opening large files (>4gb) causes a crash

[Gale]

Hello, all. I am trying to open NIFTI (.nii) files of various sizes on ITK-SNAP 4.2.2 (Linux).

These files are all subsets of the same .nii stack, just containing different numbers of slices (e.g. 50-slice subset is a 3GB .nii file, 100-slice subset is 6GB)

I can open files that are 3.6 GB and below but files 5 GB and above causes the program to crash with the below errors:

ITK-SNAP: Segmentation fault

BACKTRACE:
/opt/itksnap-4.2.2/lib/snap-4.2.2/ITK-SNAP(+0x1095714)[0x5567bfac8714]
/lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x14ab6f68a330]
/opt/itksnap-4.2.2/lib/snap-4.2.2/ITK-SNAP(+0x3c2b560)[0x5567c265e560]
/opt/itksnap-4.2.2/lib/snap-4.2.2/ITK-SNAP(+0x3c34363)[0x5567c2667363]
/opt/itksnap-4.2.2/lib/snap-4.2.2/ITK-SNAP(+0x3c35097)[0x5567c2668097]
/opt/itksnap-4.2.2/lib/snap-4.2.2/ITK-SNAP(+0x385d8c5)[0x5567c22908c5]
/opt/itksnap-4.2.2/lib/snap-4.2.2/ITK-SNAP(+0x2016a8a)[0x5567c0a49a8a]
/opt/itksnap-4.2.2/lib/snap-4.2.2/ITK-SNAP(+0x1e2bdc3)[0x5567c085edc3]
/opt/itksnap-4.2.2/lib/snap-4.2.2/ITK-SNAP(+0x12d6579)[0x5567bfd09579]
/opt/itksnap-4.2.2/lib/snap-4.2.2/ITK-SNAP(+0x10aa642)[0x5567bfadd642]
/opt/itksnap-4.2.2/lib/snap-4.2.2/ITK-SNAP(+0x10aab0c)[0x5567bfaddb0c]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(_ZN7QWizard4nextEv+0x152)[0x14ab71651582]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Core.so.6(+0x1ba078)[0x14ab6fcc2078]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(_ZN15QAbstractButton7clickedEb+0x32)[0x14ab714ee932]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(+0x29eb7a)[0x14ab714eeb7a]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(+0x2a0650)[0x14ab714f0650]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(_ZN15QAbstractButton17mouseReleaseEventEP11QMouseEvent+0xee)[0x14ab714f08ce]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(_ZN7QWidget5eventEP6QEvent+0x19e)[0x14ab71425c1e]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(_ZN19QApplicationPrivate13notify_helperEP7QObjectP6QEvent+0x82)[0x14ab713d2012]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(_ZN12QApplication6notifyEP7QObjectP6QEvent+0x430)[0x14ab713da940]
/opt/itksnap-4.2.2/lib/snap-4.2.2/ITK-SNAP(+0x109cf73)[0x5567bfacff73]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Core.so.6(_ZN16QCoreApplication15notifyInternal2EP7QObjectP6QEvent+0x11a)[0x14ab6fc656da]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(_ZN19QApplicationPrivate14sendMouseEventEP7QWidgetP11QMouseEventS1_S1_PS1_R8QPointerIS0_Ebb+0x1e0)[0x14ab713d9c90]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(+0x1e7ae1)[0x14ab71437ae1]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(+0x1ea74b)[0x14ab7143a74b]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(_ZN19QApplicationPrivate13notify_helperEP7QObjectP6QEvent+0x82)[0x14ab713d2012]
/opt/itksnap-4.2.2/lib/snap-4.2.2/ITK-SNAP(+0x109cf73)[0x5567bfacff73]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Core.so.6(_ZN16QCoreApplication15notifyInternal2EP7QObjectP6QEvent+0x11a)[0x14ab6fc656da]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Gui.so.6(_ZN22QGuiApplicationPrivate17processMouseEventEPN29QWindowSystemInterfacePrivate10MouseEventE+0x790)[0x14ab70994670]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Gui.so.6(_ZN22QWindowSystemInterface22sendWindowSystemEventsE6QFlagsIN10QEventLoop17ProcessEventsFlagEE+0xac)[0x14ab709ec20c]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6XcbQpa.so.6(+0x577fa)[0x14ab6b5477fa]
/lib/x86_64-linux-gnu/libglib-2.0.so.0(+0x5d5c5)[0x14ab6eba25c5]
/lib/x86_64-linux-gnu/libglib-2.0.so.0(+0xbc737)[0x14ab6ec01737]
/lib/x86_64-linux-gnu/libglib-2.0.so.0(g_main_context_iteration+0x33)[0x14ab6eba1a63]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Core.so.6(_ZN20QEventDispatcherGlib13processEventsE6QFlagsIN10QEventLoop17ProcessEventsFlagEE+0x6a)[0x14ab6ff0c6da]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Core.so.6(_ZN10QEventLoop4execE6QFlagsINS_17ProcessEventsFlagEE+0x1a3)[0x14ab6fc71023]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(_ZN7QDialog4execEv+0x1c5)[0x14ab71619585]
/opt/itksnap-4.2.2/lib/snap-4.2.2/ITK-SNAP(+0x10b83ac)[0x5567bfaeb3ac]
/opt/itksnap-4.2.2/lib/snap-4.2.2/ITK-SNAP(+0x1170181)[0x5567bfba3181]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Core.so.6(+0x1ba01f)[0x14ab6fcc201f]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Gui.so.6(_ZN7QAction9triggeredEb+0x32)[0x14ab70d697b2]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Gui.so.6(_ZN7QAction8activateENS_11ActionEventE+0xe9)[0x14ab70d6c409]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Core.so.6(+0x1ba078)[0x14ab6fcc2078]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(_ZN15QAbstractButton7clickedEb+0x32)[0x14ab714ee932]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(+0x29eb7a)[0x14ab714eeb7a]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(+0x2a0650)[0x14ab714f0650]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(_ZN15QAbstractButton17mouseReleaseEventEP11QMouseEvent+0xee)[0x14ab714f08ce]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(_ZN7QWidget5eventEP6QEvent+0x19e)[0x14ab71425c1e]
/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(_ZN19QApplicationPrivate13notify_helperEP7QObjectP6QEvent+0x82)[0x14ab713d2012]

/opt/itksnap-4.2.2/lib/snap-4.2.2/libQt6Widgets.so.6(_ZN12QApplication6notifyEP7QObjectP6QEvent+0x430)[0x14ab713da940]

I thought it was a memory issue but the workstation has 140 GB free RAM so I highly doubt it. Other specs for your reference: 2x Intel Xeon Gold 6226R (16 Core) CPU; NVIDIA RTX6000 GPU (24GB GDDR6 ECC memory) 

I would like to open a ~60 GB file size at once but opening a 5 GB file is already crashing the software so I am uncertain how feasible this is. 

Would anyone know what the issue is and how I could solve it?

Would appreciate any help at all. 

Warm regards,

Gale

[Jilei Hao]

Hi Gale,

Sorry for the late reply! Is it still happening now? We have a PR merged to master branch will raise a error message if the available RAM is not sufficient to open an image. https://github.com/pyushkevich/itksnap/pull/221

Was the image compressed (nii.gz) or raw (.nii)? What're the dimensions and data type? Did the computer have "140 GB free RAM" right before you opened the image?

Best,

Jilei