Ok, but is it possible then to use another NIFTI parcellation, for instance, a functional parcellation, with the CIFTI fMRI data? Or, since the subcortical regions are already defined in the CIFTI file, is not possible to re-define these ROI?
Thank you again, Vicente On 29 October 2016 at 22:07, Glasser, Matthew <glass...@wustl.edu> wrote: > The AAL parcellation is not thought of as a particularly accurate > functional parcellation of the brain. There is a nice parcellation > available here: > > https://balsa.wustl.edu/study/show/RVVG > > Peace, > > Matt. > > From: "PALLARES PICAZO, VICENTE" <vicente.palla...@upf.edu> > Date: Saturday, October 29, 2016 at 6:09 AM > To: Matt Glasser <glass...@wustl.edu> > Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] Extracting time series in grayordinates from any > brain parcellation > > Thank you for the prompt reply. We are interested in whole-brain > parcellations, in particular we would like to extract the averaged time > courses according to the AAL parcellation (Tzourio-Mazoyer et. al, 2002), > so it would include both cortical and subcortical regions. > > Best, > Vicente > > On 28 October 2016 at 23:22, Glasser, Matthew <glass...@wustl.edu> wrote: > >> What kind of a NIFTI parcellation is this? Subcortical? >> >> Peace, >> >> Matt. >> >> From: <hcp-users-boun...@humanconnectome.org> on behalf of "PALLARES >> PICAZO, VICENTE" <vicente.palla...@upf.edu> >> Date: Friday, October 28, 2016 at 10:12 AM >> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> >> Subject: [HCP-Users] Extracting time series in grayordinates from any >> brain parcellation >> >> Dear HCP data users, >> >> We would like to use the fantastic resting state fMRI data set from the >> HCP :) >> >> We are interested in extracting the time series from the minimal >> preprocessing resting fMRI data to later perform our own analysis. >> >> After checking the available information, it seems that the most >> appropriate way to extract the average signal in each region of interest is >> to use the *cifti-parcellate* command. >> >> In the help section we have seen that the cifti-parcellate command has >> four arguments: >> >> wb_command -cifti-parcellate >> >> <cifti-in> - the cifti file to parcellate >> >> <cifti-label> - a cifti label file to use for the parcellation >> >> <direction> - which mapping to parcellate (integer, ROW, or COLUMN) >> >> <cifti-out> - output - output cifti file >> >> >> Our questions are: >> >> 1) For the <cifti-label> argument, how can we transform our nifti >> parcellation atlas into a cifti label file for both cortical and >> subcortical areas? >> >> We have seen that there is a *wb_command -cifti-create-label* command, >> but we are worried that for example our hippocampus label is different from >> the hippocampus label in cifti… So, is there any way to transform our nifti >> atlas into cifti without using the already determined CIFTI structures? >> >> 2)For the for <cifti in> argument, we use the file “ >> *rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii*” >> >> from the folder >> *100307_3T_rfMRI_REST1_fixextended\100307\MNINonLinear\Results\rfMRI_REST1_LR* >> . Is that correct? >> >> Thanks in advance for your help, >> >> Vicente and Ana >> >> _______________________________________________ >> HCP-Users mailing list >> 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. >> > > > ------------------------------ > > 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
