Hi Xiangchuan, so you found recon-all stopped in the same place (writing aseg.auto_noCCseg.label_intensities.txt)?
Bruce On Wed, 18 Nov 2009, Xiangchuan Chen wrote: > 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
