Hi Colin,
On Oct 24, 2013, at 00:24 , Colin Reveley <cm...@sussex.ac.uk> wrote: > Hi - > > I wonder if anyone has experience in dealing with T1 images where there is > hyperintenisty of blood vessels? This looks like receive & transmit surface coil data to me. For MPRAGEs, in my experience, switching to receive only surface coil (and assuming a whole body scanner) and the body coil for transmit will darken the the blood vessels again. Or you could use 8mb/kg bodyweight feraheme to reduce the blood signal as well. Both methods will obviously not work retrospectively. I have no experience with MDEFT, so the fereheme might not work. (But if you go that route: feraheme is an excellent functional contrast agent in NHPs for EPIs) > > the data involved is MDEFT scans where only a head coil is used. I read it is > a long solved problem for acquisition, but these scans do not correct it and > nor will future scans. > > the difficulty is getting 3 classes (CSF,WM,GM) for nu_correct,mri_normalise > or FSL Fast or whatever. > > It's quite a big obstacle for data that is otherwise quite excellent. > > One would think one could just threshold it out after brain extraction and to > an extent one can but it's very imperfect. segmenting 4 classes doesn't > especially work either (so far) > > if anyone has experience segmenting this stuff (especially getting > mri_normalise to work) I'd be grateful for advice. How does it affect mri_normalize? I typically used: mri_normalize -n 1 -no1d -gentle ${src_dir}/${src_vol} ${targ_dir}/${targ_vol} -v -mprage on NHPs and: mri_normalize -f ${controlpoints} ${mri_normalize_options_string} -MASK ${src_dir}/${mask} ${src_dir}/${in_vol} ${targ_dir}/${unmasked_brain} -mprage for control point based normalization (which does not look required for your nice data) I guess for MDEFT I would skip -mprage. I hope that helps at least some. best Sebastian > > e.g. attached > > Colin Reveley > <CORONAL_BLOOD.png><SAGG_BLOOD.png>_______________________________________________ > 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer