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help > Skull extracted denoised output
Jul 24, 2020 02:07 AM | Panos Fotiadis
Skull extracted denoised output
Hi Alfonso,
Hope all is well! I analyzed my resting state fMRI scans using the default pre-processing pipeline (output in MNI space) and, at the end, saved the denoised dswau* file. I noticed that compared to the swau* file, dswau* seems to be skull extracted and in a few of my subjects there was a very small number of brain matter voxels that had consequently been removed, particularly in the occipital regions. A few questions that I had were:
1) Since I'm performing some analyses where I'm looking into the BOLD signal along the whole cortical ribbon (including the BOLD values of those removed voxels), I was wondering if there was a way to save the dswau* file but with the skull included (for instance by potentially commenting out the code that applies the skull removal)? Or is the skull removal an essential step for the calculation of the BOLD signal and the creation of the dswau* file?
2) If (1) is possible, should I just re-run the denoising step (which should overwrite everything?), or should I run the pipeline from the beginning?
Thanks in advance for all the help!
Best,
Panos
Hope all is well! I analyzed my resting state fMRI scans using the default pre-processing pipeline (output in MNI space) and, at the end, saved the denoised dswau* file. I noticed that compared to the swau* file, dswau* seems to be skull extracted and in a few of my subjects there was a very small number of brain matter voxels that had consequently been removed, particularly in the occipital regions. A few questions that I had were:
1) Since I'm performing some analyses where I'm looking into the BOLD signal along the whole cortical ribbon (including the BOLD values of those removed voxels), I was wondering if there was a way to save the dswau* file but with the skull included (for instance by potentially commenting out the code that applies the skull removal)? Or is the skull removal an essential step for the calculation of the BOLD signal and the creation of the dswau* file?
2) If (1) is possible, should I just re-run the denoising step (which should overwrite everything?), or should I run the pipeline from the beginning?
Thanks in advance for all the help!
Best,
Panos
Threaded View
Title | Author | Date |
---|---|---|
Panos Fotiadis | Jul 24, 2020 | |
Alfonso Nieto-Castanon | Aug 2, 2020 | |
Panos Fotiadis | Aug 4, 2020 | |
Alfonso Nieto-Castanon | Aug 12, 2020 | |
Panos Fotiadis | Aug 12, 2020 | |
Alfonso Nieto-Castanon | Aug 12, 2020 | |
Panos Fotiadis | Aug 13, 2020 | |
Panos Fotiadis | Aug 2, 2020 | |