Dear Baran,
>
> I am having exactly the same problem. Did you figure out a solution Jerod?
>
> Here is the last part of the output when --very_verbose option is used:
>
> ------------------------------------------------------------------------
> Checking for outliers
> Making predictions for scans: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
> Checking scan: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
> Segmentation violation, Address not mapped, Offending address = (nil)
> eddy_cuda8.0 ) [0x49ffd4] [
> eddy_cuda8.0 ) [0x4c6661] [
> eddy_cuda8.0 ) [0x4bbbe9] [
> eddy_cuda8.0 ) [0x412ccd] [
> eddy_cuda8.0 ) [0x413a34] [
> eddy_cuda8.0 ) [0x407a4e] [
> /lib64/libc.so.6 __libc_start_main [0x2b81ce1f4445]
> eddy_cuda8.0 ) [0x40eff1] [
I have seen this occurring in data sets I have had sent to me. In those cases it has been a problem of finding a “shape reference volume”. When doing slice-to-volume realignment one is essentially saying that any volume might have been corrupted by movement between the slices constituting the volume, and therefore that the “shape of the brain” in any volume might be wrong. Therefore eddy needs to find a volume where it can “believe in the shape” and use that as a reference for all other volumes. In order to do that it looks at a number of criteria, and one is that the volume cannot have any outliers (since those are a sign of movement).
In the cases I have seen the problem has been small timing issues in the sequence which has meant that the T1 recovery has been slightly shorter for one slice/MB-group which has meant that that slice/MB-group has looked like an outlier in all volumes. This in turn has meant that there hasn’t been any volume without outliers, and since I hadn’t foreseen that possibility there is no check for that and a null pointer get dereferenced.
If you want to check if this is your problem you need to run eddy without the slice-to-volume option and then look at the .eddy_outlier_map or the .eddy_outlier_n_stdev_map to see if there is a slice/MB-group that has been labeled as an outlier in all volumes.
Jesper
> ------------------------------------------------------------------------
>
> Thank you
>
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