After I try the code: mri_compute_layer_fractions -nlayers 4 $SUBJECTS_DIR/fMRI/register.lta $SUBJECTS_DIR/fMRI/HIP001_rest_preproc_norm.nii test.mgz
open test.mgz using freeview like this! Not binarize according different layers! Also the frontal part of the brain is missing! > On Sep 1, 2015, at 11:49, Bruce Fischl <[email protected]> wrote: > > you can use -n <name> to change the name of the surfaces, and -nlayers <n> to > specify the number of layers it computes (# of surfaces = 1+number of layers > I think) > On Tue, 1 Sep 2015, Yun Wang wrote: > >> Thanks! But it looks this script keeps looking for the lh.gwdist00N forever, >> here is the error message: >> mri_compute_layer_fractions: could not load lh surface 5 >> from/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical/out >> put/surf/lh.gwdist005 >> I do not have lh.gwdist005. How can I set up the number in this code? >> >> On Sep 1, 2015, at 11:08, Bruce Fischl >> <[email protected]> wrote: >> no, you just need to name them in the way that >> mri_compute_layer_fractions is expecting (e.g. lh.gwdist000 for white, >> etc...) >> On Tue, 1 Sep 2015, Yun Wang wrote: >> >> I do have 5 intermediate surfaces, should I combine them >> together? >> >> On Sep 1, 2015, at 10:43, Bruce Fischl >> <[email protected]> wrote: >> >> you need to use mris_expand to generate the >> family of intermediate surfaces >> >> cheers >> Bruce >> On Tue, 1 Sep 2015, Yun Wang wrote: >> >> Hi all experts, >> I have the error message when >> trying to use >> mri_compute_layer_fractions. >> mri_compute_layer_fractions >> $SUBJECTS_DIR/fMRI/register.lta >> $SUBJECTS_DIR/white_lh.mgz test >> reading >> registrationfile/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomical >> /fMR >> I/register.lta >> regio_read_register: loading lta >> regio_read_register: loading lta >> >> readingvolume/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomic >> al/out >> put/mri/aseg.mgz >> reading laminar surfaces from >> gwdist.? >> >> readingsurface/Users/emilyUS/Documents/Cortical_layer/Data/anatomical/Rest-Anatomi >> cal/out >> put/surf/lh.gwdist000 >> Anyone know the gwdist? how I can >> get it? >> Thanks! >> Yun Wang >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> 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 . 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 >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > [email protected] > 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 . 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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