[Freesurfer] Is it poosible to redistribute a part of buckner_data for group work?
Dear FreeSurfer experts, We are planning to have a one-day neuroimaging workshop in Japan. One topic of the workshop is "FreeSurfer troubleshooting", in which we go through the online tutorial you provide ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) in Japanese language. So we would like to use the buckner_data for the workshop. However, the problem is that some have difficulties downloading the data (It takes more than 2 days to download...) So I'm wondering if we can share the part of buckner_data with attendees for the workshop in a closed network (via a site with login requirements). I read through the FreeSurfer license, and README in the buckner_data, but it doesn't mention about redistributing the data. We would like to respect the license, so could you let me know if we can redistribute the part of buckner_data? Best regards, Kiyotaka -- Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Neuropsychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: kiyot...@nemotos.net ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Is it poosible to redistribute a part of buckner_data for group work?
Dear Allison, Thank you! It will be a big help to us. Best regards, Kiyotaka 2018-01-10 21:17 GMT+09:00 Allison Stevens : > Dear Kiyotaka, > It is okay to distribute the buckner_data we post on our website for > tutorial purposes. > Allison > > On Jan 8, 2018, at 6:35 AM, Kiyotaka Nemoto wrote: > > Dear FreeSurfer experts, > > We are planning to have a one-day neuroimaging workshop in Japan. One > topic of the workshop is "FreeSurfer troubleshooting", in which we go > through the online tutorial you provide (https://surfer.nmr.mgh.harvar > d.edu/fswiki/FsTutorial/TroubleshootingData) in Japanese language. > > So we would like to use the buckner_data for the workshop. However, the > problem is that some have difficulties downloading the data (It takes more > than 2 days to download...) > > So I'm wondering if we can share the part of buckner_data with attendees > for the workshop in a closed network (via a site with login requirements). > I read through the FreeSurfer license, and README in the buckner_data, but > it doesn't mention about redistributing the data. We would like to respect > the license, so could you let me know if we can redistribute the part of > buckner_data? > > Best regards, > > Kiyotaka > > -- > Kiyotaka Nemoto, M.D., Ph.D. > Associate Professor > Department of Neuropsychiatry > Division of Clinical Medicine, Faculty of Medicine > University of Tsukuba > 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan > E-mail: kiyot...@nemotos.net > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Libraries not found Freeview ubuntu 18
External Email - Use Caution Dear Renew, I use Ubuntu 18.04, and installing libjpeg62 and libpng12 resolved the problem for freeview. Copy and paste the below to your terminal and you will be able to run freeview. - cd $HOME/Downloads curl -O http://security.ubuntu.com/ubuntu/pool/universe/libj/libjpeg6b/libjpeg62_6b2-3_amd64.deb sudo apt install -y ./libjpeg62_6b2-3_amd64.deb curl -O http://security.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1.1_amd64.deb sudo apt install -y ./libpng12-0_1.2.54-1ubuntu1.1_amd64.deb - Hope this helps, Kiyotaka Renew Andrade : > External Email - Use Caution > > Dear FreeSurfer experts: > I have a problem with Freeview running I ubuntu. Some libraries missing. I > read this thread “ > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63255.html” > and my question is regarding the installation of the libraries. Do I need > to install manually one by one or is there any package to install most of > them? Plus I couldn´t find any of them by the name in "sudo apt-get install > *”. Some of them are OpenGL, qtscript, volumerendering, vtkftgl, > vtkhybrid, vtkIO, vtkDICOMParser, ... > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Psychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: kiyot...@nemotos.net ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] question about aparcstats2table
External Email - Use Caution Hi, I use the attached script to utilize aparcstats2table. This will generate surface, thickness, thickness_SD, and volume csv files. Hope this helps. Kiyotaka External Email - Use Caution > > Hi FreeSurfer experts, > I want to converts a cortical stats file into a table by the > aparcstats2table command. However, there are totally 500 subjects. And it > is really hard to input subject numbers one by one. The Numbers are > arranged in a regular way. > So, can you give me some advices? > Thanks a lot. > Cheers, > Chen > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Psychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: kiyot...@nemotos.net fs_stats_aparc.sh Description: application/shellscript ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error running "Test your FreeSurfer Installation"
External Email - Use Caution Dear Rafael, I use Ubuntu 18.04, and installing libpng12 resolved the problem for freeview. Copy and paste the below to your terminal and you will be able to run freeview. - curl -O http://security.ubuntu.com/ubuntu/pool/main/libp/libpng /libpng12-0_1.2.54-1ubuntu1.1_amd64.deb sudo apt install -y ./libpng12-0_1.2.54-1ubuntu1.1_amd64.deb - Hope this helps, Kiyotaka External Email - Use Caution > > When I changed the permissions on the directory where FreeSurfer was > installed and ran it from there, and all went well. However, when I tried > to display the results with Freeview, there was a problem:error while > loading shared libraries: libpng12.so.0 > > This was a more serious error. I saw some mention of this error > occurring, but am not sure what to do about it. The answers given don't > quite help. Somehow I need to extract a very specific library which I > have no idea how to find. I installed all this using Anaconda in a virtual > environment. I have several copies of libpng12.so.0 in various conda > environments, but not the specific version that seems to be required by > Freeview... > > On Fri, Dec 20, 2019 at 12:33 PM Hoopes, Andrew > wrote: > >> Hi Rafael, >> >> >> >> Is your subject directory stored on an external drive like an SD card? >> The “Function not implemented” error implies that symlinks are not >> supported on the filesystem that you’re saving to. Ubuntu 18 definitely >> supports symlinks and I see that SUBJECTS_DIR points to /media/rafa…. You >> should process your data on the ubuntu filesystem first, then try copying >> it onto a card after. >> >> >> >> Best, >> >> Andrew >> >> >> >> >> >> *From: * on behalf of Rafael >> Espericueta >> *Reply-To: *FS Help >> *Date: *Wednesday, December 18, 2019 at 8:57 PM >> *To: *FS Help >> *Subject: *[Freesurfer] Error running "Test your FreeSurfer Installation" >> >> >> >> *External Email - Use Caution* >> >> I was trying to run the command: recon-all -s bert -all >> >> It ran for hours, but finally output the following: >> >> writing Gaussian curvature to ./lh.white.preaparc.K...done. >> writing mean curvature to ./lh.white.preaparc.H...done. >> rm -f lh.white.H >> ln -s lh.white.preaparc.H lh.white.H >> ln: failed to create symbolic link 'lh.white.H': Function not implemented >> Linux hypatia 4.15.0-66-generic #75-Ubuntu SMP Tue Oct 1 05:24:09 UTC >> 2019 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s bert exited with ERRORS at Wed Dec 18 16:18:43 PST 2019 >> >> 1) FreeSurfer version: >> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c >> 2) Platform: Ubuntu 18.04.3 >> 3) recon-all.log: see attached >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Psychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: kiyot...@nemotos.net ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] aparcstats2table {Disarmed}
External Email - Use Caution Hi, Suppose the fsid of your subj10 is subj10 and you set SUBJECTS_DIR correctly to /home/team33/MRI4, the command should be aparcstats2table --hemi lh --subjects subj10 --parc aparc.a2009s --meas meancurv --tablefile /home/team33/aparcstats.txt I noticed that there is a space between team33/ and aparcstats.txt, which will cause another problem. Hope this helps, Kiyotaka 2020/11/5 0:24 saman fouladi : > External Email - Use Caution > > hi > > I run in linux command: > """"""""""""""""""""""""""""""""""""""""""" > aparcstats2table --hemi lh --subjects /home/team33/MRI4/subj10/stats > --parc aparc.a2009s --meas meancurv --tablefile /home/team33/ aparcstats > .txt > """"""""""""""""""""""""""""""""""""""""""" > but show below error an i can not solve it nix: > > """"""""""""""""""""""""""""""""""""""""""" > File "/usr/local/freesurfer/bin/aparcstats2table", line 156 > print 'ERROR: atleast 1 subject must be provided' > """"""""""""""""""""""""""""""""""""""""""" > > I changed the code several times, but in all cases there is this error. > This error also happens to asegstats2table. > > please help me > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1cvwnliBEQF1AmGZlpH3pfTq05Ws5G3jBZGmy_RJuGbUUDic_warS6Cj15iHHT4Rd8AuG4XHWICk9sA5AvxzSOXkRHs6_xFu-HxTxwpASsX95EWfwhebDAvNLaDVWcXX6afQVPdjvxXvn-TouU93nYJCVJu2-t8vxOOb8K_wstaLC7by_F_bHpbW84AlqnRSd1rxNsvHb5WEpSk8are55vA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer -- Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Psychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: kiyot...@nemotos.net ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ubuntu 20.4?
