Thank you very much Doug! -----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 12:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc
projfrac = -2 appears to be pointing at the ventricle. It should be 2*thickness away from the white surface into the white matter On 11/04/2016 12:11 PM, Alshikho, Mohamad J. wrote: > Hi Doug, > I am sorry for sending multiple emails. I wanted to be sure that I understand > it properly. Kindly: > My question is regarding "projfrac = -1" and "projfrc=-2" are the pointers in > the figure located correctly where the analysis will be carried out? > > Thanks again > > > > > -----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 12:09 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_preproc > > Do you have a question about the image? > > > 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 > > _______________________________________________ > 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 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 . 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