Hi Tim, Thank a lot for your fast response! Ok, clear. Ok, so I decrease the FOV before loading it in Caret. About the NaNs, I noticed that and replaced them with zeros now.
MRI is new for me so most likely I will post some more trivial issues. Kind regards, Rikkert P.S. Please delete the scan; it came from collaborator's lab. On Thu, Jun 19, 2014 at 11:45 PM, Timothy Coalson <[email protected]> wrote: > It is doing that because the FOV is so large compared to the brain - the > total number of positive voxels is only 2.1% of the total number of voxels. > Thus, the default display of clipping the top and bottom 2% of values > results in a very low "max" for palette scaling. Changing the Draw Type in > Volume Settings in display control to Min to Max shows the variation in the > data, though a bit darker than what 2% to 98% does on more > approriately-sized volumes. > > It should also be noted that ~50% of your voxels are NaN, which are > generally quite unfriendly to computation such as smoothing. > > Tim > > > > On Thu, Jun 19, 2014 at 2:41 PM, HINDRIKS, RIKKERT < > [email protected]> wrote: > >> Hi Donna, >> >> I'm sorry but I am unable to upload the file... >> >> Kind regards, >> Rikkert >> >> >> >> On Thu, Jun 19, 2014 at 5:27 PM, Donna Dierker <[email protected]> >> wrote: >> >>> Hi Rikkert, >>> >>> Please try again. There was a problem with permissions when I tried >>> just now, but I fixed it. >>> >>> Donnba >>> >>> >>> On Jun 19, 2014, at 1:12 AM, "HINDRIKS, RIKKERT" < >>> [email protected]> wrote: >>> >>> > Hi Donna, >>> > >>> > I tried to upload the file but am not sure if it worked though. >>> > Please let me know... >>> > >>> > Kind regards, >>> > Rikkert >>> > >>> > >>> > On Wed, Jun 18, 2014 at 8:30 PM, Donna Dierker < >>> [email protected]> wrote: >>> > Hi Rickert, >>> > >>> > Assuming you used File: Open Data File: type = Volume Anatomy File, >>> you should see a normal T1w image. >>> > >>> > If you see solid white, then please upload the volume here, so we can >>> try to replicate the problem: >>> > >>> > http://pulvinar.wustl.edu/cgi-bin/upload.cgi >>> > >>> > Donna >>> > >>> > >>> > On Jun 18, 2014, at 12:32 PM, "HINDRIKS, RIKKERT" < >>> [email protected]> wrote: >>> > >>> > > >>> > > Dear all, >>> > > >>> > > When I load a T1-weighted scan into Caret, the image looks like a >>> mask, that is, all white voxels covering the brain. The voxel intensities >>> themselves are, however, nicely distributed and the grey and white matter >>> peaks are clearly visible. Also, the intensities are normalized between 0 >>> and 255. This problem does not occur when I view the scan with MRIcron or >>> SPM. Does anyone know what is going on here? >>> > > >>> > > Thanks alot, >>> > > Rikkert >>> > > _______________________________________________ >>> > > caret-users mailing list >>> > > [email protected] >>> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> > >>> > >>> > _______________________________________________ >>> > caret-users mailing list >>> > [email protected] >>> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> > >>> > _______________________________________________ >>> > caret-users mailing list >>> > [email protected] >>> > http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >>> _______________________________________________ >>> caret-users mailing list >>> [email protected] >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >> >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >
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