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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korannvit
March 23, 2019 01:55AM
Thanks, Paul for assisting on a regular basis.

After updating AFNI to a new version, now things are fine. One sincere suggestion from my side is that why don't you people incorporate @SSwarper along with afni proc in example 11 and since eg. 11 does not do the intended job properly. So it would be helpful for others if you could club @SSwarper and example 11 together.

I also attached the normalization results after using the @SSwarper function along with codes. 

@SSwarper          \
        -input  SubjID-Structural.nii       \
        -base   MNI152_2009_template_SSW.nii.gz        \
        -subid  SubjID \


afni_proc.py -subj_id SubjID \
	-blocks despike tshift align tlrc volreg blur mask scale regress \
	-copy_anat anatSS.SubjID.nii \
	-anat_has_skull no \
	-anat_follower anat_w_skull anat SubjID_SurfVol.nii \
	-anat_follower_ROI aaseg anat aparc.a2009s+aseg.nii \
	-anat_follower_ROI aeseg epi aparc.a2009s+aseg.nii \
	-anat_follower_ROI FSvent epi 001_vent.nii \
	-anat_follower_ROI FSWe epi 002_wm.nii \
	-anat_follower_erode FSvent FSWe \
	-dsets Rest.nii \
	-tcat_remove_first_trs 3 \
	-align_opts_aea -giant_move -cost lpc+ZZ -check_flip \
	-volreg_tlrc_warp -tlrc_base /home/naren123/abin/MNI152_2009_template_SSW.nii.gz \
	-tlrc_NL_warp \
      	-tlrc_NL_warped_dsets \
         	anatQQ.SubjID.nii \
         	anatQQ.SubjID.aff12.1D \
         	anatQQ.SubjID_WARP.nii \
	-volreg_align_to MIN_OUTLIER \
	-volreg_align_e2a \
	-volreg_tlrc_warp \
	-mask_epi_anat yes \
	-regress_motion_per_run \
	-regress_ROI_PC FSvent 3 \
	-regress_make_corr_vols aeseg FSvent \
	-regress_anaticor_fast \
	-regress_anaticor_label FSWe \
	-regress_bandpass 0.01 0.1 \
	-regress_apply_mot_types demean deriv \
	-regress_RSFC \
	-regress_est_blur_epits \
	-regress_est_blur_errts \
	-regress_run_clustsim no

Thanks, Rick for helping at the right time.

Regards
-Korann
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Attachments:
open | download - Screenshot from 2019-03-22 13-34-01.png (168.4 KB)
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Subject Author Posted

normalization of resting data to MNI152 template Attachments

korannvit March 16, 2019 03:18AM

Re: normalization of resting data to MNI152 template

ptaylor March 16, 2019 07:17AM

Re: normalization of resting data to MNI152 template

korannvit March 19, 2019 02:37AM

Re: normalization of resting data to MNI152 template

ptaylor March 19, 2019 09:55AM

Re: normalization of resting data to MNI152 template

korannvit March 20, 2019 03:24AM

Re: normalization of resting data to MNI152 template

ptaylor March 20, 2019 08:19AM

Re: normalization of resting data to MNI152 template

rick reynolds March 20, 2019 11:22AM

Re: normalization of resting data to MNI152 template

korannvit March 21, 2019 07:03AM

Re: normalization of resting data to MNI152 template

ptaylor March 21, 2019 10:08AM

Re: normalization of resting data to MNI152 template Attachments

korannvit March 23, 2019 01:55AM

Re: normalization of resting data to MNI152 template

ptaylor March 23, 2019 07:08AM

Re: normalization of resting data to MNI152 template

korannvit March 21, 2019 06:59AM