Dear Douglas, thank you for the file and response. This new cluster-sess file works OK.
Antonin _____ From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] To: Antonin Skoch [mailto:a...@medicon.cz], Freesurfer@nmr.mgh.harvard.edu [mailto:Freesurfer@nmr.mgh.harvard.edu] Sent: Tue, 03 Mar 2015 16:56:17 +0100 Subject: Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space) Hi Antonin, please remember to send responses to the list. Thanks! I've put a new version of cluster-sess in that same location. Let me know if that works. for the mri_mcsim command, make sure to pass it a fwhm that is an integer. Also, I would probably just run it with --fwhm-max so that it does all the fwhms below the max. There is virtually no time penalty for this and it may be useful in other cases where the fwhm is not exactly the same. doug On 03/03/2015 08:42 AM, Antonin Skoch wrote: > Dear Douglas, > > thank you very much for the file. It seems, that the -cache-dir > parameter is not parsed properly in this script. > By -cache-dir you fill-in the CacheDir variable, but it is never used > and at line 182 you use for csd directory construction variable SimDir > which hard-coded points to $SUBJECTS_DIR/fsaverage/mult-comp-cor. > > But when I corrected for this, it works in principle. > > Could you please check that I understand the usage correctly? > I simulated my own distribution in subject's native space by using > mri_mcsim, for example for right hemisphere by this command > mri_mcsim --o subject_name/rh/cortex --base mc-z --surf subject_name > rh --nreps 10000 --fwhm my_fwhm(from fwhm.dat in analysis directory) > and then run cluster-sess -analysis analysis_name -thresh 2 -a2009s > -2spaces -cache-dir dir_of_my_simulation -s session_ID > > Regards, > > Antonin > > ------------------------------------------------------------------------ > *From:* Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > *To:* Antonin Skoch [mailto:a...@medicon.cz] > *Sent:* Mon, 02 Mar 2015 21:07:36 +0100 > *Subject:* Re: [Freesurfer] multiple comparisons correction for > individual hemispheres (native space) > > Sorry, try it now > > On 03/02/2015 02:42 PM, Antonin Skoch wrote: > > Dear Douglas, > > > > I am also interested in multiple comparisons correction in > first-level > > analysis for individual hemispheres in fsFast. Unfortunately, > your file > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cluster-sess > > > > which you provided for Christopher in November 2014 is not > available > > at that location. Could you please provide this file permanently > for > > other users? > > > > Regards, > > > > Antonin Skoch > > Institute for Clinical and Experimental Medicine > > Czech Republic > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > 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. > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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