Hi All,

I'm working on preprocessing an fMRI dataset, and I’m generally following the default preprocessing pipeline offered by CONN. Here are the exact steps I plan to use:

- `functional Label current functional files as "original functional data"`

- `functional Center to (0,0,0) coordinates (translation) separately for each run/session`

- `functional Realignment with correction of susceptibility distortion interactions (subject motion estimation and correction)`

- `functional Label current functional files as "realigned functional data"`

- `functional Slice timing correction (STC; correction for inter-slice differences in acquisition time)`

- `functional Outlier detection (ART-based identification of outlier scans for scrubbing)`

- `functional Direct segmentation and MNI-space normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)`

- `functional Label current functional files as "mni-space functional data"`

- `structural Label current structural files as "original structural images"`

- `structural Center to (0,0,0) coordinates (translation)`

- `structural Segmentation and normalization (simultaneous Grey/White/CSF segmentation and MNI normalization)`

- `structural Label current structural files as "mni-space structural images"`

- `functional Smoothing (spatial convolution with Gaussian kernel)`

- `functional Label current functional files as "smoothed functional data"`

However, due to the nature of my sample, I would like to use a **custom brain template** for the segmentation and normalization steps:

> **Template file:** `DLBS268MNI_111_brain.nii`  

> This is an adult lifespan sample brain template in MNI space.

To do this, my plan is to complete most preprocessing steps through the GUI, but perform **segmentation and normalization manually using the following script**:

```matlab

conn_setup_preproc( ...

 {'structural_segment&normalize'}, ...

 'applytofunctional', true, ...

 'structural_template', 'F:/ds004856-download/dlbs_templates/DLBS268MNI_brain/DLBS268MNI_111_brain.nii');

```

---

### My questions:

**1.** Is this a valid approach for replacing the default segmentation and normalization steps with a custom template?  

If yes, should I **manually remove** the following four steps from the GUI pipeline?

- `functional Direct segmentation and MNI-space normalization`

- `functional Label current functional files as "mni-space functional data"`

- `structural Segmentation and normalization`

- `structural Label current structural files as "mni-space structural images"`

**2.** Assuming everything is done correctly, in the **QA normalization** step, will CONN display the result using **my custom DLBS template**, or does it still overlay the outline of the **default MNI TPM** template regardless of what was used during normalization?

Thank you very much for your help,  

Mohammad Javad