---------- 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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>>>
>>>
>>>
>>>
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>>
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