Hi Doug, I think that you are right, the bhdr regressors did not make it into the design matrix. Your Matlab code works. Thanks for that. On a related note, in the wiki, it says that there should be only one file for external nuisance regressors (https://surfer.nmr.mgh.harvard.edu/fswiki/mkanalysis-sess), does that still apply in version 5? If I have motion plus some other nuisance regressors, should I join them into one file, or can I have multiple instances of -nuisreg in mkanalysis-sess? Thanks, Caspar
2013/7/15 Douglas N Greve greve@nmr.mgh.harvard.edu:
Did it actually get included? It looks like it would just skip it if it did not exist rather than throwing an error. It is not set up to use the bhdr, but you can create a text file easily enough, just
mc = fast_vol2mat(MRIread('mcext.bhdr')); fp = fopen('mcext.dat','w'); fprintf(fp,'%g %g %g %g %g %g \n',mc'); fclose(fp)
I think that should work, but you should double check it doug
On 07/13/2013 06:31 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, thanks for the response. Given that I already have the bhdr files, can I still use them? I did not get an error using -mcextreg, but I am not sure whether they were actually included. Caspar
2013/7/13 Douglas Greve greve@nmr.mgh.harvard.edu:
Hi Caspar, just put the regressors into a text file with number of rows equal to the number of time points doug
On 7/13/13 2:57 PM, Caspar M. Schwiedrzik wrote:
Hi! I am doing motion correction outside Freesurfer and would like to use motion nuisance regressors in my GLM, which I run in FSFAST. I am externally creating mcextreg.bhdr, mcextreg_000.blfoat and mcextreg_000.hdr for analyses in Freesurfer v4.5, but I was wondering whether I can use the same files for analysis in Freesurfer v5.x. Or should I convert them to something else? The documentation is slightly ambiguous about this. Thanks! Caspar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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