Re: [caret-users] Macaque Segmentation
Hi Eric, Based on what you describe, you probably have some non-uniformity in your volume that bias correction may help. I use FSL's fast for this purpose (which uses BET as preprocessing), but there are many other options (e.g., MNI's nu_correct and AFNI's 3dUniformize). You can upload your volume here and I can either confirm or rule out this issue: http://pulvinar.wustl.edu/cgi-bin/upload.cgi Peak tweaking makes a huge difference in segmentation quality. This page might be helpful: http://brainvis.wustl.edu/help/peak_tweaking/ If you're getting good results out of Freesurfer, then you can use the resulting surface in Caret (e.g., for registration, visualization, or other purposes). Except in cases where the quality of the structural MRI is exceptionally poor (e.g., acquisition resolution way to low; non-uniformity beyond hope -- like the surface coil scans I used to see), then bias correction and peak tweaking usually give good results in Caret. On 03/31/2006 11:03 AM, Faden, Eric (NIH/NIMH) [F] wrote: I have tried two different approaches thus far and neither seems to yield reasonable results. I first tried to feed in the full scan in ACPC coords. The image was rotated in brains, converted to AFNI, and then imported to caret. It is correctly oriented and looks ok although the contrast seems a bit off (some of the image seems to white). After cutting the brain into just the left hemi I ran it through the segmentation process which yielded a pretty bad surface that still included about 90% of the eyes and a very large chunk of the skull. I then decided to try it with just a brain image (as I already had a brain mask in brains). Following the same steps as the first attempt with the brain only image also yielded a fairly bad initial surface as well as leaving a large block of the hindbrain. Are there any other tricks people could provide? Is there a trick to picking the gray/white matter peaks? For reference I have run the same image through a modified freesurfer surface generation which works fairly well, but was curious to see if caret could top it. -Eric ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.)
[caret-users] Macaque Segmentation
Hey All, Are there any special steps required outside of the standard tutorial for segmenting a Macaque brain? Or would the normal tutorial work correctly if followed? -Eric Faden
RE: [caret-users] Macaque Segmentation + AC/PC Align
I actually resampled them at .5mm already. The other problem I am having is that the way our monkeys are scanned they need to be rotated to the correct orientation (45 degrees or so). I tried to use the AC/PC align in Volume Attributes Editor. I selected the AC and PC then clicked align. After about 10 minutes I got a white cube where my volume used to be. Any thoughts on what this is? or what is a good way to AC/PC align my volume? -Eric -Original Message- From: Donna Dierker [mailto:[EMAIL PROTECTED] Sent: Wed 3/29/2006 10:58 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Macaque Segmentation The only difference that comes to mind is the voxdims. Resampling your macaque structural to cubic 0.5mm rather than cubic 1.0mm tends to work best (although I've seen 0.75mm work well). You definitely do NOT want to resample to cubic 1.0mm for monkeys. On 03/29/2006 09:53 AM, Faden, Eric (NIH/NIMH) [F] wrote: Hey All, Are there any special steps required outside of the standard tutorial for segmenting a Macaque brain? Or would the normal tutorial work correctly if followed? -Eric Faden ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http://home.att.net/~donna.hanlon for details.) ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users winmail.dat
Re: [caret-users] Macaque Segmentation + AC/PC Align
Eric, The AC/PC align in volume attributes is something I recently added but has received only limited testing (I tried it on two volumes). I believe AFNI (afni.nimh.nih.gov) can AC-PC align a volume so you might try AFNI or another volume type program. Good luck. -- John Harwell [EMAIL PROTECTED] 314-362-3467 Department of Anatomy and Neurobiology Washington University School of Medicine 660 S. Euclid Ave.Box 8108 St. Louis, MO 63110 USA On Mar 29, 2006, at 10:57 AM, Faden, Eric ((NIH/NIMH)) [F] wrote: I actually resampled them at .5mm already. The other problem I am having is that the way our monkeys are scanned they need to be rotated to the correct orientation (45 degrees or so). I tried to use the AC/PC align in Volume Attributes Editor. I selected the AC and PC then clicked align. After about 10 minutes I got a white cube where my volume used to be. Any thoughts on what this is? or what is a good way to AC/PC align my volume? -Eric -Original Message- From: Donna Dierker [mailto:[EMAIL PROTECTED] Sent: Wed 3/29/2006 10:58 AM To: Caret, SureFit, and SuMS software users Subject: Re: [caret-users] Macaque Segmentation The only difference that comes to mind is the voxdims. Resampling your macaque structural to cubic 0.5mm rather than cubic 1.0mm tends to work best (although I've seen 0.75mm work well). You definitely do NOT want to resample to cubic 1.0mm for monkeys. On 03/29/2006 09:53 AM, Faden, Eric (NIH/NIMH) [F] wrote: Hey All, Are there any special steps required outside of the standard tutorial for segmenting a Macaque brain? Or would the normal tutorial work correctly if followed? -Eric Faden ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users -- Donna L. Dierker (Formerly Donna Hanlon; no change in marital status -- see http:// home.att.net/~donna.hanlon for details.) ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users winmail.dat ___ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
