Re: [Freesurfer] questions about cortical thickness using qdec.

On 01/09/2014 04:42 PM, yaya ya wrote:

I am sorry for this misunderstanding.

I am now performing surface-based analysis on my data, especially on cortical thickness. Since when I did this analysis based on the whole left or right hemisphere, the results were not very good.

That is why I want to limit my cortical thickness analysis / surface based analysis into a brain region in order to improve the power.

So, my question is how to build a surface mask of a brain area (e.g., left insula) to do what I want to do (performing thickness only in this mask rather than the whole left or right hemisphere).

I hope that what I described is more clear this time.

Yes, then use the method I described to get a label of insula

By the way, what do you mean by "You would only use a brain mask or a surface mask for a volume-based analysis"? My understanding is that I could use a brain mask or a surface mask to do a volume-based analysis on the cortical or subcortical area. But I could only use surface mask to do cortical thickness or cortical area analysis, right?

Depends on what you mean by a "surface mask". Usually a mask is a data structure with 1s were you want to analyze and 0s everywhere else. For a surface-based analysis, you don't need a surface mask because it is all surface.

On Thu, Jan 9, 2014 at 10:30 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

I'm still not sure I understand what you are doing. Is it a
volume-based
analysis or a surface-based analysis? You would only use a brain
mask or
a surface mask for a volume-based analysis.
doug


