Hi Doug,
Thanks for the help! I think I figured out the issue based on your
response.
1) I created a template to use for this group and named it fsaverage
(including creating monte carlo simulations) for simplicity of integrating
with freesurfer as I am newer to it. This is why the sizes didn't match up
as you expected
but the mri_glmfit still ran.
2) I deleted the folder and restarted without background processes. The
error became apparent. Of my covariates (2 fix factors and 3
quantitative), not all were orthogonal. In looking at the error more, it
seems that i need to add the
--perm-force if I wanted the simulation to run, however the background
processes were not aware of this error and kept polling as you mentioned.
This brings me to a new but related issue. From what I have read in other
freesurfer posts, it is statistically incorrect to use --perm-force for
non-orthogonal covariates (or continuous covariates). I am unsure how to
proceed.
a) If I ran permutation testing (to overcome the issue of incorrect
smoothness estimations from the gaussian distribution assumption), then I
run into the issue of non-orthogonal covariates. Is there a way to
orthogonalize the data in
freesurfer, or a solution to this issue?
b) If orthogonalizing is difficult to implement, another option is running
Qdec with the montecarlo simulation at a more conservative p value (p<
0.001). From your previous posts, the testing at this p value for 10mm
seems to meet the 5% FPR. One question is if the non-orthogonal data
affects this analysis as well for this model?
Thanks,
Ajay
On Thu, Aug 25, 2016 at 12:18 PM, Ajay Kurani <dr.ajay.kur...@gmail.com>
wrote:
> Hi Freesurfer Experts,
> I am trying to use freesurfer's mri_glmfit-sim tool to run permutation
> testing on cortical thickness data (as recommended by Doug in my previous
> post: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.
> edu/msg48653.html )
>
> Most of the tutorials I found were not related to permutation testing so
> the subsequent steps may be incorrect. Please let me know where I go
> wrong...
>
> 1) I first ran QDec to generate a folder for the analysis which would
> create the subsequent fsgd and y files needed my mri_glmfit-sim. I am
> running both left and right hemisphere cortical thickness analysis with
> 10mm smoothing. The following is for just the left hemisphere. Note I am
> doing a 3 group comparison, but for this 2 group ttest I manually centered
> the data based on the 3 group mean for age and education.
>
> 2) I ran the following command:
> /mri_glmfit-sim --glmdir ./HCvsPAT_lh_thickness_10mm/ --sim perm 10000 2
> perm.abs.2 --sim-sign abs --bg 16
>
> Prior to running the command above, from the y.fsdg file I deleted the
> fwhm estimate of 13mm since this was not correctly estimated (ACF with long
> tails). I assumed that by removing this estimate, it would force the
> permutation test to calculate based on the data but when looking at the log
> output I see the following which says fwhm 0:
>
> cmdline mri_glmfit.bin --C ./HCvsPAT_lh_thickness_10mm//
> tmp.mri_glmfit-sim-19468/lh-Avg-Intercept-thickness.mtx --C
> ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-
> Diff-Male-Female-Intercept-thickness.mtx --C ./HCvsPAT_lh_thickness_10mm//
> tmp.mri_glmfit-sim-19468/lh-Diff-PD-MCI-Intercept-thickness.mtx --C
> ./HCvsPAT_lh_thickness_10mm//tmp.mri_glmfit-sim-19468/lh-X-
> Gender-Group-Intercept-thickness.mtx --sim perm 625 2
> ./HCvsPAT_lh_thickness_10mm//csd/perm.abs.2.j013 --y
> /home/akurani/Documents/PPMI/FS_Final/qdec/HCvsPAT_lh_thickness_10mm/y.mgh
> --mask ./HCvsPAT_lh_thickness_10mm//mask.mgh --sim-sign abs --fwhm 0
> --fsgd ./HCvsPAT_lh_thickness_10mm//y.fsgd dods --surf fsaverage lh white
> --sim-done ./HCvsPAT_lh_thickness_10mm//csd/poll/done.perm.abs.2.j013
>
> 3)I started this a few days ago on a 16 core machine and it is still
> running in the terminal. I have 150 subjects in the analysis and specified
> 10000 iterations. In the terminal I assumed when I reach Poll 10000 it
> would be complete but currently I am at : Poll 13341 job 1 Thu Aug 25
> 12:03:51 CDT 2016
>
> Questions:
> a) I am curious, is this going to run 10,000 simulations X 150 patients or
> does the Poll number not have anything to do with the number of iterations
> it is on?
>
>
> b) Did I run this procedure correctly? Was I incorrect in deleting the
> fwhm estimate from y.fsgd file generated by Qdec even though we know the
> estimate is incorrect since smoothness assumed a gaussian distribution as
> opposed to gaussian with heavy tails
>
> c) I noticed in the logfile the following warning:
> INFO: gd2mtx_method is dods
> Computing normalized matrix
> Normalized matrix condition is 5.65727
> Matrix condition is 935.597
> Found 136777 voxels in mask
> Reshaping mriglm->mask...
> search space = 89675.729228
> ERROR: design matrix is not orthogonal, cannot be used with permutation.
> If this something you really want to do, run with --perm-force
> Poll 2 job 1 Tue Aug 23 22:58:18 CDT 2016
>
> I am not sure if this means my simulation is incorrect?
>
> Thanks,
> Ajay
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
