hi - I've been trying to run a set of MP-RAGE images collected on our allegra through the first part of the autorecon process, and I've run into somewhat of a problem with the skull-stripping. In all 8 of the brains that I have tried, there is a substantial amount of scalp left over after stripping (primarily on the dorsal posterior surface of the skull). I have tried the recommendations from the wiki (reducing the wsthresh to 5, and using -wsatlas) to no avail, there is still skull left over. Short of editing out the scalp by hand, are there any other tricks I might try to get the automated stripping to work?
for what it's worth, we have found these Allegra MP-RAGE images to wreak havoc on BSE and BET as well. Any suggestions would be most appreciated!
cheers russ
--- Russell A. Poldrack, Ph.d. Associate Professor UCLA Department of Psychology Franz Hall, Box 951563 Los Angeles, CA 90095-1563
phone: 310-794-1224 fax: 310-206-5895 email: poldrack@ucla.edu web: www.poldracklab.org
Hi Russ,
are you gradient unwarping them?
Bruce
On Mon, 10 Jul 2006, Russell Poldrack wrote:
hi - I've been trying to run a set of MP-RAGE images collected on our allegra through the first part of the autorecon process, and I've run into somewhat of a problem with the skull-stripping. In all 8 of the brains that I have tried, there is a substantial amount of scalp left over after stripping (primarily on the dorsal posterior surface of the skull). I have tried the recommendations from the wiki (reducing the wsthresh to 5, and using -wsatlas) to no avail, there is still skull left over. Short of editing out the scalp by hand, are there any other tricks I might try to get the automated stripping to work?
for what it's worth, we have found these Allegra MP-RAGE images to wreak havoc on BSE and BET as well. Any suggestions would be most appreciated!
cheers russ
Russell A. Poldrack, Ph.d. Associate Professor UCLA Department of Psychology Franz Hall, Box 951563 Los Angeles, CA 90095-1563
phone: 310-794-1224 fax: 310-206-5895 email: poldrack@ucla.edu web: www.poldracklab.org
not yet - we are working on getting the coordinates on this end to do that, so we should hopefully be able to do so fairly soon. cheers rp
On Jul 10, 2006, at 5:01 PM, Bruce Fischl wrote:
Hi Russ,
are you gradient unwarping them?
Bruce
On Mon, 10 Jul 2006, Russell Poldrack wrote:
hi - I've been trying to run a set of MP-RAGE images collected on our allegra through the first part of the autorecon process, and I've run into somewhat of a problem with the skull-stripping. In all 8 of the brains that I have tried, there is a substantial amount of scalp left over after stripping (primarily on the dorsal posterior surface of the skull). I have tried the recommendations from the wiki (reducing the wsthresh to 5, and using -wsatlas) to no avail, there is still skull left over. Short of editing out the scalp by hand, are there any other tricks I might try to get the automated stripping to work?
for what it's worth, we have found these Allegra MP-RAGE images to wreak havoc on BSE and BET as well. Any suggestions would be most appreciated!
cheers russ
Russell A. Poldrack, Ph.d. Associate Professor UCLA Department of Psychology Franz Hall, Box 951563 Los Angeles, CA 90095-1563
phone: 310-794-1224 fax: 310-206-5895 email: poldrack@ucla.edu web: www.poldracklab.org
--- Russell A. Poldrack, Ph.d. Associate Professor UCLA Department of Psychology Franz Hall, Box 951563 Los Angeles, CA 90095-1563
phone: 310-794-1224 fax: 310-206-5895 email: poldrack@ucla.edu web: www.poldracklab.org
you mean the coefficients from Siemens? Actually Jenni has had a lot of recent experience messing around with Allegra data. If you want to put one on the file drop we'll take a look (do they look okay?)
Bruce
On Mon, 10 Jul 2006, Russell Poldrack wrote:
not yet - we are working on getting the coordinates on this end to do that, so we should hopefully be able to do so fairly soon. cheers rp
On Jul 10, 2006, at 5:01 PM, Bruce Fischl wrote:
Hi Russ,
are you gradient unwarping them?
Bruce
On Mon, 10 Jul 2006, Russell Poldrack wrote:
hi - I've been trying to run a set of MP-RAGE images collected on our allegra through the first part of the autorecon process, and I've run into somewhat of a problem with the skull-stripping. In all 8 of the brains that I have tried, there is a substantial amount of scalp left over after stripping (primarily on the dorsal posterior surface of the skull). I have tried the recommendations from the wiki (reducing the wsthresh to 5, and using -wsatlas) to no avail, there is still skull left over. Short of editing out the scalp by hand, are there any other tricks I might try to get the automated stripping to work?
for what it's worth, we have found these Allegra MP-RAGE images to wreak havoc on BSE and BET as well. Any suggestions would be most appreciated!
cheers russ
Russell A. Poldrack, Ph.d. Associate Professor UCLA Department of Psychology Franz Hall, Box 951563 Los Angeles, CA 90095-1563
phone: 310-794-1224 fax: 310-206-5895 email: poldrack@ucla.edu web: www.poldracklab.org
Russell A. Poldrack, Ph.d. Associate Professor UCLA Department of Psychology Franz Hall, Box 951563 Los Angeles, CA 90095-1563
phone: 310-794-1224 fax: 310-206-5895 email: poldrack@ucla.edu web: www.poldracklab.org
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Russell Poldrack