Hi Martin, Thank you for getting back to me. To clarify what I did:
1. edited all cross-sectionals & reran until surfaces are accurate. 2. created the base from the cross-sectionals. 3. edited base & reran until surfaces are accurate 4. created longitudinal files from edited cross-sectionals & base 5. edited longitudinal data & reran We only edited the brain.finalsurfs.manedit.mgz file (not brainmask.mgz as it was problematic to delete the cerebellum in this file) in each case, except that when I recreated the surfaces for the longitudinal data, it appears that the edits from both cross-sectionals and base did not transfer at all! While the edits in the longitudinal data are minor, we try to be precise with our manual edits. (hence, why we edited all cross-sectionals & base prior to editing the longitudinal data). We edited these edits and reran only to find out that the surfaces look worse in the longitudinal data after rerunning than it did before editing. Based on your response, it appears that we should forego editing the cerebellum in the brain.finalsurfs.manedit.mgz file if we do not want the extra effort of reediting longitudinal surface from scratch because the existence of this file prevents edits from the cross-sectionals and base to be transferred to the longitudinal data? Do you suggest we: Accept the minor issues with the surface boundaries and not edit the longitudinal data at all? (BTW, I checked cross-sectional and base to see if these issues exist in these images. They do not.) or Just rerun recon-all -autorecon2-pial -autorecon3 -long subid_1 subid_template & edit from scratch to get most accurate surfaces? It would help if I understand what the autorecon2 & 3 codes are doing exactly with the images & edits. Also, your tutorials suggest using autorecon2-pial in one instance and autorecon3-pial in another. If possible, could you please elaborate on the differences between the 2 commands? *Regarding your inquiry about editing the brain.finalsurfs.manedit.mgz file: * When we first learned that the brain.finalsurfs.manedit.mgz file was used for editing the cerebellum, I posted the question to your group: If the brain.finalsurfs.manedit.mgz file was used as the final determinant for the surface boundaries, which ultimately determines how FS extracts the segmentation and parcellation data, why not make edits to brain.finalsurfs.manedit.mgz file only? This would've saved us a lot of time because we only had to inspect and edit one file. The response was "there doesn't seem to be any reason for not doing this," so we stuck with editing the brain.finalsurfs.manedit.mgz, which appeared to work fine until now. On Mon, Apr 1, 2013 at 3:39 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu>wrote: > Hi Vy, > > not sure what it going on in your data. Surfaces are copied from the base > and if they are not accurate there you need to fix it there. It seems you > did that and you worked the edits in the right order. > > What exactly happened? You fixed cross and base and everything look fine. > When you run long it looks fine, but when you edit long and run it again it > messes up? > > Did you edit only the brain.finalsurfs or also other things at the same > time? Also, if you edited long, these edits will be kept and not replaced > with new edits from base or cross. So if cross or base get edited it may be > good to rename or remove the edit file in the long and run long without > edits again. This way the cross and base edits get transferred to long > automatically. Only if that is not sufficient you need to do edits in the > long. > > Sorry I cannot say more right now without knowing what you did. > > Best, Martin > > > > On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh <vy_d...@rush.edu> wrote: > >> BTW, we are using Freesurfer 5.1: >> freesurfer-i686-apple-darwin9.8.0-stable5-20110525 >> >> >> On Fri, Mar 29, 2013 at 10:08 AM, Vy Dinh <vy_d...@rush.edu> wrote: >> >>> Dear Developers, >>> >>> I have a significant problem when rerunning the pial edits for the >>> longitudinal data. Our dataset consists of subjects & a followup scan (for >>> each sub). To be thorough, we edited brain.finalsurfs.manedit.mgz (as it >>> was further in the processing stream) for the cross-sectional scans, the >>> base scans, and the longitudinal scans. The longitudinal data were created >>> only after the base has been edited and rerun. Likewise, the base was only >>> created and rerun after the cross-sectionals were finalized. >>> >>> We work with a clinical population so minor edits do show up on the >>> longitudinal scans. However, after editing and recreating the surfaces from >>> these longitudinal scans, the pial surfaces has extended to include dura & >>> other voxels that were not previously included within the pial surface >>> (during the initial creation of the longitudinal data). We tried both >>> commands (listed below) and get this same problem: >>> >>> recon-all -autorecon2-pial -autorecon3 -long tpN tp_base ( >>> http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits) >>> or recon-all -autorecon3-pial -long tpN tp_base ( >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial >>> ) >>> >>> *Could you please help us figure out why the pial surface extends to >>> include nonbrain regions when recreating the surfaces? * >>> * >>> * >>> *What solutions would you suggest in resolving this problem?* >>> * >>> * >>> Thank you, >>> >>> Vy Dinh >>> Research Associate >>> Department of Neurological Sciences >>> Rush University Medical Center >>> >> >> > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Dr. Martin Reuter > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreu...@nmr.mgh.harvard.edu > reu...@mit.edu > Web : http://reuter.mit.edu > > 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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