Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Segmentation fault: 11
by priya padma 05 Oct '22

05 Oct '22

External Email - Use Caution Hello Team, I just installed freesurfer and freeview using the methods mentioned in https://secure-web.cisco.com/1oeEk1V3fGDlcuYEIm1RFYCYdQcU2m3TJysRGz7NAzZIOM… the installation was successful and after creating the environment the freeview also opened but whenever I open any volume, freeview crashes and I get an error saying line 2: 6736 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" I followed the thread https://secure-web.cisco.com/1Xm7JHZ-l0iAQ6540xdJyuY8nR4ldJU2U31IejPX9O93yn… and tried to move the terminal to the main laptop screen but still I get the same error. I am unable to open the sample data given along with freesurfer. Could you help me with this issue? -- Best Regards Padma Priya *AI Developer * *PhenoMx, Inc.* *priya(a)phenomx.ai <priya(a)phenomx.ai> | (+82)10-5405-2685*

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How to Verify That Cortical Surface Orientation Values are Accurate?
by Bansal, Krishan Chandra 04 Oct '22

04 Oct '22

External Email - Use Caution I have created a volume which is supposed to have the cortical surface orientation with respect to b0 at each voxel. To do this I got the 6 frame overlay file from mris_convert. Then I isolated the first 3 values from each row in Matlab to create an Nx3 matrix, then from this I calculated the angle between each row vector and the b0 vector (which was just [0 1 0]) using the usual angle between two vectors formula. The result was an Nx1 matrix.I then saved it as an .mgh surface file (using save_mgh) and projected it back onto the original volume using surf2vol. I believe that I did this correctly, however the professor that I am developing this method for told me he wants me to verify that the results are correct. He was not very specific in how to do this, all he told me was that I could use volumes of the individual scanner x,y,z angles to help me figure out if my b0 results are right. What I assume he meant is: since the b0 axis goes vertically down the middle of the brain when in coronal view I can tell if the b0 angles are correct by seeing where the cortical surface is with respect to the z scanner direction and seeing if the b0 angle at the corresponding location makes sense. My problem is that I can’t tell if my results make sense. In theory I believe that at the locations where the cortex appears to be orthogonal to the B0 (z scanner) axis, the overall B0 angle of the cortical surface should be closer to 90 degrees. I still don’t understand what pattern I should be seeing in the values of the z scanner volume compared to the b0 angles volume. Comparing my z scanner volume results to the B0 angle volume the only pattern I can see is that the cortical surface with respect to B0 is closer to 90 degrees when the z scanner volume is closer to 0 degrees. No B0 angle I got is actually greater than 89 though. I can’t tell if this is the right pattern or enough to verify the results in the way the professor I’m working for wants. Any help here would be GREATLY appreciated. I can send pictures of my results if someone wants to look at them.

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B0 distortion correction using 2. FSL epidewarp script
by Addison, Reuben 04 Oct '22

04 Oct '22

Hi, I am new to fsfast and I trying to create a field map using the AP and PA spin echo maps for B0 distortion correction using the FSL epidewarp script I have two fieldmaps PA_spinecho.nii and AP_spinecho.nii 1. First I want tow know if my code below is about right epidewarp.fsl --mag $dir/$subj/bold/fieldmap/ PA_spinecho.nii --dph $dir/$subj/bold/fieldmap/ PA_spinecho.nii --epi bold.nii.gz --tediff 2.46 --esp .69 --sigma 2 --vsm shiftmap.nii.gz --epidw bold_dw.nii.gz 1. If it is right, which output goes into my bold folder (“Shiftmap.nii”, I mostly suspect or “bold_dw.nii.gz” ) to be used for later preprocessing in FS-FAST 2. I want to know how to make this efficient for multiple subjects Reuben A.

