External Email - Use Caution Hi Freesurfer, I am also experiencing the same problem and everything regarding FREESURFER path looks ok just getting error that says: Reading source surface /storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white MRISread(): could not open file No such file or directory mri_surfcluster: could not read surface /storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white No such file or directory I wonder if you found the reason and solution?
Best regards, Amirhossein Manzouri On Thu, Dec 6, 2018 at 6:57 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > > > On 11/27/2018 06:46 AM, C.P.E. Rollins wrote: > > External Email - Use Caution > > Hi Douglas, > > > > Thanks a lot for your answers. > > > > 1) For the permutations, would you recommend using this for > > controlling for MC in cortical thickness analyses too? > Yes > > Why is it recommended to use permutation simulation as opposed to Z > > Monte Carlo simulation for an LGI analysis? > Because the spatial correlations are very high (which makes MCZ less > accurate) > > > > 2) I've attached here the output from ls -Rl > > $FREESURFER_HOME/subjects/fsaverage. > It looks like there is a difference in where you think FREESURFER_HOME > is. Below, you say it is in /home/cper2/BeneMin/Freesurfer, but the > attached file says it is in /applications/freesurfer/freesurfer_6.0.0. > Which one is it? > > > > > > Thanks again, > > Colleen > > > > On 2018-11-23 16:26, C.P.E. Rollins wrote: > >> Dear Freesurfer Developers, > >> I have a 2-part question: > >> 1) I was advised to use permutation to control for multiple > >> comparisons in an LGI analysis, would you mind elaborating how to do > >> this in command line (in terms of command and parameters)? > >> 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache > >> 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error > >> (attached). I was wondering if you might have any advice? The file > >> /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can > >> view it in freeview. > >> > >> Many thanks, > >> Colleen > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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