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help > RE: Using UNC_neonate template in CONN toolbox
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.
Threaded View
| Title | Author | Date |
|---|---|---|
| parinaz babaeeghazvini | May 3, 2023 | |
| Alfonso Nieto-Castanon | May 5, 2023 | |
| parinaz babaeeghazvini | May 8, 2023 | |