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Re: [Freesurfer] Freeview does not display image
by fsbuild 04 Oct '22

04 Oct '22

External Email - Use Caution With regards to WSL, there is probably something preventing the X-server from correctly displaying graphics.  Instead of running freeview you could try a simpler command to test X-window graphics.  One command is “xeyes” which you can look for and try running in the Ubuntu terminal window by typing, $ which xeyes/usr/bin/xeyes$ xeyes If a window does not open displaying something like a pair of eyes then the X-windows server is not working correctly. There are 2 different versions of WSL, i.e. version 1 and 2.  The setup for the X-server can be different depending upon which version you are running.  You can try to find the version by typing the following command at the Windows command prompt.  The number under VERSION should be the version of WSL you are running. C:\Users\sam>  wsl -l -v   NAME     STATE     VERSION* Ubuntu   Running  2   <— means you are running WSL version 2 Down the bottom of this page are some instructions for setting up the Ubuntu shell environment for WSL, https://secure-web.cisco.com/1iKRwZpgN3zDuJlFspVtdJXrVV6ghp3nndYF… If you have not already run these 2 commands, then I would do so,  $ echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc$ echo "export DISPLAY=:0" >> $HOME/.bashrc Then exit your Ubuntu terminal window and start a new one so those settings take effect.  Then try running the “xeyes” command again to see if it works.  If it does work, then try running freeview again. With regards to trying to use the VM, if uncompressing the image is crashing then you may be running out of disk space.  You should check there is at least 40 Gig of free disk space in the location where you are trying to open the zip file. - R. On Oct 4, 2022, at 03:11, Justina Lee <justinalee56(a)gmail.com> wrote:        External Email - Use Caution        Hello R,Sorry I wasn’t so clear on my part. I am using ubuntu linux on the windows subsystem linux (WSL). I followed these instructions atMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wsl to download the WSL, X-server, and the freesurfer. Is it still possible to fix the problem here internally or should I follow the instructions sent from the link previously to download Virtual Box and run freesurfer in this way? I have been trying to open the zip file Ubuntu compressed image but it seems to keep crashing as I load it. I will keep trying if the first way aforementioned is not possible. Thank you and hope this has become alittle clearer. Sincerely,Justina On Mon, Oct 3, 2022 at 8:35 PM fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello Justina,We need to know what your setup is on Windows for running Linux in order to help with running freeview.  It reads like you are not using VirtualBox to run the Linux Ubuntu OS, I do not have VirtualBox installed ....So it’s not clear to me how you are currently running Ubuntu Linux on your Windows machine in order to run freeview or other freesurfer commands.  Are you running Ubuntu linux with the Windows Subsystem for Linux (WSL)?  Maybe you are connecting remotely to a linux machine via VNC or the like from your Windows machine ? If you don’t mind running freesurfer 7..2.0 (instead of the newest 7.3.2 release), there is a smaller version of the VM to download from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1pDNeyyXnoU0PIQ7-rMdLh5tom581Kv0B3Mn8R…; with setup instructions under that link.   But you would still need to download and install VirtualBox on your Windows machine and then download and install the Freesurfer Software.- R.On Oct 3, 2022, at 09:35, Justina Lee <justinalee56(a)gmail.com> wrote:        External Email - Use Caution        To whom that can provide any insight,I am currently using Ubuntu on windows to open freeview to show some data. My issue at hand is that freeview does not show any images, despite changing the window levels (contrast and brightness). Using the command freeview -v works, and I am able to run it smoothly.. When I try to open an mgz file, it runs fine, but I am unable to see anything.  I do not have VirtualBox installed and tried to take this advice from previous but I ran across the problem of downloading the course Virtual Machine. I do think that I do not need to download the VirtualBox and can continue using Ubuntu on Windows.What could be the issue with this? Should I be downloading the Virtual machine to run Freeview?Thank you so much for your time and I hope that my issue is not too big of a problem to solve.Sincerely,Justina_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1R3cUq4RykRt6cPCE4lwjRCb05baj49mMr_HMN… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1deahsDR7bgySlDh-gqSvErXdDWMrr1x8nDI5a…; .-- Sent from Gmail Mobile_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] annex repository missing a lot of files
by fsbuild 04 Oct '22

