Quality Check
- Paul Macey (admin)
CSPM creates files to look assess the success and quality of the preprocessing.
fMRI Quality Check
Mean, stdev and individual normalized images *
Set folder, “fMRIanalysis”, preproc, “Summary”
Example :T:\HCP\ID419N596G1\fMRIanalysis\fMRI_HCP1200_rsfMRI_VOIconn_Left Hippocampus\Summary
File | Origin | What to look for |
|---|---|---|
[GROUP/ALL]mean_N[###].nii | Mean of all studies in group. If have more than one group, also have mean of all images in set (“ALL…nii”) N[###] - N followed by number of studies.
Files use to create the mean are listed in the text file “…\thefiles4[GROUP]mean_N[###].txt” | Smoothness, no weird outside-the-brain signal |
[GROUP/ALL]stdev_N[###].nii | Standard deviation; equivalent naming to mean | Artifactual regions of high stdev |
* Start with this file * [GROUP]summary_N[###].pdf | A pdf with multiple pages: 1st - Mean display 2nd - Stdev displayu A series of 15 images/page “Check Reg” are run, with the template top-left and individual studies. Multiple pages are creted as needed. | Consistent normalization of individual scans. See snapshot below The first step for problem scans is to check the project coreg with template. See Manual Coreg to MNI Step-by-Step Instructions |
Example page from file “CONTROLsummary_N596.pdf” for fMRI correlation values. The images are fuzzy because they are correction values, not anatomical scans. However, the shape should be roughly similar to the template. A good idea is to look for at one orientation at a time (for example, figure below shows two magnified axial views, one matched to the template and the other not).
