Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Setup & Configuration Error
by Hossein Shooli 01 Apr '20

01 Apr '20

External Email - Use Caution Hello FreeSurfer Development Team, I have just install the FreeSurfer (freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c) on my mac Catalina OS (10.15.2). The installation path was set as default (/Application/freesurfer). Then, in the Setup & Configuration step I have faced some troubles that I'm in need to fix it. In this step the first line " $> export FREESURFER_HOME=/Applications/freesurfer" works properly. But when I typed the " $> source $FREESURFER_HOME/SetUpFreeSurfer.sh ". an error occurred as below: Hosseins-MacBook-Pro:~ dhs$ > export FREESURFER_HOME=/Applications/freesurfer Hosseins-MacBook-Pro:~ dhs$ > source $FREESURFER_HOME/SetUpFreeSurfer.sh /Applications/freesurfer/SetUpFreeSurfer.sh: line 14: return: can only `return' from a function or sourced script /Applications/freesurfer/SetUpFreeSurfer.sh: line 42: /FreeSurferEnv.sh: No such file or directory Hosseins-MacBook-Pro:~ dhs$ I have checked the mail archives but there no answer to my problem. Please help me solve the issue and setup freesurfer successfully. Bests regard Hossein [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=sig…> 04/01/20, 11:04:28 AM

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kill recon-all programatically/remotely
by Octavian Lie 31 Mar '20

31 Mar '20

External Email - Use Caution Dear All, Is there a way to kill a recon-all run on linux via ssh/putty. Ctrl+C is not working, obviously, and it is not easy to figure out which process encodes the recon-all runs with commands such as ps aux, top etc. One gross way may be removing the subject directory all together midway, but not sure how this affects FS, subsequent runs Thank you, Octavian

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Reducing FreeSurfer recon-all time
by Xiaojiang Yang 31 Mar '20

31 Mar '20

External Email - Use Caution Freesurfer experts: I know in my powerful Linux machine, recon-all needs about 10 hours to finish all computation. What is the possible way I can use to greatly reduce this computation time from 10 hours to, say 1-3 hours? Is Sun Grid Engine (SGE), or GPU/CUDA, or any other technique, helpful? Thank you! Xiaojiang

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Problem with version of mri_surfcluster provided with fspalm
by Syam Gadde 31 Mar '20

31 Mar '20

External Email - Use Caution Hi, We have a user trying to use fspalm. I followed all the directions to install, but are getting an error with the new mri_surfcluster that we were asked to download with fspalm. Here is the dummy command I ran to replicate the error: mri_surfcluster --thmin 0 --subject fsaverage --hemi lh --in /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white and the end of its output: <...> subjectsdir = /usr/local/packages/freesurfer_v6.0.0/subjects FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; ---------------------------------------------------- Reading source surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white MRISread(x�<m�): could not open file No such file or directory mri_surfcluster: could not read surface /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white No such file or directory ----- It is the same error reported in these emails: https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su… but the error message is misleading. The problem is not in reading the surface file, but in trying to read a file name made up of non-ascii (or presumably unicode) characters. As shown by strace: ... read(3, "", 8192) = 0 open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4 read(4, "0\n", 31) = 2 close(4) = 0 close(3) = 0 munmap(0x7f8413571000, 8192) = 0 open("\310\215\26\f\376\177", O_RDONLY) = -1 ENOENT (No such file or directory) write(2, "MRISread(\310\215\26\f\376\177): could not open"..., 37MRISread(ȍ^V^L<FE>^?): c ould not open file) = 37 ... Any thoughts on how to proceed? Thanks, -syam

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Re: [Freesurfer] on Ubuntu (was FreeSurfer V 7.0 on Centos 8) {Disarmed}
by fsbuild 31 Mar '20

