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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discoraj
June 01, 2015 02:07PM
hi,
Sorry to take so long to get back to you.
I think we will be fine with the dilated mask, but to be complete, here are the alignment steps.

anat to T1
3dQwarp -iwarp -prefix ${subj}.anat2mni.${ScanNo} -nopadWARP \
-duplo -useweight -blur 0 3 -resample -base ${MNI_1mm} -allineate \
-allineate_opts '-twopass -cost nmi -autoweight -fineblur 3 -cmass -source_automask -automask' \
-source ${subj}.anat.uni.strip+orig


epi to T1
align_epi_anat.py -anat ${subj}.anat.uni.strip+orig -epi ${subj}.rest.strip+orig \
-prep_off -suffix _rest2anat -epi2anat -epi_base 0 \
-dset1_strip None -dset2_strip None -master_epi ${subj}.anat.uni.strip+orig

epi -> T1 -> MNI
3dNwarpApply -source pb07.${subj}.blur+orig \
-nwarp "${subj}.anat2mni.${ScanNo}_WARP+tlrc" \
-affter ${subj}.rest2anat.${ScanNo}_mat.aff12.1D \
-master NWARP -prefix ${subj}.rest.temp

Thanks, Justin
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Subject Author Posted

extent masking edges dilated by 1

discoraj May 19, 2015 03:40PM

Re: extent masking edges dilated by 1

rick reynolds May 20, 2015 04:12PM

Re: extent masking edges dilated by 1

discoraj May 21, 2015 09:54AM

Re: extent masking edges dilated by 1

rick reynolds May 26, 2015 12:59PM

Re: extent masking edges dilated by 1

discoraj May 26, 2015 02:17PM

Re: extent masking edges dilated by 1

rick reynolds May 26, 2015 03:24PM

Re: extent masking edges dilated by 1

discoraj June 01, 2015 02:07PM

Re: extent masking edges dilated by 1

rick reynolds June 03, 2015 10:55AM

Re: extent masking edges dilated by 1

discoraj June 04, 2015 09:56AM