On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve <greve@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

> <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
>
>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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