3dMVM error: datasets are not on the same grid

AFNI Message Board
1

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.

2

Hi Jordan,

Would you please try "3dinfo -obliquity -space" on those datasets? If they are differently oblique, they would not be on the same grid. What standard space are these datasets on?

-rick

3

Hi Rick!

These are all in MNI 151 space. Here are the results from "3dinfo -obliquity -space":

** WARNING: NIfTI file HCA6198582_V1_MR_bis_seed_1_MNI151.nii.gz dimensions altered since AFNI extension was added
11.307	TLRC
** WARNING: NIfTI file HCA6439780_V1_MR_bis_seed_1_MNI151.nii.gz dimensions altered since AFNI extension was added
22.684	TLRC
** WARNING: NIfTI file HCA6742377_V1_MR_bis_seed_1_MNI151.nii.gz dimensions altered since AFNI extension was added
13.566	TLRC

So I guess they are differently oblique. These input files are seed-connectivity images from an analysis ran through bioimage suite but I get the same findings when doing the same with the preprocessed images before seed-analysis. Is this problem from a preprocessing step (or lack thereof) and how would I adjust this now?

Jordan

4

That warning is suspicious:

** WARNING: NIfTI file HCA6198582_V1_MR_bis_seed_1_MNI151.nii.gz dimensions altered since AFNI extension was added

You might try removing the old and possibly inappropriate extensions by running:

nifti_tool -rm_ext ALL -infile XXXX.nii.gz -prefix XXXX_noext.nii.gz

on each file. Then test with the _noext versions.
-rick

5

Removing the extensions does get rid of that warning, but the obliquities are unchanged and script is still outputting the error that the datasets are not on the same grid. I also tried to remove from the preprocessed images pre-analyses and the obliquities are still different from one another.

Jordan

6

Hey Rick and anyone seeing this! I've also been asking around my lab group about this obliquity error and it seems like the problem may be that I used bioimage suite to reslice my images to MNI space, so 3dMVM works with images resliced with a different command and I'll just have to rerun those steps for this 3dMVM. Thank you for your help!!

Jordan

7

That's great, Jordan, thanks for the update!

-rick