The CIFTI fMRI data does not contain subcortical information outside those defined ROIs. If you need to redefine them, you would need to get the data from the volume fMRI files, and the resulting cifti files would be challenging to compare/use with the released cifti data.
You can incorporate volume subcortical parcellation data within the existing CIFTI subcortical ROIs into a dlabel file that also contains a cortex parcellation, see http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-create-dense-from-template . Tim On Mon, Oct 31, 2016 at 9:28 AM, PALLARES PICAZO, VICENTE < [email protected]> wrote: > 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 <[email protected]> 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" <[email protected]> >> Date: Saturday, October 29, 2016 at 6:09 AM >> To: Matt Glasser <[email protected]> >> Cc: "[email protected]" <[email protected]> >> 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 <[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. >>> >> >> >> ------------------------------ >> >> 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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
