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Hi Jessica,
the parfor_progress.m script, which is throwing the error, will create a text file in Matlab's current working directory. That file simply displays the progress of the parallelized computations.
It seems that your current working directory in Matlab is /Applications/freesurfer/matlab/lme/mass_univariate, and the error seems to arise because you do not have writing permisson for that directory.
As a solution, you could try changing to another directory within Matlab (for which you have write permissions), and run the analysis from there. Please do not forget to add the lme directory and its subfolders to the Matlab PATH before.
Best regards,
Kersten
On Fr, 2019-05-31 at 05:42 +0000, Hua, Jessica wrote:
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Dear FreeSurfer Experts,
Just reposting this since I did not see it on the forum. I am trying to run longitudinal gyrification analyses following the FreeSurfer Linear Mixed Effects Models instructions, and I ran into a problem using lme_mass_fit_vw. I have 49 participants, and each participant has 2 timepoints.
My model is: Yij = ß1 + ß2*tij +ß3*adjBACi + ß4*adjBACi *tij + ß5*sexi + ß6*ICVi + b1i + b2i*tij + eij
lhcortex 1x149955 uint32
lhsphere 1x1 struct
M 98x4 double
mri 1x1 struct
ni 49x1 double
Qdec 99x4 cell
sID 98x1 cell
X 98x6 double
Y 98x163842 double
X Column 1 = column of 1s
X Column 2 = column of alternating 0s and 1s (corresponding to either time 1 or time 2)
X Column 3 = adjBAC
X Column 4 = adjBAC * column 2
X Column 5 = participant's sex
X Column 6 = participant's ICV
After following the steps in the FreeSurfer instructions, I ran this code:
lhstats = lme_mass_fit_vw(X,[1],Y,ni,lhcortex);
And I got the following errors:
Error using parfor_progress (line 17) Do you have write permissions for /Applications/freesurfer/matlab/lme/mass_univariate?
Error in lme_mass_fit (line 155) fn = parfor_progress('init',nv);
Error in lme_mass_fit_vw (line 73) [stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);
Do you know what I am doing wrong? I am using Matlab R2018b (with parallel computing) and FreeSurfer v.6.0. Please let me know if you need me to provide you with any additional information.
Thank you!
Jessica Hua
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