Re: [HCP-Users] 2 thickness files

[Harms, Michael]

Yes, that is correct. The creation of the corrThickness file is done in the CreateMyelinMaps.sh script in the PostFreeSurfer pipeline: ${CARET7DIR}/wb_command -metric-regression "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".corrThickness.native.shape.gii -roi "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".roi.native.shape.gii -remove "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere”.curvature.native.shape.gii And the usage statement for -metric-regression is: -metric-regressionREGRESS METRICS OUT OF A METRIC FILE   wb_command -metric-regression      <metric-in> - the metric to regress from      <metric-out> - output - the output metric      [-roi] - only regress inside an roi         <roi-metric> - the area to use for regression, as a metric      [-column] - select a single column to regress from         <column> - the column number or name      [-remove] - repeatable - specify a metric to regress out         <metric> - the metric file to use         [-remove-column] - select a column to use, rather than all            <column> - the column number or name      [-keep] - repeatable - specify a metric to include in regression, but not         remove         <metric> - the metric file to use         [-keep-column] - select a column to use, rather than all            <column> - the column number or name      For each regressor, its mean across the surface is subtracted from its      data.  Each input map is then regressed against these, and a constant      term.  The resulting regressed slopes of all regressors specified with      -remove are multiplied with their respective regressor maps, and these      are subtracted from the input map. cheers, -MH --  Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO  63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of Benjamin Risk <bb...@cornell.edu> Date: Tuesday, August 16, 2016 at 11:10 AM To: "Glasser, Matthew" <glass...@wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>, Peka Savayan <savay...@umn.edu> Subject: Re: [HCP-Users] 2 thickness files I have a follow-up question on what you mean by "regressed out." If thickness_v = b0 + b1*curvature_v + error_v for the vth location, is corrThickness_v = thickness_v - b1*curvature_v? Also, I am conducting a multisubject analysis of cortical thickness. Is it your opinion that MSM-All offers the best registration across subjects? It's not clear to me if the addition of information from resting-state correlations would benefit my analysis, so I will probably also look at results using MSM-Sulc. Thank you, Ben On Tue, Aug 16, 2016 at 8:32 AM, Glasser, Matthew <glass...@wustl.edu> wrote: Thickness is the raw thickness output from FreeSurfer.  CorrThickness has the linear effects of curvature regressed out.  It is better for seeing how thickness changes across cortical areas (as the surface folding exerts a strong effect on cortical thickness by making gyri thicker and sulci thinner). Peace, Matt. From: <hcp-users-bounces@humanconnectome.org> on behalf of Peka Savayan <savay...@umn.edu> Date: Tuesday, August 16, 2016 at 7:29 AM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] 2 thickness files Dear Experts, What is the difference between subID.L.corrThickness.native.shape.gii and subID.L.thickness.native.shape.gii? Both are in the preprocessed directory, MNINonLinear/Native For example: 100307.L.corrThickness.native.shape.gii and 100307.L.thickness.native.shape.gii   Where I can obtain a detailed description of both files? best, Peka _______________________________________________ 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. 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