[Freesurfer] Longitudinal Edits, skull strip and wmcp, how to do this longitudinally

For some of my subjects, I need to make many different types of edits on my longitudinal data, but have a few questions regarding the order/how to do this. I have read the details of this website ( http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) but wanted to confirm a few things.

[Freesurfer] Please help: Registering to FSL feat- example_func2standard

Hi Freesurfers, I ran reg-feat2anat to register freesurfer data to FSL feat in order to generate some binary masks. Afterwards I edited the FEAT registration to standard space via: reg-feat2anat --feat subjectX.feat --manxfm func2std and saved the registration. i want to use these example_func2s

Re: [Freesurfer] subtracting segmented volumes

mris_calc should do what you want (although the aseg is not zero in the cortex, so you will change the cortical labels) cheers Bruce On Sat, 14 Apr 2012, Adil Javed wrote: Hi, Is there a way to subtract segmented files in freesurfer?  For example, aparc+aseg.mgz - aseg.mgz= aparc.mgz only? 

Re: [Freesurfer] mri_compute_volume_fractions

Hi Adrian this will create a voxel map with the % of each tissue class in each voxel. If you want the total %s, just read them out of the stats files and compute them directly. cheers Bruce On Sat, 14 Apr 2012, Adrian Garcia wrote: > Dear Bruce, > > thank you for the reply. So this function

[Freesurfer] subtracting segmented volumes

Hi, Is there a way to subtract segmented files in freesurfer?  For example, aparc+aseg.mgz - aseg.mgz= aparc.mgz only?  I am interested in looking only at the cortex.  I find that label to volume conversion doesn't give me a nice segmented cortex, with some patchy areas of intensities lost. tha

Re: [Freesurfer] mri_compute_volume_fractions

Just the name you give the output On Apr 14, 2012, at 4:07 AM, Adrian Garcia wrote: > I would like to have Freesurfer calculate the percentage of wm/gm/csf from an > MRI volume (produced with mri_volsynth). I have run recon-all to completion > and have a registration matrix from the MRI to

[Freesurfer] reg-feat2anat --feat --manxfm func2std

Hi Freesurfers, I ran reg-feat2anat and am now checking registration. For some subjects I had to edit the registration of feat to standard space. So, do I have to replace the example_func2standard.mat fsl's example_func2standard.mat in the reg folder or is this done automatically? Is this the onl

[Freesurfer] mri_compute_volume_fractions

I would like to have Freesurfer calculate the percentage of wm/gm/csf from an MRI volume (produced with mri_volsynth). I have run recon-all to completion and have a registration matrix from the MRI to the Freesurfer anatomical (tkregister2). It looks like mri_compute_volume_fractions will do