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: "firstname.lastname@example.org" <email@example.com> > 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. > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users