The parcellation I mentioned below is CIFTI, so it will work without issue with CIFTI fMRI data.
Peace, Matt. From: Timothy Coalson <[email protected]<mailto:[email protected]>> Date: Monday, October 31, 2016 at 3:17 PM To: "PALLARES PICAZO, VICENTE" <[email protected]<mailto:[email protected]>> Cc: Matt Glasser <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [HCP-Users] Extracting time series in grayordinates from any brain parcellation 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]<mailto:[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]<mailto:[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]<mailto:[email protected]>> Date: Saturday, October 29, 2016 at 6:09 AM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[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]<mailto:[email protected]>> wrote: What kind of a NIFTI parcellation is this? Subcortical? Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "PALLARES PICAZO, VICENTE" <[email protected]<mailto:[email protected]>> Date: Friday, October 28, 2016 at 10:12 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[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]<mailto:[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]<mailto:[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
