Re: [Freesurfer] [FreeSurfer] WM Parcellation

2016-01-27 Thread Douglas N Greve 
First you'll have to decide on which wm parcellations will go into which 
lobe. When you have that, then you can use mri_binarize with the 
--replace option to change the index of a given segmentation to that of 
the lobe

On 01/27/2016 07:00 PM, VA Research wrote:
> thank you for that,
>
> but i'm confused on how to do the rest as well .
>
> I now have the wmparc2 with unsegmented areas,
>
> how can we create the lobar regions and use those to parcelate the WM into
>
> lobar regions?
>
> On Wed, Jan 27, 2016 at 2:57 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> You can regenerate a wmparc that does not have the unsegmented wm with
> something like
>
> cd $SUBJECTS_DIR/subject
> mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown
> --volmask --ctxseg aparc+aseg.mgz --wmparc-dmax 100 --o
> mri/wmparc2.mgz
>
> Then create your lobes from that
>
>
> On 01/27/2016 05:47 PM, VA Research wrote:
> > Hello FS experts,
> >
> > Does anyone have some form of step-by-step instructions on how to do
> > this ?
> >
> > Thanks so much
> >
> > Joseph
> > Brainiac . wrote:
> > >/Hi All, />//>/I need to classify WM into different lobes
> (temporal, parietal, />/frontal, occipital). I tried to do the
> lobe mapping using />/parcellations from wmparc.mgz.
> />/http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
> />//>/My problem is the "unsegmented white matter" in wmparc.mgz.
> My />/understanding is that these unsegmented areas are classified
> so />/because they are beyond 5mm from any pre-classified cortex
> area. />//>/My questions: />/(1) So in order to classify
> "unsegmented WM" into lobes, do I need to />/take each voxel in
> the unsegmented WM region and then assign it to the />/closest
> cortex area to classify it into respective parcellations. Then
> />/re-group into lobes. Is this correct? /
> > >//>/(2) Are there any tailor made function or any other easier
> way to do />/this? Is there any easier way to segment WM into
> lobes directly that I />/have missed? />//>/Thanks, />/Brain/
> >
> > You can do this in a couple of steps. First, you'll need to create a
> > lobe annotation. You can do this in 3 ways:
> > 1. mri_annotation2label --lobesStrict
> >2. mri_annotation2label --lobes
> >3. Custom: break up annotation and recombine:
> >a. mri_annotation to create separate label files
> >b. mri_mergelabels to create single label files for each
> lobe label
> >c. mris_label2annot to create the lobe annotation
> >
> > Next, create the WM segmentation with mri_aparc2aseg, specifying
> your
> > new lobe annot and adding --labelwm. You can control the
> distance  with
> > --wmparc-dmax
> >
> > doug
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Re: [Freesurfer] [FreeSurfer] WM Parcellation

2016-01-27 Thread VA Research 
thank you for that,

but i'm confused on how to do the rest as well .

I now have the wmparc2 with unsegmented areas,

how can we create the lobar regions and use those to parcelate the WM into

lobar regions?

On Wed, Jan 27, 2016 at 2:57 PM, Douglas N Greve 
wrote:

> You can regenerate a wmparc that does not have the unsegmented wm with
> something like
>
> cd $SUBJECTS_DIR/subject
> mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown
> --volmask --ctxseg aparc+aseg.mgz --wmparc-dmax 100 --o mri/wmparc2.mgz
>
> Then create your lobes from that
>
>
> On 01/27/2016 05:47 PM, VA Research wrote:
> > Hello FS experts,
> >
> > Does anyone have some form of step-by-step instructions on how to do
> > this ?
> >
> > Thanks so much
> >
> > Joseph
> > Brainiac . wrote:
> > >/Hi All, />//>/I need to classify WM into different lobes (temporal,
> parietal, />/frontal, occipital). I tried to do the lobe mapping using
> />/parcellations from wmparc.mgz. />/
> http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation />//>/My
> problem is the "unsegmented white matter" in wmparc.mgz. My
> />/understanding is that these unsegmented areas are classified so
> />/because they are beyond 5mm from any pre-classified cortex area.
> />//>/My questions: />/(1) So in order to classify "unsegmented WM" into
> lobes, do I need to />/take each voxel in the unsegmented WM region and
> then assign it to the />/closest cortex area to classify it into respective
> parcellations. Then />/re-group into lobes. Is this correct? /
> > >//>/(2) Are there any tailor made function or any other easier way to
> do />/this? Is there any easier way to segment WM into lobes directly that
> I />/have missed? />//>/Thanks, />/Brain/
> >
> > You can do this in a couple of steps. First, you'll need to create a
> > lobe annotation. You can do this in 3 ways:
> > 1. mri_annotation2label --lobesStrict
> >2. mri_annotation2label --lobes
> >3. Custom: break up annotation and recombine:
> >a. mri_annotation to create separate label files
> >b. mri_mergelabels to create single label files for each lobe
> label
> >c. mris_label2annot to create the lobe annotation
> >
> > Next, create the WM segmentation with mri_aparc2aseg, specifying your
> > new lobe annot and adding --labelwm. You can control the distance  with
> > --wmparc-dmax
> >
> > doug
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] [FreeSurfer] WM Parcellation

2016-01-27 Thread Douglas N Greve 
You can regenerate a wmparc that does not have the unsegmented wm with 
something like

cd $SUBJECTS_DIR/subject
mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown 
--volmask --ctxseg aparc+aseg.mgz --wmparc-dmax 100 --o mri/wmparc2.mgz

Then create your lobes from that


On 01/27/2016 05:47 PM, VA Research wrote:
> Hello FS experts,
>
> Does anyone have some form of step-by-step instructions on how to do 
> this ?
>
> Thanks so much
>
> Joseph
> Brainiac . wrote:
> >/Hi All, />//>/I need to classify WM into different lobes (temporal, 
> >parietal, />/frontal, occipital). I tried to do the lobe mapping using 
> >/>/parcellations from wmparc.mgz. 
> >/>/http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation />//>/My 
> >problem is the "unsegmented white matter" in wmparc.mgz. My />/understanding 
> >is that these unsegmented areas are classified so />/because they are beyond 
> >5mm from any pre-classified cortex area. />//>/My questions: />/(1) So in 
> >order to classify "unsegmented WM" into lobes, do I need to />/take each 
> >voxel in the unsegmented WM region and then assign it to the />/closest 
> >cortex area to classify it into respective parcellations. Then />/re-group 
> >into lobes. Is this correct? /
> >//>/(2) Are there any tailor made function or any other easier way to do 
> >/>/this? Is there any easier way to segment WM into lobes directly that I 
> >/>/have missed? />//>/Thanks, />/Brain/
>
> You can do this in a couple of steps. First, you'll need to create a
> lobe annotation. You can do this in 3 ways:
> 1. mri_annotation2label --lobesStrict
>2. mri_annotation2label --lobes
>3. Custom: break up annotation and recombine:
>a. mri_annotation to create separate label files
>b. mri_mergelabels to create single label files for each lobe label
>c. mris_label2annot to create the lobe annotation
>
> Next, create the WM segmentation with mri_aparc2aseg, specifying your
> new lobe annot and adding --labelwm. You can control the distance  with
> --wmparc-dmax
>
> doug
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.