Hi again Bob and other AFNI experts,


to continue with this story, I applied 3dNwarpApply as discusted on a first set of data, everything went well. Now I have a new one, and the script keeps getting "killed". My guess is that it is because there is not enough RAM. The same issue was presented here but my data are not so far apart so I don't think that's the problem. I also saw here that I could use OpenMP but for now it seems a little complicated for me.

Some information:

- I am running on a virtual machine. My host has 16Gb of RAM, and I tried to give as much as 12.5Gb to the linux guest, but it is still not enough. The "top" function shows me that the %MEM goes up to 96.8% before the kill.
- The function is:
anat_warp= the WARP file created by 3dQWarp, from anat+orig to anat+tlrc.
epi_warp= the affine created by align_epi_anat -anat2epi.
cat_matvec -ONELINE $epi_warp -I volreg_matrix.aff12.1D > whole_matrix_volreg_epi2anat.aff12.1D
3dNwarpApply -nwarp "$anat_warp whole_matrix_volreg_epi2anat.aff12.1D" \
-source pb02.$subj.r01.tshift+orig -dxyz 3.5 -prefix rm.epi.nomask -master ~/abin/MNI152_T1_2009c+tlrc

I also checked for differences between this set of data and the previous one, when it worked:
-anat+orig: same size (256x256x256), both float.
-anat+tlrc: same size (MNI size), both float.
-anat_warp from 3dQwarp: This matrix size always varies but it is significantly bigger for the second set of data (~ 230x250x230 for the first, ~530x550x530 for the second).
-results from align_epi_anat: well aligned in both cases.
-epi data is a little bigger in the second set (80x80x34, 150 TR vs 64x64x40, 100 TR)

Do you have ideas that could help reduce the RAM needed? Crop some data with Autobox? Run a different function for every TR in pb02?

Thank you so much,


Emmanuelle



Edited 2 time(s). Last edit at 01/06/2017 11:13AM by Emmanuelle Renauld.