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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:
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
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
| September 14, 2021 03:08PM | |
Greetings AFNI experts,
I have an alignment related issue that you might be able to help with:
I have skull-stripped T1 anatomical datasets that I need to align on top of hybrid DTI/pCASL datasets. Both the T1 and DTI/pCASL datasets have been collected in the same scan session:
T1: 1mm isotropic voxels (256x256x256 voxels)
Hybrid DTI/pCASL: 3.5mmx3.5mmx8.0mm (64x63x12 voxels) The one shown is an M0 image,
I can get a relatively, maybe sort of OK alignment if I do the following:
1) Resample the Hybrid DTI/pCASL images to the T1 resolution
3dresample -master ${s}_freesurfer_brain.nii.gz -prefix IMG_PLD2000_M0_RS.nii.gz -input IMG_PLD2000_M0.nii
2) Align using align_epi_anat.py and pretending the DTI/pCASL dataset is EPI
align_epi_anat.py -anat ${s}_freesurfer_brain.nii.gz -anat_has_skull no -epi IMG_PLD2000_M0_RS.nii.gz \
-epi_strip None -anat2epi -epi_base 0 -partial_coverage -volreg off -tshift off -suffix _AL_m0_RS.nii.gz
The output is depicted in the animated gif below (image shows the TI overlaid on top of the DTI/pCASL image after alignment):
The alignment is not totally horrible but I was wondering if there is anyway this can be improved. I can share my data if this will help,
Thank you in advance for your help,
Valentinos
I have an alignment related issue that you might be able to help with:
I have skull-stripped T1 anatomical datasets that I need to align on top of hybrid DTI/pCASL datasets. Both the T1 and DTI/pCASL datasets have been collected in the same scan session:
T1: 1mm isotropic voxels (256x256x256 voxels)
Hybrid DTI/pCASL: 3.5mmx3.5mmx8.0mm (64x63x12 voxels) The one shown is an M0 image,
I can get a relatively, maybe sort of OK alignment if I do the following:
1) Resample the Hybrid DTI/pCASL images to the T1 resolution
3dresample -master ${s}_freesurfer_brain.nii.gz -prefix IMG_PLD2000_M0_RS.nii.gz -input IMG_PLD2000_M0.nii
2) Align using align_epi_anat.py and pretending the DTI/pCASL dataset is EPI
align_epi_anat.py -anat ${s}_freesurfer_brain.nii.gz -anat_has_skull no -epi IMG_PLD2000_M0_RS.nii.gz \
-epi_strip None -anat2epi -epi_base 0 -partial_coverage -volreg off -tshift off -suffix _AL_m0_RS.nii.gz
The output is depicted in the animated gif below (image shows the TI overlaid on top of the DTI/pCASL image after alignment):
The alignment is not totally horrible but I was wondering if there is anyway this can be improved. I can share my data if this will help,
Thank you in advance for your help,
Valentinos
| Subject | Author | Posted |
|---|---|---|
|
vza224 | September 14, 2021 03:08PM |
|
Daniel Glen | September 14, 2021 04:41PM |
|
vza224 | September 15, 2021 04:35PM |
