Re: [Freesurfer] hemisphere analysis

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> 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 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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