External Email - Use Caution Hi Olga, I test FS 7.1.1 on Ubuntu 20.04, and it works well so far. You need to install libjpeg62 and libpng12 beforehand. lipjpeg62 can be installed easily with apt. sudo apt install libjpeg62 As of libpng12, you need to download deb file. curl -O http://secure-web.cisco.com/1J0IxTXaTCDx69zRg7MojhMmzIRmzAYydUBXqa3tbKmV2F-ujZutGz57k1t7AOjoqnmJ153CUxEw2RzSHdQeG768Y59bvjzq5tStZzQFjgzbqxMTTcrrUxN-79TbVTppbZV6oG8GvQk8SCAXJWO-Zyq3SAIk2MV8ORxgpUHBAnF3zBhkSV4fbF-yHA1NZL7zU6OU3IBXWtmHtdB2BBXRIplS3gk8fmUuBnHFA_nYoVyByNSZ2Ov2WrStxmvITKxwTP1hkDqTgrV2pPAec2dZWPQ/http%3A%2F%2Fsecurity.ubuntu.com%2Fubuntu%2Fpool%2Fmain%2Flibp%2Flibpng%2Flibpng12-0_1.2.54-1ubuntu1.1_amd64.deb sudo apt install -y ./libpng12-0_1.2.54-1ubuntu1.1_amd64.deb Best regards, Kiyotaka On Fri, Feb 12, 2021 at 9:38 PM Olga Kepinska wrote: > External Email - Use Caution > > Dear all, > > If in the meantime any of you has had any experience with FS on Ubuntu > 20.4, please let us know the details. > > > > Thank you and kind regards, > > Olga Kepinska > > > > *From: * on behalf of Olga > Kepinska > *Reply-To: *Freesurfer support list > *Date: *Tuesday, December 22, 2020 at 5:24 PM > *To: *"freesurfer@nmr.mgh.harvard.edu" > *Subject: *[Freesurfer] ubuntu 20.4? > > > > *External Email - Use Caution* > > Dear FS community, > > I’m following up on my previous communications about FS on Ubuntu (if > interested see thread ‘FS on Ubuntu’). > > The advice (very useful, thank you!) given by the fsbuild team is to go > with Ubuntu 18. > > > > If however, anyone out there has successfully used FS 7.1 (to run the > structural pipeline) on Ubuntu 20.4, please reach out! > > > > Thank you, > > Olga > > > > -- > > Olga Kepinska, PhD > > Postdoctoral Researcher > > Brain and Language Lab > (http://secure-web.cisco.com/10zoZoVhI0MrLVBtlIMNDW06hsvdwx84ecab4agSZLT8lsURyQkHiidoZeDtd_aLESLHQmDQXQTZKv2fZajZ0JX7itHhBrQvqDqy6ZoKvjup-_0EPe3B_z041Uv1t7TRbRqYKT8VCzZYfSmwwo8hxaJeNmQKbOW03DT2u723oCOwq_RhC9Lz4nJKEX-DUtetlpa-IYJoYX1Hh1k137oyEWVwbHRLMFnaNQD4AqVwxt6i_6cigF4Ot1tolVseQPBHs4sMq9MVAgmj-ljLuxgAx7Q/http%3A%2F%2Fwww.brainandlanguagelab.org) > > @olgakepinska > > ___ Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1q1AHAKxkuZZUweoC-JyV1RKPz3QegPuK1OWYazRZvgieVSElTnEAWcf6WAIpAR23iIVEY1DPwkitRefOoTQEnQuVfYF8P9Z4nrWv60Z4TvLimzrm40W5tLyqWtnKtdpC0lkg6cg0TWxUbuPH9QYeRy7CI8oCmu46c0hmGv1zCAti9D93UU3PEVmc8EYz23yEsMM3HgNKTTSVaWxX3pk_EA_m3OSZrWVB8HeWOCPWygt3x_MbWh9mnI3bYd9cLK_MxtyfksiCDojqeA-K1xB6Zw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1q1AHAKxkuZZUweoC-JyV1RKPz3QegPuK1OWYazRZvgieVSElTnEAWcf6WAIpAR23iIVEY1DPwkitRefOoTQEnQuVfYF8P9Z4nrWv60Z4TvLimzrm40W5tLyqWtnKtdpC0lkg6cg0TWxUbuPH9QYeRy7CI8oCmu46c0hmGv1zCAti9D93UU3PEVmc8EYz23yEsMM3HgNKTTSVaWxX3pk_EA_m3OSZrWVB8HeWOCPWygt3x_MbWh9mnI3bYd9cLK_MxtyfksiCDojqeA-K1xB6Zw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer -- Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Psychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: kiyot...@nemotos.net ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Announcing FreeSurfer version 7.2
External Email - Use Caution Dear Doug, Thank you for the announcement of 7.2.0 update. I updated using freesurfer-linux-ubuntu18_amd64.tar.gz and noticed that the 'mni' directory is missing. As a result, now the shell shows warning about MNI = freesurfer-linux-ubuntu18_x86_64-7.2.0-20210714-aa8f76b Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.2.0 FSFAST_HOME /usr/local/freesurfer/7.2.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/username/freesurfer/7.2.0/subjects WARNING: MINC_BIN_DIR not defined. 'nu_correct' and other MINC tools are used by some Freesurfer utilities. Set NO_MINC to suppress this warning. WARNING: MINC_LIB_DIR not defined. Some Freesurfer utilities rely on the MINC toolkit libraries. Set NO_MINC to suppress this warning. FSL_DIR /usr/local/fsl = Is it intended? Best regards, Kiyotaka On Tue, Jul 20, 2021 at 7:45 AM Douglas N. Greve wrote: > We are please to announce version 7.2. Mostly bug fixes and > behind-the-scenes enhancements. But there are a few new goodies and one > new "known issue" about defacing. Check out > https://secure-web.cisco.com/1Nq7OG4aqL5Xu5zmIj8jgt_aBH5sIzltmYEnh37LRCC02zUZJGtxhXjbr0RAoJKh7BtiL6-idjNjfiQdlADO4shk7DLtd9JwfjdpLzmw9--jn4lSaFUiwRrKjViNKHZQtQQPksweoYvQiKRJ-y0-kRCdPvOF3aK5lht5Pyc-LXUG4if3vb5foaGHGQb-9RCQhVi2Fen9Qpcz-5KsV8t2xasvxlBFP9nxk2X0URW-y0xEiEjnPng_y6WFgp42hIhMR-bF4VfXTbQTXEZX37XNcKg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes > doug > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/160o86r0Wg5hAWXbUcGcJ_MNRJJoO9nSvvvdSf0RIWdKuZ60guHgPYdDLMWPLctFsmW8v2_W95fIQKEHtdEZoiuWj0FAFY7moIi_xp1H2fdyrRQURKgGXVkHwc2JFPcFhA9prmc4ZzBrrpb-iyq-pFoQRjufitZHAj3jtpCeIXoYBgXB2ODwVkiPK1PeBJqZf5KaW7LXbZ184ROm5g3oAAn-Aiy0Iai2Z5l3tBKnd5cJcqGiLA2Gw7hYSueg8L3hfVMOjhR_JvOcbMZN1p4dbbw/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 > http://secure-web.cisco.com/1sNbeEVtvuwqzKlXCpXC5oSagM47ENvIzIX1rje6hMrQRa0xr50lz9ftON5MKtxQ7KzUyGjFY4HQBMsg7Lfc9e6XDe7wmpXz8mgYsRTZQgO7dDQv5v0oyM6eXaFUdPe756rkK6nv1j__R8miVAPj503r7RtesN2CMzfuTvi-gVhpYtEx07MUELh2MbMAxKgvKAN7xbaW7spFL1xcXNOMq8FHW0USHm_8Lp0MfDVArOACMzjeUZ4iaCTY9fTuQUJnbOOmQRyIuaqKYpeQ3Ao4Eqw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > 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. > > -- Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Psychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: kiyot...@nemotos.net ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Announcing FreeSurfer version 7.2