31 Mar '20

External Email - Use Caution We would also like to know about any issues you are seeing on Ubuntu.. I think Ubuntu eliminated some jpeg/png packages from their repos.  Those can be downloaded and installed manually,e.g., libpng12-0_1.2.54-1ubuntu1.1_amd64.deb, libjpeg62_6b2-3_amd64.deb.  That is part of the reason we made an Ubuntu 18 VM available with everything pre-installed.  The VM is essentially what has been used for the freesurfer course which runs mostly freeview commands with some mri* commands (though I believe a recon-all also works).  The VM is running binaries built on CentOS7 - as the reference platforms for freesurfer dev are currently CentOS and MacOS.  We are looking at making a .deb installer for freesurfer on Ubuntu though. There is some info on the wiki about packages required to compile the source on Ubuntu - but you don’t need all of these to run (even the CentOS) binaries. https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements - R. On Mar 31, 2020, at 02:50, Tim Schäfer <ts+ml@rcmd..org> wrote:       External Email - Use Caution        Hi Tristan,I'm about to setup a FreeSurfer installation on an Ubuntu system, and I wondered whether you could elaborate on the kind of issues you are experiencing.Best,Tim--Dr. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, GermanyOn March 30, 2020 at 11:01 PM TRISTAN J PAUTSCH <tpautsch(a)wisc.edu> wrote:       External Email - Use Caution        Is there going to be an "official" Ubuntu build this time around (as in, built and tested in Ubuntu) that isn't the VM? Both the current CentOS and the dev builds continue to have issues (even when compiled from scratch) on my Ubuntu 18.04 servers.Thanks!T________________________________From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of fsbuild(a)contbay.com <fsbuild(a)contbay.com>Sent: Monday, March 30, 2020 9:40 AMTo: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>Cc: dr.minafakhry(a)live.com <dr.minafakhry(a)live.com>Subject: Re: [Freesurfer] FreeSurfer V 7.0 on Centos 8       External Email - Use CautionHello Mina,I see from https://www.centosblog.com/centos-eol-dates/ that CentOS 6 will no longer be updated as of 11/2020, and similarly for CentOS 7 in 6/2024.  It looks like CentOS 8 was released around September of 2019.While we do not currently build/test on CentOS8, I am sure it will eventually be supported.   Given some users will continue to use CentOS 6 even after 11/2020 and that many people have been running the freesurfer 6 release on CentOS6, then even the upcoming freesurfer 7 release is targeting CentOS6, CentOS7 and Ubuntu linux (as well as Mac OS).There is also currently an Ubuntu 18 VM with freesurfer 6 and the beta release of freesurfer 7 pre-installed which you can find here, https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67- R.On Mar 30, 2020, at 08:52, Mina Rizkallah <dr.minafakhry(a)live.com> wrote:       External Email - Use CautionGreetings FreeSurfer team,I recently upgraded by workstation from Centos 7 to 8.1 as the support for centos  7 will be over soon.I tried installing freesurfer version 7.0 beta 1 but failed due to some unresolved dependencies (tried on a  virtual centos 7 and worked fine) !!so, when will there be support for centos 8, thank youBest regardsMina_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Using freeview to view (and edit?) talairach registrations
by Ruopeng Wang 31 Mar '20

31 Mar '20

You can go to menu Tools -> Transform Volume to adjust the registration and save it as a lta registration file. Then run lta_convert to convert it to xfm: lta_convert --inlta foo.lta --outmni foo.xfm > On Mar 31, 2020, at 1:06 PM, Rachel Hoel <hoel2(a)wisc.edu <mailto:hoel2@wisc.edu>> wrote: > > External Email - Use Caution > > > Hi Ruopeng, > > I entered the full path for the transformation file, and this is what I’m seeing in freeview (screenshot attached). Is it possible to edit the talairach registrations in freeview similar to how they could be edited in tkmedit, or can freeview only be used for looking at talairach registrations? > > Thanks again, > Rachel > > <Screen Shot 2020-03-31 at 12.02.47 PM.png> > > >

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Re: [Freesurfer] tips on the gtmseg.mgz check
by Ferraro, Pilar 31 Mar '20

