Dear Guillaume,
great, that works.
Best,
Christian
On Wed, 31 Jan 2018 12:48:39 +0000, Guillaume Flandin <[log in to unmask]> wrote:
>Dear Christian,
>
>After a bit of detective work, I think I found where the overflow occurs:
>
>spm12/src> svn diff spm_mapping.c -c7250
>Index: spm_mapping.c
>===================================================================
>--- spm_mapping.c (revision 7249)
>+++ spm_mapping.c (revision 7250)
>@@ -474,7 +474,8 @@
>
> static MAPTYPE *get_maps_3dvol(const mxArray *ptr, int *n)
> {
>- int num_dims, jj, t, dtype = 0;
>+ int num_dims, jj, dtype = 0;
>+ long long t;
> const mwSize *dims;
> MAPTYPE *maps;
> unsigned char *dptr;
>
>Let me knows if it solves the issue for you (after recompilation).
>
>Best regards,
>Guillaume.
>
>
>On 31/01/18 08:59, Christian Gaser wrote:
>> 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
>>
>>
>
>--
>Guillaume Flandin, PhD
>Wellcome Trust Centre for Neuroimaging
>University College London
>12 Queen Square
>London WC1N 3BG
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