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?
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
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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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