I obtain this error: mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir Thickness.wls --nii.gz --fsgd g1v1_thickness.fsgd --C intercept.mtx --C slope.mtx --pvr $SUBJECTS_DIR/rh.MCI.thickness.10B.mgh
Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/rh.white gdfRead(): reading g1v1_thickness.fsgd ERROR: fio_FileHasCarriageReturn(): cannot open g1v1_thickness.fsgd > Il 5 febbraio 2018 alle 18.26 Douglas Greve <gr...@nmr.mgh.harvard.edu> ha > scritto: > > > > > On 2/4/18 10:06 AM, std...@virgilio.it mailto:std...@virgilio.it wrote: > > > > > > I have run: > > > > 1) > > > > mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh --meas > > thickness --out rh.GROUP1.thickness.00.mgh > > mri_surf2surf --hemi rh --s fsaverage --sval > > rh.GROUP1.thickness.00.mgh --fwhm 10 --cortex --tval > > rh.GROUP1.thickness.10B.mgh > > > > > looks good > > > > > > 2) > > > > mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage > > rh --glmdir Age.wls --nii.gz --fsgd g1v1_Age.fsgd --C intercept.mtx --C > > slope.mtx --pvr rh.GROUP1.thickness.10B.mgh > > > > The command line is correct? > > > > > Yes, though I'm not sure about the effect of using --wls and --pvr. I > > guess it will be ok, I just have not used it. > > > > > > > > My concern is on the fsgd file. > > > > I have > > > > GroupDescriptorFile 1 > > Title All > > Class Main > > Variables thickness > > Input ADNI0XX_GROUP1 Main ???? > > Input ADNI0XY_GROUP1 Main ???? > > Input ADNI0YX.GROUP1 Main ???? > > ... > > > > What I should add after Main if I would like to assess the vertex > > by vertex correlation between FC (between seed and target vertex) and > > thickness (in the target vertex)? > > > > > Don't represent the PVR in the FSGD file. You only need to include > > items in the contrast matrix. Eg, for intercept use [1 0] and for slope use > > [0 1] eventhough you only have a single class. > > > > > > Should I add the path where is contained rh.thickness.mgh of each > > subject? > > > > > No > > > > > > Please give me an help because I did not find these information > > using --help or mail list. > > > > Thanks > > > > > > Stefano > > > > > > > > Il 3 febbraio 2018 alle 19.55 Douglas Greve > > <gr...@nmr.mgh.harvard.edu> mailto:gr...@nmr.mgh.harvard.edu ha scritto: > > > > > > Yes, use the --pvr option to mri_glmfit (per-voxel regressor). > > Search through the mail archives for an example on how to use it > > > > > > On 2/3/18 12:10 PM, std...@virgilio.it mailto:std...@virgilio.it > > wrote: > > > > > > > > > > Hi list, > > > > > > Is there a way to obtain a map that report the "vertex by > > > vertex" correlation between the FC (obtained by FS-FAST) and cortical > > > thickness? > > > > > > Thanks > > > > > > > > > Stefano > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > mailto:Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > mailto:Freesurfer@nmr.mgh.harvard.edu > > > 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 . 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. > > > > > > > > > > >
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