Re: [HCP-Users] Myelin Map Summary Statistics
Use -cifti-weighted-stats, it reports the measures separately per hemisphere (and can integrate over surface area instead of a naive mean), and use the -roi option to report within an ROI. If you want to use a lot of ROIs that don't overlap, look at -cifti-parcellate. Tim On Wed, Nov 2, 2016 at 3:20 PM, Timothy Hendrickson <hendr...@umn.edu> wrote: > Thanks Matt. > > Hmm I am still confused. So here is my command to extract myelin for the > entire cortex: wb_command -cifti-stats 43387.MyelinMap.32k_fs_LR.dscalar.nii > -reduce MEAN. > Since -cifti-stats requires the -reduce flag the data I receive is only > one number. What I am hoping to accomplish is to extract the average > surface myelin for the left and right hemisphere and all surface ROIs. > For example with freesurfer I can rather easily generate a stats file > which informs me a measurement (of my choosing) at each particular > location. For example see attached: lh.allSite.aparc.thickness.csv. > > I apologize for the continued questions. I am fairly new to HCP data and > am still learning the in and outs :) > > -Tim > > Timothy Hendrickson > Department of Psychiatry > University of Minnesota > Mobile: 507-259-3434 (texts okay) > > On Wed, Nov 2, 2016 at 1:20 PM, Glasser, Matthew <glass...@wustl.edu> > wrote: > >> You should be able to do that with the commands Tim mentioned with the >> -roi sub option. >> >> Peace, >> >> Matt. >> >> From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy >> Hendrickson <hendr...@umn.edu> >> Date: Wednesday, November 2, 2016 at 11:42 AM >> To: Timothy Coalson <tsc...@mst.edu> >> Cc: "hcp-users@humanconnectome.org" <HCP-Users@humanconnectome.org> >> Subject: Re: [HCP-Users] Myelin Map Summary Statistics >> >> Hmm, I have a follow up question. I can extract average myelin for the >> entire cortex rather easily however I am having more trouble extracting >> hemispheric and ROI information. >> Suggestions? >> >> Timothy Hendrickson >> Department of Psychiatry >> University of Minnesota >> Mobile: 507-259-3434 (texts okay) >> >> On Mon, Oct 31, 2016 at 3:45 PM, Timothy Coalson <tsc...@mst.edu> wrote: >> >>> Take a look at http://www.humanconnectome.org/software/workbench-command >>> .php?function=-cifti-weighted-stats and/or http://www.humanconnect >>> ome.org/software/workbench-command.php?function=-cifti-stats . >>> >>> Tim >>> >>> >>> On Mon, Oct 31, 2016 at 3:32 PM, Timothy Hendrickson <hendr...@umn.edu> >>> wrote: >>> >>>> HCP experts, >>>> >>>> Is there a way to extract myelin values from individual dscalar CIFTI >>>> files? >>>> What I am looking for is an average myelin value at the hemispheric and >>>> ROI level. >>>> >>>> -Tim >>>> >>>> Timothy Hendrickson >>>> Department of Psychiatry >>>> University of Minnesota >>>> Mobile: 507-259-3434 (texts okay) >>>> >>>> ___ >>>> HCP-Users mailing list >>>> HCP-Users@humanconnectome.org >>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>> >>> >>> >> ___ >> 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. >> > > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Myelin Map Summary Statistics
Thanks Matt. Hmm I am still confused. So here is my command to extract myelin for the entire cortex: wb_command -cifti-stats 43387.MyelinMap.32k_fs_LR.dscalar.nii -reduce MEAN. Since -cifti-stats requires the -reduce flag the data I receive is only one number. What I am hoping to accomplish is to extract the average surface myelin for the left and right hemisphere and all surface ROIs. For example with freesurfer I can rather easily generate a stats file which informs me a measurement (of my choosing) at each particular location. For example see attached: lh.allSite.aparc.thickness.csv. I apologize for the continued questions. I am fairly new to HCP data and am still learning the in and outs :) -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) On Wed, Nov 2, 2016 at 1:20 PM, Glasser, Matthew <glass...