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
>
>
>
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