Freesurfer April 2023

freesurfer@nmr.mgh.harvard.edu

80 participants
105 discussions

Re: [Freesurfer] Freesurfer crash question
by fsbuild 17 Apr '23

17 Apr '23

External Email - Use Caution Are you using a second monitor, i.e., additional monitor besides the primary one?   There have been issues with images being displayed properly when using multiple monitors with MacOS.  I would first try everything on the primary monitor (disconnect any second monitor). If you have not tried running freeview directly from the command line, e.g., to display a volume, then please try the following.  Open a new terminal window and run the bash shell, $ bash… prompt will change ...$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh … output with variable settings … … then see if freeview opens an empty window … $ freeview … then try to display one of the existing volumes in the distribution, $ freeview $FREESURFER_HOME/subjects/bert/mri/brain.mgz If you still see a blank screen, then try setting, $ export QT_DEBUG_PLUGINS=1 … and run the command again.  The output may be useful. - R. On Apr 17, 2023, at 14:19, He, Julian H <HEJ(a)helix.mgh.harvard.edu> wrote:<freesurfercrash.pdf>

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ERROR: flag i unrecognized
by Francisco Polito haro 17 Apr '23

17 Apr '23

External Email - Use Caution I'm trying to start a scan but I can't get it to start the recon process there, I get an error, I don't know what I'm doing wrong. with the test subject of BERT that marks the tutorial if it does, but with my file it doesn't, I attach the message and screenshot of the error that appears to me: [cid:828e9b1f-c7c6-4e72-8a91-72ae7c8b800c] Sin mas por el momento, reiterando mi subordinación y respeto, reciba un caluroso saludo. Sufragio Efectivo, No Reelección LFA Francisco Polito Haro CP 12915210

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FW: Freesurfer crash question
by He, Julian H 17 Apr '23

17 Apr '23

External Email - Use Caution Hello there, FS host, I had issue with the current version of freesurfer 7.3.2 Xquartz 2.8.5, MacOS 12.6.5 (adequate video Ram), installation appears fine, just crash as soon as I load data. See attached PDF of the crash screenshots) Thanks for your time. Please help. Julian From: He, Julian H Sent: Monday, April 17, 2023 2:07 PM To: Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> Subject: RE: Freesurfer crash question Thanks, Doug, Got it, I will do. Julian From: Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> Sent: Monday, April 17, 2023 2:05 PM To: He, Julian H <HEJ(a)HELIX.MGH.HARVARD.EDU<mailto:HEJ@HELIX.MGH.HARVARD.EDU>> Subject: Re: Freesurfer crash question Hi Julian, would you mind posting this problem to the FS email list? I think others will be able to answer it better than me. Make sure to include the version you are using. doug On 4/17/2023 2:03 PM, He, Julian H wrote: Good afternoon, Doug, Could you help me with this freesurfer crash issue, ( see attached PDF) Basically, I got an loaner -previous gen Mac Pro with video card, so I can finally give a try of your Freesurfer program, the installation went fine, I can launch the freeview, but as soon as I load a volume ( even from the subject sample data), the program will crash and quit. I can’t figure out why and don’t kwon what to do. Could you mind take a time to have a look and guide me through. Cheers Julian

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recommended change to FreeSurferEnv.sh
by Aaron Tanenbaum 17 Apr '23

17 Apr '23

External Email - Use Caution Recently FSL has changed the location of the bin directory they want you to use. The FreeSurfer setup script adds the old binary folder to the PATH not the new one. This is causing quite a bit of trouble for me. I made changes to the FreeSurferEnv.sh. I removed lines 440-446 and in its place I put the following. The echo line probably needs to be changed but it works. if [ -d $FSL_DIR/share/fsl/bin ]; then > export FSL_BIN=$FSL_DIR/share/fsl/bin > elif [ -d $FSL_DIR/bin ]; then > export FSL_BIN=$FSL_DIR/bin > else > if [[ $output == 1 ]]; then > echo "WARNING: $FSL_BIN does not exist."; > fi > fi

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FLAIRpial
by Jones, Richard 17 Apr '23

17 Apr '23

External Email - Use Caution We have noted some issues with the processing of the FLAIR images when using the FLAIRpial option with 7.3.2. In the attached PDF file the top row shows the FLAIR.prenorm.mgz images while the lower row shows the FLAIR.mgz images (the FLAIR.norm.mgz looked visually to be the same as the FLAIR.mgz image). There is some interesting contrast, particularly in the brainstem and around the corpus callosum, in the FLAIR.mgz image which is not apparent in the FLAIR.prenorm image, is this really something that one would expect from the image normalization? The recon-all log file is attached, as is the expert _options file used for this subject. We also saw the same effect when running 7.3.2 on a MacBook Pro fitted with a M1 Max processor and running the Ventura OS. Richard Jones Medical Physicist | Department of Radiology | Children's Healthcare of Atlanta * 404-785-5381 | *: richard.jones(a)choa.org<mailto:richard.jones@choa.org>

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Fwd: Turku PET Centre Brain Imaging Course / September 19th-21st 2022
by Douglas N. Greve 17 Apr '23