External Email - Use Caution
Hello R,
Thank you for letting me know that the deb file is now available. It's so
useful for Ubuntu users to install FreeSurfer using the deb file.
Can I ask you one more question? Can I specify the install directory using
the deb file?
I manage different versions of FreeSurfer by installing under
/usr/local/freesurfer/{6.0.1, 7.1.1, 7.1.2}.
If I can specify the directory, then I would love to use the deb file.
As for the missing mni directory, I'm concerned about nu_correct.
In my understanding, recon-all still uses nu_correct as default unless we
set DoAntsN3 or DoAntsN4.
nu_correct is located under $FREESURFER_HOME/mni/bin, so I thought it might
be missed for some reason.
Best regards,
Kiyotaka
On Tue, Jul 20, 2021 at 3:32 PM fsbuild wrote:
> Hello Kiyotaka,
>
> You may not need to be concerned about that warning. You can suppress it
> by setting the following in your shell environment.
>
> $ export NO_MINC=1
>
> For Ubuntu linux, if you have sudo/root/admin privileges, then you could
> try running the installer file instead of using the tar file, i.e.,
>
> $ sudo apt-get install ./freesurfer_7.2.0_amd64.deb
>
> - R.
>
> On Jul 19, 2021, at 21:08, Kiyotaka Nemoto wrote:
>
> External Email - Use Caution
>
> Dear Doug,
>
> Thank you for the announcement of 7.2.0 update.
> I updated using freesurfer-linux-ubuntu18_amd64.tar.gz and noticed that
> the 'mni' directory is missing.
>
> As a result, now the shell shows warning about MNI
>
> =
> freesurfer-linux-ubuntu18_x86_64-7.2.0-20210714-aa8f76b
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME /usr/local/freesurfer/7.2.0
> FSFAST_HOME /usr/local/freesurfer/7.2.0/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR /home/username/freesurfer/7.2.0/subjects
> WARNING: MINC_BIN_DIR not defined.
> 'nu_correct' and other MINC tools
> are used by some Freesurfer utilities.
> Set NO_MINC to suppress this warning.
> WARNING: MINC_LIB_DIR not defined.
> Some Freesurfer utilities rely on the
> MINC toolkit libraries.
> Set NO_MINC to suppress this warning.
> FSL_DIR /usr/local/fsl
> =
>
>
> Is it intended?
>
> Best regards,
>
> Kiyotaka
>
>
>
> On Tue, Jul 20, 2021 at 7:45 AM Douglas N. Greve
> wrote:
>
>> We are please to announce version 7.2. Mostly bug fixes and
>> behind-the-scenes enhancements. But there are a few new goodies and one
>> new "known issue" about defacing. Check out
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1_krAiqYGYHVZbMtBtPoXz7kVN8VoPKyZpkudxNSGLvRc0XhCBMswcAPLXcx7JcA52vWpPUt66ZaFh6lW8mBJ9rhtrAK9wNSBVMyd_xFoHrI9YN2C7xwdb7Nsm-FQaJ3voMZMuAeGVCBYl9OU45AM4X07w5488PhxS218tOWihVV_IEBx-EKYTMa6YptWmpt9mMt7c9tgkgol2wYbD5b1PyyGWj5daqvp-uZZqbV1oPA_Uw1RDXb7_jvhBwDl1xiKrlkVy3mqRuXHnN5bcwHjFg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
>> <https://secure-web.cisco.com/1Nq7OG4aqL5Xu5zmIj8jgt_aBH5sIzltmYEnh37LRCC02zUZJGtxhXjbr0RAoJKh7BtiL6-idjNjfiQdlADO4shk7DLtd9JwfjdpLzmw9--jn4lSaFUiwRrKjViNKHZQtQQPksweoYvQiKRJ-y0-kRCdPvOF3aK5lht5Pyc-LXUG4if3vb5foaGHGQb-9RCQhVi2Fen9Qpcz-5KsV8t2xasvxlBFP9nxk2X0URW-y0xEiEjnPng_y6WFgp42hIhMR-bF4VfXTbQTXEZX37XNcKg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes>
>> doug
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web..cisco.com" claiming to be*
>> https://secure-web.cisco.com/1PYiesaHKg39fdFzcC9TO5yhVmP-Xs-yLSKdCzx2VNakVmXJ72isb5oLqAXFUNiSj5TXQAstSGFJGGckVErjK88y985R-IhGoOrwD9qO96gRmOd_38kC6E1nR9QgY5E_uIEu36a3bxQ5Zpl7ozmE7HkzeePinGoSfZG2Tw9b7wv0g3H0S5ds-4CY14mCPWCrKmEVaKRaqGQIDok6efJXXNyFcdcYyQe4Rr-X9fG-Emt6Ap8R83dvzdEtxaj85urDrtU7NplCWTFGERO_mrZ8fEw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <https://secure-web.cisco.com/160o86r0Wg5hAWXbUcGcJ_MNRJJoO9nSvvvdSf0RIWdKuZ60guHgPYdDLMWPLctFsmW8v2_W95fIQKEHtdEZoiuWj0FAFY7moIi_xp1H2fdyrRQURKgGXVkHwc2JFPcFhA9prmc4ZzBrrpb-iyq-pFoQRjufitZHAj3jtpCeIXoYBgXB2ODwVkiPK1PeBJqZf5KaW7LXbZ184ROm5g3oAAn-Aiy0Iai2Z5l3tBKnd5cJcqGiLA2Gw7hYSueg8L3hfVMOjhR_JvOcbMZN1p4dbbw/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, pleas
Re: [Freesurfer] Announcing FreeSurfer version 7.2
External Email - Use Caution
The default path you show me is exactly what I want! Thank you!
