Re: [Freesurfer] Gammafit vs. SPMHRF

The SPM HRF is a difference of gamma functions (one shifted in time wrt the other). I have not studied it a lot, but I have not seen much of a difference. The SPM HRF is a quasi-standard since most people in the world are using SPM, but that does not necessarily make it better:). The longer t

[Freesurfer] Gammafit vs. SPMHRF

Dear FreeSurfers, What exactly is the difference between the HRF function in gammafit vs. SPMHRF? Are there reasons to prefer one to the other? Thanks, Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 496-5222 E-

Re: [Freesurfer] make_average_subject

I think it is another case of out-of-date scripts I've put new versions of these scripts make_average_subject make_average_surface make_average_volume here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ doug Furlong, Carolyn wrote: Hi, I'm still having problems with ma

Re: [Freesurfer] reg -feat2anat error

Did you see my email from last week? It looks like the problem was fixed with new versions of a few programs. doug Furlong, Carolyn wrote: Hi Doug Please find attached the logfile that you requested, sorry for the delay, I am only able to work on this one day a week. Best wishes Carolyn

RE: [Freesurfer] tkmedit

Hi Lars, Typically the optic nerve is not a problem - it's likely included in all our subjects. If you feel you need to edit it you will want to remove it from the brainmask.mgz volume, to affect where your pial surface is. Jenni -Original Message- From: Lars Tjelta Westlye [mailto:[EMA

[Freesurfer] make_average_subject

Hi, I'm still having problems with make_average_subject, when I type the folowing command line in: >make_average_subject --debug --subjects 'subject1' 'subject2'. --out >PLP_average --no-symlink echo ERROR: Flag $flag unrecognized. echo ERROR: Flag --no-symlink unrecognized. ERROR: Flag -

[Freesurfer] reg -feat2anat error

Hi Doug Please find attached the logfile that you requested, sorry for the delay, I am only able to work on this one day a week. Best wishes Carolyn Actually, I wanted the log file found in featdir/reg/freesurfer/reg-feat2anat.log. doug Furlong, Carolyn wrote: > Hi > > > niiRead()

RE: [Freesurfer] tkmedit

Hi, I have a related question. Should the optic nerve included in the pial surface be considered a problem for the surfaces? The nerve also does create a small bump on the inflated surface as viewed in tksurfer. If so, from which volume should the optic nerve be erased? Thanks for your time. La