Freesurfer March 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
161 discussions

Hippocampal Subfield Segmentation Error
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 14 Apr '20

14 Apr '20

External Email - Use Caution Dear Freesurfer experts, I am having a problem with hippocampal subfield segmentation. The issue appears to be related to JavaVM - after I run the code: recon-all -s (subject ID) -hippocampal-subfields-T1 This is the error: JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. Fatal Error on startup: Unable to start the JVM because of a bad Java option or unknown error. Please check your java.opts file. Any suggestions? Thank you, Alex

3 8

training set
by javier quilis 13 Apr '20

13 Apr '20

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

3 7

Petsurfer: Gtmstats < 1, voxel wise mean is fine
by Eckbo, Ryan 03 Apr '20

03 Apr '20

Hello experts, I've recently run into a case the gtmstats uptake (reference region: cerebellum) for the pericarlcarine ROI's are as low as 0.40, however computing the voxel wise mean using input.rescaled.nii.gz and mgx.ctxgm.nii.gx and aux/seg.nii.gz, the values are closer to 1, as expected: | vol | psf | roi | gtmstats_uptake | mean_uptake | | --------------------- | --- | -------------------- | --------------- | ----------- | | input.rescaled.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 | 1.226… | | input.rescaled.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 | 1.083… | | input.rescaled.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 | 1.197… | | input.rescaled.nii.gz | 6 | ctx-lh-pericalcarine | 0.470 | 1.058… | | mgx.ctxgm.nii.gz | 0 | ctx-rh-pericalcarine | 0.807 | 1.007… | | mgx.ctxgm.nii.gz | 0 | ctx-lh-pericalcarine | 0.758 | 0.888… | | mgx.ctxgm.nii.gz | 6 | ctx-rh-pericalcarine | 0.409 | 0.915… | | mgx.ctxgm.nii.gz | 6 | ctx-lh-pericalcarine | 0.470 | 0.809… | This is using Freesurfer 6.0, and the PET to anatomical registration looks fine. Any ideas why we get such bad values from the GTM method? Thanks for any help, Ryan

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HP and thalamic subfield quality with a bad aparc segmentation
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 03 Apr '20

03 Apr '20

Hi all, >From my understanding from the log files, the subfield segmentations (and in general the aparc.mgz) relies on the norm.mgz (which is based off the brainmask.mgz). What if hypothetically, you have a not so good segmentation of the cerebral cortex, but willing to individually qc the subfields for the hippo, amyg and thal to see whether they are worth including in an analysis? I don't know if you would inherently discard a subject in a subfield analysis if it has a bad cerebral cortex segmentation (e.g ring artifacts) since the subfield segmentation retrieves some sort of cerebral cortex measurement in its calculations Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 3

Is it possible to "fill in" the region delimited by an ROI label?
by Mohammad Rashid 01 Apr '20

01 Apr '20

External Email - Use Caution Hi all, I'm able to load in a yellow outline for the entorhinal region by loading a file named ?h.entorhinal_exvivo.label as a volume. (I first load in a brain image such as brain.mgz, and then display the outline on top of it.) Is it possible to get a solid highlight of the entorhinal region in this manner, as opposed to just an outline of the region? (Strangely enough, if I load ?h.entorhinal_exvivo.label as a label on an surface file, such as ?h.inflated, then the entorhinal region is seen filled in with a yellow color on the 3D surface. This is the effect I want, except on a 2D volume.) Any help is greatly appreciated, Mohammad

2 4

Recon-all exited with errors
by Wang, Lily 01 Apr '20

01 Apr '20

Hi All, I have a subject whose T1 quality is quite good but reconstruction exited with errors so I am not sure what the issue could be. Attached is the recon-all.log. Could it be that the subject is very old and has a lot of degeneration? Thank you, Lily

3 5

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

2 1

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

2 4

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

2 1

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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Freesurfer March 2020