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Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Pawel

February 06, 2022 11:26AM

Registered: 5 years ago
Posts: 80

By the way, I hope you don't mind if I quickly ask about a different thing,
This sequence:

3dAllineate -base           $MPRAGE_file                             \
            -input          ${MDfile_u}+orig                         \
            -prefix         $MDfile_alMP_u                           \
            -cost           lpa                                      \
            -1Dmatrix_save  tmp                                      \
            -automask                                                \
            -source_automask                                         \
            -cmass                                                   \
            -maxrot         45

#convert transform into 3x4 format for further cat_matvec
cat_matvec tmp.aff12.1d > ${MD_MP_lin_Xfm}.1d
rm tmp.aff12.1d

works fine on Ubuntu on my laptop, but fails on CentOS Biowulf. Both cat_matvec and rm claim that tmp.aff12.1d is not there. If I check after the script finished, I see tmp.aff12.1d in the folder.

This looks like an HPC issue (because it runs fine on Ubuntu), and I have a ticket open with them, but just in case it's actually an AFNI thing, I am asking here as well. (I believe AFNI versions might be slightly different, on Ubuntu I have 22.0.01 and HPC is on AFNI_22.0.04)

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Subject	Author	Posted
afni_proc: different -align_epi_ext_dset and -volreg_base_dset	Pawel	February 03, 2022 10:58PM
Re: afni_proc: different -align_epi_ext_dset and -volreg_base_dset	rick reynolds	February 06, 2022 10:55AM
Re: afni_proc: different -align_epi_ext_dset and -volreg_base_dset	Pawel	February 06, 2022 11:14AM
Re: afni_proc: different -align_epi_ext_dset and -volreg_base_dset	rick reynolds	February 06, 2022 12:25PM
Re: afni_proc: different -align_epi_ext_dset and -volreg_base_dset	Pawel	February 06, 2022 12:28PM
Re: afni_proc: different -align_epi_ext_dset and -volreg_base_dset	rick reynolds	February 06, 2022 12:31PM
Re: afni_proc: different -align_epi_ext_dset and -volreg_base_dset	Pawel	February 06, 2022 11:26AM
Re: afni_proc: different -align_epi_ext_dset and -volreg_base_dset	rick reynolds	February 06, 2022 12:29PM
Re: afni_proc: different -align_epi_ext_dset and -volreg_base_dset	Pawel	February 07, 2022 06:54PM
Re: afni_proc: different -align_epi_ext_dset and -volreg_base_dset	rick reynolds	February 08, 2022 09:39AM
Re: afni_proc: different -align_epi_ext_dset and -volreg_base_dset	Pawel	February 08, 2022 10:01AM
Re: afni_proc: different -align_epi_ext_dset and -volreg_base_dset	Daniel Glen	February 06, 2022 05:16PM
Re: afni_proc: different -align_epi_ext_dset and -volreg_base_dset	Pawel	February 06, 2022 05:23PM
Re: afni_proc: different -align_epi_ext_dset and -volreg_base_dset	rick reynolds	March 30, 2022 10:29AM
Re: afni_proc: different -align_epi_ext_dset and -volreg_base_dset	Pawel	March 31, 2022 10:51AM