Hello,
I am currently working on a rt-fMRI project where we have 21 participants. Each participant completed two runs of the experimental condition and had 167-169 volumes per run. We created a grey matter mask. Then we utilized 3dLME, 3dFWHMx, and 3dClustSim to create thresholds and activation maps.
3dLME -prefix Arouse -jobs 16 \\
-resid 'lme_arouse_resid' \\
-mask /home/derivatives/mri/gm_mask/group_gm_mask.nii \\
-model 'arouse' \\
-ranEff '~1' \\
-num_glt 1 \\
-gltLabel 1 'ON-OFF' -gltCode 1 'arouse : 1*ON -1*OFF'
-dataTable Subj run arouse InputFile
We used the residual file provided by the 3dLME calculation
3dFWHMx -acf -input lme_arouse_resid+tlrc
Output:
++ 3dFWHMx: AFNI version=AFNI_19.1.04 (Apr 21 2019) [64-bit]
++ Authored by: The Bob
*+ WARNING: removed 262170 voxels from mask because they are constant in time
++ start ACF calculations out to radius = 12.00 mm
+ ACF done (0.00 CPU s thus far)
** ERROR: (FAILED) attempt to over-write file 3dFWHMx.1D
++ ACF 1D file [radius ACF mixed_model gaussian_NEWmodel] written to 3dFWHMx.1D
++ 1dplot: AFNI version=AFNI_19.1.04 (Apr 21 2019) [64-bit]
++ Authored by: RWC et al.
+ and 1dplot-ed to file 3dFWHMx.1D.png
['0.57608', '1.62374', '6.44495', '4.70654']
++ 3dClustSim: AFNI version=AFNI_19.1.04 (Apr 21 2019) [64-bit]
++ Authored by: RW Cox and BD Ward
** AFNI converts NIFTI_datatype=64 (FLOAT64) in file derivatives/mri/gm_mask/group_gm_mask.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ 34639 voxels in mask (10.65% of total)
++ Kernel function radius = 19.68 mm
++ ACF(0.58,1.62,6.44) => FWHM=4.67 => 65x77x65 pads to 80x96x80
+ Kernel image dimensions 39 x 47 x 39
++ Startup clock time = 0.2 s
++ Using 15 OpenMP threads
Simulating:0123456789.0123456789.0123456789.0123456789.01234567!
++ Clock time now = 192.3 s
We used the acf parameters to calculate the cluster size:
3dClustSim -acf 0.58 1.62 6.44 -nxyz 54 64 50 -pthr 0.001 -athr 0.05 -mask '+
p.path_mri_gm_mask + 'group_gm_mask.nii -prefix ' + p.path_code + 'clust_size_arouse_new
This was the afni output:
# 3dClustSim -acf 0.576086 1.62376 6.44507 -nxyz 54 64 50 -pthr 0.001 -athr 0.05 -mask /derivatives/mri/gm_mask/group_gm_mask.nii -prefix /clust_size_arouse
# bi-sided thresholding
# Grid: 65x77x65 3.00x3.00x3.00 mm^3 (34639 voxels in mask)
#
# CLUSTER SIZE THRESHOLD(pthr,alpha) in Voxels
# -NN 1 | alpha = Prob(Cluster >= given size)
# pthr | .05000
# ------ | ------
0.001000 3.6
We are concerned that a cluster size of 4 is too small. Do you have any suggestions?
Thank you,
Maegan
