Hi Antonin, I see. The problem with the intersection would be that it could be zero in spite of several edits that move around. Still would be better than nothing. Feel free to test that (e.g. you can load that in matlab, intersect and then apply to the wm from base to see if it helps). Let me know.
About 6.0 usually edits should carry through. Test it in one or two cases to make sure it works. Also you could keep 5.3 cross and (consistently for all individuals) run 6.0 for base and long. Should also work. Best, Martin > On 24 Jan 2017, at 23:40, Antonin Skoch <a...@ikem.cz> wrote: > > Dear Martin, > > thanks for the feedback. We had to edit cross due to the fact that > > 1. our dataset is involved also in cross-sectional studies > 2. we are continuously acquiring timepoints but want to do some analyses with > data we already have > > Therefore only editing the base was not an option for us. > > I was thinking (to save time spent on edits) of transferring the INTERSECTION > of wm edits from all cross points to base. > I think this should work, the only issue I see here is how to handle > resampling from space of cross to the space of base. What do you think? > > And, regarding the v6.0 is currently released, would you recommend to > re-process our cross-sectional data (originally processed with v5.3) with > v6.0? > Would you expect any issues with cross-sectional edits made on v 5.3? Most of > the edits are on the wm.mgz, some on brainmask.mgz or > brain.finalsurfs.manedit.mgz. > > Regards, > > Antonin > > > > > > Hi Antonin, > > in most cases it should be sufficient to only edit wm.mgz in the base, > instead > of editing all time points. This is a big time saving especially if you have > many time points. > I don’t think merging edits from cross will work well, as there could be > atrophy and lots of non-linear deformations in some of the fast progressing > brains. > > Best, Martin > > > On 23 Jan 2017, at 23:11, Antonin Skoch <a...@ikem.cz> wrote: > > > > Dear experts, > > > > I am currently starting longitudinal analysis of data I previously > > corrected > > in cross-sectional stream (FreeSurfer v5.3). > > The analysis comprises quite large number of subjects - approx 150 > > subjects, > > each scanned twice. > > All subjects are already inspected and errors corrected in cross-sectional > > analysis. Some of them needed quite large edits, mainly to the wm.mgz and > > the > > whole process took large time. > > > > As I read the documentation, the wm.mgz edits in cross are not currently > > transferred to base. However, wm.mgz has to be correct in base in order to > > estimate surfaces correctly. From this it implies to me that I would need > > to > > edit all wm.mgz errors in base again. > > Do you think that it could be possible/reasonable to transfer some wm.mgz > > edits from cross to base, for example to make intersection of edits of all > > cross timepoints and to transfer it to the base? This could significantly > > reduce time spent on edits. Does it make sense? > > > > Regards, > > > > Antonin Skoch > _______________________________________________ > 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 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.
