External Email - Use Caution Hello Bruce,
As suggested by you, I used tkmeditfv to view the volumetric maps on the surface and it seems like the dACC cluster is lying outside the brain. I checked the registration of the volumetric file using tkregisterfv but surprisingly nothing shows up. I also tried using bbregister and then checked the registration but the same thing happened, the volumetric map doesn't show up in either of those cases. I am confused, as to why that is happening and how can I fix it such that all the clusters are appropriately aligned. The files I am using have been exported from neuroelf program. I exported them as analyze format (.img and .hdr) and then converted it to nifti format using mri_convert. However, with both the analyze and nifti format, similar things happened. Any help is highly appreciated. Thanks, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Tue, Jun 26, 2018 at 11:56 PM, Douglas Greve <dgr...@mgh.harvard.edu> wrote: > you can try > tkmeditfv subject orig.mgz -surfs -ov clustermap.nii.gz -fminmax .01 3 > you may have to adjust the thresholds (fminmax) > > > On 6/26/18 10:43 PM, srishti goel wrote: > > External Email - Use Caution > Hello Bruce, > > You had mentioned about loading the volumetric maps with the surface to > check that all my clusters are contained within the surfaces. Since I am > very new to freesurfer, could you please guide to where I can find an > appropriate command to do that. > > Thank you so much for all the help! > > Best, > Srishti > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > > On Mon, Jun 25, 2018 at 11:50 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu > > wrote: > >> Hi Srishti >> >> you should be able to load the volumetric maps with the surfaces and make >> sure that your clusters are contained within the surface. >> >> cheers >> Bruce >> >> On Mon, 25 Jun 2018, srishti goel wrote: >> >> >>> External Email - Use Caution >>> >>> They are separate clusters not the same clusters but we both of those >>> don't show up when we >>> project the volume maps on surface. Every other cluster comes up and >>> this has happened in >>> about 2-3 files. Are you absolutely sure that the surface in freesurfer >>> includes dACC and >>> insula? >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> On Mon, Jun 25, 2018 at 10:14 AM, Douglas Greve <dgr...@mgh.harvard.edu> >>> wrote: >>> >>> It should be included. But dACC and insula are not close to each >>> other. How can >>> there be a cluster that spans both? >>> >>> >>> On 6/23/18 7:54 PM, srishti goel wrote: >>> >>> External Email - Use Caution >>> >>> Hello, >>> I am using mri_vol2surf to project my volume maps on to the surface. >>> There is a >>> dACC/insula cluster visible in my volume maps that doesn't show up when >>> I project >>> it on the surface. >>> >>> Is that because dACC/insula is not included in surfaces on Freesurfer? >>> >>> Thanks! >>> >>> Best, >>> Srishti >>> Social/Clinical Research Specialist >>> Child Imaging Research and Life Experiences Lab >>> University of North Carolina at Chapel Hill >>> email (W): srish...@email.unc.edu >>> skype: srishti.goel12 >>> >>> >>> >>> _______________________________________________ >>> 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. 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