Re: [Freesurfer] freeview registration
I think that freeview does not correctly generate the registration file. You can use it to check the regsitration, but us tkregister if you need to edit it. doug On 2/27/15 10:18 AM, Xiaomin Yue wrote: Hi All, After using freeview to manually adjust the registration between a functional and T1.mgz generated by bbregister, I saved the registration file in freeview as lta format, which seems the only option. However, the registration file has same file name for source and target volume. So, when loading it again to freeview, the registration is totally wrong. In order to avoid the problem, I converted the register.dof6.dat to lta formation, where the lta file has correct source and target volume name. Then, I loaded the lta file generated from register.dof6.dat, did manual adjustment, and then saved adjusted registration as a lta file. the final lta file has same problem. I am using freesurfer 5.3. Any suggestion is appreciated. Thanks, Xiaomin ___ 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 . 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] regional surface area differences
On 2/27/15 3:41 PM, aqure...@nmr.mgh.harvard.edu wrote: > Hi Freesurfer group, > > I wanted to use mris_preproc to calculate regional differences in surface > area between two groups. > > Ideally I would like to use something that is vertex-wise and preserves > regional area, but I've had trouble with spherical demons (using the > Winkler methodology). So I am going to first try using mris_preproc (and > compare the two methods). I found this old thread suggesting that I should > use the --area flag. > But I had some questions: > > 1) Which surfname should I use with the --area flag? area.mid vs area.pial > vs any other file We usually use area (area of the white surface) since mid and pial will have confounding thickness effects. > 2) Should I use --meas flag in addition and if so which one? (similar to > how --meas thickness is used for calculating cortical thickness) I would use --meas area without using --area. > 3) Which --surfreg file should I use? sphere.reg vs sphere. Or do I not > need the --surfreg? sphere.reg (which is the default) doug > > > Thanks, > Abid > > > -- Forwarded message -- > From: Anderson M. Winkler > Date: Tue, May 14, 2013 at 1:19 AM > Subject: Re: [Freesurfer] Usage of --area option in estimating the > vertex-wise maps of surface area > To: free > > > Hi Xi-Nian, > > As Doug said, they don't do the same thing. The method in the paper > uses a different kind of interpolation to allows the preservation of > the amount of area, whereas mris_preproc achieves the same globally > using a Jacobian correction. The results aren't expected to be > identical at the vertex level or for small regions. > > An implementation of the method we proposed in the paper is available > for Octave and/or Matlab at http://brainder.org/download/areal > It works fine, but beware that it's quite slow. > > All the best, > > Anderson > > > > 2013/5/13 Douglas Greve >> >> Hi Xi-Nian, it does not do the same thing, but it does something > similar. Anderson found that it gave similar results in a lot of cases, > but he has found some differences. If he's still following the FS list, > maybe he can comment. >> doug >> >> >> >> >> >> On 5/11/13 9:53 PM, Xinian Zuo wrote: >> >> Hello Doug, >> >> I am doing some association studies between functional measures and > surface area. In using mris_preproc, there is an option --area. Does > this do sth similar to that as Winkler et al. (2012)? >> Winkler et al., 2012. Measureing and comparing brain cortical > surfacearea and other areal quantities. >> Thank you very much. > ___ > 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 . 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] Projection of CBF maps on fsaverage and smooth
Basically looks ok. The only things that jump out at me are that you are using regheader (I would create a registration file with bbregister rather than assuming that there was no motion between the anatomical and the ASL). Where did brain.fsaverage.lh.mgh come from? doug On 2/27/15 2:16 PM, Matthieu Vanhoutte wrote: Dear Freesurfer's experts, I computed some perfusion maps from ASL data. These perfusion maps were registered on anatomical T1 and I would like to make a group analysis on surfaces. Please find below my actual commands in order to project these volumic maps on fsaverage then smooth the data projected on fsaverage : *Project CBF maps on fsaverage* : /mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi lh --o lh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg// //mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o rh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg/ *Smooth the data projected on fsaverage (native ASL data size voxel of 3mm)* : /mris_fwhm --s fsaverage --hemi lh --smooth-only --i lh.fsaverage.cbf.mgh --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh --mask brain.fsaverage.lh.mgh// //mris_fwhm --s fsaverage --hemi rh --smooth-only --i rh.fsaverage.cbf.mgh --fwhm 3 --o rh.fwhm3.fsaverage.cbf.mgh --mask brain.fsaverage.rh.mgh/ Could you advise me on these two steps and tell me first if this is the best way to project CBF maps on fsaverage, then to smooth the data on surfaces ? Is my process could be improved ? Best regards, -- - Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France ___ 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 . 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] Bad design matrix
Try demeaning your covariates. By demeaning, I mean to compute the mean across all subjects, then subtract the mean from all values (for each covariate). doug On 3/1/15 2:40 AM, Anders Hougaard wrote: Dear all, I'm comparing cortical thickness of a group of patients to a group of controls. I want to regress out the effects of gender, age, disease severity and disease duration. For the controls, the last two parameters equals zero. When running mri_glmfit, i get ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 See the design matrix attached. My contrasts are set as 1 -1 0 0 0 0 0 0 0 0 and -1 1 0 0 0 0 0 0 0 0 What should I do to improve this? All the best, Anders ___ 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 . 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.