31 Mar '20

External Email - Use Caution Dear Freesurfer experts, I’m performing an analysis using PETSurfer and, after processing all the T1 images with the Freesurfer analysis, I’m now creating the segmentation for the GTM. I’ve run the gtmseg —s command on a first subject. I was surprised though, cause I’ve read the process should have taken about an hour or two, but it actually took only 25 minutes, so, even if at the end of the process it was reported “gtmseg done”, I’ve checked the resulting gtmseg.mgz image using the command: tkmeditfv subject/ nu.mgz -seg gtmseg.mgz gtmseg.ctab -opacity 1 And this is how it looked like: [cid:A7433273-09FF-4594-A618-91107110F8B0] My question is, is there something specific I should check in this image to be sure everything has been done correctly? Sorry, I’m new to this type of analysis, so I’d rather be sure about everything before further proceeding. Many thanks, Pilar Maria Ferraro Il giorno 26 mar 2020, alle ore 2:44 PM, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> ha scritto: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Misalignment of boundaries and T1 (Freesurfer/SamSrf) (Mason Wells) 2. Re: VM_setup (fsbuild) 3. Re: mri_deface download link not found (Hoopes, Andrew) 4. Registration file types confusion (Xiaojiang Yang) 5. Freeview CLI feature request (VINCENT KOPPELMANS) 6. Re: Freeview CLI feature request (Ruopeng Wang) 7. Re: Freeview CLI feature request (VINCENT KOPPELMANS) 8. Re: training set (javier quilis) 9. Re: Misalignment of boundaries and T1 (Freesurfer/SamSrf) (Mason Wells) 10. Re: Hippocampal Volume Extraction (Devika K) 11. Re: training set (Bruce Fischl) 12. Re: Misalignment of boundaries and T1 (Freesurfer/SamSrf) (Bruce Fischl) ---------------------------------------------------------------------- Message: 1 Date: Wed, 25 Mar 2020 18:38:34 +0000 From: Mason Wells <WellsMT1(a)cardiff.ac.uk> Subject: Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <5BD22FFC-C541-42CB-964B-AA3B2186428F(a)cardiff.ac.uk> Content-Type: text/plain; charset="utf-8" External Email - Use Caution HI Bruce, Ok, great. I just thought some sections of white matter had not been traced in their entirety (see red crosshair in attached image). If you think this all looks reasonable, please can you advise on the misaligned as outlined in the original post? Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 ?On 25/03/2020, 17:29, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of fischl(a)nmr.mgh.harvard.edu> wrote: Hi Mason I can't tell from those images except that it looks reasonable cheers Bruce On Wed, 25 Mar 2020, Mason Wells wrote: External Email - Use Caution Hi again Bruce, I have now installed the relevant libpng packages and have freeview open. The segmentation doesn?t look brilliant in some areas. What do you think? Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 On 25/03/2020, 16:28, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of WellsMT1(a)cardiff.ac.uk> wrote: External Email - Use Caution Hi Bruce, I get the following error message when I try to load freeview Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl masontwells@masontwells-VIG800S:~$ freeview freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 On 25/03/2020, 16:19, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of fischl(a)nmr.mgh.harvard.edu> wrote: something like freeview -v $SUBJECTS_DIR/<subject name>/mri/norm.mgz \ -f $SUBJECTS_DIR/<subject name>/surf/?h.white cheers Bruce On Wed, 25 Mar 2020, Mason Wells wrote: External Email - Use Caution Hi Bruce, Thanks for getting back to me. Sorry, but I am not sure I follow what you mean here. Could you please explain how I would check this? Thanks again for your help. Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 On 25/03/2020, 16:11, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of fischl(a)nmr.mgh.harvard.edu> wrote: Hi Mason can you confirm that things look ok within FreeSurfer if you look at the surface over the volume in freeview? cheers Bruce On Wed, 25 Mar 2020, Mason Wells wrote: External Email - Use Caution Hello Freesurfer developers, I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all command which finished without errors. However, the white/grey matter boundaries are significantly misaligned with the subjects T1 (images attached). Below are the steps I have taken to reach this point in the analysis: 1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain. 2. Ran Feat ? Distortion correction of the EPI ? Motion correction ? No smoothing ? Highpass filter ? No registration to whole brain ? Register to T1_biascorr_brain ? Register to standard space 3. Ran recon-all on T1_biascorr 4. Convert T1/T1_brain/orig(001) from mgz to nii 5. Check registration (using the SurfaceProjection command from the SamSrf package) which leads to the attached images named S1 and S1. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: Linux 5.3.0-40-generic x86_64 Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux As you can see, the registration is significantly misaligned. Can anyone offer any advice on this/suggest a way to rectify it? Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… -------------- next part -------------- A non-text attachment was scrubbed... Name: freeview1.png Type: image/png Size: 256888 bytes Desc: freeview1.png Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200325/e… ------------------------------ Message: 2 Date: Wed, 25 Mar 2020 20:05:22 +0100 From: fsbuild <fsbuild(a)contbay.com> Subject: Re: [Freesurfer] VM_setup To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <1585163122.5e7bab72c2100(a)trashmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Pierpaolo, Just sent it to your email.  You can email me back directly if you need something. - R.On Mar 25, 2020, at 14:34, Pierpaolo Croce <pierpaolo12croce(a)gmail.com> wrote:        External Email - Use Caution        Dear List, I have followed the virtual machine setup for virtual box freesurfer installation... Starting ubuntu, ask me developers account informations. Which is the password?-- Ing. Pierpaolo Croce, PhD.Institute for Advanced Biomedical Technologies - ITABandDepartment of Neuroscience and ImagingUniversity of Chieti "G. D'Annunzio"Via dei Vestini, 3366013 Chieti, Italy_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200325/0… ------------------------------ Message: 3 Date: Wed, 25 Mar 2020 19:24:32 +0000 From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Subject: Re: [Freesurfer] mri_deface download link not found To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <A395AA58-1246-4D83-9478-B19277111303(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Ah thanks Tim, I misread. The links on that wiki page are fixed now. Sorry for the confusion. Andrew ?On 3/25/20, 3:32 AM, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Tim Sch?fer" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of ts+ml(a)rcmd.org> wrote: External Email - Use Caution I think the problem is not with running the version he downloaded, but the fact that he could not download it, because all download links on the website at https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface are dead. I downloaded mri_deface from that website about a month ago, back then the links were still okay. It seems something went wrong on the server in the meantime. Best, Tim On March 24, 2020 at 6:39 PM "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> wrote: Hi Hailey, Can you provide some more info about your issue, like what version you downloaded and a copy/paste of the command line you ran with the error message. Thanks Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "D'Silva, Hailey" <hailey.mulder(a)yale.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, March 24, 2020 at 7:24 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_deface download link not found External Email - Use Caution Hello Freesurfer Experts! I'm trying to anonymize a number of T1s by using mri_deface, but am getting a "Not Found" error when I try to download the tools for it. Thanks for your help, Hailey _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ Message: 4 Date: Wed, 25 Mar 2020 16:00:53 -0500 From: Xiaojiang Yang <xjyangxj(a)gmail.com> Subject: [Freesurfer] Registration file types confusion To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAPg=14aWe4zMno5fbWfZyNhz22bS1aMx0KYXwd36efLFJRRi2w(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi everyone, I am confused by the two types of registration files: .lta and .dat. .dat file is simpler and easier to understand. But for the .lta files, there seems to be no detailed explanation regarding it. Can anyone point out to me where can I find the detail explanation of the file? And, what's the relationship between .lta and .dat file? Also, .lta files seem to cause some compatibility issues. For example, if I use the tkregister2 utility to make some changes to the registration file of type .lta (generated by bbregister), like below tkregister2 --mov $someSeries --reg $SUBJECTS_DIR/$subjectid/mri/transforms/FLAIR.auto.lta --surf pial and save it from the GUI, then many errors occur in the console window, like below: ...... MatrixAsciiReadFrom: could not scanf parms ERROR: TransformLTA2RegDat(): type = 2011264000, must be 1 or 0 or 14 Segmentation fault (core dumped) Actually that is because the registration file has been saved in the format of .dat, although the file extension is still .lta, and the tkregister2 program finally cracks when reading the newly saved .lta file. Anyone can solve my confusion? Thank you! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200325/1… ------------------------------ Message: 5 Date: Wed, 25 Mar 2020 22:28:00 +0000 From: VINCENT KOPPELMANS <vincent.koppelmans(a)utah.edu> Subject: [Freesurfer] Freeview CLI feature request To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <FA7720A8-9593-4854-BD0E-4EEA17B7B339(a)contoso.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear FreeSurfer team, I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39 Would it be possible to add the following features as command line flags to FreeView? 1) Set opacity for a surface It is currently only possible via CLI to set opacity for volumes, surface overlays, and labels, but not for the surface itself. 