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/1mhxyoaRo0TPOzY61gZ72Ihv17F6eoLxQkrIKSVeF9WmwBbwFTfbJouz6qsqQSRdz0Uk2WJfvXwaW6obKEujB6RrViM4R4AtQHcyvw0s5Tv02rV5vVVNxaAQUzePsE4J-taB4ZdiArX0pqI79a-82dF0d5bz5ZH5kTzltCSPWFxMbefYCekHanVzKPReFwgzsuSejjoEGXHy9NKaW7Ghq6no3rgWcW9964k1EwqI7x7HZgkOOK7L8_aSbKL8d2WOL-PuMiYvqw1pdrfBJ94PeBY3FIIp-JGWZrKv4vxId9DB3o7aEtH4fVdjo1B_hZHLypqW0m8SJPadhz4FJEVQ7zw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74529.html>) and I wonder if this may be related to my graphics card? Best, Haley ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of freesurfer-requ...@nmr.mgh.harvard.edu <freesurfer-requ...@nmr.mgh.harvard.edu> Sent: Monday, June 19, 2023 3:51 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 232, Issue 12 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1NFAytgj_o7SeKzQukc41bipAEO_iD8efSPiiL9lGpNDyHnU24aG7hBviwVPliMdp6rvx3ifddV7rAz92G0sPt_9_9oSbEBKAm0_nHTmebYKIFTbDEaggo7NjKq3Jtj_lWuh_YpQhi-JJ_qhZ3QCWEY4TPFdd7YpfwkyiegWS-rlm5VWWCufAdumAPQlaKd1bVYWMz4f-31g2LFqk0WXKX2fY8jSMbB5w7vmb2Av9s_d9xDstMisi16Y8_y4LKvPquP97g19q-F3_A0ajnF1z8W3WbRCvgoWsIxJ_D-gVfns0iKKOfm4zo9xTJizVzKr2/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@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 <jb19790...@gmail.com> Subject: Re: [Freesurfer] Size of overlap between a label and a volume To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <CABPMGjnBVnozT=1BcLNrXPe5fmciy4=7iisrtj3xbxyvxy4...@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_8SwhRxwcP4XoV0QdvHT3rxvRNSBm4KwTJa8GFaC4IypTfW6sCwqLkCV8-04lx4IwpYw1bloRw_V6dP7ZHDGcAKW_GxvmcPnNpEDrGOUP0_IOqBySvJcnPNi6vhkSVi10dToaEBiERpqDFz-EnxCjEgNGIJ3XNt-k3tKuVVXCHwRVILgioT9OGbo6ypjpXFGP3ZXbaHEcno4FQfRfil7Daqyt9jtk6hu7MV49cAA-kVltRnz0XNs6FPf7MtEN0eemFGiV1vvMIp5rjRfhyA2LWaKuhK4F6Eq2uHqE_n9TYs6AsXPSvtrmL8vi3cGm-6XyMKJwBQAM1Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_overlap On Fri, Jun 16, 2023 at 10:37?PM parsa...@student.ubc.ca < parsa...@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@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1bL2PbUa0oBf3uE-dqjk6ArIqlk3Mu1XRZ0Gqm2BSbnknDXkUAv0nG7TCvgdZGtxFpMopuSoaOG1DAd2Hcb1tVsAaDmHymRYxJ4t9yMfTNp_6Rw0B6zaYk45w86NY1Q_5DrDavKtV8snTWDbKA39DB8QOeiU6rCYHTWxfs4NRznwCDaSwzoAMgi2HIHvPl7e5Zz7ADzeIMiNT_JCukW7q9IrK8z7HIKo6d9MAkW9LGj3ryNK6ZEO3Mh5dYjdNu4fpz-YXwTL-eZygw0GeYa3ZBpMSfItMm8CiO-eTtCqR0H80wtU0tr8P9m2yDn310UhLFJmxLI9Xm5rJxk4FvoVxGg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDSnWFtnDs4dDxmZ0KAaurt7X2ksh15CPKyMoFG1e_bLBE1T_ymhu-QUAx4_yJt_1k-rAAQN4ZiVDIg4Y_tN7C1oy_6FBjRoalfTUF3bw8gpxFTQgq2CkCi1aG7mPoXG2pttMvKyTe22pGcV-hg-84orMuAyku6C8FYMYvBx2wvn9egPVJBsDqGreYKUcqBi-_1Uwrahua-8-GNZRSxA7lkKttOaKGrG44K8d-XZbWzrEmOKseNEhdxJYbTkJ1qa6s-uE-1odtnhsORP79OWVcMhivoexZwjx_N4wT3CvjA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDSnWFtnDs4dDxmZ0KAaurt7X2ksh15CPKyMoFG1e_bLBE1T_ymhu-QUAx4_yJt_1k-rAAQN4ZiVDIg4Y_tN7C1oy_6FBjRoalfTUF3bw8gpxFTQgq2CkCi1aG7mPoXG2pttMvKyTe22pGcV-hg-84orMuAyku6C8FYMYvBx2wvn9egPVJBsDqGreYKUcqBi-_1Uwrahua-8-GNZRSxA7lkKttOaKGrG44K8d-XZbWzrEmOKseNEhdxJYbTkJ1qa6s-uE-1odtnhsORP79OWVcMhivoexZwjx_N4wT3CvjA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1iClcN85H7rnQ2TbMwiHw2IAh0yjytDfG77C5ivY-bJkyCCYygkJt46s7abDs7PoXw5q_336huhehE5iWnMfpytdd75Q1xoX0tIMy6N6Iyr0qRJSXJ48TCzVogAmfY6qZ6c2X_lIhWL8FTBlqxStDz1cs4jVv9mgH4ojSr11PU2agmjQkHfT-sZYRH5DGtLnwNjKfR2SIMmgQXYpuyivTCCbhiF9-57uM7mSp9jSZTRw8KA060vN_8_B0QOWHDtM2QfnI_y3FmRU0NzYBy4JEwNWsO-WwsqMl7Gl-R6rwP5F5wgwLdTUh2dTx5bvuFebA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20230617%2Fd35e185b%2Fattachment-0001.html ------------------------------ Message: 2 Date: Sun, 18 Jun 2023 00:13:40 +0000 From: Haley O Higginbotham <hhigg...