Kiyotaka
On Tue, Jul 20, 2021 at 8:23 PM fsbuild wrote:
> While it does not currently work to change the default install path, that
> default install path for the .deb (and .rpm) 7.2.0 installer files is
> /usr/local/freesurfer/7.2.0 (which reads like the path you want to use).
>
> If you already have different releases under /usr/local/freesurfer/
> that are not rev=7.2.0, e.g. from using the tar files (as this is the first
> .deb package), then the packaging tools won’t know anything about them and
> should not touch them when installing 7.2.0. Or apt install and apt remove
> will only affect /usr/local/freesurfer/7.2.0 with the
> freesurfer_7.2.0_amd64.deb
> package.
>
> Still looking into nu_correct.
>
> - R.
>
> On Jul 20, 2021, at 06:21, Kiyotaka Nemoto wrote:
>
> External Email - Use Caution
>
> Hello R,
>
> Thank you for letting me know that the deb file is now available. It's so
> useful for Ubuntu users to install FreeSurfer using the deb file.
> Can I ask you one more question? Can I specify the install directory using
> the deb file?
> I manage different versions of FreeSurfer by installing under
> /usr/local/freesurfer/{6.0.1, 7.1.1, 7.1.2}.
> If I can specify the directory, then I would love to use the deb file.
>
> As for the missing mni directory, I'm concerned about nu_correct.
> In my understanding, recon-all still uses nu_correct as default unless we
> set DoAntsN3 or DoAntsN4.
> nu_correct is located under $FREESURFER_HOME/mni/bin, so I thought it
> might be missed for some reason.
>
> Best regards,
>
> Kiyotaka
>
>
>
> On Tue, Jul 20, 2021 at 3:32 PM fsbuild wrote:
>
>> Hello Kiyotaka,
>>
>> You may not need to be concerned about that warning. You can suppress it
>> by setting the following in your shell environment.
>>
>> $ export NO_MINC=1
>>
>> For Ubuntu linux, if you have sudo/root/admin privileges, then you could
>> try running the installer file instead of using the tar file, i.e.,
>>
>> $ sudo apt-get install ./freesurfer_7.2.0_amd64.deb
>>
>> - R.
>>
>> On Jul 19, 2021, at 21:08, Kiyotaka Nemoto wrote:
>>
>> External Email - Use Caution
>>
>> Dear Doug,
>>
>> Thank you for the announcement of 7.2.0 update.
>> I updated using freesurfer-linux-ubuntu18_amd64.tar.gz and noticed that
>> the 'mni' directory is missing.
>>
>> As a result, now the shell shows warning about MNI
>>
>> =
>> freesurfer-linux-ubuntu18_x86_64-7.2.0-20210714-aa8f76b
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME /usr/local/freesurfer/7.2.0
>> FSFAST_HOME /usr/local/freesurfer/7.2.0/fsfast
>> FSF_OUTPUT_FORMAT nii.gz
>> SUBJECTS_DIR /home/username/freesurfer/7.2.0/subjects
>> WARNING: MINC_BIN_DIR not defined.
>> 'nu_correct' and other MINC tools
>> are used by some Freesurfer utilities.
>> Set NO_MINC to suppress this warning.
>> WARNING: MINC_LIB_DIR not defined.
>> Some Freesurfer utilities rely on the
>> MINC toolkit libraries.
>> Set NO_MINC to suppress this warning.
>> FSL_DIR /usr/local/fsl
>> =
>>
>>
>> Is it intended?
>>
>> Best regards,
>>
>> Kiyotaka
>>
>>
>>
>> On Tue, Jul 20, 2021 at 7:45 AM Douglas N. Greve
>> wrote:
>>
>>> We are please to announce version 7.2. Mostly bug fixes and
>>> behind-the-scenes enhancements. But there are a few new goodies and one
>>> new "known issue" about defacing. Check out
>>> *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1-DJfjJ2ump0OIrxymCZSJDyWjZ1lRUvfVbh_ALmAvflMUcQ4VbQ-rL8qJZ0CNb57YXcyvUNZBuhzNh2CljpXlJZdUE4zJ7_HWwyNWe6w5P5lT04JOCA8D6_d6HPz650QPv_q0r0-NzSCNXmkR0zvs0ELVekUvBL7SEvG3dP3RbqqeQYQ1ueLz9aKEiv-uWJ0VvFL3MBCAWtACdr-2-N8_C7zdglQcacc4rnBkvgL-jGlj1FTeHA7FFGrhOZMcnHHCcIVgLdtTsJAB27liidlKA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
>>> <https://secure-web.cisco.com/1Nq7OG4aqL5Xu5zmIj8jgt_aBH5sIzltmYEnh37LRCC02zUZJGtxhXjbr0RAoJKh7BtiL6-idjNjfiQdlADO4shk7DLtd9JwfjdpLzmw9--jn4lSaFUiwRrKjViNKHZQtQQPksweoYvQiKRJ-y0-kRCdPvOF3aK5lht5Pyc-LXUG4if3vb5foaGHGQb-9RCQhVi2Fen9Qpcz-5KsV8t2xasvxlBFP9nxk2X0URW-y0xEiEjnPng_y6WFgp42hIhMR-bF4VfXTbQTXEZX37XNcKg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes>
Re: [Freesurfer] Announcing FreeSurfer version 7.2
External Email - Use Caution Dear R, Thank you very much! I followed your instructions, and it worked perfectly. Best regards, Kiyotaka On Thu, Jul 22, 2021 at 3:20 AM fsbuild wrote: > Hello Kiyotaka, > > Please try refreshing your copy/install of the Ubuntu 7.2.0 distribution > as the packages have been updated to fix the warning below. > > I think you were using the installer, so you could try the commands below > to download and re-install with apt. (If you were using the tar file then > just change the file name in the wget command to be > freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz, expand it in the right > location and skip the commands with sum, apt remove, apt install). > > with installer ... > > $ rm -f freesurfer_7.2.0_amd64.deb > $ wget > https://secure-web.cisco.com/1FK_sXs4RH2RQpXvxlC81vWqvKNznb76Y5pxgR_orSVStzmiiJg8cCMSN_knoixqkk5nzBizJF5pgjYuljFPGf-W_5R6eKCok2vt5Sz1WIRwMqQFj8gXH4aVBW4pdHYLEJRxBQsuiMHDxCU8CxZX8d7DNZ-iFTk5K660F5iUlluHoISsEuNcPisLZbJjvEYRv7hGqRrnM8C5bo7BKMhf3PQWuQqdVQ80dDjzyn7VlNRzCsN-EZQxBRJGqlfYcAKPg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer_7.2.0_amd64.deb > $ sum freesurfer_7.2.0_amd64.deb > 20191 3199044 > $ sudo apt remove freesurfer > output deleted ... > $ apt install ./freesurfer_7.2.0_amd64.deb > output deleted ... > > ... check environment ... > > $ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0 > $ source $FREESURFER_HOME/SetUpFreeSurfer.sh > the output should have no warnings and you can also check ... > $ env | grep MINC > MINC_BIN_DIR=/usr/local/freesurfer/7.2.0/mni/bin > MINC_LIB_DIR=/usr/local/freesurfer/7.2.0/mni/lib > $ which nu_correct > /usr/local/freesurfer/7.2.0/mni/bin/nu_correct > > - R. > > freesurfer-linux-ubuntu18_x86_64-7.2.0-20210714-aa8f76b > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer/7.2.0 > FSFAST_HOME /usr/local/freesurfer/7.2.0/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /home/username/freesurfer/7.2.0/subjects > WARNING: MINC_BIN_DIR not defined. > 'nu_correct' and other MINC tools > are used by some Freesurfer utilities. > Set NO_MINC to suppress this warning. > WARNING: MINC_LIB_DIR not defined. > Some Freesurfer utilities rely on the > MINC toolkit libraries. > Set NO_MINC to suppress this warning. > FSL_DIR /usr/local/fsl > = > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all exited with ERRORS
External Email - Use Caution
Hi,
I think the problem is caused because Zhaoguang uses a VirtualBox share
folder.
The path "/media/sf_T1/" indicates the path is a shared folder of
VirtualBox.
Symbolic links can be used on some certain conditions.
Source:
https://secure-web.cisco.com/1dwlgJDipuhkA56EdBKvdgjX7GQ06QB_tibWCFgxRVp5qMyNCdaPDbahbXesxHSWfDY3t8wvp6OTfje04KDpgHFGDdkoecJv07GtKeuldJJNVJnsuffSVx9LfYzLYeh-1a5ScJN1PdZ-fDNE--Lnv1R4phboTjurWMX43qna0wem5Wa2vhWvLXwEfcGTxqY7Bduq1xk_MKqmJ0BaQptL5lOK-V0kBUTl58fCB2eRrlvBQMoLDzBscjG_cnGqeT3ZMyhoh1X1rv5D7bkil9-4mWA/https%3A%2F%2Fwww.virtualbox.org%2Fmanual%2FUserManual.html%23sharedfolders
I think there are two workaround options.
1. Avoid using shared folders
If you copy your T1 image from shared folder to somewhere on your Linux
guest, recon-all should go well.
2. Change "ln -s" to "cp" in recon-all
I tweak recon-all a little bit so that recon-all works well with files
on VirtualBox shared folders.
The commands below makes backup of recon-all first, then substitute "ln
-s" with "cp" or "cp -r"
=
cd $FREESURFER_HOME/bin
sudo cp recon-all recon-all.orig
sudo sed -i 's/ln -s \$hemi/cp \$hemi/' recon-all
sudo sed -i 's/ln -s \$FREESURFER_HOME\/subjects\/fsaverage/cp -r
\$FREESURFER_HOME\/subjects\/fsaverage \$SUBJECTS_DIR/' recon-all
sudo sed -i 's/ln -s \$FREESURFER_HOME\/subjects\/\${hemi}.EC_average/cp -r
\$FREESURFER_HOME\/subjects\/\${hemi}.EC_average \$SUBJECTS_DIR/' recon-all
=
Hope this helps,
Kiyotaka
On Thu, Aug 5, 2021 at 10:42 PM Douglas N. Greve
wrote:
> Look in /media/sf_T1/recon/demo3/surf
> Does lh.white.preaparc.H exist?
> If so, does lh.white.H exist?
> If not, what happens when you run
> ln -s lh.white.preaparc.H lh.white.H
> in that folder?
>
>
>
> On 8/5/2021 1:41 AM, guang wrote:
>
> External Email - Use Caution
> Hello FreeSurfer Developers,
> I'm attempting to preprocess my nii.gz files with FreeSurfer, But some
> errors occurred when I recon-all the data. I've attached the batch script
> and recon-all.log in case it's of any use.
> 1) FreeSurfer version:
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> 2) Platform: CentOS release 6.10 (Final)
> 3) uname -a: Linux bogon 2.6.32-754.2.1.el6.x86_64 #1 SMP Fri Jul 13
> 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
> 4) recon-all.log: see attached
> 5) batch .sh file:see attached
>
> Thank you for any reply.
>
> zhaoguang
>
>
>
>
>
>
>
>
> ___
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1-4gugTG7IJfnMSP9Kbd3NVtUKTt23hOeCLRtobg_9eugEF5QbPwyeJBMkyKRnUEycElhjwY_qKW8n3EOxMBUrO7rwxeCUSjp4j1qOzAxzrKpPV_RJTy1RSNxyqGUyCewq1f9iCpdF2RClubdfNt5C8jGFXfJPOAmLmiZk-4b-CGRZBCXllH9J5SMAGVEGteqtX-K_CxOOiuBZk0raFZN1xAeJl0qAqY_cFG8zTNfCs5wJBUhpuinkEL7eIZOHQhRGdZYRNiHtONcaVRD7crYlw/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
> http://secure-web.cisco.com/1MwgiO-I6rZmEaKP4aOBZdZ_lN3KTEvoI5tOu9SKhlrO_PjSav0ImSZjUWc6isdXJxz5MMet1p4a8vqcQSc8z7DNyPQ9UzO9tbZGawhyD4z2sdXaANthxnEH6C-Kd01XWSFmsfeNIgCkjPPrtHfQf2ldNJkcsc_68a560U4p8HW1kXnLcJK2-s-u9zKfCWu3nSu5n-OgnfnFfebyUOPY5fVUXpDRtbqxouQQv6phML8b3x6XMUqqMke9gyroDbRTWUdSbcH0NEosH9DEpE1Oj8Q/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
> . If the e-mail was sent
> to you in error but does not contain patient information, please contact
> the sender and properly dispose of the e-mail.
> 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.
>
--
Kiyotaka Nemoto, M.D., Ph.D.
Associate Professor
Department of Psychiatry
Division of Clinical Medicine, Faculty of Medicine
University of Tsukuba
1-1-1 Tennodai Tsukuba, Ibaraki 305-8575, Japan
E-mail: kiyot...@nemotos.net
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Trouble with fs_install_mcr script
9QUCLOzaN90YToafU195ETosREpYOygU2Cg_Lbbrgnkv0Jtio7GO3Lxx1hol5ndBuArG8-9JO4mCKppnbZ1D31IPGlq7xf5zZCwwrzvjTkpZAkZzVeF7Iis8xzioDFtiyzSBf6Y22UMt7LWPMGkY/https%3A%2F%2Fwww.mathworks.com%2Fproducts%2Fcompiler%2Fmatlab-runtime.html > <https://secure-web.cisco.com/1f47DuzXT9iWt3QZ-FmPoYU6PuX8nCvVAsdXGDH3F_QY6C-uhaYzYBPq2Nj-u7AAfKl7Kb1LyNWJXbZYw7f5sR25q_cZTymPGARJFrtClH0V_qQAKURS7I7-vZxCWLfSrYZEgNL0pNSZrKm7Bs1Xt0nqRgy-xLZyuWAvGaSUHej5kMWyMCk6bFgDasOXz23S9QUUmL1faKLypZNGfy27Q3s89bh7KTeOTGfEPAvEzh43iCSsXCR0GImu5Jv4ZuSqWexHF4RnSp3Hr3-3tQ5fT0XLvJvthOFMeWwemdrXx9DHN5AI4WoZQBH20RyW84cT3kRY_xBnneH-nxhjt2ERcNlYrdygesks8yeuQ_K5K2lA/https%3A%2F%2Fwww.mathworks.com%2Fproducts%2Fcompiler%2Fmatlab-runtime.html> > ? > > Thank you! > > -- > Andrei Bieger > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/18Rs4WcgeRepff5I2lpYevAjbEq_DG7hRh9NpblYAPR6vorIrAsTm8Q9PkcMOc3YtsiJ3ifz5P52qymSL0Yoak__5xaYBhPJgWVHH_WT3XWXpCC1tn33eHvexRxQP8omc9RNz3lBRefDZ0onQb935H3LOMQUYAxa1tRi2JFVWeME7fVASZRSomzULviv4KnUOGnzUj-JoGH4xuqnfc8YVRY-loJGpE7_Yg8kQAiCXREIVIhg8A7idnw1YwlqwxJKHYsLnQxULYSzmhoKzvXeotLGI3SrX8N5ojkW3hUccRX1gOjFFG8ZILmp-5Lh8FDf43OABUeh2KFevaWNiKmPC7Ofr6xrhJQMyawZUGTwL50E/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/1ID11IFjoLtkV3k1cZcwmJzNl7qpxEFfpLA1ZIub07nvNw0INVZhvYgIKbXPiaMebbKWUK6Dy09H8DN_LpLkDnui4Fr7NCsgz-E8nZ82tFfGMgEB-PxUOi6JBaXTZlaurNxrvrdiJzMfjEVjwtkxnSObqG00a83zD0ukCqFpJ4Kk3tc4GMgVWxvy-xI_rsiL6Gqwfcr9LuBNOIUuSFvYX13iAx0a71m9jqo6eDaetBpYmptqv4LgqtWQLe70x5SnjH7Y-imEGgGsVtWjWHLHDTc4QJpL7NgEFyjASKFRxxhCfRfKpeOZmKnW4sTHO9CrV4JyGKF0ZFAnQBezjYcnrE1oKI9BQMbFfVuCQj8DkrGg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1ID11IFjoLtkV3k1cZcwmJzNl7qpxEFfpLA1ZIub07nvNw0INVZhvYgIKbXPiaMebbKWUK6Dy09H8DN_LpLkDnui4Fr7NCsgz-E8nZ82tFfGMgEB-PxUOi6JBaXTZlaurNxrvrdiJzMfjEVjwtkxnSObqG00a83zD0ukCqFpJ4Kk3tc4GMgVWxvy-xI_rsiL6Gqwfcr9LuBNOIUuSFvYX13iAx0a71m9jqo6eDaetBpYmptqv4LgqtWQLe70x5SnjH7Y-imEGgGsVtWjWHLHDTc4QJpL7NgEFyjASKFRxxhCfRfKpeOZmKnW4sTHO9CrV4JyGKF0ZFAnQBezjYcnrE1oKI9BQMbFfVuCQj8DkrGg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > 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. > -- Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Psychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1 Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: kiyot...@nemotos.net ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.
Re: [Freesurfer] Trouble with fs_install_mcr script
External Email - Use Caution
Hi Andrei,
Glad to know it worked. I also encountered the problem before and found the
solution in the script itself.
Best regards,
Kiyotaka
On Sun, Mar 20, 2022 at 12:32 AM Andrei Bieger
wrote:
> External Email - Use Caution
>
> Greetings, Professor Nemoto,
>
> Your solution worked like a charm. Thank you very much!
>
> Best regards
> Andrei
>
>
> Em sáb., 19 de mar. de 2022 às 12:03, Kiyotaka Nemoto <
> kiyot...@nemotos.net> escreveu:
>
>> External Email - Use Caution
>>
>> Hi Andrei,
>>
>> You need to use sudo to use the script because it tries to install files
>> under $FREESURFER_HOME.
>> curl fails because the script tries to download a file in
>> $FREESURFER_HOME where you don't have permission to write without sudo.
>> You also need to set FREESURFER_HOME for the sudo environment.
>>
>> The command below should work for you.
