Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -
by Marina Fernández 13 May '20

13 May '20

External Email - Use Caution Thank you, Doug. That makes sense. Do you think in this case it is a good option to add the flag --illcond to run this analysis without getting an error? or is it better not to use the variable apoe in these statistical analyzes? What do you recommend us? Best wishes, Marina.

2 1

Re: [Freesurfer] Compare individual to a group
by Xiaojiang Yang 13 May '20

13 May '20

External Email - Use Caution Hi Douglas, I have tried to follow your suggestion to use the transformed thickness file like this: mris_preproc --fsgd xxx.fsgd \ --meas $meas.fwhm$smoothing.xformed.mgz \ --target fsaverage \ --hemi $hemi \ --out $hemi.$meas.$smoothing.mgh But it says $meas.fwhm$smoothing.xformed.mgz does not match surface (163842,166904). My files $meas.fwhm$smoothing.xformed.mgz come from $meas.fwhm$smoothing.fsaverage (just by multiplying it with a weight). If I use "--cache-in" in the mris_preproc like below: mris_preproc --fsgd xxx.fsgd \ --cache-in $meas.fwhm$smoothing.fsaverage \ --target fsaverage \ --hemi $hemi \ --out $hemi.$meas.$smoothing.mgh The above command line runs fine. I know the problem in the first command line might be that the files $meas.fwhm$smoothing.xformed.mgz are already on the fsaverage surface, not the subject surface. But mris_preproc is still trying to use mri_surf2surf to resample those mgh file from the subject surface to fsaverage surface, which leads to the "does not match surface" error. My question is: How can I tell mris_preproc to regard those transformed files to be on the fsaverage surface already (instead of subject's surface), just like the second command line where the "-cache-in" option is used? You know, my transformed files are Just derived from cached files $hemi.$meas.fwhm$smoothing.fsaverage.mgh in the $subject/surf directories. I do not want to use mri_surf2surf to transform them to the subject surface first, and then let mris_preproc transform them back to fsaverage surface again. Thanks! Xiao <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from :%22Douglas+N.+Greve%22> Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date :20200511> Mon, 11 May 2020 14:14:42 -0700 Just call your thickness file some other name, eg, lh.xformed.thickness.mgz, the just specify --meas xformed.thickness.mgz On 5/11/2020 3:52 PM, Xiaojiang Yang wrote: External Email - Use Caution Thank you Douglas! If I apply my transform to both the healthy controls and the patient, I guess I would lose the convenience of using mri_glmfit, which eventually loses the convenience of using mri-glmfit-sim (I don't care not using mri_glmfit, but I want to use mri_glmfit-sim to do multiple comparisons correction). That is because mri_glmfit uses the prepared output from mris_preproc, which I have no control over to use the transformed subject. The only way I can circumvent this is to use my transformed thickness file to overwrite the FS calculated thickness file, but that is what I am hesitant to do. If you have good suggestions regarding this, please let me know. Thanks! Xiao On Mon, May 11, 2020 at 12:25 PM Douglas N. Greve <dgr...(a)mgh.harvard.edu < <mailto:dgr...@mgh.harvard.edu> mailto:dgr...@mgh.harvard.edu>> wrote: I guess you could apply your transform to both the healthy controls and to your patient, can then create an FSGD file with two classes as before but no continuous variable. Then just have a contrast that computes the diff between the patient and the mean of the controls.

2 1

Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -
by Marina Fernández 13 May '20

13 May '20

External Email - Use Caution Hi Douglas, I email you the fsgd file and I have also sent it through FTP. Thank you for your attention. Best regards, Marina.

2 1

Which subject does recon-all register surfaces to?
by Ian 13 May '20

13 May '20

External Email - Use Caution Hi guys. After recon-all, the /surf/?h.sphere.reg file implies a registration has been performed to an "average" subject on a sphere. Can you please tell me which subject this is? Is it SUBJECTS_DIR/fsaverage? If so, what is SUBJECTS_DIR/fsaverage/lh.sphere.reg a registration to? If not, where can I find the subject that recon-all registers to? Thanks, Ian -- *Ian Hardingham*

3 2

Issue of freesurfer ubuntu 18 VM setup on windows 10
by Yue Liu 13 May '20

13 May '20

External Email - Use Caution Hello FreeSurfer Developers. I installed and setup freesurfer ubuntu 18VM following steps in the website https://surfer.nmr.mgh.harvard.edu/fswiki//VM_67_win. However, when I clicked green start button to run VM at the last step, it did not go directly to an empty desktop. A login interface appeared instead with the account name as "Developer" (Please see attached screeshot). I tried some passwords or using other account names, while none did work. Do you have any idea what is the problem? Thank you, Yue Liu

1 0

FreeSurfer v6.0 minimal Docker image
by Ерохин Александр 13 May '20

13 May '20

External Email - Use Caution Hello together! I’d like to share my attempt on providing minimal Docker image of the FreeSurfer that is fully operational in terms of recon-all functionality. Please see: https://hub.docker.com/r/alerokhin/freesurfer6 Compressed size is 732.6 MB Size of pulled image is 1.92GB Please follow simple instructions from Docker hub repository in order to get it running. In case of any issues or suggestions please contact me by email specified in the description of the repository. Really hope that it would be helpful for someone. Best regards, Aleksandr Erokhin.

