Hi Bruce, Thanks again for your help at the FreeSurfer course. I've corrected the pial surface manually (knowing that this invalidates the morphometry, but that by restoring the medial surface it does let me process functional data). Having done this, do I need to remake spheres and patches, or are these unchanged? For example, when using mri_vol2surf, does freesurfer know what elements to sample by consulting the ?h.orig and ?h.pial, or are there downstream files I should update as well?
Thanks! stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620 On Mon, Apr 21, 2014 at 11:28 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > Hi Stephen > > no, sorry. There are others on the list that have extensive experience in > using FS for NHP. Hopefully one of them can answer? > > Bruce > > On Mon, 21 Apr 2014, S.V.Shepherd [work] wrote: > > 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. >> >> >> >> >> > _______________________________________________ > 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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