Re: [Freesurfer] VBM by freesurfer
External Email - Use Caution Thank you! Il giorno mar 18 dic 2018 alle ore 11:43 Bruce Fischl < fis...@nmr.mgh.harvard.edu> ha scritto: > Hi Maurizio > > the orig.mgz has been converted to 1 byte/pixel and 256^3 1mm isotropic. > You can use mri_convert to go back to your original data space via: > > > mri_convert -rl orig/001.mgz > > cheers > Bruce > > > On Tue, > 18 Dec 2018, Maurizio Bergamino wrote: > > > > > External Email - Use Caution > > > > Hello,I am trying to run a VBM analysis by using the white matter and > the grey matter masks from > > Freesurfer, because, often, other tools are not able to calculate a > correct white matter and grey matter > > masks. > > When I have these masks, I have to apply them to my original T1 images. > However, the original T1 is in > > different space. I can resample the ROIs (WM and GM) in order to apply > them to my original T1, but my > > question is: > > Can I use the orig.mgz from Freesurfer as my T1 for VBM, or does it have > different intensity from my real > > T1 acquisition? > > > > Thanks, > > Maurizio > > > >___ > 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
Re: [Freesurfer] VBM by freesurfer
Hi Maurizio the orig.mgz has been converted to 1 byte/pixel and 256^3 1mm isotropic. You can use mri_convert to go back to your original data space via: mri_convert -rl orig/001.mgz cheers Bruce On Tue, 18 Dec 2018, Maurizio Bergamino wrote: External Email - Use Caution Hello,I am trying to run a VBM analysis by using the white matter and the grey matter masks from Freesurfer, because, often, other tools are not able to calculate a correct white matter and grey matter masks. When I have these masks, I have to apply them to my original T1 images. However, the original T1 is in different space. I can resample the ROIs (WM and GM) in order to apply them to my original T1, but my question is: Can I use the orig.mgz from Freesurfer as my T1 for VBM, or does it have different intensity from my real T1 acquisition? Thanks, Maurizio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] VBM by freesurfer
External Email - Use Caution Hello, I am trying to run a VBM analysis by using the white matter and the grey matter masks from Freesurfer, because, often, other tools are not able to calculate a correct white matter and grey matter masks. When I have these masks, I have to apply them to my original T1 images. However, the original T1 is in different space. I can resample the ROIs (WM and GM) in order to apply them to my original T1, but my question is: Can I use the orig.mgz from Freesurfer as my T1 for VBM, or does it have different intensity from my real T1 acquisition? Thanks, Maurizio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] VBM question
Dear Freesurfer users, I would like to study the between groups changes of volume/cortical thickness of one region (Perirhinal) belonging to the Brodmann areas. I tried to do that with Qdec tool but unfortunately Qdec does not load the Brodmann areas stat list. I am wondering if I could use the GLM formalism with of course regressing out the ITV. Any suggestion/advice will be very welcome. Many thanks in advance, Best regards, Mohamed -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.ba...@uliege.be ___ 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.
Re: [Freesurfer] VBM
we do not support vbm processing On 08/08/2017 06:21 PM, Shane S wrote: > Hello Experts, > > Can we do VBM in MNI template using the outputs from recon all? Which > file should I be using? And how do I smooth the volumes? > > Thank you for the tips! > > -- > Shane S > > > ___ > 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.
[Freesurfer] VBM
Hello Experts, Can we do VBM in MNI template using the outputs from recon all? Which file should I be using? And how do I smooth the volumes? Thank you for the tips! -- Shane S ___ 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.
Re: [Freesurfer] VBM in SPM and FreeSurfer
Hi Lijie while SPM (and others) call it "density", it's really just a smoothing of the labeled voxels over space. We tools that would allow you to do the same thing with FS segmentations, but haven't ever put them together into a pipeline as the neurobiological interpretation of such a map is very difficult. cheers Bruce On Fri, 18 Feb 2011, soft.join Huang wrote: > Hi, FreeSurfer and VBM experts > > I'm a newer in the field, and not sure if this question is relevant to the > list - any help will be appreciated. > > I am wondering about the difference between the data of FS and that of VBM > in SPM. After searching in Google, I find a topic following, url: > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-May/007710.html, > and have some different opinions. > > In the discussion in above link, all believe that FS and VBM could give the > same measurement - volume, yet I don't think so. I admit that we could get > the volume of specific ROI by multiplying the thickness by the surface area, > but through VBM in SPM, we get the mass( something like it) of the gray > matter( multiply the density of gray matter by the volume). They have > different meaning, to the best of my knowledge. > > I don't know if I get the right understanding. > > Thanks a lot in advance. > > Lijie Huang > email: huanglijie.s...@gmail.com > State Key Laboratory of Cognitive Neuroscience and Learning > Beijing Normal University > Beijing China > ___ 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] VBM in SPM and FreeSurfer
Hi, FreeSurfer and VBM experts I'm a newer in the field, and not sure if this question is relevant to the list - any help will be appreciated. I am wondering about the difference between the data of FS and that of VBM in SPM. After searching in Google, I find a topic following, url: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-May/007710.html, and have some different opinions. In the discussion in above link, all believe that FS and VBM could give the same measurement - volume, yet I don't think so. I admit that we could get the volume of specific ROI by multiplying the thickness by the surface area, but through VBM in SPM, we get the mass( something like it) of the gray matter( multiply the density of gray matter by the volume). They have different meaning, to the best of my knowledge. I don't know if I get the right understanding. Thanks a lot in advance. Lijie Huang email: huanglijie.s...@gmail.com State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing China ___ 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.
