Freesurfer June 2023

freesurfer@nmr.mgh.harvard.edu

75 participants
107 discussions

Passcode for Archive
by James 25 Jun '23

25 Jun '23

External Email - Use Caution Hello Could I please receive the password for the "FS_7_2_0_Ubuntu_18_04_06.ova.7z" archive found on this webpage? VM_67 - Free Surfer Wiki (harvard.edu) <https://secure-web.cisco.com/1E92JsdZSI1gtiuORgMd2oCcSlY4i2MfgunlqfmHQmaxG2…> Thank you for your time, James Watlington <http://secure-web.cisco.com/1JMdry0mYYRqdCZXgCAgpYd6amucC9yr_uIRr2AOKt91e2y…> Virus-free.http://secure-web.cisco.com/150KFIPXTYGg8PLLzxh2AyFWzWp-y2aUN3mF… <http://secure-web.cisco.com/1JMdry0mYYRqdCZXgCAgpYd6amucC9yr_uIRr2AOKt91e2y…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Troubleshooting "could not open file" errors in FS 5.3
by Annchen Knodt 24 Jun '23

24 Jun '23

External Email - Use Caution Hello, I'm trying to run freesurfer v5.3 recon-all and running into an error I'm not sure how to troubleshoot. I'm using essentially the same commands that i've successfully used to run version 6.0 recently, and that i've also successfully run 5.3 with in the past. On my first pass, I attempted to run this full recon-all command: /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -i /cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz And eventually got the error: MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could not open file Lots of lh surf files were produced as well as 3 of the lh stats files (aparc, curv, w-g), but nothing for rh, and I could not find the rh.white file. I then tried running rh using: /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink -all -s sub-0223_mprage -openmp 1 -hemi rh And eventually got the error: MRISread(/work/long/freesurfer_v5.3_DBIS/rh.EC_average/surf/rh.sphere.reg): could not open file One thing that seems weird about the second error is that it is looking in $SUBJECTS_DIR instead of $SUBJECTS_DIR/<subject> for the rh.sphere file, when the file does exist in $SUBJECTS_DIR/<subject>/surf (but not the top dir where it's looking) Also wanted to note that i'm running this a slightly tweaked version to remove symlinks which aren't allowed on the cluster i'm working on (which is running CentOS 8): $ diff /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink /cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all 3447c3447 < cp $subj1 ${diffsubj}_tmp --- > ln -s $subj1 ${diffsubj}_tmp 3753c3753 < cp $subj1 ${diffsubj}_tmp --- > ln -s $subj1 ${diffsubj}_tmp 3911c3911 < set cmd=(cp $FREESURFER_HOME/subjects/fsaverage) --- > set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage) 4028c4028 < set cmd=(cp $FREESURFER_HOME/subjects/fsaverage) --- > set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage) 4157c4157 < set cmd=(cp $FREESURFER_HOME/subjects/${hemi}.EC_average) --- > set cmd=(ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average) Any tips on how I can troubleshoot this? Attaching recon-all.log file. Thanks!! Annchen

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'ValueError: numpy.ndarray size changed...' in mri_synthseg&synthstrip (numpy1.20.3)
by Mu Nan 24 Jun '23

