Hi Douglas, Thanks for your reply. I created the fsgd file as you show me, and run code like this. Am I right? 1. mris_preproc --fsgd Subject.xhemi.dat \ --target fsaverage_sym --hemi lh \ --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.age.sm00.mgh \ --s subj_02_1 --s subj_04_1 --s subj_05_1 --s subj_06_1 --s subj_08_1 --s subj_09_1 --s subj_10_1 --s subj_11_1 --s subj_12_1 --s subj_13_1 --s subj_14_1 --s subj_15_1 --s subj_16_1 --s subj_17_1 --s subj_18_1 --s subj_20_1 --s subj_21_1 --s subj_22_1 --s subj_24_1 --s subj_25_1 --s subj_26_1 --s subj_27_1 --s subj_29_1 --s subj_32_1
2. mri_glmfit --y lh.lh-rh.thickness.age.sm10.mgh --glmdir glm.lh.lh-rh.thickness.age.sm10 \ --fsgd Subject.xhemi.dat \ --C Avg-thickness-age-Cor.mtx \ --surf fsaverage_sym lh Attachment is fsgd and Avg-thickness-age-cor.mtx. All best, Lanbo Wang On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Danny > > you need to give us more information if you want us to help you. Please > include the command you ran and the entire screen output. > > cheers > Bruce > > > On Tue, 7 Nov 2017, Danny Deng wrote: > > Dear FDs, >> I encountered an odd situation: >> >> My free surfer will always shut down when I run command. >> >> My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel Core i5 >> >> I don’t know if the compatibility is fine with my download version (MacOS >> Lion OS X 10.7 (64b >> intel)Stable v6.0.0) >> >> Please kindly suggest. >> >> Thanks ver much >> >> Best Regards,Danny Deng >> >> >> On Nov 7, 2017, at 7:14 AM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu> wrote: >> >> >> >> On 11/06/2017 12:03 PM, lanbo Wang wrote: >> Dear experts, >> >> I have two questions about hemisphere analysis: >> >> 1) When I run left-right hemisphere paired t-test, can I add age as >> covariate? If use fsgd to add covariate, to this paired t-test >> analysis, how to make the fsgd table? >> >> use this one-group, one-covariate example >> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V >> 2) I want to reorganize the hemisphere from left-right to >> symptom-nosymptom according to body symptom side record and compare >> different between symptom hemisphere and nosymptom hemisphere. Can I >> use freesurfer to do it? >> >> Yes, though it is a little tricky with multiple ways, each complicated >> in its own way. >> 1. Create your own design matrix. You can use the one created by >> mri_glmfit to start. Assuming you want symptomHemi-nosymptomHemi, then, >> in each subject whose symptomHemi is rh, multiply its line in the design >> matrix by -1. Then pass this design matrix to mri_glmfit with --X >> instead of passing an FSGD file. >> 2. Load the output of mris_preproc into matlab, eg, y = >> MRIread('y.mgh');, then change the sign as in #1 above, eg, >> y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on for each applicable >> subject. Then save the data with MRIwrite(y,'new.y.mgh');, then run >> mri_glmfit as normal with the new file. >> 3. Run mris_preproc for each subject separately to generate an >> lh.lh-rh.thickness.sm00.subject10.mgh file. Then change the sign as in >> #1 above with >> fscalc lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o >> lh.lh-rh.thickness.sm00.subject10.mgh >> Then run mri_concat to concatenate all the subjects together in the same >> order as they are listed in the FSGD file, then use this stack as input >> the mri_glmfit >> >> >> Thanks for your patient and help. >> >> All best, >> Lanbo Wang >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> 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 > Freesurfer@nmr.mgh.harvard.edu > 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. > >
Subject.xhemi.dat
Description: Binary data
Avg-thickness-age-Cor.mtx
Description: Binary data
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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.
