18 Jan
2018
18 Jan
'18
5:14 p.m.
Is the problem that the surfreg command is failing or that you don't know how to apply LME?
On 1/17/18 9:55 AM, lanbo Wang wrote:
Hi Martin,
I didn't try to run recon-all, I try to run flipped. The code I used is: foreach subject (subj_27_2.long.s27_base) foreach? surfreg --s $subject --t fsaverage_sym --lh foreach? surfreg --s $subject --t fsaverage_sym --lh --xhemi foreach? end
Thanks, Lanbo
On Tue, Jan 16, 2018 at 4:46 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote:
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 <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 <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@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 list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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