[Freesurfer] few oasis question

Hi. I have few questions regarding the recently published OASIS data analyzed using Freesurfer: 1. How did you produce $SUBJECT_ID/mri/wmparc.mgz. I am running recon-all -all on my subjects, but I don't get this file. 2. How did you produce segmentation of the corpus callosum. I am running rec

Re: [Freesurfer] few oasis question

Hi Martin, these are features we'll include in our next release, hopefully sometime this summer. I'll leave 3 for Doug. cheers, Bruce On Wed, 11 Jul 2007, Martin Kavec wrote: Hi. I have few questions regarding the recently published OASIS data analyzed using Freesurfer: 1. How did you pro

Re: [Freesurfer] FreeSurfer relevance for studying structures other than the bra

Howdie Doug, We are interested in studying not the ventricles, per say, but the actual cells and components of the cells that comprise these ventricles. For example, cells from a heart, spleen, sperm, or cochlea. Since we are not using an MRI machine to obtain the images, is FreeSurfer of no

[Freesurfer] flip functional using tkregister2?

Hi all, I used reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1 and then reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat --subject FREESURFERRECON_FWIO_fmri_NYU_KB_N

Re: [Freesurfer] flip functional using tkregister2?

You can't really do a left-right flip in tkregister2. ok, you can with "Sag Mirror", but I would *highly* recommend that you find out whether you really need one or not and, if so, why. LR orientation can be tricky to determine, even within the same subject. Are you using nifti? Stacy Chu

Re: [Freesurfer] flip functional using tkregister2?

Thanks, I actually ended up finding that SagMir button and after playing around with it I got it to fit the surface. By lowering the intensity and comparing the fit between the two hemi's in the sagittal view it became obvious which one fit better. The orientation was initialy completely upside d

Re: [Freesurfer] flip functional using tkregister2?

No, you should not need to do that much adjustment. Is this a full or partial volume? It could be that your nifti volume is oriented incorrectly. To check this, tkmedit -f example_func.nii Make sure that the different cardinal views are oriented correctly. doug Stacy Chu wrote: Thanks, I

Re: [Freesurfer] few oasis question

#3 is an error in the osasis data set. It has been taken down until we resolve it. doug Martin Kavec wrote: Hi. I have few questions regarding the recently published OASIS data analyzed using Freesurfer: 1. How did you produce $SUBJECT_ID/mri/wmparc.mgz. I am running recon-all -all on my

[Freesurfer] registering .gfeat

Hi Doug, I am trying to use reg-feat2anat to project FEAT results onto the FS surface. This works ok (except for some registration problems discussed earlier) for 1st level .feat directories. However, my study consists of two consecutive runs per subject (to allow the subject to take a break), so

[Freesurfer] control points

In recon-all, it says you are supposed to use -autorecon2-cp if you use control points. So I wonder why earlier normalization steps also use control points, such as Norm1 and CANormalize. What effect do the control points have in those steps? _

[Freesurfer] save a base image with an overlay together

Hi Doug: Which command should I use to save a base image with an overlay together? Thanks! Tao T. Song wrote: Thanks! I was able to create a binary mask, and the result looks good. Now how do I save a base image with an overlay, in tkmedit of which command? Tao Doug Greve wrote: You c

Re: [Freesurfer] control points

Hi Don, Nick actually just recently included something to allow you to pass the control points to mri_ca_normalize, so it can help the subcortical segmentation. Nick: what is the new flag? cheers, Bruce On Wed, 11 Jul 2007, Don Hagler wrote: In recon-all, it says you are supposed to use -