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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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/

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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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.