Re: [Freesurfer] Help with MRI segstats - Freesurfer

14 Aug 2019

      Can you send a command line and terminal output with the error?
On 8/14/19 9:38 AM, Daliah Ross wrote:
...
External Email - Use Caution
Hello,
I have tried using just one of the arguments, but I'm still not 
getting my desired output. I'm not sure if I've explained my question 
correctly. I am looking to get anatomical labels on the clusters that 
I've already created through mri_surfcluster to find out where in the 
cortex each cluster is. How would I go about doing this? I was hoping 
that mri_segstats could give an output where it lists each cluster 
starting with the biggest and where it is located. I've been able to 
get this list, but without anatomical labels. I appreciate your help!
Thank you,
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
On Thu, Aug 8, 2019 at 8:01 PM Daliah Ross <dross3@mail.yu.edu 
mailto:dross3@mail.yu.edu> wrote:
Hi,

No, we primarily wanted this for the un-permuted case, to be able
to identify the anatomical regions for each cluster. In addition,
we have thought about looking at the spatial cluster distribution
for the permutations to see if there are any regions which are
more prone to false positives, which might be indicative of e.g.
parcellation or imaging issues, but we haven’t yet figured out how
to best go about that step.  And, yes, for the permutations we are
running mri_surfcluster and extracting the max cluster size per
permutation. Thank you for the advice!

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

On Wed, Aug 7, 2019 at 4:51 PM Greve, Douglas N.,Ph.D.
<DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>> wrote:

    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> <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
    >
    >     From: freesurfer-bounces@nmr.mgh.harvard.edu
    <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
    >     <mailto: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>
    >     <mailto: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>
    >     <mailto: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>>
    >     <mailto: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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