Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

meanings of trac-all outputs
by Zeng, Qi 04 May '22

04 May '22

External Email - Use Caution Hi experts, Just want to check if dmri/dwi.nii.gz is the 4D dwi volumes after correction for B0 inhomogeneities, eddy current, and head motion? and dmri/nodif_brain_mask.nii.gz is the 3D ROI mask for the whole brain? and dmri/bvals and dmri/bvecs are rotated bvals and rotated bvecs? Thank you! Best, Qi

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Open research assistant position at Ohio State University (please share!)
by Osher, David E. 04 May '22

04 May '22

External Email - Use Caution The Cognition and Brain Circuitry Laboratory at the Ohio State University is recruiting a research assistant. Primary duties include: conducting neuroscience research on the functional and structural architecture of the human brain, and its role in cognition; programming, running, and analyzing behavioral and brain-imaging experiments using functional magnetic resonance imaging (fMRI), diffusion weighted imaging (DWI), functional connectivity, and behavioral assessments; scoring and coding data; performing statistical analyses using programs such as, MATLAB, Python, and shell scripting; recruiting research participants; maintaining participant databases; developing outreach letters. The position is available for one year with the possibility of extension based on satisfactory performance and availability of funds. Required qualifications include: Bachelor's degree in psychology, neuroscience, cognitive science, computer science, data science, engineering, physics, or math; conduct of social science research is required; experience in a social science research capacity. Highly desired: strong mathematical, statistical, and coding skills (e.g., MATLAB, Python, shell scripting); strong interpersonal skills for interacting with a diverse group of people; strong organizational skills. This position is an excellent opportunity for individuals considering future graduate studies in cognitive and computational neuroscience (every one of our research assistants has successfully been admitted into doctoral programs!). We are seeking an aspiring, self-motivated researcher with strong coding/programming skills who is excited about the brain, cognitive neuroscience, and/or clinical disorders and demonstrates evidence of a serious interest in a career in the field. If you are interested in being considered for these positions, please apply online at https://secure-web.cisco.com/1a8p8qGhoqso6oYBkudeXI8_eqsXtlC6hqmGfFmjR86taA… and submit a current CV and names of three references. If you have questions about the position or the lab, please contact Dr. David Osher at osher.6(a)osu.edu<mailto:osher.6@osu.edu> The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status. _____________________________________ David E. Osher, Ph.D. Assistant Professor of Psychology The Ohio State University davidosher.com<https://secure-web.cisco.com/1lqk_MmIM3fJEV2RfMCA4jAX9cFL53d2oDdw2rc_wWO1FR…>

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Probabilistic atlas of human thalamic nuclei
by Asa Borzabadi Farahani 03 May '22

03 May '22

External Email - Use Caution Dear Experts, I would really appreciate it if you could help me with this question: I would like to use the probabilistic atlas of human thalamic nuclei; provided by Iglesias et al. (2018); as a prior knowledge to locate the LGN within my subjects (prior knowledge would be the Atlas, the functional/structural data of subjects would be available and hence, I assume I would be able to get a better estimate for the location of LGN within the subjects). In order to do so, I need this probabilistic map to be available in the MNI or the fsaverage space. May I ask your opinion about this approach? Do you think it is feasible to have these probabilistic atlases in the MNI/fsaverage space? Best Regards, Asa Farahani

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Re: [Freesurfer] Permission denied error from -localGI
by Billah, Tashrif 02 May '22

02 May '22

Thank you Douglas. We took our time to install FreeSurfer 7.2 and retry. However, we ran into the same error: >> reading filled volume... /bin/bash: /scratch/tp44447785365264536.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp44447785365264536.load_mgh.m.mgh for reading ERROR: loading /data/pnl/FS_SUBJECTS_DIR/1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz as MGH Struct contents reference from a non-struct array object. Error in make_outer_surface (line 25) volume=vol.vol; >> ERROR: make_outer_surface did not create output file What can we do now? -Tashrif =================== Douglas N. Greve Wed, 27 Apr 2022 07:51:33 -0700 Can you just try it with 7.2? We had some problems at one point with temporary files in lGI that were fixed with 7.2 =================== On 4/27/2022 9:36 AM, Billah, Tashrif wrote: Sorry about missing your earlier question--our FreeSurfer is 7.1.0 We still need your help with this issue. Thank you, Tashrif Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700 =================== What version of FS are you running? On 3/20/2022 8:47 PM, Billah, Tashrif wrote: It does not exist and cannot be created in a shared cluster. Is there a way to define a different folder for /scratch/tp24093955057547375.load_mgh.m.mgh? =============== Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800 Do you have permission to /scratch? Does it exist? =============== Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800 Hi all, We are trying to run recon-all with -localGI but running into an unknown permission denied error: $ recon-all -s sub-1001 -localGI ``` make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 >> reading filled volume... /bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for reading ERROR: loading /path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz as MGH Struct contents reference from a non-struct array object. Error in make_outer_surface (line 25) volume=vol.vol; >> ERROR: make_outer_surface did not create output file '/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022 ``` Our MATLAB environment is properly setup and we regularly run other FreeSurfer-MATLAB commands. So I do not think that is causing the issue. Best, Tashrif

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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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