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users > RE: Affine registration stops after generating cmd.sh
Jun 29, 2018 06:06 PM | Greg Jefferis
RE: Affine registration stops after generating cmd.sh
You have log files for 3 jobs there
So you can see that the job is being aborted. If you didn't do this manually then one possibility is that your cluster job manager is aborting the job, perhaps because it is exceeding some system resource (memory, compute time). The two WARNING lines you see there are harmless but do indicate that cmtk registration has loaded the first image (the reference image I think) successfully. I wonder if it is possible that there is something corrupt about your sample image – either that it doesn't open properly or that the spatial calibration is very wrong. I suggest that you look at the nrrd header information using ImageJ's Image ... Show Info command.
Best,
Greg.
- 16632149
- 16639860
- 16643252
As far as I can tell job id 16643252
relates to another brain. The .err files for the other two jobs
look like this:
hostname = n193; short hostname = n193
INFO: number of threads set to 4 according to environment variable CMTK_NUM_THREADS
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.
User defined signal 2
Received USR2 signal
hostname = n193; short hostname = n193
INFO: number of threads set to 4 according to environment variable CMTK_NUM_THREADS
WARNING: image does not have valid orientation meta information; cannot reorient.
WARNING: image does not have valid orientation meta information; cannot reorient.
User defined signal 2
Received USR2 signal
So you can see that the job is being aborted. If you didn't do this manually then one possibility is that your cluster job manager is aborting the job, perhaps because it is exceeding some system resource (memory, compute time). The two WARNING lines you see there are harmless but do indicate that cmtk registration has loaded the first image (the reference image I think) successfully. I wonder if it is possible that there is something corrupt about your sample image – either that it doesn't open properly or that the spatial calibration is very wrong. I suggest that you look at the nrrd header information using ImageJ's Image ... Show Info command.
Best,
Greg.
Threaded View
| Title | Author | Date |
|---|---|---|
| Rob Kozol | Jun 19, 2018 | |
| Rob Kozol | Jun 28, 2018 | |
| Greg Jefferis | Jun 28, 2018 | |
| Rob Kozol | Jun 29, 2018 | |
| Greg Jefferis | Jun 29, 2018 | |
| Rob Kozol | Jul 1, 2018 | |
| Greg Jefferis | Jul 1, 2018 | |
| Rob Kozol | Jun 19, 2018 | |
| Greg Jefferis | Jun 19, 2018 | |
| Rob Kozol | Jun 19, 2018 | |
| Greg Jefferis | Jun 19, 2018 | |
| Rob Kozol | Jun 22, 2018 | |
| Greg Jefferis | Jun 23, 2018 | |
| Rob Kozol | Jun 20, 2018 | |
| Greg Jefferis | Jun 19, 2018 | |