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 <[email protected]> wrote: > What kind of a NIFTI parcellation is this? Subcortical? > > Peace, > > Matt. > > From: <[email protected]> on behalf of "PALLARES > PICAZO, VICENTE" <[email protected]> > Date: Friday, October 28, 2016 at 10:12 AM > To: "[email protected]" <[email protected]> > 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 > [email protected] > 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. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
