From dgreve@mgh.harvard.edu Fri Jun 15 09:59:01 2018
From: Douglas Greve <dgreve@mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas
Date: Fri, 15 Jun 2018 09:58:54 -0400
Message-ID: <ca3ed3de-e4b9-f12f-ff55-4aa973061ecc@mgh.harvard.edu>
In-Reply-To: <262AD86A-E490-4A26-A2A5-803DB115C586@stanford.edu>
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There are files called lh.area and lh.volume that you can use instead of=20
lh.thickness. Make sure to use the --jac flag when applying=20
mri_surf2surf to area or volume (but not thickness). This applies=20
jacobian correction to preserve the total area or volume. When you run=20
mri_segstats, include the --accumulate flag so that it reports the total=20
area or volume.


On 6/14/18 6:42 PM, Ryan Flores wrote:
>          External Email - Use Caution
>
> Hi again Doug,
>
> Sorry for not realizing this earlier, but I actually found a workflow that =
you created, which outlines the steps really well. (https://surfer.nmr.mgh.ha=
rvard.edu/fswiki/VolumeRoiCorticalThickness)
>
> However, instead of 'fsaverage' I used the the MNI brain I had previously r=
econ-ed to map the ROI to the surface. By using mri_surf2surf I mapped my sub=
ject's thickness data to the mni brain and optained the cortical thickness. M=
y questions are the following: how do I obtain the surface area and volume fo=
r this ROI? Is there a way to also obtain non-segmented stats? Also, the reas=
on I didn't map the ROI to fsaverage was because I didn=E2=80=99t have access=
...is there a way to change that?
>
> Thank you for your time.
>
> Best,
>
> Ryan
>

-- Ryan Flores Clinical Research Coordinator =EF=BB=BFOn 6/14/18, 11:32 AM,=20
"freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Douglas N. Greve"=20
<freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of=20
dgreve(a)mgh.harvard.edu> wrote: You can create an annotation with=20
mris_seg2annot and then view it in freeview. Run it with --help to get=20
docs On 06/14/2018 02:18 PM, Ryan Flores wrote: > External Email - Use=20
Caution > > Great. That seemed to have worked. Is there a way to inspect=20
that the ROIs have been correctly placed? Perhaps by using freeview? > >=20
Best, > > Ryan > - Ryan Flores Clinical Research Coordinator On 6/14/18,=20
11:02 AM,"freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of Douglas N.=20
Greve" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of=20
dgreve(a)mgh.harvard.edu> wrote: The --trgsurfval is just the output (ie,=20
lh.atlas.nii.gz sampled onto the surface of the subject). Use nii.gz or=20
mgz for the output (not img). On 06/14/2018 01:46 PM, Ryan Flores wrote:=20
 > External Email - Use Caution > > Thank you for your response. Just to=20
clarify, the first command should be mri_vol2surf, correct? It appears=20
to have worked; however, I'm not sure what my --trgsurfval should be?=20
I'm trying the following commands, where mni is the subject directory=20
for the mni brain I recon-ed and sub01 is the subject I want to transfer=20
the atlas to so that I can obtain the cortical thickness. > > 1.=20
mri_vol2surf --mov atlas.nii.gz --regheader mni --hemi lh --projfrac-max=20
0 1 .1 --o lh.atlas.nii.gz > 2. mri_surf2surf --srcsubject mni=20
--srcsurfval lh.atlas.nii.gz --trgsubject sub01 --trgsurfval=20
hammers-01-lh.img --mapmethod nnf > > I tried running mri_surf2surf=20
--help, but unfortunately the examples didn=E2=80=99t really apply to my case=
. I=20
apologize for the potential trivial question in advance. Thanks again=20
for your help. > > Best, > > Ryan > -- Ryan Flores Clinical Research=20
Coordinator On 6/14/18, 8:33 AM, "freesurfer-bounces(a)nmr.mgh.harvard.edu=20
on behalf of Douglas N. Greve" <freesurfer-bounces(a)nmr.mgh.harvard.edu=20
on behalf of dgreve(a)mgh.harvard.edu> wrote: You can always get info by=20
running the command with --help. mri_vol2vol --mov atlas.nii.gz=20
--regheader subject --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz=20
This assumes that the atlas is in registration with the mni152 (you can=20
test with tkregister --mov atlas.nii.gz --s subject --regheader --reg=20
deleteme.dat, the two volumes should be in registration) You can take=20
lh.atlas.nii.gz and use it as input to mri_surf2surf to transfer to an=20
individual. Make sure to use --mapmethod nnf On 06/13/2018 06:59 PM,=20
Ryan Flores wrote: > > External Email - Use Caution > > Hello all, > > I=20
am hoping to obtain structural information (e.g., cortical > thickness,=20
surface area, and volume) based on the n30r83 (aka > Hammersmith) atlas,=20
which is in MNI space. The atlas differentiates > between the=20
hemispheres by using odd/even numbers in the labels. > > After looking=20
through the archives I found a potential solution, which > entails using=20
the mri_vol2surf & mri_surf2surf commands. I=E2=80=99ve recon-ed > the MNI br=
ain=20
to obtain the proper space; however, I=E2=80=99m unsure of how > exactly to=20
implement the commands and which flags are relevant. Any > advice would=20
be greatly appreciated. > > Thank you for your time. I look forward to=20
hearing from you. > > Best, > > Ryan > > -- > > Ryan Flores > > Clinical=20
Research Coordinator > > > >=20
_______________________________________________ > Freesurfer mailing=20
list >Freesurfer(a)nmr.mgh.harvard.edu >=20
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer=20
_______________________________________________ Freesurfer mailing list=20
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The=20
information in this e-mail is intended only for the person to whom it is=20
addressed. If you believe this e-mail was sent to you in error and the=20
e-mail contains patient information, please contact the Partners=20
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--===============2031226638346865616==--


