Multiband data conversion from DICOM to be used in afni_proc.py

AFNI Message Board
1

Hi AFNI experts,

I have a multiband resting state fMRI acquisition with the following details.

Scanner = Seimens MAGNETOM prisma
TR = 0.681 sec
Number of slices per volume = 54
Number of Volumes = 870
Slice Thickness = 2.5mm
Series = Ascending

I tried to preprocess this data with afni_proc.py by converting dicoms using dcm2nii command. I believe there is an error in the data conversion process because I see very strange connectivity results in the output of afni_proc.py.

Can you please guide me what is the exact procedure to create the AFNI compatible dataset from these DICOMS which is also taking care of the slice timing as it is a multiband acquisition.

Waiting for your reply.
Thank you.

Naveed

2

Hi Naveed-

I generally trust dcm2nii (or the packaged version with AFNI: dcm2niix_afni) for conversion of multiband data.

  1. Are you using the CMRR sequence?

  2. What’s your afni_proc.py command?

-Peter

3

Hi Peter,

Thank you for your reply.

I am not sure about CMRR but this data is acquired at MNI Montreal following exactly the same sequence as ADNI3.

Here are my afni_proc command and subsequent commands to generate the connectivity matrix.

afni_proc.py -subj_id $line -dsets /data/data05/Studies/MCSA/RAW/MRI/$line/$RSN -copy_anat /data/data05/Studies/MCSA/RAW/MRI/$line/$T1 -blocks despike align volreg mask regress -tcat_remove_first_trs 10 -volreg_align_e2a -mask_apply epi -mask_segment_anat yes -mask_segment_erode yes -regress_apply_mot_types demean deriv -regress_run_clustsim yes -regress_est_blur_errts

3dresample -master errts.$line.tproject+orig -prefix DKT_resample -input /data/data05/melissa/MCSA_processing/t1_preproc/$line/freesurfer_DKT.nii
@MakeLabelTable -lab_file …/DKT.txt 1 0 -labeltable sub.niml.lt -dset DKT_resample+orig
3dcalc -a DKT_resample+orig -expr ‘step(a)’ -prefix DKT_mask
3dcalc -a errts.$line.tproject+orig -b DKT_mask+orig -expr ‘a*b’ -prefix errts_DKT_fs
3dNetCorr -prefix netcorr -mask mask_GM_resam+orig.BRIK -ts_out -fish_z -inset errts_DKT_fs+orig -in_rois DKT_resample+orig -output_mask_nonnull -push_thru_many_zeros -ts_wb_corr -ts_wb_strlabel
fat_mat_sel.py -m netcorr_000.netcc -P “FZ” --A_plotmin=0.27 --B_plotmax=1 --Tight_layout_on --dpi_file=75 -L 2 -d 300 -S 2

4

Ok, I’ll need some more information: Where did the file freesurfer_DKT.nii come from?

5

I preprocessed the T1 anatomical with freesurfer separately. This file is the output of freesurfer which is the registration of DKT atlas to the subject native space.