I try to use this code to compare left and right hemisphere by paired t-test and add age as covariate.
Thanks, Lanbo On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > which method are you trying to implement? If #3, then you need to run > mris_preproc separately for each subject, and then run that fscalc command > > > On 11/07/2017 11:33 AM, lanbo Wang wrote: > > 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 <mailto: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 <mailto: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 > > <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 > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > _______________________________________________ > > 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:freesur...@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 > > 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 >
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