[Freesurfer] Freesurfer and Civet

Hi everyone, I am pretty new with Freesurfer and I'd be very grateful if some of you could help me out with the following issue. I have a subject which has been processed both with Freesurfer and Civet-CLASP, and I would love to compare the two output cortical thickness maps. I have resampled

[Freesurfer] results that are difficult to explain, difference in correlation

I have subject proceed with Freesurfer 4.30 and Freesurfer 5.1. The subjects proceed with Freesurfer 5.1 appears to have thicker cortex than in Freesurfer 4.30. When I correlate the cortical thickness against continuous variables like IQ, I get a difference. Is this expected since I get a

Re: [Freesurfer] Freesurfer and Civet

Hi Gabriele unfortunately I suspect what you say is true - it's not that easy unless their vertices happen to be spatially aligned with our vertex locations, which is unlikely. You are better off computing the coordinates of each vertex then finding the nearest vertex on the other surface, or

Re: [Freesurfer] results that are difficult to explain, difference in correlation

Hi Knut have you visually inspected the surfaces? Certainly you will get differences, and our hope would be that 5.1 is more accurate. cheers Bruce On Mon, 5 Dec 2011, Knut J Bjuland wrote: I have subject proceed with Freesurfer 4.30 and Freesurfer 5.1. The subjects proceed with Freesurfer

[Freesurfer] mri_ca_register from virtual box

*Hi everyone * *I got this error while running one of my subjects* * * mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-- #@# CA Reg Inv Thu Nov 24 05:15:42 EST

[Freesurfer] How to do a group analysis of the DTI data

Dear Allison, Thank you very much for your email. 1). I wonder if the GLM group analysis that is described on the webpage you sent me (as instructed by Doug and Bruce, I was aware of this webpage and I used it for my QDEC studies but I am not sure if can be used for DTI data analysis) can

Re: [Freesurfer] How to do a group analysis of the DTI data

Hi Antonella, 1). I wonder if the GLM group analysis that is described on the webpage you sent me (as instructed by Doug and Bruce, I was aware of this webpage and I used it for my QDEC studies but I am not sure if can be used for DTI data analysis) can be used for a DTI group analysis.

Re: [Freesurfer] Contrasts in GLM

Linda Zhang wrote: Hi Doug, Thanks for the clarification. If I were to add another two class variables (patient and subject, for example) and I wanted to see if they affected thickness, assuming they come after gender in the fsgd file, would the contrasts then be [0 0 1 1 0 0 0 0 0 0 0

[Freesurfer] DTI analysis and mri_glmfit-sim \

Dear all: I am doing an FA group study (controls vs. patients without any covariant so my C = +1.0 -1.0) and I want to see if there are any clusters that survives by multiple comparison so I ran: mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\   --fsgd

Re: [Freesurfer] DTI analysis and mri_glmfit-sim \

Hi Antonella, are there any clusters listed in the summary file? It might be that you just don't have any clusters that survive. doug Antonella Kis wrote: Dear all: I am doing an FA group study (controls vs. patients without any covariant so my C = +1.0 -1.0) and I want to see if

Re: [Freesurfer] DTI analysis and mri_glmfit-sim \

You can try it with tkmedit tkmedit fsaverage orig.mgz -overlay /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/sig.mgh Also, in freeview try reducing the threshold to see if something pops up. doug Antonella Kis wrote: Hi Doug, Many thanks for your answer. Yes,

[Freesurfer] mri_cvs_register error on Mac

All, I've been trying to use mri_cvs_register on a 64-bit mac and received the following error (below). Google found a couple of hits that others are having this problem but no solution. I'm running the most recent version from version 5.1 with the patch on the release notes page ($Id:

Re: [Freesurfer] mri_cvs_register error on Mac

Hi Peter, Could you attach the log files from your process? Lilla On Mon, 5 Dec 2011, Peter J. Molfese wrote: All, I've been trying to use mri_cvs_register on a 64-bit mac and received the following error (below). Google found a couple of hits that others are having this problem but

Re: [Freesurfer] mri_ca_register from virtual box

1.5GB is probably not enough. typically we recommend that recon-all have at least 3GB available to it, which can be very hard to do on a virtual machine (since windows takes 1GB, the vm linux takes another 1GB, which leaves 2GB for processes). i would setup your vm to use the maximum memory

Re: [Freesurfer] DTI analysis and mri_glmfit-sim \

Hi Doug, Many thanks for your answer. Yes, there are four clusters as you can see below: # Reporting Coordinates in MNI305 Space # Cluster   Size(n)   Size(mm^3) MNIX   MNIY    MNIZ  Max#   GRFCWP   1 200   1600.0   8.00    5.00  -17.00  -5.47411  0.0 

[Freesurfer] color map in Freeview

Dear All, I was trying to find an explanation of the color map: min, Mid, MAx and Offset values in Freeview. Can someone please explain me if I have the color map set it up as HEAT what is the meaning of this values if for example I am viewing the existing clusters after multiple comparison

Re: [Freesurfer] color map in Freeview

They are standard parameters to linearly map a voxel value (val) into heat-scale color (c), something like this: first apply offset: val = val + offset then: if val = min, c = black if min val mid, c = between black and red if val = mid, c = red if mid val max, c = between red and

[Freesurfer] Auditory Cortex Labels missing

Dear Freesurfers, I'm looking for a suitable solution for Volumetry of the auditory Cortex. As a proxy for Heschl Gyrus I tried the Gyrus temporalis transversus label - as it is posted in the Color LUT. After typing: asegstats2table --subjects WD \ --segno 1034 \ --tablefile aseg.vol.table I

Re: [Freesurfer] overlapping of the surfaces from one hemisphere to another

Hi Eunjin what version are you using? Bruce On Tue, 6 Dec 2011, Eunjin Yoon wrote: Dear, Freesurfer users I am processing 1.5T MR images, and found some overlapping of the surfaces from one hemisphere to another. I attached captured images of that subject. you can find the error center of

Re: [Freesurfer] Contrasts in GLM

Hi Doug, Sure, my fsgd file contained two groups originally, M and F. I had three continuous variables, which were Age, MMSE, Education. I wanted to test whether thickness is correlated with MMSE scores after controlling for gender, age and education. I now want to add two more class variables

Re: [Freesurfer] overlapping of the surfaces from one hemisphere to another

Hi Bruce, I'm using Freesurfer version 5.1.0. On Dec 6, 2011, at 10:56 AM, Bruce Fischl wrote: Hi Eunjin what version are you using? Bruce On Tue, 6 Dec 2011, Eunjin Yoon wrote: Dear, Freesurfer users I am processing 1.5T MR images, and found some overlapping of the surfaces from