[Freesurfer] how to extract data that are removed effects of covariates

Dear experts, I’m new to analysis with use of the Freesurfer. I compared grey matter thickness between two groups using Qdec with several covariates (i.e. nuisance factors) such as age, gender and intracranial volume (ICV). I found regions that significantly differed between the two groups. I

Re: [Freesurfer] Medial Surface Problem

Thanks Bruce. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au

Re: [Freesurfer] Surface edits: Cortex that extends into the putamen + Missing gray matter

can you tar and gzip the entire subject and upload it to our ftp site with coordinates of the problem areas? On Mon, 3 Jul 2017, Vincent Koppelmans wrote: Hi Bruce, Thank you for your reply.  The aseg seems to be okay: https://www.dropbox.com/s/j1ac0ftxw8iiv34/Putamen.png?dl=0  Do you

Re: [Freesurfer] Surface edits: Cortex that extends into the putamen + Missing gray matter

Hi Bruce, Thank you for your reply. The aseg seems to be okay: https://www.dropbox.com/s/j1ac0ftxw8iiv34/Putamen.png?dl=0 Do you have any other suggestions? Here is an extra image of the cortical ribbon. Maybe this helps:

Re: [Freesurfer] Surface edits: Cortex that extends into the putamen + Missing gray matter

Hi Vincent the putamen error probably means that the aseg is wrong, and if so, you can correct the aseg and rerun autorecon2-wm and autorecon3 I believe. For the medial ttemporal lobe issue is that really cortex? I can't really tell from the single coronal slice. I'll cc Jean Augustinack to

[Freesurfer] Strange Discrepancy Between Activation Location on Surface vs. Volume

Hello, I am running into an odd issue. In particular, I have run a GLM analysis in *volume* space, and I am visualizing the results both on the surface using tksurfer, and on the volume using tkmedit. In both cases, I am using the register.dof6.dat file to do the registration. Oddly, when I

[Freesurfer] Matlab Problem LME

Dear FreeSurfer experts, I am following the LME tutorial for the spatiotemporal mass-univariate model on Matlab 8.2. When I get to the point where the covariance estimates are segmented into homogeneous regions I run into a problem. Nothing really happens in Matlab anymore. This is my

Re: [Freesurfer] bad file conversion

Hi Michael where did you the T1.nii file come from? Do you have the dicoms that were used to create it? It will indeed continue to fail until you fix the file so that the anatomical directions are correct (which you can verify by viewing it in freeview) cheers Bruce On Mon, 3 Jul 2017,

Re: [Freesurfer] bad file conversion

Hi Bruce, i used a T1.nii file at the beginning and performed the standard recon-all to convert the file just like i did with the rest of them. I deleted the file and run it again but it still produced the same results using this method. Kind regards, Michael > On 3 Jul 2017, at 15:05,

Re: [Freesurfer] bad file conversion

Hi Michael if it loaeds in freeview upside down then everything else will fail. What format did it start as? Best to use dicoms directly if you can, and avoid analyze. In any case, make sure that the directions are correct at the beginning (that is, for the file that you give to recon-all as

Re: [Freesurfer] Medial Surface Problem

Hi Bronwyn not yet, but we'll get to it soon cheers Bruce On Mon, 3 Jul 2017, Bronwyn Overs wrote: Hi Bruce, Just wanted to check in on the status of reviewing our medial surface problem. Any luck so far? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia

[Freesurfer] Using multimodal slab input for hippocampus subfield segmentation in FS6

Dear experts, I am trying to use T2-weighted images (0.5x0.5x1mm) as an additional scan to a T1-weighted image (0.7x0.7x0.7mm) for hippocampal subfield segmentation in Freesurfer 6. The T2-weighted data is a slab which includes the whole hippocampus and its y-axis is parallel to the hippocampal