Hi Donna, Thank you very much for the quick reply. I have uploaded a zipped file (caret.zip) using the link you suggested. I don't think the image is rotated away from the AC-PC line. How can I check if there are "bridges", and what would be the cause of it? I appreciate your help! Akiko
Akiko Ikkai PhD Candidate Department of Psychology New York University 6 Washington Place New York NY, 10003 ----- Original Message ----- From: Donna Dierker <[EMAIL PROTECTED]> Date: Thursday, August 24, 2006 12:13 pm Subject: [caret-users] Re: segmentation error > Hi Akiko, > > The likely reason you can't post is that you're not a member of > caret-users. The subscriber list doesn't show a [EMAIL PROTECTED], > which is > the address you're posting from (although there are some hidden > addresses). > I've copied caret-users. A couple of things come to mind: > > 1) Your volume is rotated significantly off AC-PC line. > > 2) There are "bridges" connecting the cerebellum to the ventral > occipital cortex. > > Create a zipped or tar/gzipped archive of your dataset (cropped > anatomical volume header and brik/img; params file; and spec file) > and > upload it here: > > http://pulvinar.wustl.edu/cgi-bin/upload.cgi > > I'll take a look at it when I get a few minutes. > > On 08/24/2006 10:51 AM, Akiko Ikkai wrote: > > Hi, > > I have been subscribing to Caret mailing list, and would like to > post a > > message below. Please let me know what procedures I should follow. > > Thanks! Akiko Ikkai > > > > ----- Original Message ----- > > From: [EMAIL PROTECTED] > > Date: Thursday, August 24, 2006 11:49 am > > Subject: [SPAM] segmentation error > > > > > >> You are not allowed to post to this mailing list, and your > message has > >> been automatically rejected. If you think that your messages are > >> being rejected in error, contact the mailing list owner at > >> [EMAIL PROTECTED] > >> > >> > >> ----------------------------------------------------------------- > ------- > >> > >> Subject: > >> [SPAM] segmentation error > >> From: > >> Akiko Ikkai <[EMAIL PROTECTED]> > >> Date: > >> Thu, 24 Aug 2006 11:49:47 -0400 > >> To: > >> caret-users@brainvis.wustl.edu > >> > >> To: > >> caret-users@brainvis.wustl.edu > >> > >> > >> Hello, > >> > >> I have been using Caret to segment brains and recently > encountered a > >> problem of getting either "Hindbrain segmentation error", or > >> segmentation that is missing most of the structures (esp. > posterior part). > >> > >> We have been using FSL's susan_smooth twice on structual, and also > >> correcting for signal intensity inhomogeneity before loading > into Caret, > >> and these procedures seem to give us good results in > segmentation in the > >> past. However, there is one brain (both hemispheres) that does > not go > >> through. During the segmentation, I usually set the peaks a > little bit > >> to the left, but it gives the same errors. I have also tried > different>> peaks, and low/high thresholds for hind brain > segmentation. > >> > >> Any idea what might be going wrong, and any suggestion for the > better>> segmentation tips? > >> Thanks in advance, Akiko > >> > >> > >> > >> Akiko Ikkai > >> PhD Candidate > >> Department of Psychology > >> New York University > >> 6 Washington Place > >> New York NY, 10003 > >> > > > -- > 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 >