>>
>> sudo FREESURFER_HOME=$FREESURFER_HOME $FREESURFER_HOME/bin/fs_install_mcr
>> R2014b
>>
>> Hope this helps,
>>
>> Kiyotaka
>>
>>
>> On Sat, Mar 19, 2022 at 11:32 PM Andrei Bieger
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> Hello, everyone,
>>>
>>> I`m having trouble installing the MatLab Runtime 2014b as required for
>>> running the new hippocampal subfields pipeline. The "fs_install_mcr 2014b"
>>> command returns me the message below:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$
>>> fs_install_mcr 2014b % Total% Received % Xferd Average Speed Time
>>> Time Time Current Dload Upload
>>> Total SpentLeft Speed10010 100100 0 2 0
>>> 0:00:05 0:00:04 0:00:01 2Archive: installer.zip
>>> End-of-central-directory signature not found. Either this file is not a
>>> zipfile, or it constitutes one disk of a multi-part archive. In the
>>> latter case the central directory and zipfile comment will be found on the
>>> last disk(s) of this archive.unzip: cannot find zipfile directory in one
>>> of installer.zip orinstaller.zip.zip, and cannot find
>>> installer.zip.ZIP, period.*
>>>
>>> Then I tried running the specific line of the script to download the
>>> file so I could take a look at it:
>>>
>>>
>>>
>>>
>>>
>>>
>>> *andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$ curl
>>> --location MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be
>>> https://secure-web.cisco.com/1OakMqmY6U2864VcIrI5u4KRZUm7H860Jb-1dbz_XneQ4EBgynqgXRHd1GIbjfQi-fzsrHVUsbDoSaQv02HbAPr72ediRT3XWN4d9pSabsBwEBwG7e6Cz7ePmJfqCLezlTARo-BqaJv_bSxGi2NOH-DScwRbaaZwlZg5ayl37rmEgSGf0ta5_1AdIyENiG0jCkoKo8qY9jWCpexQd9FFz1SdtrFbJoGxDvOrZ94hhkaYaR_RP7j8X_FDXicXtZddQ8ZfSidSG9Xl9Zd8UyF8-iq_5HH8rx27Qc-2NvQSPI2yV9Z3TnqyVctEbOLXzyw57ycvZ8xyOVKWcJ5i5fjRQ4A/https%3A%2F%2Fssd.mathworks.com%2Fsupportfiles%2Fdownloads%2F%24MCR_VER%2Fdeployment_files%2F%24MCR_VER%2Finstallers%2F%24OS_TAG%2FMCR_%24{MCR_VER}_${OS_TAG}_installer.zip
>>> <https://secure-web.cisco.com/1UHq_hHAhu7HwPLU25e5pyUgtFmgmagCCAXlBmW3qUjcEdSndPCFdsMJetPs5mQiG1LT8OodaBv-ZQNWBv1_vp2myOujucaEMsMKKejeCXm_NgQ_azXgbiexcWuqLTjDhbcKymWv7kh9Za77u2V4PamdiMmT2_uskTI1CB_o8VdP1VFVD-Hyrix0jLQGzWc7PcQw6noKSr8SwKwWssSMNt3DRZtI8NS1Kn71VPEt62tBIjM_r42c7WrlxsKK8xlNYIOEqjtfsdvdwIVgkyn1qJLVgq_LSCa0OMAJEL4UkR1a4AuwoxvOtb5UgaFsBVaVF5i2KTMEGlkZpz4bJp1UHAVo1XuRiSmDS8hT1sKf0shE/https%3A%2F%2Fssd.mathworks.com%2Fsupportfiles%2Fdownloads%2F%24MCR_VER%2Fdeployment_files%2F%24MCR_VER%2Finstallers%2F%24OS_TAG%2FMCR_%24%7BMCR_VER%7D_%24%7BOS_TAG%7D_installer.zip>
>>> -o installer.zip % Total% Received % Xferd Average Speed Time
>>> Time Time Current Dload Upload
>>> Total SpentLeft Speed10010 100100 0161 0
>>> --:--:-- --:--:-- --:--:--
>>> 161andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$ file
>>> installer.zipinstaller.zip: ASCII text*
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> *andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$ unzip
>>> installer.zipArchive: installer.zip End-of-central-directory signature
>>> not found. Either this file is not a zipfile, or it constitutes
Re: [Freesurfer] Help (Freeview fails to launch)
External Email - Use Caution Dear Akira, I agree with R that installing FreeSurfer using the deb is preferred, but if you want to stick to tar.gz, below is the list of the packages to be installed when you install FreeSurfer using the deb package. So if you install these packages, you would be able to run freeview. Hope this helps, Kiyotaka sudo apt install -y language-pack-en binutils libx11-dev gettext x11-apps \ perl make csh tcsh bash file bc gzip tar \ xorg xorg-dev xserver-xorg-video-intel libncurses5 libbsd0 libc6 libc6 \ libcom-err2 libcrypt1 libdrm2 libegl1 libexpat1 libffi7 libfontconfig1 \ libfreetype6 libgcc-s1 libgl1 libglib2.0-0 libglu1-mesa libglvnd0 libglx0 \ libgomp1 libgssapi-krb5-2 libice6 libjpeg62 libk5crypto3 libkeyutils1 \ libkrb5-3 libkrb5support0 libpcre3 libpng16-16 libquadmath0 libsm6 \ libstdc++6 libuuid1 libwayland-client0 libwayland-cursor0 libx11-6 \ libx11-xcb1 libxau6 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 \ libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 \ libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 \ libxcb-xinput0 libxcb-xkb1 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 \ libxkbcommon-x11-0 libxkbcommon0 libxmu6 libxrender1 libxss1 libxt6 zlib1g On Fri, Dec 29, 2023 at 12:14 PM fsbuild wrote: > External Email - Use Caution > > > That message could be the result of missing system libraries which the > Ubuntu 22 FS 7.4.1 .deb package will try to automatically identify, > download and install for you. You can download the package via the link > *MailScanner > has detected a possible fraud attempt from "secure-web.cisco.com" claiming > to be* > https://secure-web.cisco.com/1mKMabUX5OEUvCDYuNLL03gy4wla33dNI6Ox8dPzZ_qBoLFWXoufcqAf2xdwBE_BLgKkXD80OQ5NgOUxywRL0N0wr63y6xGFPMuYMVhScIysNXav0Y4z28Z__cNw9SgCGUW68fdgfU8QDsRvR5NNF7vdpsshn6ACHPjYJr6JQcf2sCXJjoGxWj4hC7KyiUOhaRHIYOptZ1d1TMm10pJl2Wo80JxmbN_ExW9WtWOeJE3QcI24nX9nwDsHhamhR7k-K7nlz_WIGFKPWcZpmd9U4iSiiuAC41kYHaqh3oc15rOX9GB1n5yIcEKNHfnxbQ8Q_Pl7T-Cii52ogXtnRAF4Nnw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb > <https://secure-web.cisco.com/1_U_QdXreVu6wH-joAQGYWXyzydRY-oOu_HN35KN1_Gu2EugYsBfddLu9kSjKPPIOY85f8qSjXQxvlcdHQbCEYXVWo8anAkh0AdrTtlKCaQwtww17b3P86ROK0bEpuAFeszer1A1_0OHLRUTv_M-z4R-ioKJRfHKPvCW5AMEWOI0Fz18EeZs4-TM2OkaB6BIbQtC-tkRho8ufs5oTdQLGRd5tRFsTg3W9EsFp7A1jq97JFX4N8qxa_rjgULLaBn6vZ_vO2UeqbtQSS8yEfOh13X15865cyTH35_evnYvZCQasPJPE6AdHq2BCC-D-CsYDTDeIQfKtRuffhcyHx5vFdA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb> > and > the install can be done with, > > … cd to your Downloads to wherever the .deb file is … > > $ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb > > If the install succeeds, freesurfer will be under > /usr/local/freesurfer/7.4.1 which is the path to use for the environment > variable