Hi Lanbo,
what is the exact command you use for this? The problem is that the
script or your command does not pass the right flags to recon all.
Whenever recon-all is supposed to work on a longitudinal directory it
needs to know the base and the long so the recon all command needs to show
-long subj_02_1 s02_base
as part of its arguments. So either adjust your command line, or if the
recon-all call is performed from within another script, we need to
change that script (add a -long flag so that the script performs the
correct recon-all call in those cases when working on a longitudinal
time point).
Once you have the left right difference (define on one of the
hemispheres), you can treat it similar as a thickness map and run it
through the Matlab LME code.
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
Best, Martin
Am 27.12.2017 um 16:11 schrieb lanbo Wang:
Thanks for replying me. But I still have two questions.
Firstly, when I try xhemi on pre-possessed longitudinal data, it
showed error like this:
Performing left-right swap of labels
TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00
i_ras = (-1, 3.72529e-08, 3.35276e-08)
j_ras = (-2.6077e-08, -3.72529e-09, -1)
k_ras = (-1.78814e-07, 1, 6.98492e-10)
writing to
/HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+aseg.mgz...
Wed Dec 20 17:46:35 EST 2017
recon-all -sb subj_02_1.long.s02_base/xhemi -talairach
ERROR: Are you trying to run or re-run a longitudinal time point?
If so, please specify the following parameters:
\' -long <tpNid> <templateid> \'
where <tpNid> is the time point id (SAME as cross sectional
ID) and <templateid> is the ID created in the -base run.
The directory <tpNid>.long.<templateid> will be created
automatically or used for output, if it already exists.
Secondly, how I can get the change rate after construct left -right
registration.
Thanks,
Lanbo
On Fri, Dec 22, 2017 at 5:40 AM, Martin Reuter
<mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>> wrote:
Hi Lanbo,
you could look at longitudinal changes of the left-right
difference in volume per ROI. Or do you mean on the cortical
thickness map (I have never done that, but probably works
similarly, construct left -right registration, compute difference,
then run the LME on that).
Best, Martin
Am 17.12.2017 um 17:54 schrieb lanbo Wang:
Hi, all experts.
I want to compare changes rate between left and right hemisphere
of longitudinal data, How should I do that, how to combine xhemi
with two stage or LME?
Best,
Lanbo
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