Haven't noticed it but maybe we missed something. I'd like to look at your case if I can to try to figure it out. If you'd rather not send the case, I'll try some testing on this end to see if I can replicate it.
On Fri, 13 Jan 2012, Vy Dinh wrote: > Hi Allison, > > Upon a closer look, it appears that there were still some corrections to be > made for the subject whose 5.0 corrections "were preserved," just not as many > edits for this subject as the others. (The difference in the amount of edits > we need to make were significant, however.) > > For one subject, I ran [recon-all -all -s subjid] in 5.1, the edits carried > over in 5.1. But then I took this subject again and ran [recon-all -all > -clean-bm -subjid] with brain.finalsurfs.manedit.mgz in the subj/mri/ > directory and when I checked this subject in tkmedit the next morning, I had > the same issues with the edits not being preserved. Have you observed these > results with running -clean-bm in your lab? > > Best, > > Vy T.U. Dinh > Research Assistant, Neurological Sciences > Rush University Medical Center > Phone: (312) 563-3853 > Fax: (312) 563-4660 > Email: vy_d...@rush.edu > > ________________________________________ > From: Allison Player [astev...@nmr.mgh.harvard.edu] > Sent: Thursday, January 12, 2012 3:18 PM > To: Vy Dinh > Cc: freesurfer@nmr.mgh.harvard.edu; jennifer.g.gold...@gmail.com > Subject: Re: [Freesurfer] Rerunning Freesurfer 5.1 reconall on 5.0 edited > data and recreating cerebellum in brainmask > > Hi Vy, > I'm not sure why that only seems to be working sometimes. Can you send me > a case it did work on and a case it didn't work on? > Allison > > On Thu, 12 Jan 2012, Vy Dinh wrote: > >> Dear Freesurfer experts, >> We are about to do a mass reprocessing in our lab to update our FS 5.0 data >> to the FS 5.1 and would like to do the following all in one run: >> >> 1) Preserve the wm and pial edits made in the 5.0 data in 5.1 >> From our understanding, using the command >> -------------------------------------------- >> recon-all -all -s subjid >> -------------------------------------------- >> will preserve our (wm and pial) edits when rerunning recon-all as long >> as we do not use any -clear command. We've tested this command and it works. >> However, we would also like to (go to #2) >> >> 2) Recreate the cerebellum in brainmask while preserving our edits. >> We recently learned that the cerebellum should not be edited in >> brainmask.mgz as this would affect the volumetric measurements of this >> region. Since we are interested in this measurement, we want to recreate >> brainmask.mgz when rerunning recon-all. I came across a post that suggested >> adding the option -clean-bm and using brain.finalsurfs.manedit.mgz when >> rerunning >> reconall.(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20406.html). >> The documentation on brain.finalsurfs.manedit.mgz suggests that this image >> determines the final surfaces, regardless of what brainmask.mgz looks like, >> which is why we could still use -cleanbm to recreate brainmask AND preserve >> our edits. >> >> However, when we ran the command >> -------------------------------------------- >> recon-all -all -clean-bm -s subjid (with >> brain.finalsurfs.manedit.mgz containing our edits in 5.0) >> -------------------------------------------- >> the edits were only preserved in one subject that we tested. The edits did >> not appear to be preserved at all in the other subjects. Does anyone have >> any explanations for why edits were preserved in this subject but not the >> other test subjects? Since running reconall takes a long time, we will >> really appreciate it if there is a way to carry over the edits we made but >> also recreate brainmask to get the cerebellum in one run. (Alternatively, we >> can add voxels back to the cerebellum, but this method would be more time >> consuming.) If brain.finalsurfs.manedit.mgz is indeed used to determine the >> final surface, would be possible to make all edits in >> brain.finalsurfs.manedit.mgz instead of brainmask.mgz? It seems more >> efficient and intuitive to make edits in one place. >> >> We would like to move forward with our reprocessing and are looking forward >> to your responses. >> >> Best, >> >> Vy T.U. Dinh >> Research Assistant, Neurological Sciences >> Rush University Medical Center >> Phone: (312) 563-3853 >> Fax: (312) 563-4660 >> Email: vy_d...@rush.edu >> >> Vy T.U. Dinh >> Research Assistant, Neurological Sciences >> Rush University Medical Center >> Phone: (312) 563-3853 >> Fax: (312) 563-4660 >> Email: vy_d...@rush.edu >> >> > > > _______________________________________________ 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.
