Dr. Douglas, I try #3 method, when I run mri_glmfit, get error. The code I used: [mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh Reading source surface /HD4/subjects_results_symptom//fsaverage_sym/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 61972.710938 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh sysname Linux hostname localhost.localdomain machine x86_64 user mtobia FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.thickness.sm10.mgh logyflag 0 usedti 0 labelmask /HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex.label maskinv 0 glmdir glm.lh.lh-rh.thickness.sm10 IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory glm.lh.lh-rh.thickness.sm10 Loading y from /HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.thickness.sm10.mgh Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 146902 points in label. Pruning voxels by thr: 0.000000 Found 146902 voxels in mask Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh Reshaping mriglm->mask... search space = 79288.081914 DOF = 0 ERROR: DOF = 0 The code I used before this one is How can I resolve this problem. Thanks, Lanbo On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > which code. I gave 3 options below, which one did you use? > > > On 11/07/2017 02:43 PM, lanbo Wang wrote: > > 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 <mailto: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> > > <mailto: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> > > <mailto: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> > > > <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> > > > <mailto: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> > > > <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> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu > >> > > > Phone Number: 617-724-2358 <tel:617-724-2358> > > <tel:617-724-2358 <tel:617-724-2358>> > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > > <tel:617-726-7422>> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://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> > > > <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> > > > > > <http://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/> > > > <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> > > > <mailto: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> > > > <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> > > > <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> > > <mailto: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> > > > > > <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> > > > <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> > > > > -- > > 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:freesur...@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > > > > > _______________________________________________ > > 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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