24 Jun '23

External Email - Use Caution Dear FreeSurfer experts, I have recently upgraded to the latest stable version, 7.4.1, in order to try out the new features of SynthSeg and SynthStrip. However, I have encountered some errors. My laptop's chip is M2. Could someone please provide some guidance? Initially, I was able to run mri_synthstrip, but not the mri_synthreg. I got the error message as: (base) MacBook-Pro-M2:$ mri_synthseg -i ./mci_test/mri/orig.mgz -o ./mci_test/ai_test --threads 8 Traceback (most recent call last): File "/Applications/freesurfer/7.4.1/python/scripts/mri_synthseg", line 10, in <module> import surfa as sf File "/Applications/freesurfer/7.4.1/python/lib/python3.8/site-packages/surfa/__init__.py", line 19, in <module> from .image import Volume File "/Applications/freesurfer/7.4.1/python/lib/python3.8/site-packages/surfa/image/__init__.py", line 1, in <module> from .framed import FramedImage File "/Applications/freesurfer/7.4.1/python/lib/python3.8/site-packages/surfa/image/framed.py", line 24, in <module> from surfa.image.interp import interpolate File "surfa/image/interp.pyx", line 1, in init surfa.image.interp ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject Enlightened by #msg74713 and #msg73091, I upgraded the numpy version from 1.19 to 1.20.3, and also installed a python specific for M1/M2. $ sudo /Applications/freesurfer/dev/python/bin/python3 -m pip install numpy==1.20.3 (I couldn't use $ sudo fspython -m pip install, because it said my freesurfer is not properly sources, which is weird since I am sure it was sourced in a right way. But now both mri_synthseg and mri_synthstrip can't run. Now if I enter the commands $ fspython -m pip freeze, the outputs are: ... neurite==0.2 nibabel==5.1.0 numpy==1.20.3 oauthlib==3.2.2 opencv-python==4.7.0.72 ... tensorboard==2.11.2 tensorboard-data-server==0.6.1 tensorboard-plugin-wit==1.8.1 tensorflow @ file:///Users/mu/Desktop/tensorflow-2.4.1-py3-none-any.whl tensorflow-estimator==2.4.0 tensorflow-io-gcs-filesystem==0.32.0 Best, Mu

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Re: [Freesurfer] Freesurfer Digest, Vol 232, Issue 12 - data not displayed
by Haley O Higginbotham 23 Jun '23

23 Jun '23

External Email - Use Caution Thanks Bruce, Changing the coordinates still left me with a blank screen, but I tried using glxgears to further troubleshoot and that also resulted in a blank black screen. I was able to fix this by disabling my graphics card (Intel Iris XE). While this enabled freesurfer then to display the mri data, I discovered that I am not able to click on anything within the voxel edit or recon edit pop-up menus (like in this post: Re: [Freesurfer] Freeview Edit options restricted (mail-archive.com)<https://secure-web.cisco.com/1mhxyoaRo0TPOzY61gZ72Ihv17F6eoLxQkrIKSVeF9WmwB…>) and I wonder if this may be related to my graphics card? Best, Haley ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Monday, June 19, 2023 3:51 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 232, Issue 12 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1NFAytgj_o7SeKzQukc41bipAEO_iD8efSPiiL9lGpNDyH… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Size of overlap between a label and a volume (John Anderson) 2. Freeview: data not displayed (Haley O Higginbotham) 3. Re: Freeview: data not displayed (Fischl, Bruce R.,PHD) 4. [FreeSurfer] Talairach Failure Detection (Krystal Xiwing Yau) ---------------------------------------------------------------------- Message: 1 Date: Sat, 17 Jun 2023 07:45:35 -0400 From: John Anderson <jb19790001(a)gmail.com> Subject: Re: [Freesurfer] Size of overlap between a label and a volume To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CABPMGjnBVnozT=1BcLNrXPe5fmciy4=7iisRTJ3xbXyVXY4Ctg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Let's say the red spot is overlay.nii.gz 1) convert aparc+aseg from mgz to nii.gz using: mri_convert aparc+aseg.mgz aparc+aseg.nii.gz 2) create mask between overlay and the atlas using fslmaths: fslmaths aparc+aseg.nii.gz -mas overlay.nii.gz overlay_overlap.nii.gz 3) use fslstats (or mris_cacl) to compute volume: fslstats aparc+aseg.nii.gz -k overlay_overlap.nii.gz -V this output #voxels and volume Alternatively, you might consider mri_seg_overlap https://secure-web.cisco.com/1yEdORqlIEup_8SwhRxwcP4XoV0QdvHT3rxvRNSBm4KwTJ… On Fri, Jun 16, 2023 at 10:37?PM parsatad(a)student.ubc.ca < parsatad(a)student.ubc.ca> wrote: > External Email - Use Caution > > Hello, > > Hope you are doing well. I'm new to freesurfer so I was wondering if you > could help me out with something please. > > I'm looking for a simple way to find the size (i.e. volume in mm3) of > overlap between a particular label (1027 ctx-lh-rostalmiddlefrontal) ) in > an aparc+aseg file and a NIfTI volume file that can be overlayed on the > aparc+aseg file. Please look at the attached file for a better > visualization of what I'm describing. > > I'd really appreciate it if you could point me in the right direction. > > Thank you, > > Parsa > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1bL2PbUa0oBf3uE-dqjk6ArIqlk3Mu1XRZ0Gqm2BSbnknD… > The 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 > https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yED… < > https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yED…> . >

