WM/Pial surfs Problem with SPGRs from 3T GE - Freesurfer

24 Jul 2012

  As you can see from the picture, the autorecon does not
  work properly (for WM/Pial surfs) with my files:
  Especially in the temporal lobes.

  I am working with the SPGR files of a 3T GE Machine.
  Is there any way to optimize the autorecon results for
  SPGRs?
  (Except the lavish application of CPs.)

  Best regards
  Thomas

  On Mon, Jul 23, 2012 at 6:00 PM,
  <freesurfer-request@nmr.mgh.harvard.edu> wrote:
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        Today's Topics:

           1. Re: Questions about correction over 2
        hemispheres and MCC
              (Reem Jan)
           2. More than two time-points in
        longitudinal base = Memory
              allocation error? (Liz Bowman)
           3. Re: Talairach registration (Mojdeh
        Zamyadi)
           4. Subcortical segmentations (Jordan
        Pierce)

        ----------------------------------------------------------------------

        Message: 1
        Date: Sun, 22 Jul 2012 21:12:44 +0000
        From: Reem Jan <r.jan@auckland.ac.nz>
        Subject: Re: [Freesurfer] Questions about
        correction over 2
                hemispheres and MCC
        To: "Watson, Christopher"
        <Christopher.Watson@childrens.harvard.edu>
        Cc: Freesurfer Mailinglist
        <freesurfer@nmr.mgh.harvard.edu>
        Message-ID:

        <3375B664D4A0834FB7D0C15D590A9EF11825DBC1@FMHS-MBX1.fmhs.auckland.ac.nz>

        Content-Type: text/plain; charset="iso-8859-1"

        Hi Bruce, J?rgen and Chris

        Thank you for elaborating further. I've gone
        with a Bonferroni correction as I had a
        limited number of tests (a-priori hypothesis).
        But just out of interest Chris, you mentioned
        you found correlations between subcortical
        structures, do you have a reference I could
        look at? The tool that J?rgen suggested
        requires we enter a correlation coefficient,
        so I wondered if I could use published values
        or whether I'd need to calculate my own (if
        so, could you please recommend a way of doing
        that in Freesurfer or FSL?)

        Many thanks in advance

        Kind regards
        Reem

        -----Original Message-----
        From: freesurfer-bounces@nmr.mgh.harvard.edu
        [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]
        On Behalf Of J?rgen H?nggi
        Sent: Sunday, 22 July 2012 7:47 p.m.
        To: Watson, Christopher
        Cc: Freesurfer Mailinglist
        Subject: Re: [Freesurfer] Questions about
        correction over 2 hemispheres and MCC

        Hi Chris

        Yes there are such tools. Bonferroni oder
        Sidak test that take into account the
        correlated measures. Here you can find these
        tools

        http://www.quantitativeskills.com/sisa/calculations/bonfer.htm

        Cheers
        J?rgen

        On [DATE], "Watson, Christopher" <[ADDRESS]>
        wrote:

