no, it is a matter of taste. Note that 2 is the threshold. If you are looking at sig maps, then the threshold may be important. The p-value threshold is 10^-fthresh
On 01/11/2016 02:19 PM, Hirsch, Gabriella wrote: > Thanks Doug! This is very good to know. Is there a ratio or relationship > between the fmin and fmax that is optimal, as in, should we keep a 2 to 5 > ratio? > > > Gabriella > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Monday, January 11, 2016 12:55 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] fMRI activation color inversion > > There is another parameter called -fmid. The final mapping is a complicated > combination of all three (fthresh, fmin, fslope). I usally use the -fminmax > option which is easier to explain. -fminmax 2 5 means that the threshold is > set to 2 and that at 5 the color will saturate. > doug > > On 01/11/2016 12:18 PM, Hirsch, Gabriella wrote: >> Hi FreeSurfer experts, >> >> I recently ran a simple fMRI analysis in FSL and now generating images >> of the activation in freesurfer using reg-feat2anat to register the >> functional activation to the freesurfer recon-all files, and >> generating the images using tksurfer: >> >> /tksurfer pilot_3 lh inflated -annot aparc.annot -ov >> run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg >> run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat *-fthresh 4 >> *-fslope 1/ >> >> However I have come across a strange occurrence when I change the >> threshold. Specifically, when I set the -fthresh flag (bolded) as 4 >> (i.e. p=0.0001) or less, the activation colors comes off as they >> should (see 4_blue attached) in terms of how I set up the contrasts. >> But when I set my threshold to 5 or higher (changing nothing else), >> the colors of the activation invert (see 5_red attached). >> >> What does this mean? How can I fix this? >> >> Any ideas would be greatly appreciated! >> >> Thank you! >> Gabriella >> >> >> Mass. Eye and Ear Confidentiality Notice: This e-mail and any files >> transmitted with it are confidential and are intended solely for the >> use of the individual(s) addressed in the message above. This >> communication may contain sensitive or confidential information. If >> you are not an intended recipient, dissemination, forwarding, >> printing, or copying of this e-mail is strictly prohibited. If you >> believe you have received this e-mail in error and the email contains >> patient information, please contact the Mass. Eye and Ear Compliance >> Line at 617-263-1600. If the e-mail was sent to you in error but does >> not contain patient information, please contact the sender and delete >> the e-mail. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > 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/ > > _______________________________________________ > 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. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
