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

History of AFNI updates  

Previous Message Next Message
Message List New Topic Print View
|
vferrer
September 27, 2018 05:11AM
Hi guys,

I am doing a functional to MNI transformation and therefore applying realigment+inv(anat to functional)+anat to MNI in one 3dNwarpApply. My problem is that using the MNI template as master and preserving the voxel size (3mm) the grid of my image is different. Here the 3dNwarpApply command:

3dNwarpApply -master $TEMPLATEDIR/$TEMPLATE -overwrite -dxyz ${VOXELRESZ} \
-source pb03.${SUBJ}.blip.nii.gz \
-nwarp "anat.un.aff.qw_WARP.nii.gz mat.warp.aff12.1D" \
-prefix pb04.${SUBJ}.volreg.${TSPACE}.nii.gz
++ 3dNwarpApply: AFNI version=AFNI_18.2.16 (Sep 12 2018) [64-bit]
++ Authored by: Zhark the Warped
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file /export/home/vferrer/public/PARK_VFERRER/TEMPLATES_ATLAS/MNI152_2009_template_FSL.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.
++ -master dataset is '/export/home/vferrer/public/PARK_VFERRER/TEMPLATES_ATLAS/MNI152_2009_template_FSL.nii.gz'
++ output grid size = 3 mm
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as pb03.sub-012ParkMbaaPb.blip.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:pb03.sub-012ParkMbaaPb.blip.nii.gz is 10.099990 degrees from plumb.
++ opened source dataset 'pb03.sub-012ParkMbaaPb.blip.nii.gz'
++ Processing -nwarp
++ Warping:...............................................Z
++ Output dataset ./pb04.sub-012ParkMbaaPb.volreg.MNI.nii.gz
++ total Elapsed time = 918.6 sec

Also the volume dimensions before and after the transformation:
3dinfo -n4 pb04.sub-012ParkMbaaPb.volreg.nii.gz
64 64 42 703
3dinfo -n4 pb04.sub-012ParkMbaaPb.volreg.MNI.nii.gz
61 73 61 703
This is also affecting the TR of the output image. Do you know how can I solve this issue keeping the original dimesions. I have tried by not putting a master, but then part of the brain is not shown.
Reply Quote
RSS
Subject Author Posted

Problems applying 3dNwarpApply

vferrer September 27, 2018 05:11AM

Re: Problems applying 3dNwarpApply

Daniel Glen September 27, 2018 02:32PM