Re: [Freesurfer] cortical surface area

Thanks. I ran this command: mris_anatomical_stats subjectID lh pial It gave me a total surface area of 115007 mm^2 I also tried the following command from within the 'label' directory: mris_anatomical_stats -l lh.cortex.label -f lh.cortex.stats -b subjectID lh pial It gave me a total surface

Re: [Freesurfer] cortical surface area

oh, sorry, I missed the 5.3 part. YOu can always compute it for a subject via: mris_anatomical_stats pial cheers Bruce On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: > I don't see this file in the stats directory using FS 5.3. > > Jim > > -Original Message- > From:

Re: [Freesurfer] cortical surface area

I don't see this file in the stats directory using FS 5.3. Jim -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, October 12, 2017 4:52 PM To: Freesurfer support list

Re: [Freesurfer] cortical surface area

Hi Jim check the ?h.aparc.pial.stats file. I think the total surface area should be in there. cheers Bruce On Thu, 12 Oct 2017, Alexopoulos, Dimitrios wrote: > Specifically, where in the aparc.stats file (or other file) is the cortical > surface area? > I only see default output for

Re: [Freesurfer] cortical surface area

Specifically, where in the aparc.stats file (or other file) is the cortical surface area? I only see default output for 'WhiteSurfArea'. Jim -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve

Re: [Freesurfer] cortical surface area

mm2 On 10/12/2017 02:15 PM, Alexopoulos, Dimitrios wrote: > > What measure is for the cortical surface area? > > The measure in the aparc.stats file states ‘WhiteSurfArea’ > > Jim > > > > The materials in this message are

Re: [Freesurfer] volume vs surface-based and surface smoothing

The surface is created during recon-all. rawfunc2surf-sess resamples the volumetric fMRI onto the surface. On 10/12/2017 01:42 PM, Alissa Stafford wrote: > Thanks Matt! Does rawfunc2surf-sess create the surface and smooth? > > From:

[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance

I have applied the contrasts that we discussed in the previous mails but they produce doubt results. In summary, I aim to look at: A- Difference between groups without considerer the covariate effect (I suppose that the maps will be in the intercept folder) ---> ANOVA between 4 groups B-

[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance

I have applied the contrasts that we discussed in the previous mails but they produce doubt results. In summary, I aim to look at: A- Difference between groups without considerer the covariate effect (I suppose that the maps will be in the intercept folder) ---> ANOVA between 4 groups B-

[Freesurfer] cortical surface area

What measure is for the cortical surface area? The measure in the aparc.stats file states 'WhiteSurfArea' Jim The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not

Re: [Freesurfer] volume vs surface-based and surface smoothing

My understanding of the FreeSurfer surface-based functional processing is that it adheres to the below guidelines; however, I have not personally used it so we¹ll have to see what the FreeSurfer experts say. Peace, Matt. From: on behalf of Alissa

Re: [Freesurfer] volume vs surface-based and surface smoothing

Thanks Matt! Does rawfunc2surf-sess create the surface and smooth? From: > on behalf of Matt Glasser > Reply-To: Freesurfer support list

Re: [Freesurfer] volume vs surface-based and surface smoothing

Volume-based registration is fine with subject as you have the same brain that you are registering (ideally such registrations are 6 DOF rigid registrations and any image distortions are corrected for). Surface-based registration is better when comparing across subjects due to the variability in

[Freesurfer] volume vs surface-based and surface smoothing

Hello, I am trying to understand the preprocessing functions to successfully complete surface-based analysis. I am confused about what is happening on the volume level and when exactly the surface is being created. My questions revolve around register-sess and rawfunc2surf-sess. Registration

[Freesurfer] dcmunpack

Hi There, Could someone tell me how long approximately dcmunpack should take? (I have 243 files and it has been "interrogating" now for 2 hours. Thank you! Keiko -- J. Keiko McCreary, PhD Postdoctoral Fellow SARTAN-AD Clinical Research Coordinator (Lethbridge Site) Canadian Centre for

Re: [Freesurfer] Normalize to mni

Hi Jan, Is the functional image already coregistered to the T1? If you have a registration file, you could try: mri_vol2vol --mov fstcmc.nii.gz --reg registrationfile --tal --talres 2 --o fstcmc.mni305.2mm.nii.gz .. to bring the functional image to MNI305. Are you planning to your restrict

[Freesurfer] Normalize to mni

Normalize to mni   Dear Doug,   We have a very simple question. In a first step we segmented brains using the recon all command. Our functional pipeline created a „fstcmc.nii.gz“ file. We would like to do some subcortical analysis and need to perfrorm this in MNI 305 space. We also need the

Re: [Freesurfer] Problem flipping a label into other hemisphere

Hi Doug and Bruce, I forgot to mention that I had tried that as well but without success. As a sanity check, tried flipping a label from the 'bert' subject and it still comes out wrong. I've uploaded a screen shot of the result: https://imgur.com/a/J6Phx Thank you for any input you might have!