Sorry, I'll have to defer to Bruce, who wrote the code. doug On 12/17/2012 11:24 AM, Gabriel Gonzalez Escamilla wrote: > OK the Doug, > > I know which are the voxels contained into a ROI. From all of them I > know the norm.mgz and the brainmask.mgz values, because I'm assuming > that FS always work with the brainmask.mgz to know the actual voxel > intensity, as indicated when running mri_segstats. > > I can easily calculate the mean of the norm voxel intensities, do I > need anything else? > > Could you tell me the formula to compute the PV? > > Kind Regards, > Gabriel. > > > > > El 17/12/12, *Douglas N Greve * <gr...@nmr.mgh.harvard.edu> escribió: >> The PV is done based on intensities. For each voxel an the boundary of >> an ROI, the voxel intensity is assumed to be a weighted summation of the >> the average intensities in each ROI. Knowing the average intensities in >> the ROIs and the actual intensity of the voxel, the PV can be computed. >> doug >> >> >> On 12/17/2012 09:59 AM, Gabriel Gonzalez Escamilla wrote: >> > Thanks Doug, >> > >> > In my case I did as you said but as Bruce recommend use the wmparc, so >> > the voxels less than 4000, and = 5001 were left , and more than or >> > equal to 4000, and =5002 were right. >> > >> > So different approach but I think would be the same, isn't it? >> > >> > Can you explain to me how FS makes the PV correction on the output >> > volumes in aseg.stats? >> > >> > >> > Best Regards, >> > Gabriel. >> > >> > >> > El 13/12/12, *Douglas N Greve * <gr...@nmr.mgh.harvard.edu> escribió: >> >> >> >> Gabriel, the way I've done it is to just assign WMSA to left or right >> >> based on the column number of the WMSA voxel. If it is less than 128, >> >> then it is right (78) if it is greater than 128 it is left (79). It's >> >> not perfect, but it is correct in the vast majority of cases. >> >> doug >> >> >> >> >> >> On 12/12/2012 01:56 PM, Gabriel Gonzalez Escamilla wrote: >> >> >Thanks Bruce, >> >> > >> >> >The problem is that for this set of subjects I only have the T1s, >> >> anyways I would like to give a try onto the tools for WMSA, since I >> >> have T2 from some subjects. >> >> > >> >> >On the other hand, If I'm right the way to do the assignment on >> >> matlab, would be something like opening the mgz, finding their >> >> positions and look which are the neighbors right? >> >> >If so, I would like to not assign just the neighbor voxel, as this >> >> might bias the assignment, I'm guessing that something like the >> >> assignment done during the aparc+aseg.mgz creation (using GM >> >> parcelation to map GM labels to the wm voxels - mri_aparc2aseg) >> >> should be a correct way to do so. Can you point me to an article or >> >> explain to me how this works indeed, and how the decision to the >> >> belonging voxel is made, I think I know the basis, but not enough to >> >> make my own script. >> >> > >> >> >If I do not understand bad, is something like, you take a voxel a >> >> look to some contiguous voxels till you get into a point where all >> >> the contiguous voxels are too far from the seed, and are surrounded >> >> by lots of voxels belonging to other areas. I'm not quite sure about >> >> the decision about when to stop the search. I really think that the >> >> method like the implemented in the mri_apar2aseg is the perfect >> solution. >> >> > >> >> >Regards, >> >> >Gabriel >> >> > >> >> > >> >> > >> >> > >> >> >El 12/12/12, *Bruce Fischl * <fis...@nmr.mgh.harvard.edu> escribió: >> >> >>then I would either use TRACULA (if you have DWI) or the wmparc to >> >> generate ROIs. I meant that you could count whether there are more lh >> >> or rh wm labels neighboring each one to figure out which hemi they >> are in >> >> >> >> >> >>cheers >> >> >>Bruce >> >> >> >> >> >> >> >> >>On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: >> >> >> >> >> >>>Yes I did loo at the total WH-hypointensities(77), and substract >> >> them without a problem. >> >> >>> >> >> >>>What do you mean with lateralize them based on neighboring labels? >> >> How can I perform such thing on FS? >> >> >>> >> >> >>>Actually I'm interested in knowing to wich specific label o region >> >> they are. >> >> >>> >> >> >>>Bests, >> >> >>>Gabriel >> >> >>> >> >> >>> >> >> >>>El 12/12/12, Bruce Fischl <fis...@nmr.mgh.harvard.edu> escribió: >> >> >>> Hi Gabriel >> >> >>> >> >> >>> we don't lateralize them by default, so look for >> >> WM_hypointensities (77) instead. It would be pretty easy to >> >> >>> lateralize them based on neighboring labels. >> >> >>> >> >> >>> cheers >> >> >>> Bruce >> >> >>> >> >> >>> >> >> >>> On Wed, 12 Dec 2012, Gabriel Gonzalez Escamilla wrote: >> >> >>> >> >> >>> > >> >> >>> >Dear Freesurfers, >> >> >>> > >> >> >>> >I'm looking for a way to compute the left and right >> >> WM-hypointensities, as volume values or images. They always >> >> >>> appear empty in >> >> >>> >the aseg.stats, and the corresponding segs No 78 & 79 do >> >> not appear in the aseg.mgz, and I'm a bit lost with it. >> >> >>> > >> >> >>> >Can any one help me? >> >> >>> > >> >> >>> >Best Regards, >> >> >>> >Gabriel. >> >> >>> > >> >> >>> > >> >> >>> >> >> >>> >> >> >>> 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. >> >> >>> >> >> >>> >> >> >>>-- >> >> >>>-------------------------- >> >> >>>PhD. student Gabriel González-Escamilla >> >> >>>Laboratory of Functional Neuroscience >> >> >>>Department of Physiology, Anatomy, and Cell Biology >> >> >>>University Pablo de Olavide >> >> >>>Ctra. de Utrera, Km.1 >> >> >>>41013 - Seville >> >> >>>- Spain - >> >> >>> >> >> >>>Email: ggon...@upo.es >> >> >>>http://www.upo.es/neuroaging/es/ >> >> >>> >> >> > >> >> >-- >> >> >-------------------------- >> >> >PhD. student Gabriel González-Escamilla >> >> >Laboratory of Functional Neuroscience >> >> >Department of Physiology, Anatomy, and Cell Biology >> >> >University Pablo de Olavide >> >> >Ctra. de Utrera, Km.1 >> >> >41013 - Seville >> >> >- Spain - >> >> > >> >> >Email: ggon...@upo.es >> >> >http://www.upo.es/neuroaging/es/ >> >> >> >> -- >> >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> > >> > -- >> > -------------------------- >> > PhD. student Gabriel González-Escamilla >> > Laboratory of Functional Neuroscience >> > Department of Physiology, Anatomy, and Cell Biology >> > University Pablo de Olavide >> > Ctra. de Utrera, Km.1 >> > 41013 - Seville >> > - Spain - >> > >> > Email: ggon...@upo.es >> > http://www.upo.es/neuroaging/es/ >> >> -- >> 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: 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 > > -- > -------------------------- > PhD. student Gabriel González-Escamilla > Laboratory of Functional Neuroscience > Department of Physiology, Anatomy, and Cell Biology > University Pablo de Olavide > Ctra. de Utrera, Km.1 > 41013 - Seville > - Spain - > > Email: ggon...@upo.es > http://www.upo.es/neuroaging/es/
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