2) Set smoothing iterations for isosurfaces This can only be done in the GUI, not yet via the CLI. Thank you for your consideration. - Vincent -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200325/2… ------------------------------ Message: 6 Date: Wed, 25 Mar 2020 18:41:02 -0400 From: Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview CLI feature request To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <6989E259-5D80-4BE4-8039-394262F86A78(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Sure. We?ll add those in. Best, Ruopeng On Mar 25, 2020, at 6:28 PM, VINCENT KOPPELMANS <vincent.koppelmans(a)utah.edu> wrote: External Email - Use Caution Dear FreeSurfer team, I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39 Would it be possible to add the following features as command line flags to FreeView? 1) Set opacity for a surface It is currently only possible via CLI to set opacity for volumes, surface overlays, and labels, but not for the surface itself. 2) Set smoothing iterations for isosurfaces This can only be done in the GUI, not yet via the CLI. Thank you for your consideration. - Vincent _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200325/f… ------------------------------ Message: 7 Date: Wed, 25 Mar 2020 22:43:44 +0000 From: VINCENT KOPPELMANS <vincent.koppelmans(a)utah.edu> Subject: Re: [Freesurfer] Freeview CLI feature request To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <06F52328-176F-4D3C-BD29-EF8E70BD69E4(a)umail.utah.edu> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Thank you for your quick and positive reply. Best, Vincent From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, 25 March 2020 at 16:41 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview CLI feature request Sure. We?ll add those in. Best, Ruopeng On Mar 25, 2020, at 6:28 PM, VINCENT KOPPELMANS <vincent.koppelmans(a)utah.edu<mailto:vincent.koppelmans@utah.edu>> wrote: External Email - Use Caution Dear FreeSurfer team, I am currently using FreeView v3.0, Darwin Build Mar 25 2020 00:009:39 Would it be possible to add the following features as command line flags to FreeView? 1) Set opacity for a surface It is currently only possible via CLI to set opacity for volumes, surface overlays, and labels, but not for the surface itself. 2) Set smoothing iterations for isosurfaces This can only be done in the GUI, not yet via the CLI. Thank you for your consideration. - Vincent _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200325/6… ------------------------------ Message: 8 Date: Thu, 26 Mar 2020 11:15:47 +0000 From: javier quilis <j.quilis(a)hotmail.com> Subject: Re: [Freesurfer] training set To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <HE1PR0602MB3385849CBF77626970C2C5EB90CF0(a)HE1PR0602MB3385.eurprd06.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" External Email - Use Caution Hi Bruce, thanks for the answer. Is there any paper where this is explained? I want to detail this in my paper and I would like to refer to the source. Thanks again, Javier ________________________________ De: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> en nombre de Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Enviado: mi?rcoles, 25 de marzo de 2020 14:40 Para: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Asunto: Re: [Freesurfer] training set Hi Javier no, that's not correct, depending on which training set you mean. For the Bayesian segmentation (aseg) we used 40 datasets distributed in age and pathology (10 each for young, middle age, elderly and AD). cheers Bruce On Wed, 25 Mar 2020, javier quilis wrote: External Email - Use Caution Thanks for the answer. I can not open the power point for some reason. Is there any paper where I can check this? I think the dataset used by freesurfer is in the MNI Average Brain (305 MRI) Stereotaxic Model and this dataset only use MRIs from young people, is this correct? Thanks again. Bests, Javier ____________________________________________________________________________ De: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> en nombre de Douglas N. Greve <dgreve(a)mgh.harvard.edu> Enviado: viernes, 20 de marzo de 2020 15:39 Para: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Asunto: Re: [Freesurfer] training set Try the tutorial slides https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI It does not go into a lot of detail, but it will give you the relevant lectures On 3/17/2020 8:54 AM, javier quilis wrote: External Email - Use Caution Hello everyone, I'm trying to do a study of a comparison between the automated methods to analyze structural MRI from FSL and Freesurfer. I am interested in the training set used by Freesurfer to do the brain segmentation and I can not find a detailed description of it. Is there any source where this set is described? Thanks in advance. Bests, Javier Quilis _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200326/1… ------------------------------ Message: 9 Date: Thu, 26 Mar 2020 13:25:25 +0000 From: Mason Wells <WellsMT1(a)cardiff.ac.uk> Subject: Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <9F66CFB7-6712-4267-BEA8-5577D1598C65(a)cardiff.ac.uk> Content-Type: text/plain; charset="utf-8" External Email - Use Caution In the event that Bruce might not be able to help. I ask if anyone else on the list has experience with the problem described in this thread? Any help would be greatly appreciated. Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 ?On 25/03/2020, 18:38, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of WellsMT1(a)cardiff.ac.uk> wrote: External Email - Use Caution HI Bruce, Ok, great. I just thought some sections of white matter had not been traced in their entirety (see red crosshair in attached image). If you think this all looks reasonable, please can you advise on the misaligned as outlined in the original post? Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 On 25/03/2020, 17:29, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of fischl(a)nmr.mgh.harvard.edu> wrote: Hi Mason I can't tell from those images except that it looks reasonable cheers Bruce On Wed, 25 Mar 2020, Mason Wells wrote: External Email - Use Caution Hi again Bruce, I have now installed the relevant libpng packages and have freeview open. The segmentation doesn?t look brilliant in some areas. What do you think? Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 On 25/03/2020, 16:28, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of WellsMT1(a)cardiff.ac.uk> wrote: External Email - Use Caution Hi Bruce, I get the following error message when I try to load freeview Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl masontwells@masontwells-VIG800S:~$ freeview freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 On 25/03/2020, 16:19, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of fischl(a)nmr.mgh.harvard.edu> wrote: something like freeview -v $SUBJECTS_DIR/<subject name>/mri/norm.mgz \ -f $SUBJECTS_DIR/<subject name>/surf/?h.white cheers Bruce On Wed, 25 Mar 2020, Mason Wells wrote: External Email - Use Caution Hi Bruce, Thanks for getting back to me. Sorry, but I am not sure I follow what you mean here. Could you please explain how I would check this? Thanks again for your help. Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 On 25/03/2020, 16:11, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of fischl(a)nmr.mgh.harvard.edu> wrote: Hi Mason can you confirm that things look ok within FreeSurfer if you look at the surface over the volume in freeview? cheers Bruce On Wed, 25 Mar 2020, Mason Wells wrote: External Email - Use Caution Hello Freesurfer developers, I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all command which finished without errors. However, the white/grey matter boundaries are significantly misaligned with the subjects T1 (images attached). Below are the steps I have taken to reach this point in the analysis: 1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain. 2. Ran Feat ? Distortion correction of the EPI ? Motion correction ? No smoothing ? Highpass filter ? No registration to whole brain ? Register to T1_biascorr_brain ? Register to standard space 3. Ran recon-all on T1_biascorr 4. Convert T1/T1_brain/orig(001) from mgz to nii 5. Check registration (using the SurfaceProjection command from the SamSrf package) which leads to the attached images named S1 and S1. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: Linux 5.3.0-40-generic x86_64 Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux As you can see, the registration is significantly misaligned. Can anyone offer any advice on this/suggest a way to rectify it? Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… ------------------------------ Message: 10 Date: Thu, 26 Mar 2020 19:02:11 +0530 From: Devika K <devikakuttala(a)gmail.com> Subject: Re: [Freesurfer] Hippocampal Volume Extraction To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CA+m7eQEugcK9hM3M0_ouwC6MXoG=VnL4ShDL9PL9U-dT=kR1vA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi, I want to extract hippocampal volume from longitudinal samples. I am less aware of it. I ran recon-all-all with longitudinal pipeline for all those samples. How I need to process further (Commands that I need to follow). Would you please help me out? Thanks and Regards Devika K -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200326/7… ------------------------------ Message: 11 Date: Thu, 26 Mar 2020 09:36:02 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] training set To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.21.2003260935250.13248(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" Have you checked the original aseg paper? If not, then it will be in Rahul's cortical parcellation one as it is the same data cheers Bruce On Thu, 26 Mar 2020, javier quilis wrote: ????????External Email - Use Caution???????? Hi Bruce,? thanks for the answer. Is there any paper where this is explained? I want to detail this in my paper and I would like to refer to the source.? Thanks again,? Javier ____________________________________________________________________________ De: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> en nombre de Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Enviado: mi?rcoles, 25 de marzo de 2020 14:40 Para: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Asunto: Re: [Freesurfer] training set ? Hi Javier no, that's not correct, depending on which training set you mean. For the Bayesian segmentation (aseg) we used 40 datasets distributed in age and pathology (10 each for young, middle age, elderly and AD). cheers Bruce On Wed, 25 Mar 2020, javier quilis wrote: ????????External Email - Use Caution???????? Thanks for the answer.? I can not open the power point for some reason. Is there any paper where I can check this? I think the dataset used by freesurfer is in the MNI Average Brain (305 MRI) Stereotaxic Model and this dataset only use MRIs from young people, is this correct? Thanks again. Bests,? Javier ___________________________________________________________________________ _ De: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> en nombre de Douglas N. Greve <dgreve(a)mgh.harvard.edu> Enviado: viernes, 20 de marzo de 2020 15:39 Para: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Asunto: Re: [Freesurfer] training set ? Try the tutorial slides https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI It does not go into a lot of detail, but it will give you the relevant lectures On 3/17/2020 8:54 AM, javier quilis wrote: ?????? ????????External Email - Use Caution???????? ?????? Hello everyone,? I'm trying to do a study of a comparison between the automated methods to analyze structural MRI from FSL and Freesurfer. I am interested in the training set used by Freesurfer to do the brain segmentation and I can not find a detailed description of it. Is there any source where this set is described? Thanks in advance. Bests,? Javier Quilis _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ Message: 12 Date: Thu, 26 Mar 2020 09:44:08 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Misalignment of boundaries and T1 (Freesurfer/SamSrf) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.21.2003260943340.13248(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Mason not sure we can help if everything looks good in freeview. Doesn't that make it a SamSrf issue? Or an interface between the two packages? Have you checked with their support? cheers Bruce On Thu, 26 Mar 2020, Mason Wells wrote: External Email - Use Caution In the event that Bruce might not be able to help. I ask if anyone else on the list has experience with the problem described in this thread? Any help would be greatly appreciated. Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 ?On 25/03/2020, 18:38, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of WellsMT1(a)cardiff.ac.uk> wrote: External Email - Use Caution HI Bruce, Ok, great. I just thought some sections of white matter had not been traced in their entirety (see red crosshair in attached image). If you think this all looks reasonable, please can you advise on the misaligned as outlined in the original post? Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 On 25/03/2020, 17:29, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of fischl(a)nmr.mgh.harvard.edu> wrote: Hi Mason I can't tell from those images except that it looks reasonable cheers Bruce On Wed, 25 Mar 2020, Mason Wells wrote: External Email - Use Caution Hi again Bruce, I have now installed the relevant libpng packages and have freeview open. The segmentation doesn?t look brilliant in some areas. What do you think? Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 On 25/03/2020, 16:28, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Mason Wells" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of WellsMT1(a)cardiff.ac.uk> wrote: External Email - Use Caution Hi Bruce, I get the following error message when I try to load freeview Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl masontwells@masontwells-VIG800S:~$ freeview freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 On 25/03/2020, 16:19, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of fischl(a)nmr.mgh.harvard.edu> wrote: something like freeview -v $SUBJECTS_DIR/<subject name>/mri/norm.mgz \ -f $SUBJECTS_DIR/<subject name>/surf/?h.white cheers Bruce On Wed, 25 Mar 2020, Mason Wells wrote: External Email - Use Caution Hi Bruce, Thanks for getting back to me. Sorry, but I am not sure I follow what you mean here. Could you please explain how I would check this? Thanks again for your help. Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 On 25/03/2020, 16:11, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of fischl(a)nmr.mgh.harvard.edu> wrote: Hi Mason can you confirm that things look ok within FreeSurfer if you look at the surface over the volume in freeview? cheers Bruce On Wed, 25 Mar 2020, Mason Wells wrote: External Email - Use Caution Hello Freesurfer developers, I am using Freesurfer and SamSrf for prf mapping. I have ran the recon-all command which finished without errors. However, the white/grey matter boundaries are significantly misaligned with the subjects T1 (images attached). Below are the steps I have taken to reach this point in the analysis: 1. Run fsl_anat to get a bias corrected T1 and T1_biascor_brain. 2. Ran Feat ? Distortion correction of the EPI ? Motion correction ? No smoothing ? Highpass filter ? No registration to whole brain ? Register to T1_biascorr_brain ? Register to standard space 3. Ran recon-all on T1_biascorr 4. Convert T1/T1_brain/orig(001) from mgz to nii 5. Check registration (using the SurfaceProjection command from the SamSrf package) which leads to the attached images named S1 and S1. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: Linux 5.3.0-40-generic x86_64 Uname: Linux masontwells-VIG800S 5.3.0-40-generic #32~18.04.1-Ubuntu SMP Mon Feb 3 14:05:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux As you can see, the registration is significantly misaligned. Can anyone offer any advice on this/suggest a way to rectify it? Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau?r Golwg & Canolfan Ymchwil Delweddu?r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ff?n: 02920 879628 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 193, Issue 37 *******************************************

