Re: [HCP-Users] White matter mask availability in HCP

[Glasser, Matthew]

Great to hear! Matt. From: Eleftherios Garyfallidis <garyfalli...@gmail.com> Date: Tuesday, December 9, 2014 at 7:59 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] White matter mask availability in HCP Thank you Matthew.  Your suggestions were very helpful.  I had to do a few more corrections on selecting the labels for creating whole brain white matter mask from the ribbon.nii.gz and wmparc.nii.gz files. Here what worked at the end:     #_WHITE_MATTER_LEFT CEREBRAL_WHITE_MATTER_RIGHT     ribbon_structures = [2, 41]     # CEREBELLAR_WHITE_MATTER_LEFT CEREBELLUM_LEFT THALAMUS_LEFT CAUDATE_LEFT PUTAMEN_LEFT PALLIDUM_LEFT BRAIN_STEM HIPPOCAMPUS_LEFT AMYGDALA_LEFT ACCUMBENS_LEFT DIENCEPHALON_VENTRAL_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_RIGHT THALAMUS_RIGHT CAUDATE_RIGHT PUTAMEN_RIGHT PALLIDUM_RIGHT HIPPOCAMPUS_RIGHT AMYGDALA_RIGHT ACCUMBENS_RIGHT DIENCEPHALON_VENTRAL_RIGHT     # wmparc_structures = [7, 8, 10, 11, 12, 13, 16, 17, 18, 26, 28, 46, 47, 49, 50, 51, 52, 53, 54, 58, 60]     # CEREBELLAR_WHITE_MATTER_LEFT CEREBELLAR_WHITE_MATTER_RIGHT BRAIN_STEM     wmparc_structures = [7, 46, 16]     #Fornix, CC_Posterior, CC_Mid_Posterior, CC_Central, CC_MidAnterior, CC_Anterior     wmparc_cc_structures = [250, 251, 252, 253, 254, 255]     #LeftLateralVentricle, LeftInfLatVent, 3rdVentricle, 4thVentricle, CSF, LeftChoroidPlexus, RightLateralVentricle, RightInfLatVent, RightChoroidPlexus     wmparc_del_structures = [4, 5, 14, 15, 24, 31, 43, 44, 63]     #LeftCaudate RightCaudate       wmparc_del_structures2 = [11, 50] Thx again!  Best regards, Eleftherios On Fri, Dec 5, 2014 at 2:54 AM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: For whitematter/greymatter interface, it sounds like you need a surface (the white matter surface).   This will be much more exact than a volume mask (e.g. if you are doing tractography, you can get quite misleading results if you use masks vs surfaces for cortex).   As for a white matter mask, you can use the ribbon.nii.gz and wmparc.nii.gz files to construct this (indices for ribbon.nii.gz or wmparc.nii.gz are listed below with the appropriate names): #CORTEX_LEFT CEREBRAL_WHITE_MATTER_LEFT CORTEX_RIGHT CEREBRAL_WHITE_MATTER_RIGHT RibbonStructures="2 3 41 42" #CEREBELLAR_WHITE_MATTER_LEFT CEREBELLUM_LEFT THALAMUS_LEFT CAUDATE_LEFT PUTAMEN_LEFT PALLIDUM_LEFT BRAIN_STEM HIPPOCAMPUS_LEFT AMYGDALA_LEFT ACCUMBENS_LEFT DIENCEPHALON_VENTRAL_LEFT CEREBELLAR_WHITE_MATTER_RIGHT CEREBELLUM_RIGHT THALAMUS_RIGHT CAUDATE_RIGHT PUTAMEN_RIGHT PALLIDUM_RIGHT HIPPOCAMPUS_RIGHT AMYGDALA_RIGHT ACCUMBENS_RIGHT DIENCEPHALON_VENTRAL_RIGHT wmparcStructuresToKeepSTRING="7 8 10 11 12 13 16 17 18 26 28 46 47 49 50 51 52 53 54 58 60" #Fornix, CC_Posterior, CC_Mid_Posterior, CC_Central, CC_MidAnterior, CC_Anterior CorpusCallosumToAdd="250 251 252 253 254 255” #LeftLateralVentricle, LeftInfLatVent, 3rdVentricle, 4thVentricle, CSF, LeftChoroidPlexus, RightLateralVentricle, RightInfLatVent, RightChoroidPlexus wmparcStructuresToDeleteSTRING="4 5 14 15 24 31 43 44 63" Peace, Matt. From: Eleftherios Garyfallidis <garyfalli...@gmail.com> Date: Thursday, December 4, 2014 at 6:43 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] White matter mask availability in HCP Hello HCP crew, For my current analysis I need to get a whole brain white matter mask and if possible the white-matter/gray-matter interface mask for each subject. I am aware that such a mask one can get by using FSL/FAST on the T1 but I was wondering if you already provide such masks in your processed data so that I don't need to recompute them. Do you? I have seen for example that you provide the wmparc.nii.gz file but I am not sure if using that  I can get a subject specific and whole brain white matter mask (with cerebral and cerebellum  bundles and for example the full CST included all in the same mask). If I use wmparc.nii.gz then it seems that I need to provide a great number of labels until I get the full coverage of the white matter mask. Is there a simpler way?   What is crucial here is that the white matter mask should fit really well in the native space of the subject. Any ideas?  Best regards, Eleftherios _______________________________________________ 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.   The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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