Hi Bruce, Is -seg the correct flag to input an .mgz file instead of a .gca atlas? After making the recommened changes, the command will not seem to work. My input is as follows:
mri_ca_normalize -seg /Volumes/Wong_Lab/LabMRIData/FreeSurfer/CMH-7549/mri/nu.mgz /Volumes/Wong_Lab/CochlearImplant/UNC_NiFTI/infant-neo-mgz/mri/seg.mgz /Applications/freesurfer/subjects/CMH-7259/mri/transforms/talairach.lta /Volumes/Wong_Lab/norm.mgz Thanks for all the help - Mark On Tue, Jul 2, 2013 at 11:13 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Mark > > for mri_ca_normalize all the optional arguments (prefixed with a dash) > must come before all the mandatory ones. Also, you shouldn't give it the > mri directory - give it an input volume (like nu.mgz). > > cheers > Bruce > > > On Tue, 2 Jul 2013, Mark Plantz wrote: > > Hello, >> I am currently having some difficulties with the mri_ca_normalize >> command. I am attempting to create a normalized volume file using an input >> brain with the following command: >> >> mri_ca_normalize >> /Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/**infant-neo-mgz/mri/ -seg >> /Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/** >> infant-neo-mgz/mri/seg.mgz/ >> /Applications/freesurfer/**subjects/CMH-7259/mri/** >> transforms/talairach.lta >> /Volumes/Wong_Lab/norm.mgz >> >> However, I am getting an error that my seg.mgz file could not be read: >> >> Operation not permitted >> dhcp-165-124-23-240:~ IngvalsonLab$ mri_ca_normalize >> /Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/**infant-neo-mgz/mri/ -seg >> /Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/** >> infant-neo-mgz/mri/seg.mgz/ >> /Applications/freesurfer/**subjects/CMH-7259/mri/** >> transforms/talairach.lta >> /Volumes/Wong_Lab/neo-atlas.**gca >> reading 2 input volumes >> reading atlas from'/Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/** >> infant-neo-mgz/mri/seg.mgz/'.. >> . >> GCAread(/Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/** >> infant-neo-mgz/mri/seg. >> mgz/): could not read file >> Operation not permitted >> mri_ca_normalize: could not open GCA >> /Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/** >> infant-neo-mgz/mri/seg.mgz/. >> >> I don't believe it is a permissions issue. Any ideas? >> >> Thanks, >> >> Mark >> >> >> > > 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. >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
