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help > Using UNC_neonate template in CONN toolbox
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May 3, 2023 06:05 PM | parinaz babaeeghazvini - New York State Psychiatric Institute
Using UNC_neonate template in CONN toolbox
Hi all,
I am analyzing infants' fMRI data, and I would like to use the UNC template provided for neonates instead of the SPM template. I am using the following pipeline:
functional Label current functional files as "original data"
functional Realignment with correction of susceptibility distortion interactions (subject motion estimation and correction)
functional Center to (0,0,0) coordinates (translation)
functional Slice timing correction (STC; correction for inter-slice differences in acquisition time)
functional Outlier detection (ART-based identification of outlier scans for scrubbing)
structural Center to (0,0,0) coordinates (translation)
functional Indirect segmentation and MNI-space normalization (coregister functional/structural; structural segmentation & normalization; apply same deformation field to functional)
functional Label current functional files as "mni-space data"
functional Smoothing (spatial convolution with Gaussian kernel)
functional Label current functional files as "smoothed data"
and in settings, I used custom TPM for that. The preprocessing runs with no problem, and the outcomes look fine except for "QA normalization: functional data + outline of MNI TPM template (1)" and "QA normalization: structural data + outline of MNI TPM template (1)". This problem continues to denoising step, and there is a mismatch between functional data and structural data.
Can I skip MNI normalization and normalize my data into the UNC template instead?
Best,
Parinaz.
I am analyzing infants' fMRI data, and I would like to use the UNC template provided for neonates instead of the SPM template. I am using the following pipeline:
functional Label current functional files as "original data"
functional Realignment with correction of susceptibility distortion interactions (subject motion estimation and correction)
functional Center to (0,0,0) coordinates (translation)
functional Slice timing correction (STC; correction for inter-slice differences in acquisition time)
functional Outlier detection (ART-based identification of outlier scans for scrubbing)
structural Center to (0,0,0) coordinates (translation)
functional Indirect segmentation and MNI-space normalization (coregister functional/structural; structural segmentation & normalization; apply same deformation field to functional)
functional Label current functional files as "mni-space data"
functional Smoothing (spatial convolution with Gaussian kernel)
functional Label current functional files as "smoothed data"
and in settings, I used custom TPM for that. The preprocessing runs with no problem, and the outcomes look fine except for "QA normalization: functional data + outline of MNI TPM template (1)" and "QA normalization: structural data + outline of MNI TPM template (1)". This problem continues to denoising step, and there is a mismatch between functional data and structural data.
Can I skip MNI normalization and normalize my data into the UNC template instead?
Best,
Parinaz.
May 5, 2023 11:05 AM | Alfonso Nieto-Castanon - Boston University
RE: Using UNC_neonate template in CONN toolbox
Hi Parinaz
I believe the issue with the QC plot is just that the "QA normalization: * data + outline of MNI TPM template" plots are not yet adapted to use non-standard TPM files (they still plot the default MNI boundaries there irrespective of what TPM file you used during normalization) so they are not useful/informative in your case, sorry about that. If you want you may temporally change the file conn/utils/surf/referenceGM.nii, referenceWM.nii and referenceCSF.nii to suitable gray matter, white matter, and CSF template masks for those areas in your atlas as CONN will use the information in these files for these QA plots.
And regarding the issue in the denoising tab, that indicates that the "analysis mask" file specified in Setup.Options is not appropriate for the new reference space of your data. To fix this you can simply change the 'analysis mask' setting in the Setup.Options tab and enter there a different file (this should be a somewhat liberal mask file identifying voxels within the brain in your neonates template), and then re-run the Setup step to extract the BOLD signal from this new analysis mask.
Hope this helps
Alfonso
Originally posted by parinaz babaeeghazvini:
I believe the issue with the QC plot is just that the "QA normalization: * data + outline of MNI TPM template" plots are not yet adapted to use non-standard TPM files (they still plot the default MNI boundaries there irrespective of what TPM file you used during normalization) so they are not useful/informative in your case, sorry about that. If you want you may temporally change the file conn/utils/surf/referenceGM.nii, referenceWM.nii and referenceCSF.nii to suitable gray matter, white matter, and CSF template masks for those areas in your atlas as CONN will use the information in these files for these QA plots.
And regarding the issue in the denoising tab, that indicates that the "analysis mask" file specified in Setup.Options is not appropriate for the new reference space of your data. To fix this you can simply change the 'analysis mask' setting in the Setup.Options tab and enter there a different file (this should be a somewhat liberal mask file identifying voxels within the brain in your neonates template), and then re-run the Setup step to extract the BOLD signal from this new analysis mask.
Hope this helps
Alfonso
Originally posted by parinaz babaeeghazvini:
Hi all,
I am analyzing infants' fMRI data, and I would like to use the UNC template provided for neonates instead of the SPM template. I am using the following pipeline:
functional Label current functional files as "original data"
functional Realignment with correction of susceptibility distortion interactions (subject motion estimation and correction)
functional Center to (0,0,0) coordinates (translation)
functional Slice timing correction (STC; correction for inter-slice differences in acquisition time)
functional Outlier detection (ART-based identification of outlier scans for scrubbing)
structural Center to (0,0,0) coordinates (translation)
functional Indirect segmentation and MNI-space normalization (coregister functional/structural; structural segmentation & normalization; apply same deformation field to functional)
functional Label current functional files as "mni-space data"
functional Smoothing (spatial convolution with Gaussian kernel)
functional Label current functional files as "smoothed data"
and in settings, I used custom TPM for that. The preprocessing runs with no problem, and the outcomes look fine except for "QA normalization: functional data + outline of MNI TPM template (1)" and "QA normalization: structural data + outline of MNI TPM template (1)". This problem continues to denoising step, and there is a mismatch between functional data and structural data.
Can I skip MNI normalization and normalize my data into the UNC template instead?
Best,
Parinaz.
I am analyzing infants' fMRI data, and I would like to use the UNC template provided for neonates instead of the SPM template. I am using the following pipeline:
functional Label current functional files as "original data"
functional Realignment with correction of susceptibility distortion interactions (subject motion estimation and correction)
functional Center to (0,0,0) coordinates (translation)
functional Slice timing correction (STC; correction for inter-slice differences in acquisition time)
functional Outlier detection (ART-based identification of outlier scans for scrubbing)
structural Center to (0,0,0) coordinates (translation)
functional Indirect segmentation and MNI-space normalization (coregister functional/structural; structural segmentation & normalization; apply same deformation field to functional)
functional Label current functional files as "mni-space data"
functional Smoothing (spatial convolution with Gaussian kernel)
functional Label current functional files as "smoothed data"
and in settings, I used custom TPM for that. The preprocessing runs with no problem, and the outcomes look fine except for "QA normalization: functional data + outline of MNI TPM template (1)" and "QA normalization: structural data + outline of MNI TPM template (1)". This problem continues to denoising step, and there is a mismatch between functional data and structural data.
Can I skip MNI normalization and normalize my data into the UNC template instead?
Best,
Parinaz.
May 8, 2023 06:05 PM | parinaz babaeeghazvini - New York State Psychiatric Institute
RE: Using UNC_neonate template in CONN toolbox
Hi Alfonso,
Thank you very much for your help. I applied your suggestions and my problem completely solved.
Best,
Parinaz.
Thank you very much for your help. I applied your suggestions and my problem completely solved.
Best,
Parinaz.
Aug 8, 2025 09:08 AM | Mohammad Javad Mousavi
Using New template in CONN toolbox for segmentation and normalization steps
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