        > What about, for example, the correlations
        I've seen in a cohort of subjects.
        >
        > In 158 subjects aged 10-19 (both controls
        and patients), the
        > correlation between L & R thalamus is 0.91,
        and the correlations
        > between L & R of caudate, putamen, pallidum,
        hippocampus, and amygdala were all 0.75 or
        higher.
        >
        > I would think that a Bonferroni correction
        would be incredibly
        > conservative and, in my opinion, just plain
        wrong because true
        > significant diff's would be missed. Is there
        any principled way of
        > dealing with multiple tests that are
        correlated?
        >
        > Thanks,
        > Chris
        > ________________________________________
        > From: Bruce Fischl
        [fischl@nmr.mgh.harvard.edu]
        > Sent: Saturday, July 21, 2012 12:01 PM
        > To: Watson, Christopher
        > Cc: Douglas N Greve;
        freesurfer@nmr.mgh.harvard.edu
        > Subject: Re: [Freesurfer] Questions about
        correction over 2
        > hemispheres and MCC
        >
        > Hi Chris,
        >
        > bonferroni will be overly conservative in
        that case, but we rarely
        > really know the true covariance structure of
        the data, so we would
        > rather err on the side of being
        conservative.
        >
        > cheers
        > Bruce
        > On Fri, 20 Jul 2012, Watson, Christopher
        > wrote:
        >
        >> Hi Doug et al,
        >>
        >> The 2nd question is something I've wondered
        about. Doesn't a
        >> Bonferroni correction assume that the
        measures are independent?
        >> If so, I think in the case of subcortical
        structures, it is incorrect
        >> to use this method, as e.g. the putamen and
        pallidal volumes are not
        >> independent of one another.
        >> If not, and it is acceptable to use when
        there are dependencies
        >> between measures, how do you calculate the
        FWE? It wouldn't be equal
        >> to alpha/n, unless I am misunderstanding
        something.
        >>
        >> Thanks,
        >> Chris
        >> ________________________________________
        >> From:
        freesurfer-bounces@nmr.mgh.harvard.edu
        >> [freesurfer-bounces@nmr.mgh.harvard.edu] on
        behalf of Douglas N Greve
        >> [greve@nmr.mgh.harvard.edu]
        >> Sent: Friday, July 20, 2012 2:38 PM
        >> To: freesurfer@nmr.mgh.harvard.edu
        >> Subject: Re: [Freesurfer] Questions about
        correction over 2
        >> hemispheres and MCC
        >>
        >> Hi Reem, it looks like you've done
        everything correctly (sorry for
        >> the null result). As for your second,
        question, I don't think there
        >> is a way other than Bonferroni. You can try
        FDR, but it makes the
        >> interpretation a little messy.
        >> doug
        >>
        >> On 07/19/2012 07:59 PM, Reem Jan wrote:
        >>>
        >>> Hi Doug
        >>>
        >>> I hope it?s okay that I double check I?m
        doing the correction over 2
        >>> hemispheres correctly and ask a question
        regarding correction for
        >>> multiple comparisons. I will briefly
        describe what I have done:
        >>>
        >>> I have 2 groups of subjects ? Drug addicts
        (n= 17) and controls (n=20).
        >>>
        >>> 1.I ran a surface thickness study:
        >>>
        >>> ?For the ?mri_glmfit? command, I used DOSS
        and specified a contrast
        >>> of
        >>> +1 -1 0 (Controls > MA)
        >>>
        >>> ?I ran a pre-cached simulation with the
        following command:
        >>> mri_glmfit-sim --glmdir
        lh.group_age.glmdir --cache 4 pos
        >>>
        >>> ?This simulation should only have
        corrected for the left hemisphere
        >>> as I understand it. My cluster summary
        text file showed me that a
        >>> cluster survived in the insula. I
        interpreted this as ?controls had
        >>> higher grey matter thickness in this
        cluster located in the insula
        >>> than drug addicts?. However, this was only
        corrected over the left
        >>> hemisphere (when I ran the same simulation
        in the right hemisphere,
        >>> nothing survived multiple comparison
        correction).
        >>>
        >>> ?I now wanted to correct the lh results
        for 2 hemispheres. From the
        >>> help menu of ?mri_glmfit-sim?, I
        understood you can do this in 2
        >>> ways, are both of these correct and give
        the same result?
        >>>
        >>> a.mri_glmfit-sim --glmdir
        lh.group_age.glmdir --cache 4 pos --2
        >>> spaces --no-sim csdbase
        >>>
        >>> b.mri_glmfit-sim --glmdir
        lh.group_age.glmdir --cache 4 pos
        >>> --cwpvalthresh 0.025
        >>>
        >>> ?No clusters survived the Bonferroni
        correction over both hemispheres.
        >>> So I assume I can no longer report this
        result?
        >>>
        >>> 2.I ran a subcortical volume study:
        >>>
        >>> ?I used SPSS to perform the statistical
        analysis on each of 14
        >>> subcortical structures (left and right).
        Is there a good way to
        >>> correct for multiple comparisons, apart
        from Bonferroni, which would
        >>> be very conservative?
        >>>
        >>> Many thanks for your advice.
        >>>
        >>> Kind regards
        >>>
        >>> Reem
        >>>
        >>> *Reem Jan***
        >>>
        >>> BPharm (Hons), RegPharmNZ
        >>>
        >>> PhD Student / Pharmacist
        >>>
        >>> School of Pharmacy, Faculty of Medical &
        Health Sciences, The
        >>> University of Auckland, Private Bag 92019,
        Auckland, New Zealand.
        >>>
        >>> Ph: +64 9 373 7599 ext 81138. DDI: +64 9
        923 1138
        >>>
        >>> F: +64 9 367 7192
        >>>
        >>>
        *From:*freesurfer-bounces@nmr.mgh.harvard.edu
        >>>
        [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]
        *On Behalf Of
        >>> *Douglas Greve
        >>> *Sent:* Friday, 20 July 2012 11:52 a.m.
        >>> *To:* freesurfer@nmr.mgh.harvard.edu
        >>> *Subject:* Re: [Freesurfer] slice-by-slice
        predictors
        >>>
        >>> Sorry, not possible.
        >>>
        >>> On 7/19/12 6:56 PM, Caspar M. Schwiedrzik
        wrote:
        >>>
        >>> Hi!
        >>> Is it possible to have slice-by-slice
        predictors in Freesurfer, and
        >>> if so, how?
        >>> Thanks,
        >>> Caspar
        >>>
        >>>
        >>>
        >>>
        >>>
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        >>>
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        >>
        >> --
        >> Douglas N. Greve, Ph.D.
        >> MGH-NMR Center
        >> greve@nmr.mgh.harvard.edu
        >> Phone Number: 617-724-2358
        >> Fax: 617-726-7422
        >>
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        surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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        >>
        >>
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        >
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