Re: [caret-users] Issue with displaying voxel intensities
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 do...@brainvis.wustl.edu 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 rikkert.hindr...@upf.edu 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 caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Issue with displaying voxel intensities
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 rikkert.hindr...@upf.edu 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 do...@brainvis.wustl.edu 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 rikkert.hindr...@upf.edu 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 caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Issue with displaying voxel intensities
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 do...@brainvis.wustl.edu 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 rikkert.hindr...@upf.edu 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 do...@brainvis.wustl.edu 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 rikkert.hindr...@upf.edu 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 caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Issue with displaying voxel intensities
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 tsc...@mst.edu 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 rikkert.hindr...@upf.edu 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 do...@brainvis.wustl.edu 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 rikkert.hindr...@upf.edu 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 do...@brainvis.wustl.edu 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 rikkert.hindr...@upf.edu 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 caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] Issue with displaying voxel intensities
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 caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Issue with displaying voxel intensities
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 rikkert.hindr...@upf.edu 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 caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
