workshop Date: September 18, 2022

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