Re: [Freesurfer] Analysis question
Hi Corey, you can try smoothing the individual data, but of course you won't have the power that you have in a group study (which is why you do the group study in the first place). cheers, Bruce On Wed, 9 Jan 2008, Corey Keller wrote: Hi, I have a quick and hopefully simple question. The picture on the left is an individual fmri mean functional display. To get it I used Tksurfer-sess -hemi rh -aparc -s PROZ06004 -analysis simple_v_complex -c simple_v_complex while in /space/multnomah/3/users/gow/PROZ06/fMRI The picture is splotchy whereas the second picture which is the average of all subjects for this same analysis and contrast is smooth and cleaner. In order to display the averaged data I used Tksurfer fsaverage rh inflated -annot aparc -overlay group-analysis/simple_v_complex/rh.meanfunc.nii -fthresh 2 while in the same directory I'm trying to get the individual subjects to look like the smooth averaged output. Can you help me with this? Thanks so much. Best, Corey Corey Keller Epilepsy Unit Clinical Research Coordinator Massachusetts General Hospital Wang 735, 55 Fruit Street Boston, MA 02114 Phone 802.578.6292 Email [EMAIL PROTECTED] [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Gray Matter Mask - twist on previous post
Dear Group, Back in April, Anil Roy posted a question about methods to generate a gray matter mask that can be fed into AFNI . . . I'm wondering if the opposite can be done? Can a functional mask made in AFNI be fed easily into Freesurfer? Currently this mask is saved as a NIFTI dataset. Thank you. Emily Emily Trittschuh, PhD Neuropsychology Post-doctoral Fellow Cognitive Neurology and Alzheimer's Disease Center Northwestern University Feinberg School of Medicine 320 E. Superior Street, Searle 11-579 Chicago, IL 60611 phone 312/503-1155 fax 312/908-8789 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Gray Matter Mask - twist on previous post
Hi Emily, is it a volume or surface functional map? If volume, I think it should be pretty straightforward to sample it onto the surface with mri_vol2surf then go from there. There is probably a way to do this in SUMA also. cheers, Bruce On Wed, 9 Jan 2008, Emily Trittschuh wrote: Dear Group, Back in April, Anil Roy posted a question about methods to generate a gray matter mask that can be fed into AFNI . . . I'm wondering if the opposite can be done? Can a functional mask made in AFNI be fed easily into Freesurfer? Currently this mask is saved as a NIFTI dataset. Thank you. Emily Emily Trittschuh, PhD Neuropsychology Post-doctoral Fellow Cognitive Neurology and Alzheimer's Disease Center Northwestern University Feinberg School of Medicine 320 E. Superior Street, Searle 11-579 Chicago, IL 60611 phone 312/503-1155 fax 312/908-8789 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] segmentation of brain of age 8-13
Dear freesurfer experts, I got uncorrected segmentation results, especially occipital cortex, from brain of age 8-13. I found similar problem in adult brain in freesurfer mailing list and the resolving answer like below. use the control points with the mri_ca_normalize flag as part of the aseg. I've not used the command much, but you should be able to add the flag '-f tmp/control.dat' to the normal mri_ca_normalize command to run this step Do I have to do any procedure for brain of age 8-13 in addition to suggestion like above? Thanks, bsjeong ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] segmentation of brain of age 8-13
Hi, we don't in general use the aseg.mgz for cortical stuff, so if it look inaccurate, but the ?h.white and ?h.pial surfaces look accurate then I wouldn't worry about it. It's hard to diagnoe without any images though. cheers, Bruce On Thu, 10 Jan 2008, BumSeok Jeong wrote: Dear freesurfer experts, I got uncorrected segmentation results, especially occipital cortex, from brain of age 8-13. I found similar problem in adult brain in freesurfer mailing list and the resolving answer like below. use the control points with the mri_ca_normalize flag as part of the aseg. I've not used the command much, but you should be able to add the flag '-f tmp/control.dat' to the normal mri_ca_normalize command to run this step Do I have to do any procedure for brain of age 8-13 in addition to suggestion like above? Thanks, bsjeong ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
