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Hi again,

Just wanted to confirm the randomness of the issue… and see if there was any potential explanation for this.

I decided to go back from scratch, using a copy of my scans processed with FS5.3. I re-ran the thalamic nuclei pipeline from FS7.2.0 a first time: 3 subjects only (out of 139) were actually processed for thalamic nuclei. I ran it a second time (did not change any parameter), “excluding" the 3 scans that were processed in the previous round (deleted from a text file I call to identify my subjects), and got 2 new scans to be processed; these 2 were not processed in the previous round, giving me the segmentation violation error! I am currently running a third round (minus the previous 5 scans), and at least 1 new scan is being processed…. that sent an error at the 2 previous round.

Any idea of what could go wrong?

Thanks for your time.

Yann

On 31 Aug 2022, at 2:12 pm, Yann Quidé yannquide@gmail.com wrote:

This is the error I get when for example, I use MCRv93

sub-BA_IGP001

ERROR: cannot find Matlab 2014b runtime in location:

/Applications/freesurfer/7.2.0/MCRv84

It is looking for either: bin/glnxa64/libmwlaunchermain.so (Linux 64b) or bin/maci64/libmwlaunchermain.dylib (Mac 64b)

The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime. You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2014b. To do so, please run the following command (you might need root permissions):

fs_install_mcr R2014b

For further details, please visit https://secure-web.cisco.com/1iHk6T6OBHrbNMB24br5MdKlQzlWpJc9EKeEEEWfb83XfMZ... https://secure-web.cisco.com/1iHk6T6OBHrbNMB24br5MdKlQzlWpJc9EKeEEEWfb83XfMZNGLZlNDf_C94nMo-BGlBDTHzq-uenqgExMJzSMxCkpy8UXx9M_E3LKgK1YvKPdZXqe741pw2e1vMl9SnnqoJMzU8KczGbLwq_xDm-Th_sZppO0z28c15TDv8QgzBl_VIr2BfO3LQr3i-8oYepIUkuGdwnFw-giMjOa2yz3HLN5WTX0GIG2XpigmIk278UwRJDF4DYSYdptvTVAtCR4ssdaw-FsZNSWZXGx_rX1y2SriVzesQcY7Vx5GhzNBZluKcGYQHsVBfdZnUyYHMdP/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMatlabRuntime

/Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.volumes.txt /Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.mgz /Volumes/MacintoshHD2/mridata/IGP/Subjects/sub-BA_IGP001/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz .

Yann

...

On 31 Aug 2022, at 1:51 pm, fsbuild <fsbuild@contbay.com mailto:fsbuild@contbay.com> wrote:

It’s possible something in 7.2.0 still requires MCRv84. If so, it is probably not going to work to use a soft link to fake out the name, and using a different version of Matlab run time could explain the crashes. Please send along the output showing MCRv84 is required.

• R.