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
