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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