29 Apr
2013
29 Apr
'13
10:38 a.m.
Yes it's my doubt too, but how can I check this?
2013/4/29 Bruce Fischl fischl@nmr.mgh.harvard.edu
then it's not rerunning the -cp. And is it really wm if it's that dark?
On Mon, 29 Apr 2013, Claudia Dacquino wrote:
Bruce,no the intensity is lesser then 110 at those voxels, it's like
60-70.
Claudia
2013/4/29 Bruce Fischl fischl@nmr.mgh.harvard.edu is the intensity at those voxels 110 after you have processed with autorecon2-cp? On Mon, 29 Apr 2013, Claudia Dacquino wrote:
The problem is that after editng manually WM by adding control points, I still have some WM and GM areas not included in either the pial or WM boundaries, but I can see that there are control points added (green cosses), but they seem not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Claudia can you describe the problems? And cc the list so that others can help? thanks Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Bruce,I think wm.mgz it's accurate enough, but what you mean? I'm trying to upload data, but I've problems with your server. Cheers, Claudia 2013/4/29 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Claudia it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the expected gray matter intensities in the xopts file, but that is rarely necessary and only if your gray matter looks very different than the sequences we are used to. If you can't sort it out feel free to upload you data. cheers Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote: Hi Freesurfers,I have a question about pial editing. I have some reconructions in which there's a lot of grey matter excluded, and consequently white metter too. I did correct these images manually by control points editing, and then autorecon2-cp autorecon3, but some cortical grey matter continues to not be included in the pial surface, and I have white matter areas that are still not included in either the pial or white matter boundaries. Is there anyother ethods for adding grey matter in the pial surfeces other than editing control points (such as by editing voxels to add grey matter), or something like that? Thanks for your help. Claudia The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.