Freesurfer April 2022

freesurfer@nmr.mgh.harvard.edu

97 participants
155 discussions

mri_segment_hypothalamic_subunits error
by Chen ZY 22 Apr '22

22 Apr '22

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to use the mri_segment_hypothalamic_subunits tool on subjects that have been analyzed with recon-all as described on the wiki page (https://secure-web.cisco.com/1A9dGY6OywLZ30vDfBWiSZqvoBp25mO3nhNd6jDNfiis58…) but I received the following error when I run the mri_segment_hypothalamic_subunits command (mri_segment_hypothalamic_subunits --s): (tensorflow) brain@neurodebian:/usr/local/apps/freesurfer/subjects$ mri_segment_hypothalamic_subunits --s bert using 1 thread processing 1/1 *** Error in `/usr/local/apps/freesurfer/python/bin/python3': munmap_chunk(): invalid pointer: 0x00007fa1707b3400 *** Aborted I would be appreciated if you can help me solve this problem. Thank you very much! Regrads, 发送自 Windows 10 版邮件<https://secure-web.cisco.com/1CLa9ah2pQJGRCoKdiDPebrBBXr4zULmqXF8tkJypVTxDs…>应用

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Re: [Freesurfer] License for 5.X versions of FreeSurfer
by fsbuild 21 Apr '22

21 Apr '22

External Email - Use Caution Responding to you off the list. - R. On Apr 21, 2022, at 15:08, Paul Wighton <paul(a)corticometrics.com> wrote:        External Email - Use Caution        Hi Jacob,Can you provide more details on how FreeSurfer was installed, how you are using the license key and the errors you are receiving?I just created a docker container with FreeSurfer v5.3.0-HCP (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1J8ksi9SDc5fMzjSvEALj9L1iRGatYnyqft703…) and tried my license file and things work fine.The container is at pwighton/freesurfer:5.3.0-HCP if you would like to try it yourself.You can run `docker run -it --rm pwighton/freesurfer:5.3.0-HCP` to get an interactive shell inside this container.Once inside the container, running this test command:```mri_convert /opt/freesurfer-5.3.0-HCP/subjects/sample-001.mgz /tmp/sample-001.nii.gz```Does indeed give me a license error```--------------------------------------------------------------------------ERROR: FreeSurfer license file /opt/freesurfer-5.3.0-HCP/license.txt not found.  If you are outside the NMR-Martinos Center,  go to MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1ky0Zkng4jenq5LESezo6mVh5Nj2QyMfpmBaZ_E… get a valid license file (it's free).  If you are inside the NMR-Martinos Center,  make sure to source the standard environment.--------------------------------------------------------------------------```However after copying my license file to `$FREESURFER_HOME/license.txt` the same command works fine.-PaulOn Thu, Apr 21, 2022 at 3:42 AM Jacob Breiting Sönnichsen <jbs(a)brainreader.net> wrote:        External Email - Use Caution        Hi all, Are there really no one out there, who knows, how we can get a FreeSurfer 5.1 and 5.3 running?How do we obtain/create a license for these versions? Kind regards / Cordialement / Med venlig hilsen Jacob From: Jacob Breiting Sönnichsen Sent: Friday, 15 April 2022 10.03To: freesurfer@nmr.mgh.harvard.eduSubject: License for 5.X versions of FreeSurfer How do I obtain a license to run old versions of FreeSurfer?I need to replicate some research done with an old 5.1 and 5.3 version of FreeSurfer and using a current license does not seem to work?Is it possible to convert the new license to the old license somehow? Kind regardsJacob_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/16KPMReTC7GusLUXzm69NkGs_u2h1TtCJQJxIH… 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/193_FpqrceBj1EcwaA5EiWd5AF7LL6sUh3tGks… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1qAm2kFjt5n_Pli8LvxfUKUqwOvUgLPLr8BxRp…; .Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Failed to open FS 7.2 on Virtual Machine
by fsbuild 21 Apr '22

21 Apr '22

External Email - Use Caution Check to make sure that you are not running low on disk space on your C drive.  I would try to keep at least 10 - 30G of free space on your boot (C) drive. If there is no issue with disk space, then it’s possible the Windows “hypervisor” is interfering with VirtualBox.  See the instructions at this URL a little more than half way down the page, about how to Disable Hyper-V in the Control Panel on Windows 10, https://secure-web.cisco.com/1x_usMKyN8ZX9GNmZTRHorph5mDk2mkFj83CH… You should reboot your machine after disabling it. - R. On Apr 20, 2022, at 23:06, krystaly <krystaly(a)hku.hk> wrote:0x80004005

