I firstly did mris_preproc separately. Secondly used fscalc to reverse left symptom subjects. Thirdly used mri_concat --conjunct to combine all the subjects together.
The code is: 1.mris_preproc --target fsaverage_sym --hemi lh \ --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.sm00.s02.mgh \ --s subj_02_1 2. fscalc lh.lh-rh.thickness.sm00.s09.mgh mul -1 -o lh.lh-rh.thickness.sm00.s09.mgh 3.mri_concat --conjunct --i lh.lh-rh.thickness.sm00.s02.mgh lh.lh-rh.thickness.sm00.s03.mgh lh.lh-rh.thickness.sm00.s04.mgh lh.lh-rh.thickness.sm00.s05.mgh lh.lh-rh.thickness.sm00.s06.mgh lh.lh-rh.thickness.sm00.s08.mgh lh.lh-rh.thickness.sm00.s09.mgh lh.lh-rh.thickness.sm00.s10.mgh lh.lh-rh.thickness.sm00.s11.mgh lh.lh-rh.thickness.sm00.s12.mgh lh.lh-rh.thickness.sm00.s13.mgh lh.lh-rh.thickness.sm00.s14.mgh lh.lh-rh.thickness.sm00.s15.mgh lh.lh-rh.thickness.sm00.s16.mgh lh.lh-rh.thickness.sm00.s17.mgh lh.lh-rh.thickness.sm00.s18.mgh lh.lh-rh.thickness.sm00.s19.mgh lh.lh-rh.thickness.sm00.s20.mgh lh.lh-rh.thickness.sm00.s21.mgh lh.lh-rh.thickness.sm00.s22.mgh lh.lh-rh.thickness.sm00.s24.mgh lh.lh-rh.thickness.sm00.s25.mgh lh.lh-rh.thickness.sm00.s26.mgh lh.lh-rh.thickness.sm00.s27.mgh lh.lh-rh.thickness.sm00.s29.mgh lh.lh-rh.thickness.sm00.s32.mgh --o lh.lh-rh.thickness.sm00.mgh 4.smooth 5.mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
On Fri, Nov 10, 2017 at 11:17 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Do you only have one subject in your input file? You need to run mris_preproc separately for each subject, create a different file for each, then mri_concat the files together
On 11/9/17 6:20 PM, lanbo Wang wrote:
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 <greve@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
which method are you trying to implement? If #3, then you need torun
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 > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto: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 helpyou.
> Please include the command you ran and the entire screenoutput.
> > 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 GHzIntel
> 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> <mailto: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> > <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 changethe
> 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 subjectstogether
> 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
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