Re: [Freesurfer] Longitudinal analysis question

The fsaverage space is MNI305. $FREESURFER_HOME/average/mni152.register.dat is a registration matrix between the two. doug

On 07/20/2012 11:01 AM, Martin Reuter wrote:

Have never done that, probably someone else knows.

Martin

Sent from my phone, please excuse brevity.

"Kairys, Anson" aekairys@med.umich.edu wrote:

Thanks Dr. Reuter,

Finally, if I have an ROI in MNI space from a VBM result, can I build this accurately in FS space? I guess I still don't understand how the two spaces are related...

Any advice on best way to approach this?

Thanks for all the help

-Anson K.

-----Original Message-----
From: Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu]
Sent: Friday, July 20, 2012 9:39 AM
To: Kairys, Anson; 'Martin Reuter'
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Longitudinal analysis question

Hi Anson

Yes, mixed effects models is the better option. I'd use aparc.stats (but maybe someone else can say better)

Yes, you can also draw a ROI on the base and use it with mri_segstats on each time point to get statistics.

Best Martin
--
Sent from my phone, please
excuse brevity.

"Kairys, Anson"<aekairys@med.umich.edu>  wrote:

Hello Dr. Reuter,

Thanks for the reply!

Two more questions if I may:

1) can I simply take the Tpn.long.basename/stats/?h.aparc.stats data for e.g. the insula and look at thickness this way using a program such as SPSS. For example. I would look across time simply taking each measure from each time point and doing 2 sample ttests/mixed effects. If so would I use aparc.stats or aparc2009?

2) I would like to do an ROI approach, should I stick with TKsurfer and simply draw a region (I would assume on subjects base images?) Basically, I am interested in insular thickness across treatment.


Best

Anson K.

-----Original Message-----
From: Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu]
Sent: Thursday, July 19, 2012 5:51 PM
To: Kairys, Anson
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re:
[Freesurfer] Longitudinal analysis question

Hi Anson,

Qdec can only do cross sectional analyses, therefore currently we supply scripts for a very simple 2 stage approach:
1. create within subjects linear fits to compute the rate of atrophy or percent change. This gives a single number per subjects (per region or vertex).
2. compare that measure across subjects (or across groups). For this you can use QDEC, e.g. to ask where is the atrophy rate significantly different from zero or where does it differ between groups. All columns with numerical variables are averaged across time and you have a single entry per subject. Since the atrophy rate was computed from all time points, the average seemed more appropriate, than e.g. the baseline value. For time you would put the actual time between your scans, e.g.
the age of the subject at that time point, or 0 and 1.2 ... in years (or weeks). This is important to interpret your 'rate' e.g. mm/years . For
test retest you can put anything that has a difference of 1, e.g. (0 and
1) or (1 and 2) because you want the difference in mm (not divided by some number).

So everything is fine as you describe it below.

Best, Martin


On Wed, 2012-07-18 at 18:06 +0000, Kairys, Anson wrote:
>  Hello FS experts,
>
>
>
>  I am running a group up subjects pre/post treatment.
>
>
>
>  When trying to do group analysis, after converting data with the
>  mri_slope command, when I made the long table into a cross table, I
>  noticed in qdec it averaged my “time” variable and only supplies a
>  mean and there is no longer separate timepoints for subjects, just one
>  value per subject. Do I need to define time as something more
>  descriptive than 0 (tp1) and 1 (tp2)? I am so close to analyzing these
>  data, just need a little help with the
group analysis
>
>
>
>  Thanks
>
>
>
>  Anson
>
>
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--
Sent from my phone, please excuse brevity.
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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