FREESURFER_HOME, > > $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1 > > If they are not already set in your environment, you should also set, > > $ export XDG_RUNTIME_DIR=$HOME/.xdg > > $ export DISPLAY=:0 > > - R. > > On Dec 27, 2023, at 23:17, Akira Kita wrote: > > External Email - Use Caution > > I have installed FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tar > archive freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz. > > Freeview fails to launch with the following error message: > > This application failed to start because no Qt platform plugin could be > initialized. Reinstalling the application may fix this problem. > Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, > offscreen, > vnc, wayland-egl, wayland, webgl, > > How can I solve this? > > > Akira > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1QI73ha0dZUxEGvYoEY_1bYLyCUQHOXV-uF3VAAGaEPKSzyD1nk2DxAarPrXJTqvTusR8gBzTyWOW2-kKzsxSeIadM-y30LBoFcSz5mxwl6BrxdQ6Inv507a1TZr765rV_NZR-bk698jbJ-vqcPvC4EKJ5UTWDndvRP0uBpApG-TtOsQUPPG8ZHqP6nuQ0_aya37i0g22_g_ZxtO8xo3uJ7k-zPCumS_Eh5wFjz0kMaNw8xK2i_tLxfm9uND_vZiF4BA8RBWhfWCKe3bjJxORg6txWtP7nqolZUOmiK8132YcfTy76x54nkehXXP1lKggt5vEVxPG3qW4ilDrAduriw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1QI73ha0dZUxEGvYoEY_1bYLyCUQHOXV-uF3VAAGaEPKSzyD1nk2DxAarPrXJTqvTusR8gBzTyWOW2-kKzsxSeIadM-y30LBoFcSz5mxwl6BrxdQ6Inv507a1TZr765rV_NZR-bk698jbJ-vqcPvC4EKJ5UTWDndvRP0uBpApG-TtOsQUPPG8ZHqP6nuQ0_aya37i0g22_g_ZxtO8xo3uJ7k-zPCumS_Eh5wFjz0kMaNw8xK2i_tLxfm9uND_vZiF4BA8RBWhfWCKe3bjJxORg6txWtP7nqolZUOmiK8132YcfTy76x54n
Re: [Freesurfer] Help (Freeview fails to launch)
External Email - Use Caution Dear R, Thank you for the information. The deb package is useful so I agree with you. Only one point is that using deb cannot handle installing two different versions. Do you have any recommendation managing two (or more) different versions using deb package? Best regards, Kiyotaka On Sat, Dec 30, 2023 at 1:21 PM fsbuild wrote: > External Email - Use Caution > > > Depending upon the state of a machine, there is no guarantee a list of > "required" packages will encompass everything that needs to be > installed/updated, or that a manual install will work. So we neither > recommend or support manual/piecemal installs, e.g., via the list below, > instead of using the built-in linux package management tools. > > - R. > > On Dec 29, 2023, at 22:32, Kiyotaka Nemoto wrote: > > External Email - Use Caution > > Dear Akira, > > I agree with R that installing FreeSurfer using the deb is preferred, but > if you want to stick to tar.gz, > below is the list of the packages to be installed when you install > FreeSurfer using the deb package. > So if you install these packages, you would be able to run freeview. > > Hope this helps, > > Kiyotaka > > sudo apt install -y language-pack-en binutils libx11-dev gettext x11-apps \ > perl make csh tcsh bash file bc gzip tar \ > xorg xorg-dev xserver-xorg-video-intel libncurses5 libbsd0 libc6 libc6 \ > libcom-err2 libcrypt1 libdrm2 libegl1 libexpat1 libffi7 libfontconfig1 \ > libfreetype6 libgcc-s1 libgl1 libglib2.0-0 libglu1-mesa libglvnd0 > libglx0 \ > libgomp1 libgssapi-krb5-2 libice6 libjpeg62 libk5crypto3 libkeyutils1 \ > libkrb5-3 libkrb5support0 libpcre3 libpng16-16 libquadmath0 libsm6 \ > libstdc++6 libuuid1 libwayland-client0 libwayland-cursor0 libx11-6 \ > libx11-xcb1 libxau6 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 \ > libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 \ > libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 \ > libxcb-xinput0 libxcb-xkb1 libxcb1 libxdmcp6 libxext6 libxft2 libxi6 \ > libxkbcommon-x11-0 libxkbcommon0 libxmu6 libxrender1 libxss1 libxt6 > zlib1g > > On Fri, Dec 29, 2023 at 12:14 PM fsbuild wrote: > >> External Email - Use Caution >> >> >> That message could be the result of missing system libraries which the >> Ubuntu 22 FS 7.4.1 .deb package will try to automatically identify, >> download and install for you. You can download the package via the link >> *MailScanner >> has detected a possible fraud attempt from "secure-web.cisco.com" claiming >> to be* >> https://secure-web.cisco.com/1J9_Z0HLKDYWwXrGPXi_fqFTQLygJlwVaU-141E5zzDhAkkw1xXapN0nnVgWhTS6XGCgfkc5ueirEA_jvddWCTdYAfUcAH7SxCSaFAzawZC4lvbC8y_9NKqsjhD5ZFMrWt7X3muEEOwu9TlGI9rdd8dbC5nuG2Ghq2KLE70SI4ZxUWWmXSVkXCZyhhXZq5f4wFQyAvLrAHPX0lR7gws9mQ_Q3UYrjc-3musq7AJqT7K0xWCpNBXEO5jRyNhN_5IQyFWAx8la8y0nyTkV52oB8n6sf4nY9sqgm_KaTMe8Mr5-hIcABk8sdULBQpIZmVLKy5JEVPha5YlG51rCIN7H38g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb >> <https://secure-web.cisco.com/1_U_QdXreVu6wH-joAQGYWXyzydRY-oOu_HN35KN1_Gu2EugYsBfddLu9kSjKPPIOY85f8qSjXQxvlcdHQbCEYXVWo8anAkh0AdrTtlKCaQwtww17b3P86ROK0bEpuAFeszer1A1_0OHLRUTv_M-z4R-ioKJRfHKPvCW5AMEWOI0Fz18EeZs4-TM2OkaB6BIbQtC-tkRho8ufs5oTdQLGRd5tRFsTg3W9EsFp7A1jq97JFX4N8qxa_rjgULLaBn6vZ_vO2UeqbtQSS8yEfOh13X15865cyTH35_evnYvZCQasPJPE6AdHq2BCC-D-CsYDTDeIQfKtRuffhcyHx5vFdA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb> >> and >> the install can be done with, >> >> … cd to your Downloads to wherever the .deb file is … >> >> $ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb >> >> If the install succeeds, freesurfer will be under >> /usr/local/freesurfer/7.4.1 which is the path to use for the environment >> variable FREESURFER_HOME, >> >> $ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1 >> >> If they are not already set in your environment, you should also set, >> >> $ export XDG_RUNTIME_DIR=$HOME/.xdg >> >> $ export DISPLAY=:0 >> >> - R. >> >> On Dec 27, 2023, at 23:17, Akira Kita wrote: >> >> External Email - Use Caution >> >> I have installed FreeSurfer 7.4.1 on Ubuntu 22.04 using the binary tar >> archive freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz. >> >> Freeview fails to launch with the following error message: >> >> This application failed to start because no Qt platform plugin could be >> initialized. Reinstalling the application may fix this p
