AFNI Message Board

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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Doughboys
January 08, 2020 11:21AM
Hi ptaylor,
Thank you so much for that answer I think now the origin of my problem is now obvious: 
3dinfo -space -prefix /home/cgarin/Documents/1_Macaque_MRI/2_Atlas/nmt_1.2/NMT_SS.nii.gz
** AFNI converts NIFTI_datatype=4 (INT16) in file1_Macaque_MRI/2_Atlas/nmt_1.2/NMT_SS.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
ORIG	NMT_SS.nii.gz

3dinfo -space -prefix /home/cgarin/Documents/1_Macaque_MRI/3_Nifti5/Oliver2019_02_02/anatT1_warp2std_nsu.nii.gz
ORIG	anatT1_warp2std_nsu.nii.gz
But I really don't understand why the space has been modified....
and my code for the co-registration 

@animal_warper input anatT1.nii.gz -base 1_Macaque_MRI/2_Atlas/nmt_1.2/NMT_SS.nii.gz -atlas 1_Macaque_MRI/2_Atlas/nmt_1.2/F99_WOcerv_NMT.nii.gz -outdir ouput_dir_a_id

afni_proc.py -subj_id Oliver2019_02_02 /
-script 1_Macaque_MRI/8_Func_AFNI/Oliver2019_02_02/proc.Oliver2019_02_02 /
-scr_overwrite -out_dir 1_Macaque_MRI/8_Func_AFNI/Oliver2019_02_02/Oliver2019_02_02.results /
-blocks tshift align tlrc volreg blur mask scale regress -dsets 1_Macaque_MRI/3_Nifti/Oliver2019_02_02/BOLD_restingstate.nii.gz /
-copy_anat 1_Macaque_MRI/3_Nifti5/Oliver2019_02_02/anatT1_ns.nii.gz -anat_has_skull no -tcat_remove_first_trs 10 /
-volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -align_opts_aea -cost lpa+zz -giant_move -align_epi_strip_method None /
-tlrc_base 1_Macaque_MRI/2_Atlas/nmt_1.2/NMT_SS.nii.gz', '-tlrc_NL_warp /
-tlrc_NL_warped_dsets 1_Macaque_MRI/3_Nifti5/Oliver2019_02_02/anatT1_warp2std_nsu.nii.gz /
1_Macaque_MRI/3_Nifti5/Oliver2019_02_02/anatT1_shft_al2std_mat.aff12.1D /
1_Macaque_MRI/3_Nifti5/Oliver2019_02_02/anatT1_shft_WARP.nii.gz /
-blur_size 2.0 -regress_censor_motion 0.35 -regress_censor_outliers 0.02 -regress_motion_per_run -regress_est_blur_errts /
-regress_est_blur_epits -regress_run_clustsim no -execute

Let me know if everything sounds good for simple resting state acquisition,
again thanks a lot for the help!

Clément
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Re: can't malloc -1437173116 bytes in 3dNwarpApply

Doughboys January 03, 2020 05:38PM

Re: can't malloc -1437173116 bytes in 3dNwarpApply

Daniel Glen January 03, 2020 05:58PM

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Doughboys January 07, 2020 05:48PM

Re: can't malloc -1437173116 bytes in 3dNwarpApply

ptaylor January 08, 2020 09:46AM

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Doughboys January 08, 2020 11:47AM

Re: can't malloc -1437173116 bytes in 3dNwarpApply

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Re: can't malloc -1437173116 bytes in 3dNwarpApply

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Re: can't malloc -1437173116 bytes in 3dNwarpApply

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Re: can't malloc -1437173116 bytes in 3dNwarpApply

ptaylor January 09, 2020 09:54AM

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Re: can't malloc -1437173116 bytes in 3dNwarpApply

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