When creating a laterality-free atlas one needs to make sure to do the
same thing to the left and right hemi. Eg, the mni152 is not laterally
symmetric, so you will get a different registration when you register
your volume directly to the mni152 vs left-right reversing your volume
and then registering (and why people will register to a symmetric mni152
when doing such studies). These biases can creep in in other ways. Eg,
when manually labeling the brain, the labeler might do the left slightly
different than the right, and this might creep into the atlas (though
this can be reduced by including left-right reversed labels in the
atlas). Our standard labels (eg, aparc) are susceptible to these
problems. Any clearer?
On 3/6/2024 10:52 AM, Joost Janssen wrote:
External Email - Use Caution
Dear Doug,
Thanks. A regional Laterality Index can be calculated using XHEMI (as
described on the wiki) but also in a different way, e.g. using the
default FS output from ?h*.stats files and e.g. doing
(LH-RH)/((LH+RH)/2) or some other formula. You once mentioned about
this latter approach "But the atlas was not created in a symmetrical
way, so there might be biases". Could you elaborate on what these
biases might be?
I read *MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767398/
<https://secure-web.cisco.com/1TELdMKGVJpKa4ZNA0JT1c2M5j92hscTUXojMSwfCRgHWMi4h330-7qb3M2OGXIYrgOSZICxTxnpti-05ncWdhR6JaJbIx73FVjtEzOdBqK1bpmrufIS7sOC5rf9sTVNVfUF_2k02iDbUNyl8qoOsQMWS5KZS1t7h7JfI_o3K8yrj9LhxQ2EB54r2L_4CsVC3HXfzZQIQW58QvmALvYxzjqKSlL7ZlrmqwXDwD2yTC98P_wzNSIBNXBRqjKkZWOhCZR0piY0tJiFCGuAw6DMfILX-TiwrTwsyjwWmBqI1d_rxSHX5j2-2gRTFnUWbv9ua4qItxp5KwGEhL5PxfcxxZg/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC3767398%2F>
and it mentions biases when doing registration of a hemisphere to
either LH or RH but I am not sure if these are the same biases.
Thanks!
-joost
On Wed, Nov 29, 2023 at 12:02 AM Douglas N. Greve
<dgr...@mgh.harvard.edu> wrote:
Yes, they are. BTW, you should not need to mri_convert the
thickness to mgh format
On 11/27/2023 10:01 AM, Joost Janssen wrote:
External Email - Use Caution
Dear Doug,
The objective is to have _regional_ laterality index for
thickness for aparc mapped to the left hemisphere. The following
commands work without error but are they correct for meeting my
objective? Thanks.
surfreg --s $subject --t fsaverage_sym --lh --no-annot
surfreg --s $subject --t fsaverage_sym --lh --no-annot --xhemi
mri_convert $subject/surf/lh.thickness $subject/surf/lh.thickness.mgh
mri_convert $subject/surf/rh.thickness $subject/surf/rh.thickness.mgh
mris_apply_reg --src $subject/surf/lh.thickness.mgh --trg
$subject/surf/lh.thickness.lh.fsaverage_sym.mgh --streg
$subject/surf/lh.fsaverage_sym.sphere.reg
fsaverage_sym/surf/lh.sphere.reg
mris_apply_reg --src $subject/surf/rh.thickness.mgh --trg
$subject/surf/rh.thickness.lh.fsaverage_sym.mgh --streg
$subject/xhemi/surf/lh.fsaverage_sym.sphere.reg
fsaverage_sym/surf/lh.sphere.reg
fscalc $subject/surf/lh.thickness.lh.fsaverage_sym.mgh pctdiff0
$subject/surf/rh.thickness.lh.fsaverage_sym.mgh div 200 -o
$subject/surf/li.thickness.lh.fsaverage_sym.mgh
mri_segstats --annot fsaverage lh aparc --i
$subject/surf/li.thickness.lh.fsaverage_sym.mgh --sum
$subject/stats/li.thickness.aparc.stats
-joost
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