Hi, Did you have a chance to take a look at this? The basics shouldn't be NHP-specific, so I'd still value your input even though I know you work only with humans.
stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620 On Wed, Apr 16, 2014 at 10:48 PM, S.V.Shepherd [work] < stephen.v.sheph...@gmail.com> wrote: > Hi Bruce, > > As requested, I'm transferring over the entire folder. It's saved as > 140107OTIS_from_Shepherd_attn_Fischl.tar.gz > > Our pipeline appears to sidestep aseg (I'm not precisely sure why or how). > I have what I think are a reasonable brainmask.mgz and wm.mgz, which appear > to be the two key files to target for manual edits. But when I proceed to > the next step: > recon-all -autorecon2-wm -subjid 140107OTIS -cc-crs 128 108 168 > -pons-crs 128 255 128 -noaseg > there are divots in the grey matter in the ACC just anterior and dorsal to > the genu and in middle OFC. I'm not sure why. Additionally, the wm edits in > occipital do not appear to be helping. This is easiest to see if I run > > tkmedit 140107OTIS brain.mgz -aux wm.mgz -surfs > select a point just to the side of midline (e.g. 125 103 128) and switch > to a sagittal view. > > Thanks for your help. > > stephen > > > > *stephen v. shepherd phd* > The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA > // 212.327.7620 > > > On Wed, Apr 16, 2014 at 10:05 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu > > wrote: > >> Hi Stephen >> >> can you upload the whole subject dir? Also, why is there no aseg for this >> subject? >> >> Bruce >> On Tue, 8 Apr 2014, S.V.Shepherd [work] wrote: >> >> I believe ventricles and callosum are correctly labeled. I've been >>> viewing with ''' tkmedit 140107OTIS brain.mgz -aux wm.mgz >>> -surfs '''. I've uploaded ( as per the instructions here: >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange ) the file >>> contents of my Otis's mri/ directory, as >>> SVSHEPHERD_subj_OTIS_for_DOUG_on_20140408.tar.gz. >>> I hope this will be enough? >>> >>> Ares of concern are >>> * ACC (e.g. 123 105 208) - maybe misses a thin wm bundle? or won't grow >>> grey from CC? >>> * OFC (e.g. 123 133 218) - may be excluded as Olfactory Bulb, or bc too >>> bright. >>> * Occ (e.g. 115 109 97) - mostly poor scan quality; may require manual >>> overpaint. >>> >>> stephen >>> >>> Hi Stephen >>> >>> Are the ventricles and callosum correctly labeled? If you upload a >>> subject I'll >>> try to take a look >>> Cheers >>> Bruce >>> >>> >>> > On Apr 7, 2014, at 8:38 PM, "S.V.Shepherd [work]" >>> > <stephen.v.sheph...@gmail.com> wrote: >>> > >>> > Greetings, >>> > >>> > I've been reconstructing a surface in an NHP using a Kolster T1 >>> scan and >>> > FS5.3. It went very well, at first, but I've hit a wall. I >>> have trouble in >>> > occipital (due to poor signal strength/constrast) and some >>> typical-with-NHP >>> > problems in ACC and OFC. I think there are three related >>> questions. >>> > >>> > 1) I lose parts of the ACC near the genu of the corpus >>> callosum. I have >>> > attached a screen shot -- the white matter and gray matter both >>> look decent. >>> > I wondered if the corpus callosum might be handled specially, >>> and if >>> > differences between human and nhp callosi might prevent the ACC >>> from growing >>> > normally? >>> > >>> > 2) In trying to deal with this, I greyed out the ACA, which was >>> bright and >>> > potentially confounding. I wasn't sure how to do this in >>> > brain.finalsurfs.manedit, since my understanding is that only 1s >>> (nonbrain) >>> > and 255s (wm) were preserved. I tried brain, which got >>> overwritten, but >>> > ultimately succeeded by editing brainmask and rerunning >>> -autorecon2-wm. Is >>> > there a way to repain gray matter in brain.finalsurfs.manedit? >>> Alternately, >>> > if I continue editing brainmask (or equivalent) directly, should >>> I be >>> > darkening or lightening the gray matter in the excluded section >>> of the ACC? >>> > I would assume lighten -- but in the OFC, some gray matter (not >>> shown) >>> > appears to be excluded for being too bright. >>> > >>> > 3) In some places I've specified wm (e.g. in the ACC, here) but >>> it hasn't >>> > stuck. I assume this is because autorecon isn't convinced by the >>> wm >>> > specification after looking at brain.finalsurfs -- how might I >>> (gently!) >>> > override this? >>> > >>> > Thanks very much for your time and patience. >>> > >>> > stephen >>> > >>> > <Capture1.PNG><Capture2.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. >> >> >
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