We don't recommend doing bandpass filtering on HCP data, however if you must, you can convert the file to a fake NIFTI with wb_command -cifti-convert, run fslmaths on it, and then convert it back to CIFTI.
Peace, Matt. From: Ferdaus Kawsar <ferdaus.kaw...@gmail.com<mailto:ferdaus.kaw...@gmail.com>> Date: Tuesday, October 25, 2016 at 10:17 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] (no subject) Hi Matt, This is how I am removing noise from Volume file. Following is a AFNI command. 3dTproject -input rfMRI_REST1_AP.nii.gz -prefix rfMRI_REST1_AP_cleaned.nii.gz -ort rfMRI_REST1_AP_WM_Timecourse.1D -ort rfMRI_REST1_AP_CSF_Timecourse.1D -ort rfMRI_REST1_AP_GS_Timecourse.1D -polort 2 -passband 0.01 0.1 However, this only removes "noise" from the voxels in the volume file. How do I clean the surface data in a similar process? I want to create a cifti file by using -cifti-create-dense-timeseries and use the cleaned volume data and cleaned surafce data for input of this command. Best regards -Ferdaus On Tue, Oct 25, 2016 at 4:01 AM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: We don't support using ft_read_cifti for MRI data, as it currently has some bugs. Also I am not sure what you mean by "remove noise." Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Ferdaus Kawsar <ferdaus.kaw...@gmail.com<mailto:ferdaus.kaw...@gmail.com>> Date: Tuesday, October 25, 2016 at 12:31 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> Subject: [HCP-Users] (no subject) Hi HCP Experts, I need some help with resting analysis of my data. I have extracted average time course for each sub-cortical parcels. I have also extracted average time course for each cortical parcels (BA, aparc, aparc.2009 and Glasser parcellation). For this I used -cifti-parcellate command from workbench. However, to remove noise I used 3dTproject command of Afni on the volume file. My plan was to use -cifti-create-dense-timeseries to convert the volume data into dtseries.nii format so that I can read it into matlab using ft_read_cifti. However, I think 3dTproject only removed noise from volume file (sub-cortical areas?). How do I remove noise from cortical data? Thanks in advance. Best -Ferdaus Ferdaus A. Kawsar, PhD Research Scientist II Department of Neurology Medical College of Wisconsin Milwaukee, WI _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. -- Ferdaus A. Kawsar, PhD Research Scientist II Department of Neurology Medical College of Wisconsin Milwaukee, WI ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
