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Dear Yann, On 8 Nov 2017, at 20:06, Yann Quidé wrote: > Dear Christian, > > Thank you so much for your reply! > > Regarding my question 2.b: this is surprising, as I used the raw T1 > image. > This file also went through the cross-sectional pipeline successfully. This is surprising because the long mode is calling the cross-sectional processing pipeline after realigning the images. Anyway, you can try to change the flag cat.extopts.APP in cat_defaults.m to 0 or 1. Best, Christian > > Do you have any additional thought on that problem? > > Thanks again for your time. > > Yann > >> On 9 Nov 2017, at 3:31 am, Christian Gaser >> <[log in to unmask]> wrote: >> >> Dear Yann, >> >> On 8 Nov 2017, at 9:44, Yann Quidé wrote: >> >>> Dear Christian and other CAT12 users, >>> >>> I am using CAT12 v1204, SPM v6909, Matlab 8.1 (R2013A) on Mac OSX >>> 10.9.5 >>> >>> 1) Cross sectional preprocessing >>> >>> On few subjects, I get this kind of warning: >>> "Internal WMH correction for spatial normalization (WMHCstr=0.50): >>> WARNING: Uncorrected WM lesions (5.16% of the WM)! “ >>> >>> The preprocessing continues normally, and the average quality >>> assessment indicates, for example: 86.49% (B). >>> >>> Is there anything to “fix”? Do I need to include the WMH values >>> to any subsequent analysis? To what extend these WMH are considered >>> fine? I attached a copy of the log for one of my subject (file: >>> catlog_1) >> >> This warning can be ignored. CAT12 contains a very basic detection of >> white matter hyperintensities (WMH), that is intended to internally >> fill these regions to obtain a spatial registration that is less >> affected by these WMHs. Of course there exist more appropriate >> approaches based on the additional use of FLAIR or T2 images, but at >> least the method tries to roughly detect these WMHs for a less biased >> spatial registration. >> >>> >>> 2) Longitudinal preprocessing (2 sessions) >>> >>> 2.a) Related to question 1: >>> Surprisingly, while they did not show up after the cross-sectional >>> preprocessing stream, some WMH warnings appeared for some subjects >>> (different from those from the cross-sectional stream!) during the >>> longitudinal preprocessing. >>> Is there anything I can do to potentially solve that? >> No. >> >>> >>> 2.b) Unrelated to question 1: >>> For 1 subject during the longitudinal stream, the preprocessing is >>> working well for the average and Session 1 scan, but crashes for the >>> Session 2 scan. These scans were normally processed during the >>> cross-sectional pipeline. >> >> It looks like you are using skull-tripped images which is never a >> good idea and sometimes causes these problems. In this case I would >> strongly recommend to use the original images with skull. >> >> Best, >> >> Christian >> >>> Do you have any suggestion on this error? I attached a copy of the >>> log (file: catlog_2). >>> >>> Thanks for your time. >>> >>> Cheers, >>> >>> Yann