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: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 > 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