2 1

freevieer This application failed to start because no Qt platform plugin could be initialized.
by Knut J Bjuland 13 May '20

13 May '20

External Email - Use Caution Dear FreeSurfer experts I have used this script to start Freeview from within Matlab fs=getenv('FREESURFER_HOME'); setenv('FS_QT_HOME',fullfile(fs,'lib','qt')); setenv('QTLIBPATH',fullfile(fs,'lib','qt','lib')) setenv('qtplugin',fullfile(fs,'lib','qt','plugins')) setenv('vtk',fullfile(fs,'lib','vtk')) lib=getenv('LD_LIBRARY_PATH'); qtlib=getenv('QTLIBPATH'); plugins=getenv('qtplugin'); setenv('LD_LIBRARY_PATH',strcat(lib,':',qtlib,':',plugins,fullfile(fs,'lib','vtk'))) if upper < fdrtreshold upper = fdrtreshold + 1; fdrtreshold=num2str(fdrtreshold);upper=num2str(upper); fdrtreshold=sprintf('%s,%s',fdrtreshold,upper); leftcommand=sprintf('%s/%s/surf/lh.%s:annot=aparc.annot:annot_outline=1:overlay=%s:overlay_threshold=%s',SUBJECTS_DIR,template,surface,leftmgh,fdrtreshold); rightcommand=sprintf('%s/%s/surf/rh.%s:annot=aparc.annot:annot_outline=1:overlay=%s:overlay_threshold=%s ',SUBJECTS_DIR,template,surface,rightmgh,fdrtreshold); freeview='freeview'; commandline=sprintf('%s -f %s -f %s -viewport 3d &',freeview,leftcommand,rightcommand); system(commandline) but with Freesurfer 7 I have been unable to start Freeview. Are there any option that I am missing. I get this 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: linuxfb, minimal, offscreen, vnc, xcb. /usr/local/freesurfer/7.0.0-1/bin/freeview_matlab: line 13: 330961 Aborted (core dumped) freeview $argv:q /usr/local/freesurfer/7.0.0-1/bin/freeview_matlab: Aborted Do I miss something that was setup by qt_setup? Knut Jørgen Bjuland

1 0

Re: [Freesurfer] Solving the Lazy Symbol binding errors
by fsbuild 13 May '20

13 May '20

External Email - Use Caution Hello Renxi, You can try downloading and applying the FreeSurfer_6_0_0_Patch.zip file from here, https://doc-0o-60-docs.googleusercontent.com/docs/securesc/4lv0ah5ralk0bh0a… Open the archive and try to follow the instructions in README.patch file to replace the Freeview application and one of the libraries. - R. On May 13, 2020, at 00:10, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Sorry - forgot the download link,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfe… May 12, 2020, at 23:59, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello Renxi,You could try downloading the 6.0.0 release from here and use the installer package.  Since the package is unsigned, you will need sudo/admin privileges to install it, but you should not need to disable SIP.  After downloading and launching the installer, you will need to go into the System Preferences menu -> Security & Privacy - and give the installer permission to run, as well as maybe click thru some subsequent permission prompts.-R.On May 12, 2020, at 23:25, RENXI LI <rli296(a)wisc.edu> wrote:        External Email - Use Caution        Hi, I was trying to get through the lazy symbol binding errors and I have disable the SIP. I have the following errors, would you mind taking a look to see what might goes wrong?Build is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c   Running this will update some of your freesurfer binaries. Shall I proceed? [y/n/Abort]: yrsync -zbrlv --progress --suffix=.1589339130_bak rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/* /Applications/freesurferreceiving file list .... rsync: change_dir "/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in pub) failed: No such file or directory (2)0 files to considersent 4 bytes  received 9 bytes  8.67 bytes/sectotal size is 0  speedup is 0.00rsync error: some files could not be transferred (code 23) at /BuildRoot/Library/Caches/com..apple.xbs/Sources/rsync/rsync-54/rsync/main.c(1404) [receiver=2.6.9]Best,Renxi_______________________________________________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_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Updating the freesurfer Ubuntu VM to the latest 7.1.0 release
by fsbuild 13 May '20

