Select Structural Images

If the user chooses to calculate tissue-based regressors and/or DVARS, the TMFC_denoise GUI prompts them to select unprocessed T1-weighted structural images (in native space).

Select structural images GUI.

First, select the parent folder that contains the subject folders with ANAT subfolders for unprocessed T1-weighted structural images (if necessary). By default, the parent folders for first-level GLMs and ANAT subfolders are assumed to be the same (in BIDS they differ).

Second, select the ANAT subfolder for the first subject. Third, apply a text filter (e.g., *T1*.nii*) to match all T1 images. Images may be in *.img/*.hdr, *.nii or *.nii.gz format.

Alternatively, all structural images can be selected manually — for example, when they are stored in a single folder. To do this, press: Select all structural files manually

To open Select structural images GUI independently of the main TMFC_denoise function, run:

anat_paths = tmfc_select_anat_GUI(subject_paths);

Output:

• anat_paths — Full paths to unprocessed (native-space) T1-weighted structural images (cell array)

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Example 1 — SPM-like Folder Structure

In this case, there is no need to change the parent folder to select structural images.

project/
├─ rawdata/      # DICOM
└─ derivatives/  <-------- [Parent folder with ANAT subfolders (BY DEFAULT)]
   ├─ sub-01/    <-------------------------------- [Selected subject folder]
   │  ├─ anat/   <-------- [Select the ANAT subfolder for the first subject] (1)
   │  │  ├─ *T1*.nii  <--------------------------------- [Apply text filter] (2)
   │  │  └─ *T1*.nii derivatives (tissue seg., bias-corrected T1, etc.)
   │  ├─ func/
   │  │  ├─ sess-01/
   │  │  │  ├─ Unprocessed functional files (*.nii)
   │  │  │  └─ Preprocessed functional files:
   │  │  │       • smoothed + normalized + realigned (e.g., swar*.nii)
   │  │  │       • unsmoothed + normalized + realigned (e.g., war*.nii)
   │  │  └─ sess-02/ ...
   │  └─ stat/       # First-level models (one folder per GLM)
   │     ├─ GLM-01/
   │     │  ├─ SPM.mat    <------------------------- [Selected SPM.mat file]
   │     │  └─ TMFC_denoise/  <----------------------------- [Output folder]
   │     └─ GLM-02/ ...
   └─ sub-02/ ...

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Example 2 — BIDS-like Folder Structure

1. Select the parent folder that contains all subject folders with ANAT subfolders (if necessary).

2. Select the ANAT subfolder for the first subject and apply text filter (e.g., *T1*.nii) to match all T1 images.

Here, the default parent folder project/derivatives/firstlevel-spm (with STAT subfolders) needs to be changed to project — the parent folder with ANAT subfolders.

project/   <------------------- [Select parent folder (contains sub-*/anat)]  (1)
├── sub-01/
│   ├── ses-01/
│   │   ├── anat/   <----- [Select the ANAT subfolder for the first subject]  (2)
│   │   │   └── *T1*.nii   <---------------------------- [Apply text filter]  (3)
│   │   └── func/         # Unprocessed functional files
│   └── ses-02/ ...
├── sub-02/ ...
└── derivatives/
    ├── fmriprep/
    │   ├── sub-01/
    │   │   ├── ses-01/
    │   │   │   └── func/
    │   │   │       └── Preprocessed functional files:
    │   │   │           • smoothed + normalized + realigned
    │   │   │           • unsmoothed + normalized + realigned
    │   │   └── ses-02/ ...
    │   └── sub-02/ ...
    └── firstlevel-spm/<-[Parent folder with ANAT (BY DEFAULT)](Needs to be changed)
        ├── sub-01/   <--------------------------- [Selected subject folder]
        │   ├── GLM-01/
        │   │   ├── SPM.mat   <--------------------- [Selected SPM.mat file]
        │   │   └── TMFC_denoise/  <------------------------ [Output folder]
        │   └── GLM-02/ ...
        └── sub-02/ ...

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Example 3 — Other (Non-BIDS) Folder Structure

1. Select the parent folder that contains all subject folders with ANAT subfolders (if necessary).

2. Select the ANAT subfolder for the first subject and apply text filter (e.g., *T1*.nii) to match all T1 images.

Here, the default parent folder project/firstlevel-spm (with STAT subfolders) needs to be changed to project/nifti — the parent folder with ANAT subfolders.

project/
├─ rawdata/   # DICOM
├─ nifti/   <------------------- [Select parent folder (contains sub-*/anat)]  (1)
│  ├─ sub-01/
│  │  ├─ anat/  <---------- [Select the ANAT subfolder for the first subject]  (2)
│  │  │  ├─ *T1*.nii  <---------------------------------- [Apply text filter]  (3)
│  │  │  └─ *T1*.nii derivatives (tissue seg., bias-corrected T1, etc.)
│  │  └─ func/
│  │     ├─ sess-01/
│  │     │  ├─ Unprocessed functional files (*.nii)
│  │     │  └─ Preprocessed functional files (*.nii):
│  │     │     • smoothed + normalized + realigned
│  │     │     • unsmoothed + normalized + realigned
│  │     └─ sess-02/ ...
│  └─ sub-02/ ...
└─ firstlevel-spm/ <-------[Parent folder (BY DEFAULT)](Needs to be changed!)
   ├─ sub-01/   <---------------------------------- [Selected subject folder]
   │  ├─ GLM-01/
   │  │  ├─ SPM.mat   <------------------------------ [Selected SPM.mat file]
   │  │  └─ TMFC_denoise/   <-------------------------------- [Output folder]
   │  └─ GLM-02/ ...
   └─ sub-02/ ...