Dear Bruce, Many thanks for you kind answer. I sampled the perirhinal roi label into the volume using the suggested command line: "mri_label2vol --subject s6904 --fill-ribbon --label lh.perirhinal.label --o lh.perirhinal.volume.nii --hemi lh --identity". The obtained mask seems to cover well the perirhinal structure.
Now, I calculate the perirhinal volmue (mm3) based on the obtained mask but I found that the obtained value does not match the one obtained during the Freesurfer cortical reconstruction (values in the stat folder: files : rh/lh-BA_exvivo.stats). did I messed something? Thank you very much in advance, Best regards, Mohamed ----- Mail original ----- De: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> À: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Envoyé: Lundi 22 Janvier 2018 16:12:10 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi oh, then I think you are just showing the surface-based label, which will only fill voxels that intersect with the white surface I believe. To sample it into the volume try mri_label2vol with the --fill-ribbon flag (the help is pretty extensive). cheers Bruce On Mon, 22 Jan 2018, m.ba...@uliege.be wrote: > Dear Bruce, > > Thank you for your answer! > > I just display the "T1.mgz" image (mri folder) using Freeview and then loaded > the "lh/rh.perirhinal_exvivo.label" rois (label folder). > > If this is not the good way to do it, please, could you explain more the > procedure? What do you mean by MT and PC? > > Thank you very much in advance, > > Best regards, > > Mohamed > > > ----- Mail original ----- > De: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > À: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Envoyé: Vendredi 19 Janvier 2018 16:53:18 > Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi > > Hi Mohamed > > how are you visualizing the MT or PC ROIs. Did you sample them into the > volume? If so, can you tell me where the file ROIs are in the data you > sent me? > > cheers > Bruce > On Fri, 19 Jan 2018, m.ba...@uliege.be wrote: > >> Dear Bruce, >> >> Many thanks for your kind help! >> >> I put the subject data on your ftp site (s8201.tar). >> >> Best regards, >> >> Mohamed >> >> >> >> ----- Mail original ----- >> De: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> >> À: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> >> Envoyé: Jeudi 18 Janvier 2018 16:37:10 >> Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi >> >> Hi Mohamed >> >> if you tar, gzip and ftp this subject to our ftp site we will take a look >> cheers >> Bruce >> On >> Thu, 18 Jan 2018, m.ba...@uliege.be wrote: >> >>> Dear Bruce, >>> >>> Attached is the screen shot of the results of the segmentation of the >>> perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented >>> Roi does not cover the entire cortical thickness of the region. Is there >>> any other alternative to get a better segmentation of this region? >>> >>> Many thanks in advance, >>> >>> Best regards, >>> >>> Mohamed >>> >>> ----- Mail original ----- >>> De: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> >>> À: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> >>> Envoyé: Mardi 9 Janvier 2018 14:50:16 >>> Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi >>> >>> Hi Mohamed >>> >>> I'm pretty sure this was an issue with the ribbon-filling in V5 that is >>> better in V6. Try using it and see if it is fixed. >>> >>> cheers >>> Bruce >>> On Tue, 9 Jan 2018, >>> m.ba...@uliege.be wrote: >>> >>>> Dear Freesurfer experts, >>>> >>>> We would like to use volume and cortical thickness measures obtained for >>>> the perirhinal cortex in Freesurfer 5. When checking the region that has >>>> been segmented (using lh/rh.perirhinal.label), we noticed that the ROI >>>> does not seem to cover the entire cortical thickness of the region. On the >>>> coronal slice shown in example (attached file), one can see that there are >>>> still a few voxels of gray matter between the external border of the ROI >>>> and the external boundary of the cortex. How reliable is this >>>> segmentation? Is there a reason why the ROI appears so thin? >>>> >>>> Many thanks in advance, >>>> >>>> Best regards, >>>> >>>> >>>> >>> _______________________________________________ >>> 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. >>> >> _______________________________________________ >> 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. >> > _______________________________________________ > 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. > _______________________________________________ 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. -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Université de Liège - University of Liège GIGA-Cyclotron Research Centre: In Vivo Imaging, Bât B30, Quartier Agora Allée du six Aout n°8 4000 Liège, Belgium m.ba...@uliege.be Tel : + 32-4-3662304 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
