I realize the files I included were rather limited. I zipped the entire output folder and uploaded it:
-> subj161.bz2 (477.45 MiB) <http://gate.nmr.mgh.harvard.edu/filedrop2/?p=bmuvoddq6g1> Cheers, Eve LoCastro Senior Research Assistant IDEAL, Radiology Department Weill Cornell Medical College 515 E. 71st St S118 Tel: 212-746-1289 Fax: 212-746-4189 http://ideal-cornell.com/ ________________________________________ From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, December 06, 2013 5:02 PM To: Eve M. LoCastro Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation misses sulci in posterior ok, I'll take a look On Fri, 6 Dec 2013, Eve M. LoCastro wrote: > Thank you, Bruce. I have uploaded the 001.mgz here: > > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=8xy0v6sj50o > > And the segmentation (aparc+aseg.mgz). > > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=7ibj59tsn6p > > > If there are any other files of interest, please let me know. > > > Much thanks, > > Eve LoCastro > Senior Research Assistant > IDEAL, Radiology Department > Weill Cornell Medical College > 515 E. 71st St S118 > Tel: 212-746-1289 > Fax: 212-746-4189 > http://ideal-cornell.com/ > > ________________________________________ > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: Friday, December 06, 2013 4:28 PM > To: Eve M. LoCastro > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Segmentation misses sulci in posterior > > Hi Eve > > if you upload the subject we will take a look > Bruce > On Fri, 6 Dec 2013, Eve M. > LoCastro wrote: > >> We have a T1 image that has been problematic to process. This patient has >> thicker skull and extensive hypointensities in the white matter along with >> big vents. >> >> Skullstripping by modifying the watershed parameter either leaves too much >> skull or removes entire chunks of the brain in this Siemens image; >> unfortunately there seems to be no middle ground. >> >> In recon-all FreeSurfer has been unable to discern the gray matter boundary >> in the posterior of the brain and omits folding detail of the sulci. I am >> attaching a screenshot overview of the "best" attempt so far, which finished >> this morning (there is a bit of skull left over on this run; on previous >> runs where the skull is cleanly removed this problem persists). As a >> last-ditch effort I had re-sliced the axis-reformat T1 images as additional >> images (002.mgz, 003.mgz, 004.mgz) (any feedback on the feasibility of this >> approach is welcomed also). >> >> Any suggestions to improve the processing on these cortical problem areas >> are very much appreciated (ventricles are as good as I can hope for today; >> that's matter for a whole other post!). >> >> >> Much thanks, >> >> Eve LoCastro >> Senior Research Assistant >> IDEAL, Radiology Department >> Weill Cornell Medical College >> 515 E. 71st St S118 >> Tel: 212-746-1289 >> Fax: 212-746-4189 >> http://ideal-cornell.com/ >> >> >> > > > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
