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>
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
>
>
> _______________________________________________
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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/usr/local/freesurfer/bin/xhemireg
--s subj_02_1.long.s02_base
$Id: xhemireg,v 1.12.4.3 2012/05/02 21:28:58 greve Exp $
Wed Dec 20 17:46:00 EST 2017
Linux localhost.localdomain 3.10.0-693.5.2.el7.x86_64 #1 SMP Fri Oct 20 20:32:50 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
/HD4/symptom_test/subj_02_1.long.s02_base
setenv SUBJECTS_DIR /HD4/symptom_test/
Wed Dec 20 17:46:00 EST 2017
Wed Dec 20 17:46:00 EST 2017
mri_vol2vol --mov mri/orig.mgz --targ mri/orig.mgz --reg /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat --o /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/orig.mgz --keep-precision --no-save-reg
Matrix from regfile:
-1.000 0.000 0.000 1.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
movvol mri/orig.mgz
targvol mri/orig.mgz
outvol /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/orig.mgz
regfile /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat
invert 0
tal 0
talres 2
regheader 0
noresample 0
interp trilinear (1)
precision uchar (0)
Gdiag_no -1
Synth 0
SynthSeed 1514107653
Final tkRAS-to-tkRAS Matrix is:
-1.000 0.000 0.000 1.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Vox2Vox Matrix is:
-1.000 0.000 0.000 255.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Resampling
Output registration matrix is identity
mri_vol2vol done
mri_vol2vol --mov mri/T1.mgz --targ mri/T1.mgz --reg /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat --o /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/T1.mgz --keep-precision --no-save-reg
Matrix from regfile:
-1.000 0.000 0.000 1.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
movvol mri/T1.mgz
targvol mri/T1.mgz
outvol /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/T1.mgz
regfile /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat
invert 0
tal 0
talres 2
regheader 0
noresample 0
interp trilinear (1)
precision uchar (0)
Gdiag_no -1
Synth 0
SynthSeed 1514410525
Final tkRAS-to-tkRAS Matrix is:
-1.000 0.000 0.000 1.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Vox2Vox Matrix is:
-1.000 0.000 0.000 255.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Resampling
Output registration matrix is identity
mri_vol2vol done
mri_vol2vol --mov mri/brain.mgz --targ mri/brain.mgz --reg /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat --o /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/brain.mgz --keep-precision --no-save-reg
Matrix from regfile:
-1.000 0.000 0.000 1.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
movvol mri/brain.mgz
targvol mri/brain.mgz
outvol /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/brain.mgz
regfile /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat
invert 0
tal 0
talres 2
regheader 0
noresample 0
interp trilinear (1)
precision uchar (0)
Gdiag_no -1
Synth 0
SynthSeed 1514238224
Final tkRAS-to-tkRAS Matrix is:
-1.000 0.000 0.000 1.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Vox2Vox Matrix is:
-1.000 0.000 0.000 255.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Resampling
Output registration matrix is identity
mri_vol2vol done
mri_vol2vol --mov mri/brainmask.mgz --targ mri/brainmask.mgz --reg /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat --o /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/brainmask.mgz --keep-precision --no-save-reg
Matrix from regfile:
-1.000 0.000 0.000 1.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
movvol mri/brainmask.mgz
targvol mri/brainmask.mgz
outvol /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/brainmask.mgz
regfile /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat
invert 0
tal 0
talres 2
regheader 0
noresample 0
interp trilinear (1)
precision uchar (0)
Gdiag_no -1
Synth 0
SynthSeed 1514430001
Final tkRAS-to-tkRAS Matrix is:
-1.000 0.000 0.000 1.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Vox2Vox Matrix is:
-1.000 0.000 0.000 255.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Resampling
Output registration matrix is identity
mri_vol2vol done
mri_vol2vol --mov mri/norm.mgz --targ mri/norm.mgz --reg /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat --o /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/norm.mgz --keep-precision --no-save-reg
Matrix from regfile:
-1.000 0.000 0.000 1.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
movvol mri/norm.mgz
targvol mri/norm.mgz
outvol /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/norm.mgz
regfile /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat
invert 0
tal 0
talres 2
regheader 0
noresample 0
interp trilinear (1)
precision uchar (0)
Gdiag_no -1
Synth 0
SynthSeed 1514650673
Final tkRAS-to-tkRAS Matrix is:
-1.000 0.000 0.000 1.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Vox2Vox Matrix is:
-1.000 0.000 0.000 255.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Resampling
Output registration matrix is identity
mri_vol2vol done
mri_vol2vol --mov mri/aseg.mgz --targ mri/aseg.mgz --reg /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat --o /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aseg.mgz --keep-precision --no-save-reg
Matrix from regfile:
-1.000 0.000 0.000 1.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
movvol mri/aseg.mgz
targvol mri/aseg.mgz
outvol /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aseg.mgz
regfile /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat
invert 0
tal 0
talres 2
regheader 0
noresample 0
interp trilinear (1)
precision uchar (0)
Gdiag_no -1
Synth 0
SynthSeed 1513841262
Final tkRAS-to-tkRAS Matrix is:
-1.000 0.000 0.000 1.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Vox2Vox Matrix is:
-1.000 0.000 0.000 255.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Resampling
Output registration matrix is identity
mri_vol2vol done
mri_convert /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aseg.mgz /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aseg.mgz --left-right-swap-label
mri_convert /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aseg.mgz /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aseg.mgz --left-right-swap-label
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aseg.mgz...
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/aseg.mgz...
mri_vol2vol --mov mri/aparc+aseg.mgz --targ mri/aparc+aseg.mgz --reg /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat --o /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+aseg.mgz --keep-precision --no-save-reg
Matrix from regfile:
-1.000 0.000 0.000 1.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
movvol mri/aparc+aseg.mgz
targvol mri/aparc+aseg.mgz
outvol /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+aseg.mgz
regfile /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat
invert 0
tal 0
talres 2
regheader 0
noresample 0
interp trilinear (1)
precision int (1)
Gdiag_no -1
Synth 0
SynthSeed 1514546383
Final tkRAS-to-tkRAS Matrix is:
-1.000 0.000 0.000 1.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Vox2Vox Matrix is:
-1.000 0.000 0.000 255.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Resampling
Output registration matrix is identity
mri_vol2vol done
mri_convert /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+aseg.mgz /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+aseg.mgz --left-right-swap-label
mri_convert /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+aseg.mgz /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+aseg.mgz --left-right-swap-label
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+aseg.mgz...
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.
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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