@wustl.edu> wrote: > You should be able to do that with the commands Tim mentioned with the > -roi sub option. > > Peace, > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of Timothy > Hendrickson <hendr...@umn.edu> > Date: Wednesday, November 2, 2016 at 11:42 AM > To: Timothy Coalson <tsc...@mst.edu> > Cc: "hcp-users@humanconnectome.org" <HCP-Users@humanconnectome.org> > Subject: Re: [HCP-Users] Myelin Map Summary Statistics > > Hmm, I have a follow up question. I can extract average myelin for the > entire cortex rather easily however I am having more trouble extracting > hemispheric and ROI information. > Suggestions? > > Timothy Hendrickson > Department of Psychiatry > University of Minnesota > Mobile: 507-259-3434 (texts okay) > > On Mon, Oct 31, 2016 at 3:45 PM, Timothy Coalson <tsc...@mst.edu> wrote: > >> Take a look at http://www.humanconnectome.org/software/workbench-command >> .php?function=-cifti-weighted-stats and/or http://www.humanconnect >> ome.org/software/workbench-command.php?function=-cifti-stats . >> >> Tim >> >> >> On Mon, Oct 31, 2016 at 3:32 PM, Timothy Hendrickson <hendr...@umn.edu> >> wrote: >> >>> HCP experts, >>> >>> Is there a way to extract myelin values from individual dscalar CIFTI >>> files? >>> What I am looking for is an average myelin value at the hemispheric and >>> ROI level. >>> >>> -Tim >>> >>> Timothy Hendrickson >>> Department of Psychiatry >>> University of Minnesota >>> Mobile: 507-259-3434 (texts okay) >>> >>> ___ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >> > ___ > 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. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users Subject Number,lh_bankssts_thickness,lh_caudalanteriorcingulate_thickness,lh_caudalmiddlefrontal_thickness,lh_cuneus_thickness,lh_entorhinal_thickness,lh_fusiform_thickness,lh_inferiorparietal_thickness,lh_inferiortemporal_thickness,lh_isthmuscingulate_thickness,lh_lateraloccipital_thickness,lh_lateralorbitofrontal_thickness,lh_lingual_thickness,lh_medialorbitofrontal_thickness,lh_middletemporal_thickness,lh_parahippocampal_thickness,lh_paracentral_thickness,lh_parsopercularis_thickness,lh_parsorbitalis_thickness,lh_parstriangularis_thickness,lh_pericalcarine_thickness,lh_postcentral_thickness,lh_posteriorcingulate_thickness,lh_precentral_thickness,lh_precuneus_thickness,lh_rostralanteriorcingulate_thickness,lh_rostralmiddlefrontal_thickness,lh_superiorfrontal_thickness,lh_superiorparietal_thickness,lh_superiortemporal_thickness,lh_supramarginal_thickness,lh_frontalpole_thickness,lh_temporalpole_thickness,lh_transversetemporal_thickness,lh_insula_thickness,lh_MeanThickness_thickness CCA239,2.84
Re: [HCP-Users] Myelin Map Summary Statistics
You should be able to do that with the commands Tim mentioned with the -roi sub option. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Hendrickson <hendr...@umn.edu<mailto:hendr...@umn.edu>> Date: Wednesday, November 2, 2016 at 11:42 AM To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> Subject: Re: [HCP-Users] Myelin Map Summary Statistics Hmm, I have a follow up question. I can extract average myelin for the entire cortex rather easily however I am having more trouble extracting hemispheric and ROI information. Suggestions? Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) On Mon, Oct 31, 2016 at 3:45 PM, Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote: Take a look at http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-weighted-stats and/or http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-stats . Tim On Mon, Oct 31, 2016 at 3:32 PM, Timothy Hendrickson <hendr...@umn.edu<mailto:hendr...@umn.edu>> wrote: HCP experts, Is there a way to extract myelin values from individual dscalar CIFTI files? What I am looking for is an average myelin value at the hemispheric and ROI level. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
