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On 11/04/2016 11:09 AM, Alshikho, Mohamad J. wrote: > Thank you Doug! > Kindly in the attached figure are the "projfrac" values for #4 and #5 correct > for at which level the analysis will be carried out. > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Friday, November 4, 2016 10:29 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_preproc > > > > On 11/04/2016 07:25 AM, Alshikho, Mohamad J. wrote: >> Dear FS experts, >> >> I ran surface based analysis using PET maps, and the pipeline >> reported, in FS list, by multiple colleagues as the following: >> >> ·spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh >> >> ·mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii >> subject1/pet/pet_2_T1_register.dat ..... --projfrac 0.5 --out lh.mgh >> >> ·mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh >> --tval lh.sm6.mgh >> >> ·mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage >> lh --cortex --glmdir lh.glmdir// >> >> ·then mri_glmfit-sim to correct for multiple comparison. >> >> I wanted to know the correct usage of the flag "*_projfrac_*" in the >> command "*_mris_preproc_*": >> >> My understanding is that this flag control running the surface based >> analysis far from the surface (i.e. close to the surface or deep in >> the white matter) >> >> ·If it is 0.5 èthat means the surface based analysis is running in the >> middle area between white and pial >> >> ·if it is zero èthe surface based analysis is running close to white >> matter >> >> ·if it is +1 èthat means the surface based analysis is running close >> to the pial >> >> ·if it is -1 èthat means the surface based analysis is running deep in >> the white matter >> >> Kindly: >> >> 1.Is this correct? >> > Yes >> 2.Can I use values like -2 or -3 ... etc to run the analysis deep in >> the white matter. I aim to run surface based analysis on multiple >> layers of the brain deep from the pial to investigate how the PET >> signal is going to change between these layers? >> > In principle, yes, but often what happens is that when you follow the normal > vector into the white matter that far, you end up in GM or CSF and not WM. >> 3.What is the difference between the flag "*_projfrac_*" and the flag >> "*_projdis_*" >> > projdist will project an absolute distance (in mm). projfrac will project a > fraction of the thickness (as you describe above) >> 4.If I replace the PET maps in the previous pipeline by diffusion >> maps? Is it keep valid for diffusion data? >> > I guess it depends on what you mean by "valid". As I mention above, it will > not necessarily sample WM, and that probably invalidates it somewhat >> Many Thank! >> >> Mohamad >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/ _______________________________________________ Freesurfer mailing list 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.
