Re: [caret-users] Distorted COMPMEDWALL
There were two problems in the previous email, one of which appears not to be sorted: * hole in what looked like the medial wall, but which caret thought was ventral view * surface does not appear to be in LPI orientation Until the surface is in the right orientation, this isn't going to work. The medial wall won't be where caret expects it to be. On Feb 18, 2014, at 8:26 PM, Ahmad Khan 110ahmadk...@gmail.com wrote: Hi Donna, Thanks for the help. That problem has been sorted out, but now the COMPMEDWALL orientation is like the figure given below (front view and back view) . Please help! With Best Regards Ahmad image.pngimage.png Ahmad Raza Khan (Postdoctoral fellow) Advanced Imaging Research Center (AIRC),Division of Neuroscience Oregon National Primate Research Center (ONPRC) Oregon Health and Science University (OSHU),Portland Oregon- 97006 Ph no.503-614-3755 Mob No.-503-799-7204 On Thu, Feb 13, 2014 at 9:02 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Hi Ahmad, Even if your anatomical volume is in LPI orientation, I don't think your surface is. Does the segmentation volume used to generate that surface align properly with the anatomical volume (T1/T2)? The attached capture shows what I see when I set your fiducial surface to medial view (ferret_medial.jpg). It doesn't look medial to me. But the source of your compressed medial wall woes is the hole shown in the ventral view (ventral_hole.jpg). I'm not sure this really is ventral; I suspect it might be the real medial view, but it is closer to what you see when you press the V button on the toolbar. The fact that the subcortical stuff isn't filled in the segmentation used to generate the surface means your surface is more topologically equivalent to a sheet than a sphere, and Caret needs the latter to do its CMW/registration thing. So can you fill the subcortical stuff and regenerate the surface, so it's more sphere-like? Donna ferret_medial.jpg ventral_hole.jpg On Feb 12, 2014, at 4:54 PM, Ahmad Khan 110ahmadk...@gmail.com wrote: Hi Donna, I have uploaded the file as zip file name Data_Ferret. Thanks for your timely help. With Regards Ahmad Ahmad Raza Khan (Postdoctoral fellow) Advanced Imaging Research Center (AIRC),Division of Neuroscience Oregon National Primate Research Center (ONPRC) Oregon Health and Science University (OSHU),Portland Oregon- 97006 Ph no.503-614-3755 Mob No.-503-799-7204 On Wed, Feb 12, 2014 at 6:41 AM, Donna Dierker do...@brainvis.wustl.edu wrote: Can you trim your working directory down to a gigabyte zipped and upload it here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi The only other thing that comes to mind is that maybe your mesh density is so high that inflation isn't taking out enough folds for the projection to sphere / compressed medial wall thing to happen properly. Looking at the data seems like the most efficient way to troubleshoot. On Feb 11, 2014, at 6:19 PM, Ahmad Khan 110ahmadk...@gmail.com wrote: Hi, I am still getting the same problem and the orientation is x axis: increases left to right y axis: increases posterior to anterior z axis: increases inferior to superior. Surface don't have any topological defects or other defects. Please help! image.png Ahmad Raza Khan (Postdoctoral fellow) Advanced Imaging Research Center (AIRC),Division of Neuroscience Oregon National Primate Research Center (ONPRC) Oregon Health and Science University (OSHU),Portland Oregon- 97006 Ph no.503-614-3755 Mob No.-503-799-7204 On Thu, Jan 16, 2014 at 5:42 PM, Donna Dierker donna.dier...@sbcglobal.net wrote: When I see something like that, I wonder if your fiducial surface was in the right orientation: x axis: increases left to right y axis: increases posterior to anterior z axis: increases inferior to superior On Jan 16, 2014, at 6:45 PM, Ahmad Khan kh...@ohsu.edu wrote: Hi, I am wondering that despite of having good fiducial surface , when I try to make inflated and ellipsoidal surface from fiducial. I get this type of COMPMEDWAL surface. Please help me in this regard. Thanks Ahmad image003.png ___ 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] Distorted COMPMEDWALL
Can you trim your working directory down to a gigabyte zipped and upload it here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi The only other thing that comes to mind is that maybe your mesh density is so high that inflation isn't taking out enough folds for the projection to sphere / compressed medial wall thing to happen properly. Looking at the data seems like the most efficient way to troubleshoot. On Feb 11, 2014, at 6:19 PM, Ahmad Khan 110ahmadk...@gmail.com wrote: Hi, I am still getting the same problem and the orientation is x axis: increases left to right y axis: increases posterior to anterior z axis: increases inferior to superior. Surface don't have any topological defects or other defects. Please help! image.png Ahmad Raza Khan (Postdoctoral fellow) Advanced Imaging Research Center (AIRC),Division of Neuroscience Oregon National Primate Research Center (ONPRC) Oregon Health and Science University (OSHU),Portland Oregon- 97006 Ph no.503-614-3755 Mob No.-503-799-7204 On Thu, Jan 16, 2014 at 5:42 PM, Donna Dierker donna.dier...@sbcglobal.net wrote: When I see something like that, I wonder if your fiducial surface was in the right orientation: x axis: increases left to right y axis: increases posterior to anterior z axis: increases inferior to superior On Jan 16, 2014, at 6:45 PM, Ahmad Khan kh...@ohsu.edu wrote: Hi, I am wondering that despite of having good fiducial surface , when I try to make inflated and ellipsoidal surface from fiducial. I get this type of COMPMEDWAL surface. Please help me in this regard. Thanks Ahmad image003.png ___ 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] Distorted COMPMEDWALL
Hi Donna, I have uploaded the file as zip file name Data_Ferret. Thanks for your timely help. With Regards Ahmad Ahmad Raza Khan (Postdoctoral fellow) Advanced Imaging Research Center (AIRC),Division of Neuroscience Oregon National Primate Research Center (ONPRC) Oregon Health and Science University (OSHU),Portland Oregon- 97006 Ph no.503-614-3755 Mob No.-503-799-7204 On Wed, Feb 12, 2014 at 6:41 AM, Donna Dierker do...@brainvis.wustl.eduwrote: Can you trim your working directory down to a gigabyte zipped and upload it here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi The only other thing that comes to mind is that maybe your mesh density is so high that inflation isn't taking out enough folds for the projection to sphere / compressed medial wall thing to happen properly. Looking at the data seems like the most efficient way to troubleshoot. On Feb 11, 2014, at 6:19 PM, Ahmad Khan 110ahmadk...@gmail.com wrote: Hi, I am still getting the same problem and the orientation is x axis: increases left to right y axis: increases posterior to anterior z axis: increases inferior to superior. Surface don't have any topological defects or other defects. Please help! image.png Ahmad Raza Khan (Postdoctoral fellow) Advanced Imaging Research Center (AIRC),Division of Neuroscience Oregon National Primate Research Center (ONPRC) Oregon Health and Science University (OSHU),Portland Oregon- 97006 Ph no.503-614-3755 Mob No.-503-799-7204 On Thu, Jan 16, 2014 at 5:42 PM, Donna Dierker donna.dier...@sbcglobal.net wrote: When I see something like that, I wonder if your fiducial surface was in the right orientation: x axis: increases left to right y axis: increases posterior to anterior z axis: increases inferior to superior On Jan 16, 2014, at 6:45 PM, Ahmad Khan kh...@ohsu.edu wrote: Hi, I am wondering that despite of having good fiducial surface , when I try to make inflated and ellipsoidal surface from fiducial. I get this type of COMPMEDWAL surface. Please help me in this regard. Thanks Ahmad image003.png ___ 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
