ps, here are slides that explain the masking (along with a bunch of other stuff) http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt
On 09/24/2012 04:22 PM, Andrew Bock wrote: > Hi Doug, > > I uploaded two example files, as far as I can tell the raw f.nii and > talairach transform look okay. I obtained these files from the > tutorial data set, so I'm assuming they were processed properly. > > Andrew > > On Mon, Sep 24, 2012 at 1:03 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Actually, before you do that, can you check two things > 1. Does the raw data (eg, f.nii) look ok? > 2. Does the talairach transform for this subject look ok? > doug > > On 09/24/2012 04:02 PM, Douglas N Greve wrote: > > Can you upload it to our file drop at > www.nmr.mgh.harvard.edu/facility/filedrop/ > <http://www.nmr.mgh.harvard.edu/facility/filedrop/> > > > > > > > > On 09/24/2012 02:58 PM, Andrew Bock wrote: > >> It looks like a very patchy, warped version of the brain. I > find that > >> this is true for all subjects > >> > (/fsfast-functional/sess???/bold/001/fmcpr.up.sm5.mni305.2mm.nii.gz). > >> I used both freeview and fslview to visualize the images. > >> > >> On Fri, Sep 21, 2012 at 4:06 PM, Douglas N Greve > >> <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > wrote: > >> > >> yes, you would expect that. what does it look like? how > are you > >> visualizing it? > >> > >> On 09/20/2012 06:18 PM, Andrew Bock wrote: > >> > Hello, > >> > > >> > I am attempting to run preproc-sess on my functional data, > and am > >> > following the tutorial found here: > >> > > >> > http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc > >> > > >> > I downloaded the tutorial data, and find that when I view > >> > fmcpr.up.sm5.mni305.2mm.nii.gz it looks quite ugly (i.e. does > >> not look > >> > like a brain). I would expect this file to look like the > fsaverage > >> > brain, is that not correct? > >> > > >> > Andrew > >> > > >> > > >> > > >> > > >> > > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 > <mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > >> Phone Number: 617-724-2358 > <tel:617-724-2358><tel:617-724-2358 <tel:617-724-2358>> > >> Fax: 617-726-7422 <tel:617-726-7422><tel:617-726-7422 > <tel:617-726-7422>> > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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. > >> > >> > >> > >> > >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