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Re: [Freesurfer] QXcbConnection
by fsbuild 23 Jun '23

23 Jun '23

External Email - Use Caution glxgears not displaying anything is usually an indication something is wrong with the X windows connection/setup, i.e., nothing displayed or black screen.  WSL and configuring an X-server is a moving target, and MS changed how this works with WSL2 compared to WSL1.   We have some notes on the setup with Xming under 'surfer.nmr.mgh.harvard.edu/fswiki/FS7_wsl’ which might help if you have not already seen them.  I have not run into a case where images work but mouse events do not, however there are postings about this, 'stackoverflow.com/questions/62203272/how-to-fix-nonfunctional-x11-mouse-on-…' As Ruopeng mentioned, you might want to try configuring MobaXterm instead of XMing,   'mobaxterm.mobatek.net/download.html’. Some users avoid the above by using our Ubuntu 18 VM image hosted by Virtualbox on Windows since the OS running in the VM uses its own built-in X-server.  The FS 7.2.0 release is already installed and tested in that Ubuntu OS image and it should work to upgrade the OS and/or change the FS release on it as you like,  'surfer.nmr.mgh.harvard.edu/fswiki/VM_67' - R. On Dec 30, 2021, at 11:28, Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:        External Email - Use Caution        Can you try MobaXterm instead of Xming:MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1jxT0_T88bRNfrSo8C6hC6oO7OWFMSDEC_LFDP… Dec 30, 2021, at 7:51 AM, Carina Forster <carinaforster0611(a)gmail.com> wrote:        External Email - Use Caution        Dear Freesurfer community,I am using Windows 11 and Ubuntu on WSL2 to access freesurfer. I installed Xming. Unfortunately I get the following error msg when I try to open freeview:QXcbConnection: Could not connect to display 172.20.16.1Could not connect to any X display.I added my IP adress to the HOST file as suggested but that doesn't help. I also played around with export DISPLAY (setting it to my IP adress, setting it to 0.0 etc). Nothing helped.This is the Xming log (I thought that might help).Xming :0 -multiwindow -clipboard -acXdmcpRegisterConnection: newAddress 172..20.16.1winAdjustVideoModeShadowGDI - Using Windows display depth of 32 bits per pixelwinAllocateFBShadowGDI - Creating DIB with width: 1536 height: 864 depth: 32winInitVisualsShadowGDI - Masks 00ff0000 0000ff00 000000ff BPRGB 8 d 24 bpp 32glWinInitVisuals:1596: glWinInitVisualsglWinInitVisualConfigs:1503: glWinInitVisualConfigs glWinSetVisualConfigs:1581: glWinSetVisualConfigsinit_visuals:1055: init_visualsnull screen fn ReparentWindownull screen fn RestackWindowInitQueue - Calling pthread_mutex_initInitQueue - pthread_mutex_init returnedInitQueue - Calling pthread_cond_initInitQueue - pthread_cond_init returnedwinInitMultiWindowWM - HellowinInitMultiWindowWM - Calling pthread_mutex_lock ()winMultiWindowXMsgProc - HellowinMultiWindowXMsgProc - Calling pthread_mutex_lock ()glWinScreenProbe:1390: glWinScreenProbefixup_visuals:1303: fixup_visualsinit_screen_visuals:1336: init_screen_visuals(--) 5 mouse buttons found(--) Setting autorepeat to delay=500, rate=31(--) winConfigKeyboard - Layout: "00000407" (00000407)(--) Using preset keyboard for "German (Germany)" (407), type "4"Could not init font path element C:\Program Files (x86)\Xming/fonts/Type1/, removing from list!Could not init font path element C:\Program Files\Xming\fonts\dejavu, removing from list!Could not init font path element C:\Program Files\Xming\fonts\cyrillic, removing from list!Could not init font path element C:\WINDOWS\Fonts, removing from list!winInitMultiWindowWM - pthread_mutex_lock () returned.winInitMultiWindowWM - pthread_mutex_unlock () returned.winInitMultiWindowWM - DISPLAY=127.0.0.1:0.0winMultiWindowXMsgProc - pthread_mutex_lock () returned.winMultiWindowXMsgProc - pthread_mutex_unlock () returned.winMultiWindowXMsgProc - DISPLAY=127.0.0.1:0.0winProcEstablishConnection - HellowinInitClipboard ()winProcEstablishConnection - winInitClipboard returned.winClipboardProc - HelloDetectUnicodeSupport - Windows VistawinClipboardProc - DISPLAY=127.0.0.1:0.0winMultiWindowXMsgProc - XOpenDisplay () returned and successfully opened the display.winInitMultiWindowWM - XOpenDisplay () returned and successfully opened the display.winClipboardProc - XOpenDisplay () returned and successfully opened the display.Anyone ideas on what could be the problem?Thank you so much.Best,CarinaVirenfrei. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1C5jhXE-PbTYYBTaHJWgRDhKIHbs3Qbt83CSGBl… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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MICCAI Workshop on Machine Learning in Clinical NeuroImaging: Paper Submissions & Talent Award
by Fischl, Bruce R.,PHD 23 Jun '23