04 Oct '22

External Email - Use Caution Hello Ahmed, Maybe you could further explain what you are trying to accomplish, e.g., you don’t need the annex files to compile the freesurfer source. - R. On Oct 4, 2022, at 04:33, Ahmed Abou Aliaa <ahmed.s.aboualiaa(a)gmail.com> wrote:        External Email - Use Caution        Good day everyone,I did a clean clone of the annex repository for my local workflow to check that I have all files. Unfortunately there are a lot of missing (or maybe stale/private/copyrighted) files which are not available. I've appended the output of the "git annex get" command below.Is there a way to fix this?-- kind regards,Ahmed Abou-Aliaa<annex.txt>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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annex repository missing a lot of files
by Ahmed Abou Aliaa 04 Oct '22

04 Oct '22

External Email - Use Caution Good day everyone, I did a clean clone of the annex repository for my local workflow to check that I have all files. Unfortunately there are a lot of missing (or maybe stale/private/copyrighted) files which are not available. I've appended the output of the "git annex get" command below. Is there a way to fix this? -- kind regards, Ahmed Abou-Aliaa

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Re: [Freesurfer] Freeview does not display image
by fsbuild 04 Oct '22

04 Oct '22

External Email - Use Caution Hello Justina, We need to know what your setup is on Windows for running Linux in order to help with running freeview.  It reads like you are not using VirtualBox to run the Linux Ubuntu OS,  I do not have VirtualBox installed ... So it’s not clear to me how you are currently running Ubuntu Linux on your Windows machine in order to run freeview or other freesurfer commands.  Are you running Ubuntu linux with the Windows Subsystem for Linux (WSL)?  Maybe you are connecting remotely to a linux machine via VNC or the like from your Windows machine ? If you don’t mind running freesurfer 7.2.0 (instead of the newest 7.3.2 release), there is a smaller version of the VM to download from https://secure-web.cisco.com/1YWO9PWAWb2dUg45HhJ8-Uf5BVRKini-Plt5…; with setup instructions under that link.   But you would still need to download and install VirtualBox on your Windows machine and then download and install the Freesurfer Software. - R. On Oct 3, 2022, at 09:35, Justina Lee <justinalee56(a)gmail.com> wrote:        External Email - Use Caution        To whom that can provide any insight,I am currently using Ubuntu on windows to open freeview to show some data. My issue at hand is that freeview does not show any images, despite changing the window levels (contrast and brightness). Using the command freeview -v works, and I am able to run it smoothly. When I try to open an mgz file, it runs fine, but I am unable to see anything.  I do not have VirtualBox installed and tried to take this advice from previous but I ran across the problem of downloading the course Virtual Machine. I do think that I do not need to download the VirtualBox and can continue using Ubuntu on Windows.What could be the issue with this? Should I be downloading the Virtual machine to run Freeview?Thank you so much for your time and I hope that my issue is not too big of a problem to solve.Sincerely,Justina_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview does not display image
by Justina Lee 03 Oct '22

03 Oct '22

External Email - Use Caution To whom that can provide any insight, I am currently using Ubuntu on windows to open freeview to show some data. My issue at hand is that freeview does not show any images, despite changing the window levels (contrast and brightness). Using the command freeview -v works, and I am able to run it smoothly. When I try to open an mgz file, it runs fine, but I am unable to see anything. I do not have VirtualBox installed and tried to take this advice from previous but I ran across the problem of downloading the course Virtual Machine. I do think that I do not need to download the VirtualBox and can continue using Ubuntu on Windows. What could be the issue with this? Should I be downloading the Virtual machine to run Freeview? Thank you so much for your time and I hope that my issue is not too big of a problem to solve. Sincerely, Justina

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mri_glmfit error
by fernanda rohrsetzer 03 Oct '22

03 Oct '22

External Email - Use Caution Hi, I attempted to execute mri_glmfit on my structural data through the following command - mri_glmfit --y lh.10.teste.thickness.mgh --fsgd testCT.fsgd --C Contrasts/LR-HR_testcov.mtx --C Contrasts/LR-MDD_testcov.mtx --C Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir lh.groupteste.thickness.glmdir --eres-save But it gives me an error (attached below) indicating a formatting problem in my FSGD file (attached). I have been trying to figure that out for a while. But I am unable to debug it. Could someone please help me resolve it? Thanks for your time.

