Hello FreeSurfer experts!

 

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:  MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels

 

At 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.

 

Has anyone run into this error before or have any tips for troubleshooting it?

 

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.  An aparcstats2table for thickness doesn’t reveal any NaNs.

 

My design matrix is created with X = [ones(length(M),1) M] after following the suggested sortData code from the wiki

Contrast is [0 1]

This is my qdec file:

 

fsid    fsid-base       yearsfromBL

108_MR1       108   0.00

199_MR1       199   0.00

199_MR2       199   1.10

199_MR3       199   2.25

202_MR1       202   0.00

204_MR1       204   0.00

204_MR2       204   1.16

204_MR3       204   2.30

223_MR1       223   0.00

0821_MR1      0821  0.00

0931_MR1      0931  0.00

1010_MR1      1010  0.00

1010_MR2      1010  1.84

1031_MR1      1031  0.00

1031_MR2      1031  1.00

1031_MR3      1031  2.13

1064_MR1      1064  0.00

1064_MR2      1064  2.01

1125_MR1      1125  0.00

1134_MR1      1134  0.00

1134_MR2      1134  1.17

1134_MR3      1134  2.28

1233_MR1      1233  0.00

1233_MR2      1233  1.05

1373_MR1      1373  0.00

1439_MR1      1439  0.00

1439_MR2      1439  1.14

1439_MR3      1439  2.28

1475_MR1      1475  0.00

1475_MR2      1475  1.04

1475_MR3      1475  2.03

1522_MR1      1522  0.00

1522_MR2      1522  2.07

1541_MR1      1541  0.00

1541_MR2      1541  1.47

1551_MR1      1551  0.00

1551_MR2      1551  0.98

1551_MR3      1551  2.05

1572_MR1      1572  0.00

1572_MR2      1572  1.03

1625_MR1      1625  0.00

1625_MR2      1625  1.06

1637_MR1      1637  0.00

1641_MR1      1641  0.00

1656_MR1      1656  0.00

1656_MR2      1656  0.94

1656_MR3      1656  2.26

1755_MR1      1755  0.00

1755_MR2      1755  1.04

1755_MR3      1755  2.01

1829_MR1      1829  0.00

09154_MR1     09154 0.00

09154_MR2     09154 1.01

09154_MR3     09154 2.01

12110_MR1     12110 0.00

12110_MR2     12110 1.04

 

 

Any help appreciated!

 

Thank you,

 

Sophie Matis | Data Management & Research Officer

School of Health Sciences & Brain and Mind Centre 

Faculty of Medicine and Health 
 
The University of Sydney  
Brain and Mind Centre, 94-100 Mallett Street, Camperdown (M02G) | The University of Sydney | NSW | 06 
sophie.matis@sydney.edu.au  | sydney.edu.au

 

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