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 ====================================

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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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