help
help > RE: What happened to niftiDATA* confound-corrected time series files?
Feb 28, 2020 07:02 PM | Sarah Kark - UCI
RE: What happened to niftiDATA* confound-corrected time series files?
Dear Alfonso,
I see the files thank you very much for your quick response to this inquiry.
I'm not sure I understand the 2nd difference between this version and prior versions.
I am using CONN to pre-process and de-noise my time-series. I will then extract activity from the d*nii files for each ROI in an atlas and for each participant (this will be entered into a k means clustering analysis). Are the d* files still outputting confounded-corrected activation values for each voxel and volume?
All best,
Sarah Kark
Originally posted by Alfonso Nieto-Castanon:
I see the files thank you very much for your quick response to this inquiry.
I'm not sure I understand the 2nd difference between this version and prior versions.
I am using CONN to pre-process and de-noise my time-series. I will then extract activity from the d*nii files for each ROI in an atlas and for each participant (this will be entered into a k means clustering analysis). Are the d* files still outputting confounded-corrected activation values for each voxel and volume?
All best,
Sarah Kark
Originally posted by Alfonso Nieto-Castanon:
Hi
Sarah,
In the new version the denoised files will be stored in the same folder as your original functional data and will be named using SPM naming convention by simply prepending the letter 'd' to the original functional filenames (e.g. if you have used CONN's default preprocessing pipeline your fully-preprocessed files will be named swau*.nii, so the denoised data will be named dswau*.nii).
Also note that there are two differences with the old nifti*.nii files: 1) CONN now creates one separate NIFTI file per run/session (prepending 'd' letter to original functional filenames) instead of a single file concatenating all sessions (named nifti*Condition000.nii); and 2) CONN now adds back the average BOLD timeseries (one value per voxel) in the resulting denoised volumes (this is intended to maintain anatomical-feature information in the denoised data; e.g. for compatibility with SPM grand-mean computation and implicit masking procedures).
If you prefer to skip these changes, you may simply edit the file conn_process.m and change the line that reads "DONEWOUTPUTCONFCORR=1;" to "DONEWOUTPUTCONFCORR=0;" and that will generate the old-style nifti*.nii files instead. You may also change that line to "DONEWOUTPUTCONFCORR=2" and that will generate both the old- and new- style denoised files.
Hope this helps
Alfonso
Originally posted by Sarah Kark:
In the new version the denoised files will be stored in the same folder as your original functional data and will be named using SPM naming convention by simply prepending the letter 'd' to the original functional filenames (e.g. if you have used CONN's default preprocessing pipeline your fully-preprocessed files will be named swau*.nii, so the denoised data will be named dswau*.nii).
Also note that there are two differences with the old nifti*.nii files: 1) CONN now creates one separate NIFTI file per run/session (prepending 'd' letter to original functional filenames) instead of a single file concatenating all sessions (named nifti*Condition000.nii); and 2) CONN now adds back the average BOLD timeseries (one value per voxel) in the resulting denoised volumes (this is intended to maintain anatomical-feature information in the denoised data; e.g. for compatibility with SPM grand-mean computation and implicit masking procedures).
If you prefer to skip these changes, you may simply edit the file conn_process.m and change the line that reads "DONEWOUTPUTCONFCORR=1;" to "DONEWOUTPUTCONFCORR=0;" and that will generate the old-style nifti*.nii files instead. You may also change that line to "DONEWOUTPUTCONFCORR=2" and that will generate both the old- and new- style denoised files.
Hope this helps
Alfonso
Originally posted by Sarah Kark:
Hello,
I typically check the SET-UP OPTION to save the confound-corrected time series, which outputs after denoising in pre-processing/niftiDATA*.
Now that I've upgraded to 19b I only get the niftiNORM*nii files, and no niftiDATA* files (even though I checked the set-up option to save).
Has anyone been able to save the niftiDATA files for each participant?
Best,
Sarah
I typically check the SET-UP OPTION to save the confound-corrected time series, which outputs after denoising in pre-processing/niftiDATA*.
Now that I've upgraded to 19b I only get the niftiNORM*nii files, and no niftiDATA* files (even though I checked the set-up option to save).
Has anyone been able to save the niftiDATA files for each participant?
Best,
Sarah
Threaded View
| Title | Author | Date |
|---|---|---|
| Sarah Kark | Feb 28, 2020 | |
| Alfonso Nieto-Castanon | Feb 28, 2020 | |
| Sarah Kark | Feb 28, 2020 | |
| Stephen L. | Feb 28, 2020 | |