Thank Dr. Smith very much for his very helpful answers. I have one more question about the extensively processed rfMRI data of “parcellation-timeseries-netmats”. I think I saw the vitamin E capsule in the left side of the unprocessed structural image, which should be the subject’s right side, based on the description in the HCP manual. Will the HCP preprocessing and parcellation-timeseries-netmats extensively processing pipeline keep the left and right? For these ICA spatial maps in the volumetric file “melodic_IC_sum.nii.gz”, may I confirm that the left side of the ICA spatial maps displayed in FSLView is still the subject’s right side? Thanks again. Subject: Re: [HCP-Users] Questions about the extensively processed rfMRI data From: st...@fmrib.ox.ac.uk Date: Wed, 25 Feb 2015 06:21:36 +0100 CC: hcp-users@humanconnectome.org To: aaroncr...@outlook.com
Hi On 25 Feb 2015, at 03:39, Aaron C <aaroncr...@outlook.com> wrote:Dear HCP users,I have some questions about the extensively processed rfMRI data of “parcellation-timeseries-netmats”. Their filenames are “groupICA_3T_Q1-Q6related468_MSMsulc.tar.gz”, “NodeTimeseries_3T_Q1-Q6related468_MSMsulc_ICAd*_ts*.tar.gz”, and “netmats_3T_Q1-Q6related468_MSMsulc_ICAd*_ts*.tar.gz”. 1. For nodes, is there any specific threshold applied to the ICA spatial map to obtain the parcel? No - thresholding was only used to generate the thumbnail overlays. I see from an old message of this mailing list that the thumbnail images were obtained by thresholding the ICA spatial map at Z>6. But how about the threshold for obtaining that parcellation? Is that also Z>6? 2. These ICA spatial maps were obtained from the ICA+FIX preprocessed data, therefore, given the dimensionality of 100 as an example, are all these 100 components non- artifactual? Not necessarily; there can still be some artefactual processes left in the data, and out of (eg) 100 components there can possibly be a few artefactual ones. We have not attempted to classify those group-level components in the PTN release. 3. For these netmat *.pconn.nii files, are the first column corresponded to the first ICA component shown in the thumbnail image “0000.png” in the folder “melodic_IC_sum.sum”, the second column corresponded to the second thumbnail image “0001.png” in the folder, and so on? Yes 4. For these thumbnail PNG images, could I find any annotation regarding the corresponding dominant brain region on the HCP website (e.g., something similar to the annotations in Figure 4(A) of Dr. Smith et al.’s paper http://www.ncbi.nlm.nih.gov/pubmed/24238796)? Sorry - we haven't tried to annotate the PTN components. 5. Have these data ever been global signal regressed? No. Cheers, Steve. Many thanks! _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
