Re: [Freesurfer] Longitudinal LME matlab error - Matrix singular or badly scaled

11 Dec 2023


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I don’t think there is any GUI or graphical interface with the runtime environment (which does not require a Matlab license). &nbsp;Neither does it contain the matlab compiler to build matlab executables, etc. &nbsp;So if you still need to create Matlab executables either with the GUI or from the command line, you would need to have your own site or personal installation of Matlab with a license. &nbsp;The Matlab runtime environment in freesurfer subsequently allows you to run what has already been built with Matlab.
- R.
On Dec 10, 2023, at 21:31, Sophie Matis &lt;sophie.matis@sydney.edu.au&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hi there,&nbsp;Thanks for the advice, I have followed these suggestions and used the fs_install_mcr command and can see the the libmwm* libraries are installed under $FREESURFER_HOME/MCRv97/bin/glnxa64. I also added the path the script suggested once finished to LD_LIBRARY_PATH. I’m now not sure how to open matlab now though as I can’t find any executable matlab file? There were no error with the command but it doesn’t look like matlab was installed…&nbsp;Thanks again for the help,&nbsp;Sophie Matis&nbsp;| Data Management &amp; Research OfficerSchool of Health Sciences &amp; Brain and Mind Centre&nbsp;Faculty of Medicine and Health&nbsp;&nbsp;The University of Sydney&nbsp;&nbsp;Brain and Mind Centre, 94-100 Mallett Street, Camperdown (M02G)&nbsp;| The University of Sydney | NSW | 2006&nbsp;sophie.matis@sydney.edu.au&nbsp; |&nbsp;sydney.edu.au&nbsp;CRICOS 00026AThis email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments.&nbsp;Please think of our environment and only print this email if necessary.&nbsp;From:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu&nbsp;&lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt;&nbsp;On Behalf Of&nbsp;fsbuildSent:&nbsp;Saturday, November 25, 2023 6:43 AMTo:&nbsp;freesurfer@nmr.mgh.harvard.eduSubject:&nbsp;Re: [Freesurfer] Longitudinal LME matlab error - Matrix singular or badly scaled&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello Sophie,Just FYI, there is no matlab distribution included in the 7.4.1 release and we so not support using R2023b.&nbsp; So I presume someone at your site installed R2023b separately via a Mathworks matlab installer.&nbsp; We do provide a script, fs_install_mcr, to install either the R2014b or R2019b matlab runtime environment into the freesurfer tree for use.&nbsp; I don't know if running R2019b would affect what you report below, but you could try it via the commands below.- R.$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &lt;--- linux install path$ source $FREESURFER_HOME/SetUpFreeSurfer.sh&lt;... output showing SUBJECTS_DIR and other environment variables&gt;$ cd &nbsp;$FREESURFER_HOME/bin$ sudo FREESURFER_HOME=$FREESURFER_HOME &nbsp;./fs_install_mcr &nbsp;R2019bI believe this sets things up so the libmwm* libraries are installed under $FREESURFER_HOME/MCRv97/bin/glnxa64.&nbsp; You can try adding that path (or any path the script output recommends) to the start of LD_LIBRARY_PATH.&nbsp; You should remove any other entries to a different MATLAB distribution.On 11/23/23 20:42, Sophie Matis (sophie.matis@sydney.edu.au) wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Hello FreeSurfer experts!&nbsp;I have carried out some analysis of changes in cortical thickness over time using the LME Matlab (R23b) Toolbox distributed within Freesurfer (7.4.1) in line with the instructions on this page: &nbsp;MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels%C2%A0At this stage I just want to look at changes over time within each of three groups. For two groups I have been able to proceed through the steps fine and have my significance files which look normal. For the last group I am running into an error on the “[lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3); “ step. MATLAB returns “Warning: Matrix is singular, close to singular or badly scaled” and lhTh0 and lhRe are created as matrices with only NaN values.&nbsp;&nbsp;Has anyone run into this error before or have any tips for troubleshooting it?&nbsp;I haven’t had any errors on the longitudinal processing steps and visual QC on my files looks normal. No errors on mris_preproc or mri_surf2surf. &nbsp;An aparcstats2table for thickness doesn’t reveal any NaNs.