@mit.edu> Subject: [Freesurfer] Freeview: data not displayed To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <aa577d2c-2c58-423c-8ab4-b92f3e74b...@mit.edu> Content-Type: text/plain; charset="utf-8" External Email - Use Caution ? Hi FreeSurfer Developers, I've just installed Freesurfer and am trying to view a sample subject's data in Freeview (bert T1.mgz) but nothing is displayed (blank black screen - see attached screenshot). Xming is running and I've confirmed graphics function with xeyes. The progress bar in Freeview also completes and zooming in/out hasn't helped. I've also tested other volumes, surfaces, and patients with the same results. I'm running freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 on Ubuntu 20.04.6 LTS via WSL2 Has anyone experienced something like this before or have any clue what might be going on? Sorry if it's a simple solution - I'm new here Thanks in advance, Haley [cid:71a16993-26fc-4e0c-b21c-e03609ba5b22] -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1ia8l8-m09Smv2a8ShWjH1nT8oCBpsByAhfOIoZn-YG-eqAZZG6k8-e2p4Xa-qev-93-6M3B67XZl7i-aDgwib6a-vs5mOWbuqYgSz2Deb9JCxdYPaKRYLrnUjBuptyZVbKe-LwLqZpi2R2f5VScez0Db8qVyejRtm4UW2goxBh6ywxlIFLK-iKUtrzNUBoyZPWt8qTIm-A-TD-NynREg6byh3ARfexpwrfvjnzZcFV_8pvm6T8CoUBgsyngMGFZdlvuGk5hd801ZnJb_TSmvYE5cbgTYJhCxBFp2UVYKOxbkl0FsETD3reEng5aLiBps/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20230618%2Fc8326ad9%2Fattachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2023-06-17 195051.png Type: image/png Size: 107187 bytes Desc: Screenshot 2023-06-17 195051.png Url : http://secure-web.cisco.com/1w-3c32cFx7gBmtcX21h0f2SafQxdtd85_PlHWJFmLJ8DKi6zNFmi4GVHx9Vgaodntihhi9-M57u3EJZSDvkfAUfkZ9U-TsZoLkhDJyFkdpD2Iq4i8Uw9ZAza7eD-n8SyP1z6IbdCtCxI9SiVe1xcXmuup0OVJYDf4VMVDxDLeNAkUJhuDJEiaeCWi7yLlTaZ4ACfIFGkozjOxQhFm3SE3cW2CulAssYtCi1rA1rjFsMS7rFCJ68nPtLUUL-mibAymYjMHmQymaIeVXpLtI_ZDC9psTI0zOQCs0yGDW5-CAZ78nhaB69EP6PHRR_cDE-6/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20230618%2Fc8326ad9%2Fattachment-0001.png ------------------------------ Message: 3 Date: Sun, 18 Jun 2023 01:17:07 +0000 From: "Fischl, Bruce R.,PHD" <bfis...@mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview: data not displayed To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <ch0pr04mb79726387219f05e5ebb92d6cef...@ch0pr04mb7972.namprd04.prod.outlook.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution The voxel coordinate shown at the bottom is -59, so for some reason the cursor is outside the FOV. Try clicking there and typing in 100,100,100 or something like that Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Haley O Higginbotham Sent: Saturday, June 17, 2023 8:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freeview: data not displayed External Email - Use Caution ? Hi FreeSurfer Developers, I've just installed Freesurfer and am trying to view a sample subject's data in Freeview (bert T1.mgz) but nothing is displayed (blank black screen - see attached screenshot). Xming is running and I've confirmed graphics function with xeyes. The progress bar in Freeview also completes and zooming in/out hasn't helped. I've also tested other volumes, surfaces, and patients with the same results. I'm running freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 on Ubuntu 20.04.6 LTS via WSL2 Has anyone experienced something like this before or have any clue what might be going on? Sorry if it's a simple solution - I'm new here Thanks in advance, Haley [cid:image001.png@01D9A161.116FCEA0] -------------- next part -------------- An HTML attachment was scrubbed... URL: http://secure-web.cisco.com/1BU19WajzR_mT6Bwl91x1aCZ1FFP1H3AuYQE_0_lxyFsNrNddwR4mFctUaL5ykGF8T-fE-nEWbAinQQWpSNcX6gVbSwIWOT5LeRiRmzU25zD7vbo5LOeSyPj5SAR2J-GIeQbsxFyCfzw4BILivvGGsmLKSLYFzK1c5SwY0Jd0yJVHgh4pXPEUaX8Z7WX3-hE73V8ekSUnTrJYjpHndjv7VLfZkAWV-Qk7rhAo0v6AfQ7y-2clXEV7h6fG12G9hUpkfZCWIQRNL9curA7s8oXdcKMRH7zCo6GdusXQC157gmalLGcYM4AqTd5IFyapoINl/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20230618%2F167178a8%2Fattachment-0001.html -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 107187 bytes Desc: image001.png Url : http://secure-web.cisco.com/1lpzdsdPt769JPvuOHTQeUuIOw4qW_75mE2ImaVgMnsQZJ3vZxspIfgJRU25Ayzg-0VPAUTqoD7xy4-VMSs6bhohvgI8qTmolQwehYpzLnnrSg0b9BWCx9a882yzLcu2lHg_T5mZgMvhfEi0jC1sMrKXWT8_eN0QSJyArKJNxxJ9tG07R6wq8E4EcSppeplb3TC9y9DHpKfmc0jmeXMzEM0btWfmUNO_JkRJSqPPGzacWWFIGJxNxwVQNWBX3Q0WcqfTcq1vt-TqOeSOC07nGix4iW2WoHNbMOuP7MnLoQaVmZJH8fgVk1QhK1i_C3ARL/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20230618%2F167178a8%2Fattachment-0001.png ------------------------------ Message: 4 Date: Mon, 19 Jun 2023 07:50:57 +0000 From: Krystal Xiwing Yau <kryst...@hku.hk> Subject: [Freesurfer] [FreeSurfer] Talairach Failure Detection To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <7bc4fde85b5e41469fb369a18589c...@hku.hk> Content-Type: text/plain; charset="iso-8859-1" External Email - Use Caution Dear Freesurfer experts, I would like to seek for help regarding talairach error. I have browsed through the forum about it but still not solving my problem... The following steps are the solutions I have tried: * Re-run recon-all with -notal-check * Re-run recon-all with -notalairach * The above flags gave the same error message as follow: * WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=100, mri_peak=108 after smoothing, mri peak at 0, scaling input intensities by inf error: Numerical result out of range error: GCAhistoScaleImageIntensities: could not find wm peak Command exited with non-zero status 252 * Ran the command to fix the registration: tkregisterfv --s Sub-108 --fstal --no-surfs * The view for this subject is weird because it shows the axial view when the coronal view is selected * [cid:49cf1b63-a35e-4003-8f38-a1def3b7bd64] * The correct view showed up when the coronal view is selected * [cid:abd68344-6bc3-489a-9eef-20569a419c02] When I viewed 001.mgz in Freeview, there was no such problem. However, some artifact (i.e. the weird lines) occurred in certain slices, as circled in pink: [cid:0c0b2ea4-3b3e-4361-ad0c-c5dec191c85c] [cid:eadbe192-c57a-48db-b429-b162b0154d0f] [cid:229941cf-2005-44c6-a979-0bf60c03da18] I am not sure how to fix it with tkregisterfv and what are the standards for it. It would be so much appreciated if someone could help out with this issue. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong. -------------- next part -------------- An HTML attachment was scrubbed... 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