External Email - Use Caution
Hi Douglas,
According to your suggestion, I used the permutation simulation approach. I
chose a cluster forming threshold set at 0.05 and explored how the number
of iterations effects the data. For example, I used this command for 1,000
iterations:
mri_glmfit-sim \
--glmdir lh.longMRI.glmdir \
--sim perm 1000 1.3 perm.abs.13 \
--sim-sign abs\
--cwpvalthresh 0.05
I did not observe any difference on the size of the cluster between 1,000
vs 5,000 vs 10,000 iterations. As I thought the results were pretty odd, I
tried running the command with 5 permutations just to make sure it's not
also the same and I did not find any significant clusters.
Is the absence of cluster size difference between different number of
iterations expected? Just wanted to make sure with you that this approach
is working as it should.
Thanks!
Regards,
On Fri, Feb 22, 2019 at 6:50 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> You can make the bonferroni correction from of mri_glmfit-sim the same as
> qdec by not including --2spaces (the bonferroni correction in qdec is
> actually 1, not 0). Also, if you want to use such a low cluster forming
> threshold (1.3=p<.05), then you should use permutation and not MC (MC is
> not valid at such low thresholds).
>
> On 2/22/19 7:49 AM, Giuliana Klencklen wrote:
>
> External Email - Use Caution
> Thanks Douglas, that makes sense. I have run mri_glmfit-sim and have that
> table file.
> However, the cortical thickness values for each cluster displayed in that
> table can’t be used because the clusters (something.sig.cluster.mgh opened
> with tksurfer) do not match exactly (but are very similar to) those
> previously generated with QDEC. I do not understand the cause of this issue
> because all the stats I used, i.e., threshold, statistical correction,
> level of smooting, seem to be the same between both qdec and
> mri_glmfit-sim.
>
> I send you here a typical example of the problematic clusters, as well as
> the summary for both qdec and mri_glmfit-sim. They appear similar except
> for the Bonferroni correction that is set at 2 for the mri_glmfit-sim while
> it is set at 0 for the qdec version? If it is the source of the current
> issue, how can I configure the Bonferroni correction? If not, do you have
> any idea how I can resolve the problem?
>
> Many thanks in advance.
>
> Regards,
> Giuliana Klencklen
> [image: QdecGroupComparison.jpg]
>
> On Fri, Feb 15, 2019 at 5:24 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> This can happen if the label is small and/or you've used a lot of
>> smoothing. It is better to do this kind of thing in fsaverage space rather
>> than moving the labels back to the individual space. If you've run
>> mri_glmfit-sim, then it should have created a table file
>> (something.y.ocn.dat). This file will have a row for each subject and a
>> column for each cluster. The value will be the mean for that subject in
>> that cluster.
>>
>> On 2/15/19 6:23 AM, Giuliana Klencklen wrote:
>>
>> External Email - Use Caution
>> Hi FS experts,
>>
>> I did group-level, surface-based, vertex-wise analysis for baseline and
>> longitudinal data. I used Qdec and do the same work with the fsgd version
>> (mri_glmfit-sim command) to double-check the data.
>>
>> I created label files with tksurfer for each of the clusters showing a
>> significant between-group difference. Then, I used the following command
>> stream to extract the cortical thickness values for each subject and
>> cluster: mri_label2label, mris_anatomical_stats, and aparcstats2table.
>> E.g.,
>> mri_label2label --srcsubject fsaverage --srclabel
>> /home/jagust/gklenck/Long_MRI/lh.ac-baseline-rostralmiddlefrontal.label
>> --trgsubject ${s}_tp1 --trglabel
>> ${s}_tp1/label/lh.ac-baseline-rostralmiddlefrontal.label --hemi lh
>> --regmethod surface
>>
>> mris_anatomical_stats -l lh.ac-baseline-rostralmiddlefrontal.label -t
>> lh.thickness -b -f ${s}_tp1/stats/lh.ac-baseline-rostralmiddlefrontal.stats
>> ${s}_tp1 lh
>>
>> aparcstats2table --subjects ${s}_tp1 --hemi lh --parc
>> ac-baseline-rostralmiddlefrontal --meas thickness --tablefile
>> ${out_dir}/lh.ac-baseline-rostralmiddlefrontal.aparc_stats.txt
>>
>> Subsequently, when I conducted between-group comparisons for each
>> cluster, a couple of clusters (7 out of 16) do not show a significant
>> difference - which does not make sense. This problem seems to appear
>> randomly.
>>
>> Help to the FS archives, I tried to use mri_segstats command but was not
>> able to find a correct combination of arguments. If this is the right track
>> to solve this problem, what combination of arguments should I use? And if
>> this is not, do you have any idea how I can solve this problem?
>>
>> Many thanks in advance.
>>
>> Regards,
>> Giuliana
>>
>>
>> --
>> Giuliana Klencklen, Ph.D.
>>
>> Helen Wills Neuroscience Institute
>> University of California, Berkeley
>> 118 Barker Hall
>> Berkeley, CA 94720-3190
>> 510-395-0040
>> giuliana.klenck...@berkeley.edu
>>
>> _______________________________________________
>> Freesurfer mailing
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>>
>>
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>
>
>
> --
> Giuliana Klencklen, Ph.D.
>
> Helen Wills Neuroscience Institute
> University of California, Berkeley
> 118 Barker Hall
> Berkeley, CA 94720-3190
> 510-395-0040
> giuliana.klenck...@berkeley.edu
>
> _______________________________________________
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
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--
Giuliana Klencklen, Ph.D.
Helen Wills Neuroscience Institute
University of California, Berkeley
118 Barker Hall
Berkeley, CA 94720-3190
510-395-0040
giuliana.klenck...@berkeley.edu
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