Re: [Freesurfer] Help with MRI segstats - Freesurfer

7 Aug 2019

      You should only pass one of --seg, --annot, or --slabel  to 
mri_segstats. I don't understand how you are trying to use this in the 
context of your permutation. Is this something that you are running on 
each iteration? If so, it is probably not what you want to do. Probably 
you want to run mri_surfcluster to get the cluster sizes out.
On 8/7/19 1:31 PM, Daliah Ross wrote:
...
External Email - Use Caution
This is the command line:
mri_segstats --seg F_lhstats_6covars_ sm5_Interaction_negNumCl_F7.mgh 
--annot lh.aparc.annot lh parc --slabel fsaverage lh cortex --sum 
F_lhstats_6covars_ sm5_Interaction_negNumCl_F7.txt
We are running the permutations within FS, but because our model is a 
linear mixed model, and we didn't think that this would be compatible 
with fspalm. So, we are running the permutations "manually" (i.e. we 
are generating the random permutations, which in our case is just 
switching the subject labels for the thickness data. We are then using 
mri_surfcluster to extract the maximum cluster size per permutation 
and will use the permutation distribution to determine our the 
statistical significance of our results). In addition, our analyses 
are a bit out of the ordinary in that the thickness data are an 
independent variable in our model, for which we have a repeated 
non-imaging measure as the outcome. Effectively, we are using the 
thickness maps to generate vertex-wise regressors, with a fixed 
outcome measure (fixed in the sense that it doesn't vary across the 
brain).
If you have any thoughts about how we could use fspalm in our case, 
your advice would be most appreciated.
Thanks again,
Daliah
*Daliah Ross* | dross3@mail.yu.edu mailto:dross3@mail.yu.edu
Ph.D. Student, Clinical Psychology with Health Emphasis
Ferkauf Graduate School of Psychology
Yeshiva University
Albert Einstein College of Medicine
From: freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
<freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of
Greve, Douglas N.,Ph.D.
Sent: Tuesday, August 6, 2019 12:56 PM
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Help with MRI segstats

Can you send command lines? Also, are you using the built-in
permutation tool or trying to do something outside of FS?

On 8/6/19 8:40 AM, Daliah Ross wrote:
>
>         External Email - Use Caution
>
> Hi FreeSurfer experts,
>
> I have a couple of questions regarding mri_segstats tool for an
> analysis on vertex-wise cortical thickness data. We are
attempting to
> compare maximum cluster sizes among permutations. We are having
> trouble figuring out how to get the anatomical label for each
cluster
> using the --slabel argument. We are also wondering if the
difference
> between cluster sizes between mri_surfcluster and mri_segstats
is due
> to partial volumes, and if so, how to correctly use the --pv
argument.
> It suggests in the wiki page that mri/norm.mgz volume is usually
used
> but I believe we need something surface-based since we are using
> thickness data.
>
> Thank you in advance for any help you can provide.
>
> Best,
> Daliah
>
> *Daliah Ross* | dross3@mail.yu.edu <mailto:dross3@mail.yu.edu>
<mailto:dross3@mail.yu.edu <mailto:dross3@mail.yu.edu>>
>
> Ph.D. Student, Clinical Psychology with Health Emphasis Ferkauf
> Graduate School of Psychology Yeshiva University Albert Einstein
> College of Medicine
>
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