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Re: [Freesurfer] FSFAST first level covariates
by Emily Iannazzi 03 Oct '22

03 Oct '22

External Email - Use Caution Apologies, that was a bad example! Yes, like you said we want to have two variables (one binary & one continuous) that represent different aspects of the same stimulus. We’re wondering if we can rescale the values to incorporate both responses – do you know whether Freesurfer allows negative modulation values in the par files? We would essentially make negative values represent the valence ratings of stimuli with “no” responses and positive values represent those with “yes” responses. Additionally, do you have any advice for debugging the “design is ill-conditioned” error we received before? We still don’t know why our XCond was calculated to be so high at 5.45e16. Here was our setup: 1 SelfRelevant (=1, included only for trials rated as self-relevant) 2 ValenceOffset (=1, included only for trials rated as self-relevant) 3 ValenceSlope (=valence rating) 4 SelfIrrelevant (=1, included only for trials rated as self-IRrelevant) 5 ValenceOffset (=1, included only for trials rated as self-IRrelevant) 6 ValenceSlope (=valence rating) 0 Other 0 Case 0 Fixation Thank you very much for your continued help! ------------------------------ Message: 2 Date: Tue, 27 Sep 2022 09:51:58 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] FSFAST first level covariates To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <d4a6ad9a-6463-6e7e-1c19-e951622915e7(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" See https://secure-web.cisco.com/1p1LwpSgcETesv4kjUKw_dC03qPRgQywmg0EAB7vjcgsoO…<https://secure-web.cisco.com/18_XTBGtGCKWwG3rq2kI81hxXtDx-uxj7639kO0xJN6cc4…> where group1=female, group2=male, and variable=age On 9/26/2022 10:45 PM, Emily Iannazzi wrote: > > ????????External Email - Use Caution > > Hi Doug, > > Thanks for the reply! We basically want to test an equation like y = > age + sex + age*sex. How would you set up the par files for that? > > ------------------------------------------------------------------------ > *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:* Friday, September 23, 2022 6:58 AM > *To:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Freesurfer Digest, Vol 223, Issue 39 > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1WCS_x94kVz8QXVOecVfY7eRj6O05PqvwIbbUxk-BOZiKo…<https://secure-web.cisco.com/1uhSofRCBHzEwOVNvZAcm8rKoTjVfBVXE277darP8MyDhD…> > <https://secure-web.cisco.com/1Rba_aZxOkZUlSMnOdqT1LxdC3ROZ9V_xXtNg8xpYG12MU… > > > 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: Running v7 with recon-all v6 files (fsbuild) > ?? 2. Fwd: Error (Ahmad Khan) > ?? 3. Re: Error (fsbuild) > ?? 4. dcmunpack (O'Dor, Sarah,PHD) > ?? 5. Re: Fwd: Error (Douglas N. Greve) > ?? 6. Re: dcmunpack (Douglas N. Greve) > ?? 7. Re: FSFAST first level covariates (Douglas N. Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 23 Sep 2022 08:00:38 +0200 > From: fsbuild <fsbuild(a)contbay.com> > Subject: Re: [Freesurfer] Running v7 with recon-all v6 files > To: freesurfer(a)nmr.mgh.harvard.edu > Cc: brouillard.alexandra(a)gmail.com > Message-ID: <9bf58e7024ed99c7c06379a6876dda10(a)trashmail.com> > Content-Type: text/plain; charset="utf-8" > > ??????? External Email - Use Caution > > Hello Alexandra > Please let us know if you are on an Intel or a > newer Mac with an arm processor, e.g., M1, M2 chip.  