Hi Paul
I was waiting for Lilla to respond :)
Bruce
On Wed, 18 Oct 2017, miracle ozzoude
wrote:
Hello Bruce,
I wasn't sure if you answered my previous message hence, I'm sending it again.
Thank you.
Best,
Paul
---------- Forwarded message ----------
From: miracle ozzoude <miracoo...@gmail.com>
Date: Sat, Oct 14, 2017 at 3:32 PM
Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Hello Bruce,
Thank you for the response. I was able to look into CVS command and I wrote a
command on how to
register each subjects to cvs_avg35_inMNI152 template using the following:
mri_cvs_register --mov
subID --mni /Application/freesurfer/subjects/cvs_avg35_inMNI152/T1.mgz --step1
--step2 --step3
--outdir $SUBJECTS_DIR/$subID/cvs --asegfname aparc+aseg --openmp 8. Do i
need to use the T1 in
the mri folder or mri.2mm folder when performing mri_cvs_register?
My next goals are to:
1) sample the volumes created using mri_cvs_register to the cvs_avg35_inMNI152
template using
mri_vol2vol -reg .
-which of the outputs from mri_cvs_register should i use
to achieve?final_CVSmorphed_toTEMPLATE_norm.mgz,final_CVSmorph_toTEMPLATE.m3z,
or
final_CVSmorphed_toTEMPLATE_aseg.mgz
2)Use a cortical+subcortical mask from cvs_avg35_inMNI152 to smooth the output
from mri_vol2vol.
- How can I create the cortical mask from the cvs_avg35_inMNI152/mri.2mm
folder? This is
because the folder already has a subcortical mask and I want to create a
cortical mask, combine both
(using mri_merge) and use it to smooth with 8mm.
3) Lastly, use mri_concat to combine the smoothened maps in order to perform
group level analysis on
them.
- when performing mri_glmfit on the combined maps, i don't need to
specify the --surf
fsaverage and lh/rh flags because it is a volume based analysis and it was done
on MNI template not
fsaverage?
Thank you very much
Best,
Paul
On Sat, Oct 14, 2017 at 12:38 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Paul
I guess you could use CVS for this.
cheers
Bruce
On Sat, 14 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you very much. Can I still general cortical and subcortical
maps with
the Spherical warp of r/lh.white surface? If yes, please what are
the steps
to achieve this? can I still analyze it with mri_glm?
Best,
Paul
Sent from my BlackBerry 10 smartphone.
Original Message
From: Bruce Fischl
Sent: Saturday, October 14, 2017 11:27 AM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] cortical/subcortical volume based analysis
Hi Paul
if you use a property (like gm) to drive intersubject registration
it then
becomes difficult to also analyze it. If your warp was truly
perfect you
could just analyze the properties of the warp, but even then it is
hard to
localize effects (e.g. if you changed the smoothness of the warp
field
would the effect move somewhere else?). If the warp is not perfect
then
some of the effect is in your warp and some in the residual
anatomical
differences. There are lots of caveats like this you have to worry
about.
It's the reason we drive our spherical warp with the ?h.white
surface. It
is invariant to gm atrophy and so can be used to assess it without
worrying
about this kind of thing
cheers
Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello Bruce,
Thank you for the response. I meant the latter ( making maps
etc). I want to do something similar to the subcortical volume
based analysis on PETSurfer page however, on freesurfer T1.
Freesurfer doesn't perform VBM hence, why should there be a
problem with interpretation?
Best,
Miracle
Sent from my BlackBerry 10 smartphone.
Original Message
From: Bruce Fischl
Sent: Friday, October 13, 2017 6:53 PM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] cortical/subcortical volume based
analysis
Hi Paul
we typically do this type of analysis by looking at scatter
plots of
structure volumes (e.g. hippocampus). Alternatively, you can
make maps,
but that opens up all the problems/difficulties of
interpretation of VBM.
Which did you mean?
cheers
Bruce
On Fri, 13 Oct 2017, miracle ozzoude wrote:
Hello FreeSurfer experts,
I want to perform a whole brain volume based group
analysis for cortical and subcortical regions.
That's something very similar to surface based group
analysis for cortical thickness however, for
volume. Is there a tutorial on how to do it? if yes,
please can i get the link. If not, please can
someone direct me how to go about doing it? My goal
is to perform a group comparison between control
and PD patients based on volume. Thank you very
much.
Best,
Paul
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contains patient information, please contact the Partners Compliance HelpLine at
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