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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bes2037
July 27, 2018 10:20AM
Here is the output from the 3dinfo command:

-108.727364 91.842567 -74.730621 3.000000 3.000000 3.000000 RPI pb01.MOV008_20180330.r01.e1.tcat.2NEW.REF-EPI1_forallineate.nii.gz
-109.027374 92.142578 -74.430626 2.400000 2.400000 2.400000 RPI pb01.MOV008_20180330.r01.e1.tcat.2NEW.nii.gz

I should also clarify that the command I sent you was one I did for just testing out the banding, which is why I had the same input and base (I was just keeping it simple). The actual original command from my script that caused the banding was this:

3dAllineate \
-overwrite \
-base mprage.noskull_at.nii.gz \
-input pb01.${sub}.r${run}.e${echo}.tcat.nii.gz \
-1Dmatrix_apply pb01.${sub}.r${run}.e${echo}.tcat.XFM.EPI2EPI2MPR2ATL_motionINT_EPIxEPI1.aff12.1D \
-mast_dxyz 3 \
-prefix pb01.${sub}.r${run}.e${echo}.tcat.atlas_motionINT_EPIxEPI1.nii.gz

I also reran 3dAllineate using -master (code below) and the image still had bands:

3dAllineate -overwrite -base pb01.MOV008_20180330.r01.e1.tcat.2NEW.nii.gz -master pb01.MOV008_20180330.r01.e1.tcat.2NEW.REF-EPI1_forallineate.nii.gz -input pb01.MOV008_20180330.r01.e1.tcat.2NEW.nii.gz -1Dmatrix_apply pb01.MOV008_20180330.r01.e1.tcat.2NEW.motion_REF-EPI1.aff12.1D -prefix pb01.MOV008_20180330.r01.e1.tcat.2NEW.REF-EPI1_allineate_forcedresample_withmaster.nii.gz

Thanks!

Ben
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Subject Author Posted

3dAllineate issue

bes2037 July 27, 2018 09:42AM

Re: 3dAllineate issue

ptaylor July 27, 2018 09:47AM

Re: 3dAllineate issue

bes2037 July 27, 2018 09:54AM

Re: 3dAllineate issue

ptaylor July 27, 2018 10:05AM

Re: 3dAllineate issue

bes2037 July 27, 2018 10:20AM

Re: 3dAllineate issue

ptaylor July 27, 2018 12:19PM

Re: 3dAllineate issue

ptaylor August 10, 2018 04:03PM

Re: 3dAllineate issue

Daniel Glen August 10, 2018 06:53PM