Luke, It is just mris_make_surfaces that has changed (and a bug was found and fixed in mri_mask, but that bug only affected certain edits, and you would get a blank volume if you encountered that bug) so you can do the following to patch 5.2 to match 5.3:
get mris_make_surfaces (and mri_mask) for your platform from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/ then run: recon-all -s <subjid> \ -white \ -autorecon3 \ -nosphere \ -nosurfreg which should take about an hour. This regenerates the white and pial surfaces, and creates new stats files. Nick > > > Hi Bruce, > > Thanks a lot for the info. Would it mean we have to completely reprocess > the data processed with 5.2? Or at which point of the preprocessing > pipeline we should step in to fix the problems of 5.2...? I just have > finished to process about 200 data sets with 5.2... > > Best wishes, > > Luke > > Am 03.05.2013 um 02:58 schrieb "Bruce Fischl" > <fis...@nmr.mgh.harvard.edu>: > >> Hi All, >> >> We have recently uncovered problems with version 5.2. Based on these >> problems, we are recommending that people stop using 5.2, mainly in >> regards to usage of the surface data. A new version, 5.3, will be >> released within two weeks, and a beta version for each platform will be >> available within a couple days. >> >> There were two main problems that were uncovered. First, a change was > made >> that was only meant to affect the white surface placement in >> high-resolution data sets, but unfortunately is being applied to all >> data >> sets. This causes the white surface to contract a small amount. This > causes >> the surface area to be smaller and cortex to be measured as thicker >> relative to version 5.1. Visually, the surfaces do not necessarily look >> less accurate, but we feel that the systematic differences with previous >> versions are ill-advised without a clear reason for the change. >> >> Second, a change made to the placement of the pial surface in order to >> improve the positioning based on T2/FLAIR that caused it to extend too > far >> in some data sets during the T1-based pial surface deformation. This >> unfortunately became the default behavior, which was not intended. None > of >> the dozens of test data sets we ran displayed this problem. The behavior >> was reported by other users which led us to the bug. >> >> In general, we rigorously test each version. However, our systematic >> comparison of a new version with previous versions which would have > caught >> these problems was conducted prior to these changes. We are now > tightening >> and regimenting our testing procedures to ensure this doesnt happen > again. >> Note that there are no problems with the volumetric segmentation (aseg) >> in version 5.2. >> >> We realize that this will cause a substantial inconvenience for users. >> We >> have isolated and fixed the problems and have run two rounds of alpha >> testing and have one more to go, after which we will release a beta > version >> in a couple of days to anyone that wants it. >> >> sorry for the problems. >> >> Bruce >> _______________________________________________ >> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