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Failed to load MRI error
by HYE JUNG YOUN 21 Apr '22

21 Apr '22

External Email - Use Caution Dear freesurfer devleopers, I am experiencing an error while loading freeview using the following code: This always worked for me but now when I try to load and view it, a message "failed to load MRI" pops up on freeview after loading T1.mgz. >From the terminal it says: error: mghRead(/Applications/freesurfer/7.2.0/subjects/211025/1079_4/mri/wm.mgz, -1): read error MRIread failed: Unable to read from /Applications/freesurfer/7.2.0/subjects/211025/1079_4/mri/wm.mgz Also, when I check the mri containing file, eg: 1079_4 folder, after loading freeview, the folder contains automatically generated -v and -f file. I have seen a few similar errors on google and mail archive but they did not solve my issue. I would very much appreciate any solution to this. Thank you in advance. Best, HJ

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Re: [Freesurfer] differences between Freesurfer 6.0 and 6.0-beta
by Hoptman, Matthew (NKI) 21 Apr '22

21 Apr '22

External Email - Use Caution Hi all, I have access to a system that has both freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c vs. freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 Could someone please let me know what the primary differences are between these versions? They have been used exclusively to get volumes/thickness/surface area. Should those values be identical? Thanks, Matt Prounouns: He/Him/His IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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License for 5.X versions of FreeSurfer
by Jacob Breiting Sönnichsen 21 Apr '22

21 Apr '22

External Email - Use Caution How do I obtain a license to run old versions of FreeSurfer? I need to replicate some research done with an old 5.1 and 5.3 version of FreeSurfer and using a current license does not seem to work? Is it possible to convert the new license to the old license somehow? Kind regards Jacob

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FS 7.2 using ANTs N3
by Alexopoulos, Dimitrios 21 Apr '22

21 Apr '22

External Email - Use Caution Hi, We've been running some 2-3yo data (1mm isotropic T1s) through the FS 7.2 and are seeing some issues with WM segmentations that appear to be caused by the new ANTS N4 bias correction. We ran the same subjects with just the MNI N3 correction and also configuring FS7.2 to use ANTs N3 correction. Empirically, the output volumes/surfaces look most accurate using ANTs N3 (See outputs below). Infant Freesurfer did not do as well on these data. I just want to confirm that this is an acceptable approach, using ANTS N3 within the FS7.2 pipeline?? Jim See below: [cid:image001.jpg@01D853E8.7ECB9960] [cid:image002.jpg@01D853E8.7ECB9960] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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recontruction of an elephant brain
by Malav Shah 21 Apr '22

21 Apr '22

External Email - Use Caution hi, I am trying to reconstruct elephant brain MRI. I am wondering if FreeSurfer can manage this, or does the recon-all command has an inherent bias for human data. Does anyone have an experience using FreeSurfer with a non-human mammal for such purposes? I have some hopes with this idea, because I am not trying to achieve parcellation or segmentation. Rather, we want to separate White matter from grey Matter, and then probe into various surface measurements across cortical regions. So as per my understanding, all I am expecting from FreeSurfer, is WM-GM segregation, and later (if possible) cortical surface flattening, and DTI. All words of advice are welcome. Thanks :) Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. (+49) 163-216-9391

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rerunning on 7.2 with edited brainmask using hi-res
by Alexopoulos, Dimitrios 21 Apr '22

21 Apr '22

External Email - Use Caution We are running some hi-res 0.8mm3 isotropic data through FS 7.2 using the following command. recon-all -s subj -all -hires We are adding back brain which has been removed by the masking process by cloning the T1/brainmask images in freeview and adding back voxels. A revised brainmask.mgz is saved. Can/should the same command be used to rerun using hi-res data? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Recon process for skull-stripted data
by Muhammed Görünen 21 Apr '22

21 Apr '22

External Email - Use Caution Hi, How can I run a recon process if I have just skull stripted data? I need surface and annot files. Does the process need the volume files produced before the skull-stripting process? Thanks in advance. Best, --Muhammed

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Freesurfer April 2022