13 May '20

External Email - Use Caution Hello Everyone, If you previously downloaded the Ubuntu VM via the link,https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 - then without any modifications, it should contain both the previous freesurfer 6.0.0 release and the 7.0.0 beta 1 release from April 2020. Please note that latest version 7 release is now 7.1.0 (May 2020) which contains an important update by development that you will want to have if you are using the version 7 release (see copy of email below posted to the list yesterday). Use the following steps to update the 7.0.0-1 release to the 7.1.0 release in the VM.  There is also an attached bashrc file to replace the existing one in the home directory for the default user, developer. - R. - - - - -  Update Steps - - - - Download the latest release - currently 7.1.0 - from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/freesurfer-lin… Let's assume after the download the archive file is located in your downloads folder under the path, ~/Downloads/freesurfer-linux-centos7_x86_64-7.1.0.tar.gz Locate your previous version 7 release under the path /usr/local/freesurfer $ ls /usr/local/freesurfer 6.0.0-1  7.0.0-1 Remove the previous version 7 release, here 7.0.0-1, $ cd /usr/local/freesurfer $ sudo rm -rf  7.0.0-1 Expand the archive for the new release from your downloads folder, $ sudo  tar  zxpf  ~/Downloads/freesurfer-linux-centos7_x86_64-7.1.0.tar.gz Now move the newly created ./freesurfer subdirectory from the archive to be the name of the new release, $ sudo mv freesurfer 7.1.0-1 Check to see files are there, $ ls 7.1.0-1 <output deleted> Finally, replace your existing $HOME/.bashrc file with the attached bashrc file which will allow you to run either the 6.0.0 or 7.1.0 release.  NOTE - if you have made changes to your $HOME/.bashrc file since you started using the VM, then you may want to merge your current $HOME/.bashrc with the contents of the attached bashrc in order not to lose your changes. You could also diff the 2 files and add manually edit in the changes from the attached bashrc. With the new bashrc in your downloads folder as ~/Downloads/bashrc, then to diff the files, $ diff  ~/Downloads/bashrc  $HOME/.bashrc To simply replace the old bashrc in its entirety, $ cp -p -f  ~/Downloads/bashrc  $HOME/.bashrc Once your new $HOME/.bashrc file is in place (which should use use the 7.1.0-1 release by default), then start a new terminal window.  You should see the following output: -------- freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /usr/local/freesurfer/7.1.0-1 FSFAST_HOME       /usr/local/freesurfer/7.1.0-1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /usr/local/freesurfer/7.1.0-1/subjects TUTORIAL_DATA     /home/developer/tutorial_data MNI_DIR           /usr/local/freesurfer/7.1.0-1/mni WARNING: /usr/local/freesurfer/7.1.0-1/fsl_507/bin does not exist. FSL_DIR           /usr/local/freesurfer/7.1.0-1/fsl_507 -------- Forwarded Message -------- Subject: [Freesurfer] Release 7.0.0 is being recalled, 7.1.0 is ready for downloadDate: Mon, 11 May 2020 21:58:31 -0400From: Douglas N. Greve <dgreve@mgh.harvard.edu>Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>Hi All, I regret to inform you that we are recalling 7.0.0 because we found some small issues with the way that conforming step was being performed. The conforming step takes your input volume and converts it to 256x256x256 1mm and converts the type to UCHAR (8 bit). When converting to UCHAR, it has to do some intensity rescaling. The method for doing this was changed in 7.0.0. In most data sets, this results in small changes to the output. However, we just discovered that it can result in large problems in some data sets, so, for 7.1.0, we are reverting back to the pre-7.0.0 method. Going forward, we recommend that people NOT use 7.0.0 and use 7.1.0 instead. We apologize for any inconvenience this has caused.. We hope that not many data sets have been analyzed yet in the 11 days since the release. I'd like to thank our research assistant Devani Cordero for ferreting out this problem.Release notes are here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes7.1.0 can be obtained from here https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloadsPlease let us know if you have any problemsbestdoug

1 0

Re: [Freesurfer] Solving the Lazy Symbol binding errors
by fsbuild 13 May '20

13 May '20

External Email - Use Caution Sorry - forgot the download link, https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Dar… On May 12, 2020, at 23:59, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello Renxi,You could try downloading the 6.0.0 release from here and use the installer package.  Since the package is unsigned, you will need sudo/admin privileges to install it, but you should not need to disable SIP.  After downloading and launching the installer, you will need to go into the System Preferences menu -> Security & Privacy - and give the installer permission to run, as well as maybe click thru some subsequent permission prompts.-R.On May 12, 2020, at 23:25, RENXI LI <rli296(a)wisc.edu> wrote:        External Email - Use Caution        Hi, I was trying to get through the lazy symbol binding errors and I have disable the SIP. I have the following errors, would you mind taking a look to see what might goes wrong?Build is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c   Running this will update some of your freesurfer binaries. Shall I proceed? [y/n/Abort]: yrsync -zbrlv --progress --suffix=.1589339130_bak rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/* /Applications/freesurferreceiving file list ... rsync: change_dir "/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in pub) failed: No such file or directory (2)0 files to considersent 4 bytes  received 9 bytes  8.67 bytes/sectotal size is 0  speedup is 0.00rsync error: some files could not be transferred (code 23) at /BuildRoot/Library/Caches/com..apple.xbs/Sources/rsync/rsync-54/rsync/main.c(1404) [receiver=2.6.9]Best,Renxi_______________________________________________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

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer