help
487 Subscribers 
help > denoising output
Showing 1-4 of 4 posts
Feb 19, 2020 07:02 AM | inbar_meni
denoising output
Hello,
I want to run an analysis only up to the denoising stage (including denoising). I would like to use the nii files after the denoising but I can't find any nii output files. Is it possible to export the nii files after the denoising, prior to the level 1 and level 2 analysis?
Thank you!
Inbar
I want to run an analysis only up to the denoising stage (including denoising). I would like to use the nii files after the denoising but I can't find any nii output files. Is it possible to export the nii files after the denoising, prior to the level 1 and level 2 analysis?
Thank you!
Inbar
Feb 19, 2020 08:02 PM | Alfonso Nieto-Castanon - Boston University
RE: denoising output
Hi Inbar,
Sure, if you are working with the latest release and you select in the Setup.Options tab the "create confound-corrected time-series" checkbox, a version of your functional data after denoising will be saved in the same folder as your original functional data, with 'd' prepended to the filename (e.g. dswau*.nii files).
See also this thread for alternative/simpler ways to create denoised timeseries (mostly tailored to task-activation or other non-connectivity applications/analyses)
Best
Alfonso
Originally posted by inbar_meni:
Sure, if you are working with the latest release and you select in the Setup.Options tab the "create confound-corrected time-series" checkbox, a version of your functional data after denoising will be saved in the same folder as your original functional data, with 'd' prepended to the filename (e.g. dswau*.nii files).
See also this thread for alternative/simpler ways to create denoised timeseries (mostly tailored to task-activation or other non-connectivity applications/analyses)
Best
Alfonso
Originally posted by inbar_meni:
Hello,
I want to run an analysis only up to the denoising stage (including denoising). I would like to use the nii files after the denoising but I can't find any nii output files. Is it possible to export the nii files after the denoising, prior to the level 1 and level 2 analysis?
Thank you!
Inbar
I want to run an analysis only up to the denoising stage (including denoising). I would like to use the nii files after the denoising but I can't find any nii output files. Is it possible to export the nii files after the denoising, prior to the level 1 and level 2 analysis?
Thank you!
Inbar
Mar 29, 2020 11:03 AM | inbar_meni
RE: denoising output
Dear Alfonso,
Thank you so much for this answer! It worked great. I have another question- we want to stay in the subject volumetric space (not a surface). Our preprocessing output has a u*.nii file name, and is still in the native space. The problem is that after denoising the du*.nii file is no longer in the original resolution ans space, but in the mni space. That said, it seems that the brain itself did not go through the normalization process but only been resliced, probably due to our need to use the denoising step of csf\WM\GM regressors.
Is there a way to recieve the du*.nii output in both the original space and resolution of the subject?
Thank you!
Inbar
Thank you so much for this answer! It worked great. I have another question- we want to stay in the subject volumetric space (not a surface). Our preprocessing output has a u*.nii file name, and is still in the native space. The problem is that after denoising the du*.nii file is no longer in the original resolution ans space, but in the mni space. That said, it seems that the brain itself did not go through the normalization process but only been resliced, probably due to our need to use the denoising step of csf\WM\GM regressors.
Is there a way to recieve the du*.nii output in both the original space and resolution of the subject?
Thank you!
Inbar
Apr 4, 2020 11:04 PM | Alfonso Nieto-Castanon - Boston University
RE: denoising output
Dear Inbar,
Yes, that resampling is likely due to your choice of 'analysis space' (this is defined in Setup.Options). The default option there is "Volume: same as mask (default 2mm voxels)" which means that you want all of your functional data resampled to the same space as CONN's default mask (mask.volume.brainmask.nii). If you prefer not to apply any resampling to your functional data, you may, for example, change the 'analysis space' option to "Volume: same as functional".
Best
Alfonso
Originally posted by inbar_meni:
Yes, that resampling is likely due to your choice of 'analysis space' (this is defined in Setup.Options). The default option there is "Volume: same as mask (default 2mm voxels)" which means that you want all of your functional data resampled to the same space as CONN's default mask (mask.volume.brainmask.nii). If you prefer not to apply any resampling to your functional data, you may, for example, change the 'analysis space' option to "Volume: same as functional".
Best
Alfonso
Originally posted by inbar_meni:
Dear Alfonso,
Thank you so much for this answer! It worked great. I have another question- we want to stay in the subject volumetric space (not a surface). Our preprocessing output has a u*.nii file name, and is still in the native space. The problem is that after denoising the du*.nii file is no longer in the original resolution ans space, but in the mni space. That said, it seems that the brain itself did not go through the normalization process but only been resliced, probably due to our need to use the denoising step of csf\WM\GM regressors.
Is there a way to recieve the du*.nii output in both the original space and resolution of the subject?
Thank you!
Inbar
Thank you so much for this answer! It worked great. I have another question- we want to stay in the subject volumetric space (not a surface). Our preprocessing output has a u*.nii file name, and is still in the native space. The problem is that after denoising the du*.nii file is no longer in the original resolution ans space, but in the mni space. That said, it seems that the brain itself did not go through the normalization process but only been resliced, probably due to our need to use the denoising step of csf\WM\GM regressors.
Is there a way to recieve the du*.nii output in both the original space and resolution of the subject?
Thank you!
Inbar