Dear Christian and Guillaume,
thanks for the quick reply and thanks for digging into the issue.
Is it be possible to include an option for single precision in the expert options? This could allow me to split the job into separate processes without running out of memory.
Best,
Falk
-----Ursprüngliche Nachricht-----
Von: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] Im Auftrag von Christian Gaser
Gesendet: Mittwoch, 31. Januar 2018 09:59
An: [log in to unmask]
Betreff: Re: [SPM] CAT12: Segmentation fault while processing high resolution dataset
Dear Guillaume,
it's exactly as you suspect and the crash occurs during calling spm_conv_vol. The data are challenging:
vol 642x882x882 3995417664 double
Changing the data to single was successful, so I try to optimize that part of the code to be not that memory demanding.
Best,
Christian
On Tue, 30 Jan 2018 17:39:54 +0000, Guillaume Flandin <[log in to unmask]> wrote:
>Dear Falk,
>
>Let's wait for Christian's feedback if this issue is CAT12 specific but
>I'm curious because the segmentation fault takes place in spm_conv_vol.
>From what you are saying, it seems that there is a minimal voxel size
>under which the crash occurs so it could relate to file size or numeric
>overflow. Would you be able to stop CAT12 just before the call to
>spm_conv_vol during "SPM preprocessing 2 (write)" and report what the
>sizes of the input variables are?
>
>Best regards,
>Guillaume.
>
>
>On 29/01/18 13:38, Falk L sebrink wrote:
>> Dear all,
>>
>>
>>
>> I m trying to process a high resolution dataset with 0.25 mm
>> isotropic resolution using CAT12 (r1258) and SPM12 (v7219). It used
>> to work with older versions, however, now it crashes during the SPM
>> preprocessing 2 (write). See attached log file. Downsampling the
>> dataset to a resolution worse or equal to 0.4 mm works fine, i.e. 0.33 mm does not work either.
>> Bias field correction and such of SPM12 work without issues even at
>> full resolution. So I suppose it is unrelated to SPM12.
>>
>>
>>
>> RAM and disk space is available plentiful (128 GB and a few TB
>> respectively). Changing parameters (i.e. bias field correction
>> strength, sampling distance, etc.) did not seem to help either.
>>
>>
>>
>> Any help is appreciated!
>>
>>
>>
>> Best,
>>
>> Falk
>>
>
>--
>Guillaume Flandin, PhD
>Wellcome Trust Centre for Neuroimaging
>University College London
>12 Queen Square
>London WC1N 3BG
|