You could send > along a screen shot of what "About this Mac" displays. > Per the "Important Note" at the bottom of the freesurfer release page, > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1G0PkeFaLvOIRrn1MIK2_iZ9z6soqbvDnv5IRSAtAu0Vjk…<https://secure-web.cisco.com/1J_qi8yBmzKfxh4irpKkAx2HOSBPQb6Sep4ufVusAmr6D0…> > <https://secure-web.cisco.com/1xGoLsU1v9x_WJOz_jz46yX4Kqn77z6kQ5d1UM97vcLfuM… > > , you may not get exactly the same (floating point) results when > running v6 on a different/newer version of MacOS. > > - R. > > > On 9/22/22 09:36, Alexandra Brouillard > (brouillard.alexandra(a)gmail.com) wrote: > > > > > > > >         External Email - Use > Caution         > > > Hi >   > I ran recon-all on an external server using the version 6. I recently > downloaded the v6 on my Mac v12.6. > ?I was able to set a home directory but get a ?permission denied? > ?error when typing ?$FREESURFER_HOME? (but have the permissions/sudo). I > ?also can?t open Freeview: by double clicking on the app, the GUI > crashes, or by typing ?freeview? in the terminal > ?I get a PETSC error.  > According > ?to some previous forum threads, I?m thinking of downloading the v7 but > would like to validate that it?s OK when using recon-all v6 > ?files. >   > Thank you for your support, >   > Alexandra >   > > > > > > > > > ? _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/14kn_bB-iqSxYYBorx6tYbCA2oF3qeUI4Wx92HackpsboZ…<https://secure-web.cisco.com/1gbLJj5Ss62qOQb_h0V-5Hjd2rYPJDtwniatKhJz7qsIvi…> > <https://secure-web.cisco.com/12Xm2UG55yhwvp_SD445TSDlYU7qDkQtbcAxgAa1hPxmu6… > > > 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 *MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1XLqiQGGciftaJJf4IEmMwzFtnbd4PwcOuGsPas_-_8FSy…<https://secure-web.cisco.com/1ClrBOcX09ZV8oxYPLZnM6bfotSY4GjrBndnqvUT1oax8m…> > <https://secure-web.cisco.com/1VfHcQd78F8lWAln7dxGeqsla_w1QLy6b-qHUpK9i8Gf1j… > > <https://secure-web.cisco.com/1DBaRDxd12iOhxclW6Qeu-Qisec-Dz6mXPSrXki6ba2--4aP-1KUZOHTmn4djjjdndA9X9awKPiD1OBkULr__Lq7CBVhYBhC2dfDHkgvi83IrDtBDTkL3fHDuidZyLsKppjsl4b5boiolVj_GOvpmkY6fZpboqD0klywe80BrAeC7cTHNFz2p97AhioWI8BZSAXsNTm3-j9MyP0k5sbDjXd7IF0I-qNWhTcgC3AAT1VBGBBItmHGf-66q3EighSvYErFAGVakpGdOgUVNkMyrNRjlfyHt-fBkDrQHIIuKArHFAzi3ehd0vj9ppxhfLpcs/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1QEu65hJzFz0Qlr-f85ovtCCFPcEQTuVjkATuX8Dzuz3-aNImRz08NXygo1pKr2Wbp8Y7ERP6XX_QXuwwA7OQtL95Jy8KMvQkj8V15v6C3snSGsuYEymHIorCwk50lasrKb8M0DVESSb7lpsfhGW7Z8XrutrhY2vETqwYjoknqZ2L7coJdB9m0JwsRPxH88FkJaPyuapnujCIKZ0QiH7JLW_PxPUN1xjG8C0rI2ClwPd8PHXFdDo4ft_5ujxHY0YquA5UdKOwf3hc1himt1m2KKha9Xl8__;!!K-Hz7m0Vt54!hWPRRQX1ylRbES6rjr3vNJsvbbqtepENAz09egFLWkJFKIYvnFhNkJcjBYIXolLfsm45BoW1QBeS9mtry47EyJ2pUC7hKRKUCg$ > > ?cwmMraWndDu5-S3ei8hubimZcdWjlXmybq7wVZ40Jt_OHoyghzrMyO1mZg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; > . > Please note that this e-mail is not secure (encrypted).? 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