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Dear AFNI users-

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Sincerely, AFNI HQ

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Philipp

April 10, 2023 05:40PM

Registered: 2 years ago
Posts: 137

Hi Paul,

here is the output:

1	1	1	1	1	              ACW_Awake_Global.nii
1	1	1	1	1	     Resample_Yeo7N_1000ribbon.nii
1	1	1	1	1	     errts.Subject1_Awake.anaticor

And you are right. I guess that I can skip using the "Resample_Yeo7N_1000ribbon.nii" here, and directly use the coordinates from the .errts file.

However, now I tell you something interesting.
When I don't mirror the y coordinates in Python, that is, when I don't run y = y * -1 on them, I again get the

*+ WARNING: File /volumes/sandisk/fmri/dataset_3/processed/Extracted_ACW_Awake/acw_Global.1D line 14333: y coord=-97.5 is outside -96.003 .. 132.003
*+ WARNING: File /volumes/sandisk/fmri/dataset_3/processed/Extracted_ACW_Awake/acw_Global.1D line 14334: y coord=-97.5 is outside -96.003 .. 132.003
*+ WARNING: File /volumes/sandisk/fmri/dataset_3/processed/Extracted_ACW_Awake/acw_Global.1D line 14335: y coord=-97.5 is outside -96.003 .. 132.003
*+ WARNING: File /volumes/sandisk/fmri/dataset_3/processed/Extracted_ACW_Awake/acw_Global.1D line 14336: y coord=-97.5 is outside -96.003 .. 132.003
*+ WARNING: File /volumes/sandisk/fmri/dataset_3/processed/Extracted_ACW_Awake/acw_Global.1D line 14987: y coord=-97.5 is outside -96.003 .. 132.003
*+ WARNING: File /volumes/sandisk/fmri/dataset_3/processed/Extracted_ACW_Awake/acw_Global.1D line 14988: y coord=-97.5 is outside -96.003 .. 132.003
*+ WARNING: File /volumes/sandisk/fmri/dataset_3/processed/Extracted_ACW_Awake/acw_Global.1D line 14989: y coord=-97.5 is outside -96.003 .. 132.003
*+ WARNING: File /volumes/sandisk/fmri/dataset_3/processed/Extracted_ACW_Awake/acw_Global.1D line 14990: y coord=-97.5 is outside -96.003 .. 132.003

error for maaaaannyyy voxels in AFNI’s 3dUndump. However, even when I now run the 3dinfo grid check on those files, that is, including the 3dUndump NIfTI file that uses the original y-coordinates (and not the ones mirrored in Python), I get the following output:

1	1	1	1	1	              ACW_Awake_Global.nii
1	1	1	1	1	     Resample_Yeo7N_1000ribbon.nii
1	1	1	1	1	     errts.Subject1_Awake.anaticor

Isn't that strange?

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Subject	Author	Posted
Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	Philipp	April 10, 2023 07:59AM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	Philipp	April 10, 2023 08:13AM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	ptaylor	April 10, 2023 09:23AM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	Philipp	April 10, 2023 12:53PM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	ptaylor	April 10, 2023 03:18PM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	Philipp	April 10, 2023 03:20PM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	Philipp	April 10, 2023 03:31PM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	ptaylor	April 10, 2023 03:38PM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	Philipp	April 10, 2023 03:47PM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	ptaylor	April 10, 2023 04:56PM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	Philipp	April 10, 2023 05:11PM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	ptaylor	April 10, 2023 05:29PM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	Philipp	April 10, 2023 05:40PM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	Philipp	April 10, 2023 05:47PM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	Philipp	April 11, 2023 04:01AM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	ptaylor	April 11, 2023 09:54AM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	Philipp	April 11, 2023 02:14PM
Re: Extracting voxel-wise data with 3dmaskdump and recombing it with 3dUndump	rick reynolds	April 18, 2023 04:12PM