&nbsp;&nbsp;My design matrix is created with X = [ones(length(M),1) M] after following the suggested sortData code from the wikiContrast is [0 1]This is my qdec file:&nbsp;fsid&nbsp;&nbsp;&nbsp; fsid-base&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; yearsfromBL108_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 108&nbsp;&nbsp; 0.00199_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 199&nbsp;&nbsp; 0.00199_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 199&nbsp;&nbsp; 1.10199_MR3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 199&nbsp;&nbsp; 2.25202_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 202&nbsp;&nbsp; 0.00204_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 204&nbsp;&nbsp; 0.00204_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 204&nbsp;&nbsp; 1.16204_MR3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 204&nbsp;&nbsp; 2.30223_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 223&nbsp;&nbsp; 0.000821_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0821&nbsp; 0.000931_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0931&nbsp; 0.001010_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1010&nbsp; 0.001010_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1010&nbsp; 1.841031_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1031&nbsp; 0..001031_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1031&nbsp; 1.001031_MR3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1031&nbsp; 2.131064_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1064&nbsp; 0.001064_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1064&nbsp; 2.011125_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1125&nbsp; 0.001134_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1134&nbsp; 0.001134_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1134&nbsp; 1.171134_MR3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1134&nbsp; 2.281233_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1233&nbsp; 0.001233_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1233&nbsp; 1.051373_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1373&nbsp; 0.001439_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1439&nbsp; 0.001439_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1439&nbsp; 1.141439_MR3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1439&nbsp; 2.281475_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1475&nbsp; 0.001475_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1475&nbsp; 1.041475_MR3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1475&nbsp; 2.031522_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1522&nbsp; 0.001522_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1522&nbsp; 2.071541_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1541&nbsp; 0.001541_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1541&nbsp; 1.471551_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1551&nbsp; 0.001551_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1551&nbsp; 0.981551_MR3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1551&nbsp; 2.051572_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1572&nbsp; 0..001572_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1572&nbsp; 1.031625_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1625&nbsp; 0.001625_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1625&nbsp; 1.061637_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1637&nbsp; 0.001641_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1641&nbsp; 0.001656_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1656&nbsp; 0.001656_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1656&nbsp; 0.941656_MR3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1656&nbsp; 2.261755_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1755&nbsp; 0.001755_MR2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1755&nbsp; 1.041755_MR3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1755&nbsp; 2.011829_MR1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1829&nbsp; 0.0009154_MR1&nbsp;&nbsp;&nbsp;&nbsp; 09154 0.0009154_MR2&nbsp;&nbsp;&nbsp;&nbsp; 09154 1.0109154_MR3&nbsp;&nbsp;&nbsp;&nbsp; 09154 2.0112110_MR1&nbsp;&nbsp;&nbsp;&nbsp; 12110 0.0012110_MR2&nbsp;&nbsp;&nbsp;&nbsp; 12110 1.04&nbsp;&nbsp;Any help appreciated!&nbsp;Thank you,&nbsp;Sophie Matis&nbsp;| Data Management &amp; Research OfficerSchool of Health Sciences &amp; Brain and Mind Centre&nbsp;Faculty of Medicine and Health&nbsp;&nbsp;The University of Sydney&nbsp;&nbsp;Brain and Mind Centre, 94-100 Mallett Street, Camperdown (M02G)&nbsp;| The University of Sydney | NSW | 06&nbsp;sophie.matis@sydney.edu.au&nbsp; |&nbsp;sydney.edu.au&nbsp;CRICOS 00026AThis email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments.&nbsp;Please think of our environment and only print this email if necessary.&nbsp;_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1p2Xe7gNwGMHP6pOnr2RizRPipeaYfciNCVH_GRWyTs7KkI... note that this e-mail is not secure (encrypted).&nbsp; If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.&nbsp; Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. &nbsp;_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Longitudinal LME matlab error - Matrix singular or badly scaled