17 Apr '23

External Email - Use Caution -------- Forwarded Message -------- Subject: Re: Turku PET Centre Brain Imaging Course / September 19th-21st 2022 Date: Mon, 17 Apr 2023 06:34:32 +0000 From: Lauri Nummenmaa <latanu(a)utu.fi> To: PETpublic(a)tyks.fi <PETpublic(a)tyks.fi> External Email - Use Caution Dear friends and colleagues, we are delighted to announce that the fourth edition of the *Turku PET Centre Neuroimaging Course* will be held in September 11th-15th 2023. The course will give a hands-on overview on processing, modelling, and statistical analysis of brain-PET data, but we also cover principles of analyzing structural and functional MR images. The course is aimed at PhD students, post-docs, and scientists working on medical, cognitive, and computational neuroimaging. The course will be held on site, but all the lectures will be also streamed live on Echo360 and stored permanently for viewing. The *course is free of charge* but registration is mandatory as we have limited seats on site (yet unlimited capacity for participating online). Please see the course webpage for schedule, registration and further information: http://secure-web.cisco.com/1I_1yioEhKGCtw0sMY5h8PNj8csB-rEYYtEnf7iVnPHNsBN… Please pass this information to your students and colleagues, we hope to see you in Turku in September! All the best Lauri P.S. The lectures, slides and other materials from last year’s course are also available for viewing here: https://secure-web.cisco.com/1sXxvtRBEukIO3TS0NLxM536AwMBVlWxgjYn8OK-nThBFj… <https://secure-web.cisco.com/1sjY07BzZXG_0eOVi4FPaqryK-4BnuFUQmauu59a9oJniZ…> ----------------------------- Dr Lauri Nummenmaa Professor, Turku PET Centre University of Turku FI-20014, Turku, Finland tel +358 50 574 7933 www http://secure-web.cisco.com/1lX4q7XtRnK8MPnSKpWbdQ3khprqntVBga2D-EFxjd1GStE… <http://secure-web.cisco.com/1OVRsD60sLQkN7lIEI-t8_pDFXZ0z2sarAdheKXRqgBK5rg…>

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FsFast retinotopy and its flags
by IOANNUCCI Stefano 17 Apr '23

17 Apr '23

External Email - Use Caution Dear Freesurfer experts, I am attempting to run an old-fashioned polar angle retinotopy analysis through FsFast. Unsurprisingly, the tutorials I've found on the topic are somewhat outdated (>10 years ago) and seem to suggest employing flags that are no longer valid in mkanalysis-sess. For instance, it seems that -ncycles is no longer a valid flag, instead giving -retinotopy with the period of a cycle seems to be sufficient. Yet, from my understanding, this implies giving a -tpef flag pointing to a file that has the timepoints to exclude (i.e. before and and after the wedge stimulus has been displayed, in my case both 'off' periods last 12 seconds). My functional images have gone through fmriprep, so are already preprocessed and have the motion parameters estimated. Accordingly, I have put these in a file to give through the flag -extreg to mkanalysis-sess. However, I get the "flag unrecognized" error if I attempt to include it in my call. Is there some other way to do this? Moreover, the wiki page on mkanalysis-sess mentions that retinotopy runs must be analyzed through sfa-sess command, yet a tutorial I've found employs selxavg3-sess, I assume this is wrong? Telling the difference between the two based on their pages in the wiki is challenging. Many thanks in advance for any help you may provide. Best, Stefano Ioannucci

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FreeSurfer VirtualBox VM Archive Password
by Kunal Kapoor 16 Apr '23

16 Apr '23

External Email - Use Caution Hello, I am trying to establish a Linux VM with Freesurfer on my personal computer, and have been prompted with an archive password. Could you please help with this? I am working on segmentation at LCN and hoping to transition to a different computer. Warmly, Kunal

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Fwd: FS VM zip password
by Kiarash Danesh 14 Apr '23

14 Apr '23

External Email - Use Caution ---------- Forwarded message --------- From: Kiarash Danesh <kiarash.danesh(a)gmail.com> Date: Fri, Apr 14, 2023 at 9:43 PM Subject: FS VM zip password To: <Freesurfer(a)nmr.mgh.harvard.edu> Dear developers, I am attempting to set up virtual box with the Ubuntu image provided in the installation guide. I would like to request the password to unzip 'FS_7_2_0_ubuntu_18_04_06.ova.7z'. Thank you in advance! - Kiarash Danesh

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[FreeSurfer] Error: mri_ca_register with non-zero status 143
by Krystal Xiwing Yau 13 Apr '23

13 Apr '23

External Email - Use Caution Dear FreeSurfer experts, I am running recon-all for an MS patient but the process was exited with error as described in the title of this email. The attached file is the log file for your reference. The below T1 image looks fine too: [cid:18540d76-7d70-4831-a4cc-ab3762da93b2] It's generated from a 3T scanner, Siemen. Would someone kindly advise on how to fix the issue? Thank you so much in advance. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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Freesurfer April 2023