Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

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

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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

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Re: [Freesurfer] Solving the Lazy Symbol binding errors
by fsbuild 12 May '20

12 May '20

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

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Fw: Error: Command Not Found
by Chung, Evan R. 12 May '20

12 May '20

________________________________ From: Chung, Evan R. Sent: Tuesday, May 12, 2020 10:30 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Error: Command Not Found Hello Freesurfer Developers, I'm attempting to run the command "mri2mesh --all (specific folder and files)" but a "command not found" error after it runs for a few minutes. I've attached a screenshot showing this error. I couldn't find a similar error in the list. I'm using Freesurfer 6.0 on macOS Catalina, and I've installed the patch. Do you know how I might troubleshoot this? Best, Evan

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Solving the Lazy Symbol binding errors
by RENXI LI 12 May '20

12 May '20

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]: y rsync -zbrlv --progress --suffix=.1589339130_bak rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-D… /Applications/freesurfer receiving 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 consider sent 4 bytes received 9 bytes 8.67 bytes/sec total size is 0 speedup is 0.00 rsync 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

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Information regarding FreeSurferColorLUT.txt
by Safi Ullah . 12 May '20

12 May '20

External Email - Use Caution Dear Freesurfer, *Q.1*: The colors of FreeSurferColorLUT.txt corresponds to which mgz file? I wanted to extract Substancia-Nigra but with reference to a conversion, held in 2019, https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63560.html, segmentation for the serial # of Substancia-Nigra is not supported in version 6, is it supported by Version 7? if not then i would like to write a code to extract labels for Substancia-Nigra based on the color code (RGB). is it possible? as the slices are in grayscale. *Q.2*: I also need to extract Anterior Commissure and Posterior Commissure. *Q.3*: While reading the brainstem-structures.log, I came across this statement (it appears multiple times) " * WARNING: Registration did not converge in 5 steps! * Problem might be ill posed. * Please inspect output manually! " why i get this warning and how to get rid of it? because i think the segmented midbrain does not cover the whole midbrain area. Thanks in advance Safi

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Re: [Freesurfer] tkmedit in FreeSurfer 7.0
by Hoopes, Andrew 12 May '20

12 May '20

Hi Aylin, You can add this to your SetUpFreeSurfer script in $FREESURFER_HOME, but in general tkmedit is no longer supported after v6, please just use freeview. Best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Dincer, Aylin" <aylin.dincer(a)wustl.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, May 11, 2020 at 3:17 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] tkmedit in FreeSurfer 7.0 External Email - Use Caution Hi FreeSurfer Experts, We are unable to use tkmedit using FreeSurfer 7.0 (centos 7). In the .xdebug_tkmedit file, it outputs the following error: “Tcl_Init returned 1: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4” It looks like when we manually set the environmental variable TCL_LIBRARY to point to the tcl location in the $FREESURFER_HOME folder, tkmedit will open. Is there a way to fix this so it automatically sets this environmental variable? Thanks! Aylin _____________________________ Aylin Dincer Senior Research Technician NeuroImaging Laboratories Imaging Core, Benzinger Lab 314-362-3629 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -
by Marina Fernández 12 May '20

12 May '20

External Email - Use Caution Dear Freesurfer experts, I get the error that you can find at the end of this message when I am running mri_glmfit. Whenever I run an analysis in which the experimental design has more than 12 columns, I get the same error, whereas if the experimental design has less than 12 columns, the analysis is successful. I also send you the fsgd.txt file (through FTP File Exchange). In this file you can see that there are four groups that have been created by the combination of two discrete variables (sex and apoe-type). How can I solve this problem? Thank you in advance. ERROR MESSAGE: (...) Saving design matrix to /usr/local/freesurfer/subjects/amy_frapsaliva_stats/stats/cortex/cortex_caseageeducfrap/pruebax_frapsalgroup_NEG/lh.fsgd_subj_gauss001/Xg.dat Computing normalized matrix Normalized matrix condition is 1e+08 Design matrix ------------------ 0.00000 1.00000 0.00000 0.00000 0.00000 0.83619 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 0.79984 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.39700 0.00000 0.00000 0.00000 -0.73337 0.00000 0.00000 0.00000 -0.84287 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.74935 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 -0.82284 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 -1.45403 0.00000 0.00000 0.00000 -0.32012 0.00000 0.00000 0.00000 0.17882 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.57318 0.00000 0.00000 0.00000 0.91963 0.00000 0.00000 0.00000 0.33908 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 1.71704 0.00000 0.00000 0.00000 0.09313 0.00000 0.00000 0.00000 -0.02652 0.00000; 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0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.30768 0.00000 0.00000 0.00000 -0.32012 0.00000 0.00000 0.00000 1.10534; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 1.01236 0.00000 0.00000 0.00000 0.09313 0.00000 0.00000 0.00000 0.46429; 0.00000 1.00000 0.00000 0.00000 0.00000 0.48385 0.00000 0.00000 0.00000 0.09313 0.00000 0.00000 0.00000 0.33908 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 -0.04466 0.00000 0.00000 0.00000 -0.52675 0.00000 0.00000 0.00000 0.32906 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 0.83619 0.00000 0.00000 0.00000 -1.55987 0.00000 0.00000 0.00000 -1.73434 0.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 1.01236 0.00000 0.00000 0.00000 1.12625 0.00000 0.00000 0.00000 1.63622; 0.00000 1.00000 0.00000 0.00000 0.00000 0.66002 0.00000 0.00000 0.00000 -0.73337 0.00000 0.00000 0.00000 -0.98310 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000 0.00000 0.83619 0.00000 0.00000 0.00000 2.36600 0.00000 0.00000 0.00000 -2.40545 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00000 -0.57318 0.00000 0.00000 0.00000 -0.52675 0.00000 0.00000 0.00000 1.24557 0.00000 0.00000 0.00000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --surf amy_frapsaliva_average lh --C /usr/local/freesurfer/subjects/amy_frapsaliva_stats/contrast.mat --fsgd /usr/local/freesurfer/subjects/amy_frapsaliva_stats/fsgd.txt dods --label /usr/local/freesurfer/subjects/amy_frapsaliva_average/label/lh.cortex.label --y /usr/local/freesurfer/subjects/amy_frapsaliva_stats/lh.fsgd_subj_gauss001.mgh --no-prune --glmdir /usr/local/freesurfer/subjects/amy_frapsaliva_stats/stats/cortex/cortex_caseageeducfrap/pruebax_frapsalgroup_NEG/lh.fsgd_subj_gauss001 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.768203 (col 15), Max=6.706254 (col 10) ... could not determine the cause of the problem

2 1

mri_glmfit error
by Marina Fernández 12 May '20

12 May '20

1 0

Robust Regression with Univariate LME
by Hua, Jessica 12 May '20

12 May '20

External Email - Use Caution Hi FreeSurfer Experts, There are a couple of outliers in my data. I had winsorized the variable, but now I am trying to use robust regression to weight these outliers in my longitudinal analyses. In Matlab there is a robustfit function. Is there a way to modify the lme_fit_FS code to incorporate robust regression? Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

1 0

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