Dear CONN users,

I am encountering an issue with my preprocessing/denoising pipeline that I cannot explain.

Dataset:

• Structural images: T1.nii (256×256×256, 1×1×1 mm)


• Functional images: fmri.nii (96×96×54×400 volumes, 2.5×2.5×2.5 mm)


• N = 100 subjects

Pipeline:

• Default CONN preprocessing pipeline


• No custom modifications

Preprocessing results:

• Functional (smoothed, MNI space): swaufmri.nii (91×109×91×400, 2×2×2 mm)


• Structural (MNI space): wc0T1.nii (181×217×181, 1×1×1 mm)

The preprocessing step completes successfully for all subjects with no errors.

Importantly:

• swaufmri.nii and wc0T1.nii are perfectly aligned for every subject


• Same origin


• Alignment verified using SPM CheckReg and MRIcroGL

Issue:
The problem appears only at the denoising step:

1. In the CONN denoising viewer:
   
   
   
   • Functional and structural images appear strongly misaligned (Fig. 1)
   
   
   • In some cases, the functional images look visibly deformed
   
   
   
   
   
2. After denoising:
   
   
   
   • The resulting dswaufmri.nii images appear distorted (Fig. 2)
   
   
   • This deformation was not present in any earlier preprocessing outputs
   
   
   
   
   
3. No error messages are produced at any stage
   
4. Final connectivity results are clearly invalid
   

FIGURE 1

FIGURE 2

Importantly:

• All preprocessing outputs (including swaufmri.nii) look correct outside CONN (Fig. 3)


• The issue seems to appear only within CONN at the denoising stage and in the resulting dswaufmri.nii files

FIGURE 3

Questions:

• Are there known issues that could produce deformation at this stage without triggering errors?

Any suggestions or similar experiences would be greatly appreciated.

Thank you very much for your help.