Freesurfer February 2023

freesurfer@nmr.mgh.harvard.edu

85 participants
122 discussions

Pial Surface errors
by KennethSPrice 17 Feb '23

17 Feb '23

External Email - Use Caution Hello all, I am having trouble generating a pial surface on the right hemisphere. There seems to be some signal dropoff in 3 areas: insula, supplementary motor, and somatosensory cortex. I have added control points and run -autorecon2 -autorecon3 again. Any suggestions? Thanks, Ken

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error with synthsr
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 17 Feb '23

17 Feb '23

External Email - Use Caution Hi developers, Using freesurfer-linux-centos7_x86_64-dev-20230216-9bc2be6, I receive an error following mri_synthsr. It says : get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj). * deprecated from version: 3.0 * Raises <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0 resuming program execution Since this seems to be a python problem, I am using python 3.7.7 and python 3.9.12, and neither seem to work. Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://secure-web.cisco.com/1dK_bHHkDS4VkptJxydJWEsTpLGrrOWpg6cDRwbGoBle5Ul… for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

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Password for archive FS_7_2_0_ubuntu_18_04_06.ova.7z
by Yoann Thiébaut-George 17 Feb '23

17 Feb '23

External Email - Use Caution Hello, I'd like to request the password for FS_7_2_0_ubuntu_18_04_06.ova.7z in order to install the virtual image and run Freesurfer in a Virtualbox VM. Thanks a lot !

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Re: [Freesurfer] Password to FS_7_2_0_Ubuntu_18_04_06.ova.7z file
by Richard Nkrumah 17 Feb '23

17 Feb '23

External Email - Use Caution Dear Freesurfer Admin, Can I kindly get the password to extract your FS_7_2_0_Ubuntu_18_04_06.ova.7z file? I want to try Freesurfer on a Windows device using VirtualBox. Thank you. Best Richard

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Re: [Freesurfer] Request for passcode
by Chris Allis 16 Feb '23

16 Feb '23

External Email - Use Caution Hello , Requesting the passcode to uncompress this archive. FS_7_2_0_Ubuntu_18_04_06.ova.7z Thank you very much!

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Along- tract multiple comparison result visualisation and summary interpretation
by miracle ozzoude 16 Feb '23

16 Feb '23

External Email - Use Caution Hello, I have questions regarding the along-tract stats using mri_glmfit and mri_glmfit-sim with permutation for version 7.2. 1) I ran it and I found a significant result (see attached summary file) where I expected/found a negative association between FA and clinical score. how do I know the entire length of the tract and how much was affected based on the summary file; should I be interpreting the results from the summary file differently? 2) Also when performing clusterwise correction for multiple comparison for along-tract analyses, should the bonferroni flag (--2spaces) be included? This is because it wasn't mentioned/included in the tracula statistics tutorial nor the publication "Using diffusion MRI data acquired with ultra-high gradient strength to improve tractography in routine-quality data ". 3) Lastly, is it appropriate to embed the perm.th13.neg.sig.cluster.mgh from mri_glmfit-sim in dmri_trk2trk? Many thanks, Paul

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recon-all does not produce ?h.white files
by Faraz Yazdanibanafshedaragh 15 Feb '23

15 Feb '23

External Email - Use Caution Hello, When I use the command recon-all -autorecon2-wm -subjid ${tmp_subj} -noaseg -xopts-use I only get ?h.white.K and ?h.white.H files, but not the ?h.white file that I need for mri_vol2surf script (so it exits with error). What am I doing wrong? Thank you

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Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS
by fsbuild 15 Feb '23

15 Feb '23

External Email - Use Caution You can try and piecemeal install missing libraries as Bennet suggested, however that is no guarantee everything you need will be installed.   Installing the .deb package (as I originally suggested) should install that and anything else needed.  And if an administrator has permission to run the command Bennet suggested, then you will have permission to run the installer you download from https://secure-web.cisco.com/1dTe66faitgItOrZ5LFcDBU07rjhW-8GQsdy…  Just ask your administrator to look at that page and install the correct package from it. - R. On Feb 15, 2023, at 09:17, behçet ayyıldız <behcetayyildizz(a)gmail.com> wrote:        External Email - Use Caution        Dear Bennet, Thank you very much for your help and suggestion. I tried it but it didn't work by indicating the following error "drodriguez (the ID that I use to login the computers) is not in the sudoers file. This incident will be reported. I think I should consult with my system administrator.Thanks for your suggestion.Bennet Fauber <bennet(a)umich.edu>, 15 Şub 2023 Çar, 14:07 tarihinde şunu yazdı:        External Email - Use Caution        Behçet,This message is the key:> error while loading shared libraries: libncurses...so.5: cannot open shared object file: No such file or directoryFreeSurfer is looking for a supporting library that it expects youroperating system installation to have but that is not there.If you can use `sudo` on your system, then you should be able toinstall this library with$ sudo apt-get install libncurses5If not, then ask your system administrator to install the libncurses5package.  If that is truly the only problem, installing the missingncurses library should fix it.On Wed, Feb 15, 2023 at 7:59 AM behçet ayyıldız<behcetayyildizz(a)gmail.com> wrote:>>         External Email - Use Caution>> Hello,> Thank you for your valuable reply. I would ask something before checking it. I forgot to say something, even after the computers change  "recon-all" is running, just like it runs before the change, however not the segmentThalamicNuclei.sh command. So yeah, I would also say that the problem is only in the segmentation module of Freesurfer for now.> Thanks in advance,>> fsbuild <fsbuild(a)contbay.com>, 15 Şub 2023 Çar, 13:07 tarihinde şunu yazdı:>>>>>> Hello Behçet,>>>> Are you saying the version of the Ubuntu operating system changed and now when you run the same command you get this error about the missing library ?>>>> If so, I would check with your system administrators to see if they have installed the freesurfer 7.1..1 .deb freesurfer package from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1At8QKM5oUsIZmRsMRNPvhsQysuzVxU0In_cXK… matches the version of Ubuntu you are now running..   Running the installer package should try to fix that missing library dependency.>>>> - R.>>>> On Feb 15, 2023, at 05:36, behçet ayyıldız <behcetayyildizz(a)gmail.com> wrote:>>>>         External Email - Use Caution>>>>>> Dear All,>> I was using Linux Ubuntu to perform my analysis. However, they were changed with Linux ..... a couple of days ago. And while the segmentThalamicNuclei.sh command was running before the change, after the change it didn't run and I got the following message.>>>>>> drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ segmentThalamicNuclei.sh con_HaJa93>> Setting ITK threads to 1>> #-------------------------------------------->> #@# Thalamic Nuclei processing Wed 15 Feb 2023 11:09:10 AM CET>> ------------------------------------------>> Setting up environment variables>> --->> LD_LIBRARY_PATH is ..:/sw/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/sw/freesurfer/7.1..1//MCRv84//bin/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sw/freesurfer/7..1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:>> /sw/freesurfer/7.1.1//bin/SegmentThalamicNuclei: error while loading shared libraries: libncurses..so.5: cannot open shared object file: No such file or directory>> 127>> Linux causal.brain.mri.tu-muenchen.de 5..10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux>>>> Do you guys have any idea how to fix it ?>>>> Thanks in advance.>>>> -->>>> Behçet Ayyıldız..>>>> _______________________________________________>> 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/1C2qT0kjSdOsO4Urhs8YV1g41i7E88v5A13FUD… -->> Behçet Ayyıldız..>> _______________________________________________> Freesurfer mailing list> Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1C2qT0kjSdOsO4Urhs8YV1g41i7E88v5A13FUDYy7LmlSF2EiRbuT9gvgVLFnERelVG7_YRTnwqm0aXquB-vbmJ0jQAxSOTe8uQyFN_P8ZL1FwAFmhQ8FfLjY3Z5HTT-HZfbruZjUbDfH5fkjSchgybsVsgQwgfAxATRkNUwCqRksjrUUh8wBE4CJj8DQDm45HtuhuXqDun2aXI-UcJwyYkVHt4PVNsRQHNDiVhBOTSN6bvp28B7EiOm3mheAspAgjxXwS71tqnTYhrR88RP87ovsHucfO-sn26KZ23WDaP_GEnfP8f-LDa-HmtzJQlieoYJhxj9F7fbm26glFDKxPA/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/1ud1ykrOdc9YoV_4X5XaFkvrONTcVWrgb6Uukm… .> 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(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 behttps://http://secure-web.cisco.com/1f2TRP1uqxlaYesltAMsyMHo_l-V5RYiDmioq… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ji_U3JB1P4m2GTdB7gxZzx3l0y-DQBvBcxWZa…; .-- Behçet Ayyıldız.._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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neurological view on command line
by Aaron Tanenbaum 15 Feb '23

15 Feb '23

External Email - Use Caution Is there a flag on the command line to turn on neurological view or do I have to turn it on in the GUI.

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Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS
by fsbuild 15 Feb '23

15 Feb '23

External Email - Use Caution Hello Behçet, Are you saying the version of the Ubuntu operating system changed and now when you run the same command you get this error about the missing library ? If so, I would check with your system administrators to see if they have installed the freesurfer 7.1.1 .deb freesurfer package from https://secure-web.cisco.com/1kZqy9BcKMr7diHAAdkyYDg2sSQj5AQELQZUIDe_I964ho… which matches the version of Ubuntu you are now running.   Running the installer package should try to fix that missing library dependency. - R. On Feb 15, 2023, at 05:36, behçet ayyıldız <behcetayyildizz(a)gmail.com> wrote:        External Email - Use Caution        Dear All, I was using Linux Ubuntu to perform my analysis. However, they were changed with Linux ..... a couple of days ago. And while the segmentThalamicNuclei.sh command was running before the change, after the change it didn't run and I got the following message.drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ segmentThalamicNuclei.sh con_HaJa93Setting ITK threads to 1#--------------------------------------------#@# Thalamic Nuclei processing Wed 15 Feb 2023 11:09:10 AM CET------------------------------------------Setting up environment variables---LD_LIBRARY_PATH is .:/sw/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/sw/freesurfer/7.1.1//MCRv84//bin/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sw/freesurfer/7.1.1//bin/SegmentThalamicNuclei: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory127Linux causal.brain.mri.tu-muenchen.de 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/LinuxDo you guys have any idea how to fix it ?Thanks in advance.-- Behçet Ayyıldız.._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer February 2023