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
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