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Using freeview to view (and edit?) talairach registrations
by Rachel Hoel 31 Mar '20

31 Mar '20

External Email - Use Caution Dear Freesurfer Developers, I'm working with v6.0 on OS Catalina 10.15 and I'm trying to use freeview to check talairach registrations - I've always used tkmedit, so I am running into some issues with the command line for viewing the transform. When I run the following command: freeview -v <mysubjid>/mri/T1.mgz \ <mysubjid>/mri/brainmask.mgz:reg=/mri/transforms/talairach.xfm I get the following errors: regio_read_mincxfm: No such file or directory ERROR: could not read /mri/transforms/talairach.xfm ERROR: could not read /mri/transforms/talairach.xfm Thanks in advance! Rachel

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Re: [Freesurfer] FreeSurfer V 7.0 on Centos 8
by fsbuild 31 Mar '20

31 Mar '20

External Email - Use Caution Hello Mina, I see from https://www.centosblog.com/centos-eol-dates/ that CentOS 6 will no longer be updated as of 11/2020, and similarly for CentOS 7 in 6/2024.  It looks like CentOS 8 was released around September of 2019.   While we do not currently build/test on CentOS8, I am sure it will eventually be supported.   Given some users will continue to use CentOS 6 even after 11/2020 and that many people have been running the freesurfer 6 release on CentOS6, then even the upcoming freesurfer 7 release is targeting CentOS6, CentOS7 and Ubuntu linux (as well as Mac OS). There is also currently an Ubuntu 18 VM with freesurfer 6 and the beta release of freesurfer 7 pre-installed which you can find here, https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 - R.. On Mar 30, 2020, at 08:52, Mina Rizkallah <dr.minafakhry(a)live.com> wrote:        External Email - Use Caution        Greetings FreeSurfer team,I recently upgraded by workstation from Centos 7 to 8..1 as the support for centos  7 will be over soon.I tried installing freesurfer version 7.0 beta 1 but failed due to some unresolved dependencies (tried on a  virtual centos 7 and worked fine) !!so, when will there be support for centos 8, thank youBest regardsMina_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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segmentThalamicNuclei.sh - Undefined symbol error, Invalid MEX file
by Chester Kang 30 Mar '20

30 Mar '20

External Email - Use Caution Hi, We are wanting to run the hippocampal subfields which is part of the developmental version of FreeSurfer ("freesurfer-darwin-macOS-dev.pkg"). The FreeSurfer v7.0.0 Dev and the Matlab2014b (Run Time Version) has also been installed. But are getting errors. E.g., "... Invalid MEX-file '/tmp/MCR_488630323/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/ig lesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64' ..." It looks like a similar problem existed in 2018 (though I cannot find a fix). https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg56815.html Any help would be greatly appreciated. Thanks in advance! Regards, Chester

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