Resting state analysis on Surface

AFNI Message Board
1

Hello AFNI team,

I would like to do resting state analysis on surface. I’ve created afni_proc.py script file for each hemisphere and I’ve got an error saying…** FATAL ERROR: Mask creation fails for unknown reasons!

My afni_proc.py command is below.

afni_proc.py -subj_id ${subj}${hemisphere}
-script proc.${subject}${hemisphere} -scr_overwrite
-blocks despike tshift align volreg surf blur mask regress
-copy_anat $top_dir/${subj}_MPRAGE_wo_skull+orig
-anat_has_skull no -tcat_remove_first_trs 0
-dsets
$top_dir/${subj}.s.01_RS+orig
$top_dir/${subj}.s.02_RS+orig
$top_dir/${subj}.s.03_RS+orig
$top_dir/${subj}.s.04_RS+orig
-surf_anat /Applications/freesurfer/subjects/${subject}/SUMA/${subject}SurfVol.nii
-surf_spec /Applications/freesurfer/subjects/${subject}/SUMA/std.141.${subject}${hemisphere}.spec
-volreg_align_to third -volreg_align_e2a
-blur_size 4
-regress_censor_motion 0.2
-regress_bandpass 0.01 0.1
-regress_apply_mot_types demean deriv
-regress_est_blur_errts
-regress_run_clustsim no

When I generated the script file for task related experiment, I excludes mask option. I tested this on resting state analysis on surface but I could not generate the script file without mask option (e.g. I’ve got an error that ** script creation failure for block ‘regress’).

Any suggestions?

Thanks,
Taek

2

You should remove the “mask” from your -blocks line. That should fix that error.

You may need to also remove the “-regress_est_blur_errts” which may also give an error.

3

Yes, the -regress_est_blur_errts option requires the
mask block, so remove them both.

  • rick
4

It works! Thank you Peter and Rick!

I have one more question. well…this is something that i would like to get confirmation from you whether or not i am doing right thing.

I have a TLRC coordinate to create a ROI as a 1D file. (e.g. Intersection_tlrc.1D). The file contains x y z coordinates 40.931076 2.956589 55.040066 (placed on left hemisphere).

  1. Find the closest node to ROI’s coordinate:
    SurfaceMetrics -closest_node Intersection_tlrc.1D -spec /Applications/freesurfer/subjects/suma_TT_N27/std.141.TT_N27_lh.spec -prefix Intersection
  2. Expand nodes
    ROIgrow -i /Applications/freesurfer/subjects/suma_TT_N27/std.141.lh.smoothwm.gii -roi_nodes Intersection.closest.1D.dset"[0]" -lim 3 -prefix ROImask_s01
  3. Convert 1D file to .niml.dset file to visualize in SUMA
    ConvertDset -o_niml -input ROImask_s01.1D -prefix ROImask_s01

Do these make sense to you or do you have any suggestions?

Thanks!
Taek

5

Hi Taek,

That seems quite reasonable to me, for what it’s worth.

  • rick