23 Jun '23

External Email - Use Caution FYI Subject: MICCAI Workshop on Machine Learning in Clinical NeuroImaging: Paper Submissions & Talent Award Dear Researchers! We are excited to announce that the paper submissions for the #MICCAI Workshop on Machine Learning in Clinical NeuroImaging are now open! This workshop aims to bring together experts from the fields of machine learning and clinical neuroimaging to explore innovative solutions and advancements in this rapidly evolving domain - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1pSUoWTVMKYWxChqQz69sFrut_YC-PkwAzxQSukiUstQc5…<https://secure-web.cisco.com/1rNtnwKlQf30WooXb1YzG8h_KbYzNPhyuXtYxh_JhZ55t9…>. If you have been working on cutting-edge research related to machine learning techniques applied to clinical neuroimaging data, we invite you to submit your work for consideration. This is a remarkable opportunity to showcase your expertise and contribute to the advancement of the field. Benefits: * Accepted papers will be presented during the workshop, providing an opportunity for valuable discussions and feedback from experts in the field. * The top 3 papers will receive recognition and prize money of 1.500 USD will be awarded to the authors of these top papers. * Accepted papers will be published in conference proceedings, Springer (MLCN 22 Proceeding:MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1xw0VVICgMrlgRf11PYDqYCXiJkFtk45wCAqZIOtfAf8Ep…<https://secure-web.cisco.com/1TKfkPCfFLiOp2cax6rs8rOz_Yqx6iIDPuJFvLtWspfGNQ…>) Join us in exploring the frontiers of machine learning in clinical neuroimaging and help shape the future of this exciting field. We encourage you to spread the word among your colleagues and fellow researchers who may be interested. For more information, including the workshop schedule, submission guidelines, and important dates, please visit our workshop website - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1pSUoWTVMKYWxChqQz69sFrut_YC-PkwAzxQSukiUstQc5…<https://secure-web.cisco.com/1rNtnwKlQf30WooXb1YzG8h_KbYzNPhyuXtYxh_JhZ55t9…> . Important Dates Paper submission deadline: 30 June, 2023 Notification of Acceptance: 21 July, 2023 Camera-ready Submission: 28 July, 2023 Workshop Date: 8 October, 2023 We look forward to your submissions and your presence at the workshop. Donders Talent Award: Donders Talent Award enables free virtual attendance (#MLCN23<https://secure-web.cisco.com/1vv3TtYxGHezumTXLOurZFnc1ffpkrQk3sCv1hi3HlDpWn…>) for underrepresented researchers from developing countries! Apply with your CV and a letter of motivation (Email: mlcn.team(a)gmail.com<mailto:mlcn.team@gmail.com>) Best regards, MLCN Organizing Committee Email communicated by: Vinod Kumar Max Planck Institute for Biological Cybernetics, Tuebingen, Germany

