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BIC-MNI / minc-tools

Basic minc-tools from former minc repository
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mnc2nii error - "floating point exception (core dumped)" #118

Open KarissaChan1 opened 2 years ago

KarissaChan1 commented 2 years ago

Some of my MINC DWI files get the "floating point exception (core dumped)" error when trying to convert to NII using mnc2nii, but others don't. Looking through the data, there doesn't seem to be any differences in data type between volumes that show the error and those that get converted successfully. Anyone have any suggestions on what might be wrong and how I could debug this?

gdevenyi commented 2 years ago

Hi, to help here we'll need what version you're using, how you installed it, and preferably some example data of working and non-working.

KarissaChan1 commented 2 years ago

Hi Gabriel, I tried it with the two most recent versions of the VM found here: https://packages.bic.mni.mcgill.ca/virtual-machines/ I ran a python script from command line in the VM to batch process my data. I've linked a OneDrive folder with 2 MNC files: one that gave the error that I named with "FLAG" at the end of the filename, and the other that didn't with "Working".

https://1drv.ms/u/s!Agw9KH9oSI3DgZUOKldGlEWayCyyxQ?e=ywXHwG

vfonov commented 2 years ago

Probably the same bug as https://github.com/BIC-MNI/minc-tools/issues/90, got fixed in 1.9.17

gdevenyi commented 2 years ago

I will look into updating the VM.

In the meantime, you could download the .deb file here, https://bic-mni.github.io/#v2-version-1918, install with dpkg -i inside the VM and source the new installed version to get the up-to-date converter manually.

KarissaChan1 commented 2 years ago

Great, thanks so much. I installed the new version, and it worked fine with about half of my files, but for the other half I got another error:

HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 139822491150720:

000: ../../../src/H5Dio.c line 199 in H5Dread(): can't read data

major: Dataset
minor: Read failed

001: ../../../src/H5Dio.c line 601 in H5D__read(): can't read data

major: Dataset
minor: Read failed

002: ../../../src/H5Dchunk.c line 2201 in H5D__chunk_read(): error looking up chunk address

major: Dataset
minor: Can't get value

003: ../../../src/H5Dchunk.c line 2931 in H5D__chunk_lookup(): can't query chunk address

major: Dataset
minor: Can't get value

004: ../../../src/H5Dbtree.c line 1049 in H5D__btree_idx_get_addr(): can't get chunk info

major: Dataset
minor: Can't get value

005: ../../../src/H5B.c line 357 in H5B_find(): can't lookup key in subtree

major: B-Tree node
minor: Object not found

006: ../../../src/H5B.c line 335 in H5B_find(): unable to load B-tree node

major: B-Tree node
minor: Unable to protect metadata

007: ../../../src/H5AC.c line 1625 in H5AC_protect(): H5C_protect() failed

major: Object cache
minor: Unable to protect metadata

008: ../../../src/H5C.c line 2362 in H5C_protect(): can't load entry

major: Object cache
minor: Unable to load metadata into cache

009: ../../../src/H5C.c line 6726 in H5C_load_entry(): Can't deserialize image

major: Object cache
minor: Unable to load metadata into cache

010: ../../../src/H5Bcache.c line 181 in H5B__cache_deserialize(): wrong B-tree signature

major: B-Tree node
minor: Bad value

/build/libminc-qiT4Yv/libminc-2.4.03/libsrc/hdf_convenience.c:1554 (from miicv_get): Can't read dataset /minc-2.0/image/0/image Read error

I can't seem to figure out what's wrong with those input files (they're from the same dataset, same scanner, same centers).