AFNI version: afni 25.1.10
Hi all!
I am interested in how changing hormones ("FSH" - quantitative, between-subjects) in the menopause transition relate to seed-connectivity and wrote a script using 3dMVM to investigate this:
3dMVM -prefix MVM_FSH_peri.nii.gz -jobs 4 \
-mask /data1/software/bioimagesuite35/images/MNI_T1_1mm_mask.nii.gz \
-bsVars 'FSH' \
-qVars 'FSH' \
-qVarCenters '13.2' \
-SS_type 3 \
-num_glt 1 \
-gltLabel 1 'FSH-Zscore' -gltCode 1 'FSH : ' \
-resid MVM_FSH_peri_resid.nii.gz \
-dataTable \
Subj FSH InputFile \
It gives me an error that the datasets are not on the same grid:
Dimensions:
rows: 48 | columns: 3
Data summary:
Variable Detected_Type Details
Subj Subjects Num Subjects=48
FSH Quantitative Min=0.81 | Max=61.56 | Num outliers=5
InputFile Data Number of InputFiles=48
++ Good: All InputFiles exist.
++ Good: All InputFiles have exactly 1 volume.
** ERROR: Datasets are NOT on the same grid!!!
-- Note: Grids are compared to the 1st InputFile.
When I do 3dinfo -ad3 -n4 -dc3, all of my input files populate like this:
** WARNING: NIfTI file HCA6198582_V1_MR_bis_seed_1_MNI151.nii.gz dimensions altered since AFNI extension was added
1.000000 1.000000 1.000000 181 217 181 1 -13.344810 -9.775955 42.264732 HCA6198582_V1_MR_bis_seed_1_MNI151.nii.gz
** WARNING: NIfTI file HCA6439780_V1_MR_bis_seed_1_MNI151.nii.gz dimensions altered since AFNI extension was added
1.000000 1.000000 1.000000 181 217 181 1 -13.291008 -25.699692 88.080994 HCA6439780_V1_MR_bis_seed_1_MNI151.nii.gz
** WARNING: NIfTI file HCA6742377_V1_MR_bis_seed_1_MNI151.nii.gz dimensions altered since AFNI extension was added
1.000000 1.000000 1.000000 181 217 181 1 -19.238884 -15.837227 64.392929 HCA6742377_V1_MR_bis_seed_1_MNI151.nii.gz
So it seems like the problem is that the geometric centers are off but I am not sure how, since the matrix and voxel sizes are the same. All the data were collected from the HCP-A project and preprocessed in the same pipeline. I also don't know if that Warning that prints out matters, since that has printed in many previous analyses from my lab and I was told to ignore it. Please let me know how else to investigate this error and what I can do to fix it!
Jordan
Also, for bonus points - I originally ran this analysis using 3dLME and specifying -ranEff '~1' as had been done in my lab with similar analyses, which ran completely fine. However, I was told here to use 3dMVM since there are no within-subjects effects and I am wondering if someone could comment on my lab's justification for doing this from a prior study and if running it as 3dLME vs 3dMVM would be expected to have different outcomes: We have clarified in the revision that we did use a regression and not linear mixed effects modeling. While AFNI’s 3dLME is an excellent tool for linear mixed effects modeling, in a case (such as this one) without repeated measurements, we also find it to be a straightforward tool for modeling linear regressions.