I had got the same error output with v4.50 but not v4.01 for one of my subjects. I guessed that something might be wrong with the skull-strip process. So, I ran this step with different wsthresh values (from 20 to 30, increased by 1), and found that the brainmask looked very similar if the wsthresh value was set as 20-22 (if it was larger than 22, too much non-brain tissue was left in the brainmask). Then, I ran autorecon2. If the wsthresh was 20, no luck; if it was 22, the autorecon2 went through without error.
There were other strange outputs from the skull-strip process for this specific subject (sorry, it is off-topic): when wsthresh=23~30, too much non-brain tissue was left in the brainmask, except for wsthresh=25 (part of the cerebellum was removed). Hope that this information helps. Xiangchuan -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Narly A Golestani Sent: Wednesday, November 18, 2009 8:15 AM To: Bruce Fischl Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] recon-all -all error with version 4.5 Hi Bruce, There is plenty of disk space, and the 'aseg.auto_noCCseg.label_intensities.txt' file *has* successfully been written to the subject's 'mri' directory. best, Narly. On Wed, 18 Nov 2009, Bruce Fischl wrote: > did you run out of disk space? Is the file > aseg.auto_noCCseg.label_intensities.txt writeable in the subject's dir? > On > Wed, 18 Nov 2009, Narly A Golestani wrote: > > > > > > > Dear all, > > > > I am encountering a problem with 'recon-all -all' with one subject using > > freesurfer version 4.5 which I did not encounter when using version 4.4. > > With the older version, the stream ran without error, whereas the > > processing produces the following error with version 4.5: > > > > > > ######################## > > > > ..... > > > > gca peak WM_hypointensities = 0.15609 (88) > > gca peak non_WM_hypointensities = 0.10304 (57) > > gca peak Optic_Chiasm = 0.34849 (76) > > mri_ca_label GCA sequential renormalization: label 28 not consistently > > computed. > > > > not using caudate to estimate GM means > > setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 > > estimating mean gm scale to be 1.00 x + 0.0 > > estimating mean wm scale to be 1.00 x + 0.0 > > estimating mean csf scale to be 0.97 x + 0.0 > > Left_Pallidum too bright - rescaling by 0.998 (from 1.000) to 107.8 (was > > 108.0) > > Right_Pallidum too bright - rescaling by 0.998 (from 1.000) to 107.8 (was > > 108.0) > > saving intensity scales to aseg.auto_noCCseg.label_intensities.txt > > Linux aria 2.6.16.60-0.39.3-smp #1 SMP Mon May 11 11:46:34 UTC 2009 x86_64 > > x86_64 x86_64 GNU/Linux > > > > recon-all exited with ERRORS at Wed Nov 18 04:02:23 CET 2009 > > > > ######################## > > > > I have tried simply rerunning the recon-all -all stream but the error is > > reproduced consistently. This seems strange since there was no such > > error with the very same data using version 4.4. > > > > Is there any way to correct for this problem so that the stream can run > > successfully? > > > > > > Thanks in advance and best wishes, > > Narly. > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > ==================================== Narly Golestani Institute of Cognitive Neuroscience 17 Queen Square London WC1N 3AR United Kingdom Tel: +44 (0)20 7679 7529 ==================================== _______________________________________________ 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