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recon-all-clinical problems
by Michael Mc Laughlin 23 Jun '23

23 Jun '23

External Email - Use Caution I tried recon-all-clinical and there are two main problems 1) I ran it on a T1-MPRAGE image and it looks fine except that there are no lateral ventricles in the output. See attached. 2) I get lots of errors at the end. I read the following note in the release notes: *Please replace $FREESURFER_HOME/bin/recon-all-clinical.sh with the latest version HERE <https://secure-web.cisco.com/1by8vHZBkgali1lqEExldl9RRMDAvkcckApenn9NS-6rjg…>. Development versions newer than June 15th 2023 do not have this problem.]* I am not a linux expert, so I don't know how to download that file. If I could download it I am sure I could manage to replace it in the bin directory. I made an attempt by clicking on the link and copying the text from my browser into a new text file. I used this to replace the supplied file, but I still get errors. Maybe I screwed up. Michael McLaughlin, Island View, Beulah Court, Harbour Road, Dalkey Co. Dublin Ph:+353 87 688 2514

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Freesurfer installation help
by Michael Mc Laughlin 23 Jun '23

23 Jun '23

External Email - Use Caution You seriously need to improve the installation help for non-linux experts. I spent six hours trying to upgrade from 7.3.2 to 7.4.1. The first 40 minutes was going through your help pages and reading very carefully starting here: https://secure-web.cisco.com/19ID4blh6dH7zLY1eBU3QOvif6gsUtz6XQjFV1RthoGhJD… and here: https://secure-web.cisco.com/1G2hfa6Pr6IRUiy_FTikis58foj-czVVon8c5s59_Asqy8… and many other linked pages Only to find that there are not actually any instructions on what to do. All you needed to say was: *Find out what version of Linux you have with the command:* cat /etc/os-release *Download the appropriate file e.g. for Ubuntu 22 use the Deb installation file* freesurfer_ubuntu22-7.4.1_amd64.deb <https://secure-web.cisco.com/1-yCca0DS1VPostBIzb--8M5elp1jaN909370VQ3Cl48vQ…> *Then, for Ubuntu, install with the command* sudo dpkg --install <filename> That would have saved me 6 hours! I don't know linux so I don't know these basic commands. A big problem for me was that I didn't know what version of Ubuntu I had but I didn't know that I didn't know that and none of the installation tools I tried told me, they just gave me unintelligible errors. I think that because you are all linux fluent you have blind spots about some of this basic stuff. Michael McLaughlin,

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FreeSurfer VM passcode
by Hamied Haroon 22 Jun '23

22 Jun '23

External Email - Use Caution Hello Team FreeSurfer, Please could you send me the passcode to extract this FreeSurfer VM? * FS_7_2_0_Ubuntu_18_04_06.ova.7z Many thanks. Best wishes, Hamied

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aseg stats meaning
by Michael Mc Laughlin 22 Jun '23

22 Jun '23

External Email - Use Caution What do the numbers in these columns mean? I cannot find an explanation in any of the documentation. normMean normStdDev normMin normMax normRange Also, there are two rows labelled Supratentorial volume. Is one a typo? Supratentorial volume 1304730 mm^3 Supratentorial volume 1228063 mm^3 Michael McLaughlin,

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Freesurfer June 2023