On 01/09/2014 04:15 PM, yaya ya wrote:
> Thank you very much for your patience, douglas.
>
> I just want to create a surface mask. What you said is use
> mri_annotation2label to create a surface mask. Then when do
mri_glmfit
> analysis on the surface, I need to use the flag --label my
surface mask.
>
> If my understanding is wrong, don't hesitate to tell me.
>
> By the way, if I want to do a volume mask, which command do I
need to
> use?
>
> Thanks again.
>
>
> On Thu, Jan 9, 2014 at 10:02 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:
>
>
>     Is this an analysis of volume/voxel data or surface/vertex
data? If
>     surface, then you'll need to extract the left insula label from
>     lh.aparc.annot (use mri_annotation2label), then pass this
label to
>     mri_glmfit with --label
>
>     doug
>
>
>     On 01/09/2014 03:52 PM, yaya ya wrote:
>     > Thanks, Doug.
>     >
>     > I just searched the list to find how to generate a mask.
Let us say
>     > the surface of the left insula.
>     >
>     > It seems that I need to use mri_mask command and the brain
which
>     I use
>     > to get the mask should be brainmask.mgz in the fsaverage,
right?
>     >
>     > Then I use this mask in mri_glmfit command.
>     >
>     > Any suggstions, feel free to let me know.
>     >
>     >
>     > On Thu, Jan 9, 2014 at 9:13 PM, Douglas N Greve
>     > <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>> wrote:
>     >
>     >
>     >     On 01/09/2014 02:18 PM, yaya ya wrote:
>     >     > Dear Doug,
>     >     >
>     >     > I am sorry. It is my first time to post the message in
>     this way.
>     >     I am
>     >     > now used to it:)
>     >     >
>     >     > The results from the contrast 0 0 1 -1 did not
survive the
>     multiple
>     >     > comparision corrections. In other words, I guess that it
>     should
>     >     imply
>     >     > that I could try DOSS.
>     >     >
>     >     > If my thought is wrong, please feel free to let me know.
>     >     You are correct.
>     >     >
>     >     > By the way, is it possible to do SVC (small volume
>     correction) using
>     >     > an anatomical image from a particular brain region,
which
>     is the
>     >     > conventional way to improve statistical power?
>     >     You can specify a mask for an ROI when you run mri_glmfit.
>     But that
>     >     means you have to run your own simulation to do the
correction.
>     >     doug
>     >
>     >
>     >     >
>     >     > Thanks, again.
>     >     >
>     >     >
>     >     > On Thu, Jan 9, 2014 at 6:23 PM, Douglas N Greve
>     >     > <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
>     >     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
>     >     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>> wrote:
>     >     >
>     >     >
>     >     >     Please remember to post to the list. For the 0 0
1 -1
>     contrast,
>     >     >     did any results survive multiple comparisons
>     correction? If so,
>     >     >     then at least the voxels in that region cannot
be used
>     with
>     >     DOSS.
>     >     >     I'm not sure why the patter was opposite between
the two
>     >     >     contrasts. I could mean that there is a nonlinear
>     relationship
>     >     >     with age.
>     >     >
>     >     >     doug
>     >     >
>     >     >
>     >     >     On 01/09/2014 03:54 AM, yaya ya wrote:
>     >     >
>     >     >         Dear Greve,
>     >     >
>     >     >         Thank you very much for your response. I am
now a
>     little
>     >     more
>     >     >         clear, although I still have some further
questions.
>     >     >
>     >     >         According to your suggestion, I just tried
to test
>     whether
>     >     >         there is a difference between group age. I
>     included age as a
>     >     >         continuous variable in qdec. After running,
I got the
>     >     results
>     >     >         arising from the contrast 0 0 1 -1 (which is
>     called does the
>     >     >         thickness-age correlation differ between two
>     groups?). That
>     >     >         is, the results revealed the thinner in some
brain
>     >     areas. But
>     >     >         when I checked the results relating to the
>     comparision of
>     >     >         groups (1 -1 0 0 ), the results were the same
>     expect the
>     >     >         opposite pattern. That is, the results became
>     thicker in the
>     >     >         same region.
>     >     >
>     >     >         Does this imply that there is an age effect? It
>     means I
>     >     could
>     >     >         not use DOSS to do analysis, right?
>     >     >
>     >     >         Best,
>     >     >         Lickey
>     >     >
>     >     >
>     >     >         On Thu, Jan 9, 2014 at 12:32 AM, Douglas N Greve
>     >     >         <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
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<mailto:greve@nmr.mgh.harvard.edu>
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<mailto:greve@nmr.mgh.harvard.edu>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>>> wrote:
>     >     >
>     >     >
>     >     >             On 01/08/2014 04:28 PM, yaya ya wrote:
>     >     >             > Dear Freesurfer experts,
>     >     >             >
>     >     >             > I have a question about cortical thickness
>     >     analysis using
>     >     >             freesurfer.
>     >     >             > Since I don't know how to post my
question in
>     >     freesurfer
>     >     >         mailing
>     >     >             > list,  that is why I am writing to you to
>     get some
>     >     help.
>     >     >             Hopefully, my
>     >     >             > email will not cause you any troubles.
>     >     >             Thanks for posting to the list.
>     >     >             >
>     >     >             > My question is : When I compared thickness
>     from two
>     >     >         groups (a
>     >     >             patient
>     >     >             > group and a healthy contrl group),
that is say I
>     >     got the
>     >     >         thinner
>     >     >             in a
>     >     >             > subdivision of a particular brain
region in
>     patients
>     >     >         than that in
>     >     >             > controls. But when I added age as a
nusiance
>     factors
>     >     >         (not in the
>     >     >             > continuous covariate because I want to
>     control for or
>     >     >         regress
>     >     >             out the
>     >     >             > age effect) in qdec, the results
changed. In
>     the same
>     >     >         region,  the
>     >     >             > thickness became thicker in the patients
>     than that
>     >     in the
>     >     >             controls.  I
>     >     >             > have no idea what happened. Which of
them do
>     I need to
>     >     >         trust?
>     >     >             The age
>     >     >             > between two groups has been matched.
>     >     >             It depends on several things. It might
be that
>     there
>     >     is an
>     >     >         interaction
>     >     >             between group and age. Try testing for a
>     difference
>     >     >         between the age
>     >     >             slopes of the two groups. If there is no
>     difference,
>     >     then
>     >     >         re-run using
>     >     >             DOSS (DOSS was removed from QDEC so
you'll have to
>     >     create
>     >     >         an FSGD file
>     >     >             and use mri_glmfit).
>     >     >             >
>     >     >             > In addition, when I do FDR correction
on the
>     results,
>     >     >         the min in the
>     >     >             > threshold jumped to more than 5 ,
making all the
>     >     clusters
>     >     >             disappear. I
>     >     >             > think this correction is too high,
unabling the
>     >     genious
>     >     >         effects to
>     >     >             > show up. How to deal with it?
>     >     >             Try using a cluster correction instead
of FDR.
>     >     >             doug
>     >     >
>     >     >             >
>     >     >             > By the way, our lab's IT staffs
install the
>     >     lastest released
>     >     >             > freesurfer. But when I use the qdec, I
could
>     not find
>     >     >         the option of
>     >     >             > DODS and DOSS, as discussed in the mailing
>     list. I am
>     >     >         wondering
>     >     >             if it
>     >     >             > has been deleted in this new version.
>     >     >             >
>     >     >             > I really appreciate your help in advance.
>     >     >             >
>     >     >             > Best,
>     >     >             > Lickey
>     >     >             >
>     >     >             >
>     >     >             >
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>     >     >             --
>     >     >             Douglas N. Greve, Ph.D.
>     >     >             MGH-NMR Center
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>     >     >     MGH-NMR Center
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<mailto:greve@nmr.mgh.harvard.edu>>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
>     >     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>
>     >     >     Phone Number: 617-724-2358 <tel:617-724-2358>
>     >     <tel:617-724-2358 <tel:617-724-2358>>
>     >     >     Fax: 617-726-7422 <tel:617-726-7422>
<tel:617-726-7422
>     >     <tel:617-726-7422>>
>     >     >
>     >     >     Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     >     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     >     >    
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     >     >     FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>     >     > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>     >    
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>     >     >
>     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>     >     >     Outgoing:
>     >     >
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>     >     >
>     >     >
>     >     >
>     >     >
>     >     > _______________________________________________
>     >     > Freesurfer mailing list
>     >     > Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>     <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>     >     <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>     <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>     >     >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>     >
>     >     --
>     >     Douglas N. Greve, Ph.D.
>     >     MGH-NMR Center
>     > greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
>     <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
>     >     Phone Number: 617-724-2358
>     >     Fax: 617-726-7422
>     >
>     >     Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     >     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     >     FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>     > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>     >    
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>     >     Outgoing:
>     > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>     >
>     > _______________________________________________
>     >     Freesurfer mailing list
>     > Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>     <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>     <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>     <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>>
>     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>     >
>     >
>     >
>     >
>     > _______________________________________________
>     > Freesurfer mailing list
>     > Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>     <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>     --
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
>     Phone Number: 617-724-2358
>     Fax: 617-726-7422
>
>     Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>     Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
>     Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
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