Re: [Freesurfer] Desikan-Kilany atlas

Hi Norman perhaps you can take a step back and tell us what you want to use it for? We might be able to suggest a better analysis strategy Bruce On Tue, 24 Feb 2015, Norman Benbrahim wrote: Hi, I want to use the Desikan-Kilany atlas to run some analysis in some regions, however I am very

Re: [Freesurfer] Desikan-Kilany atlas

No problem, I want to take certain regions and use them as masks in order to compute the joint histogram between a thresholded z-score map obtained from ICA (a resting state network) masked in that region, and the variance of the BOLD image. I already have scripts set up to do this in matlab, so I

Re: [Freesurfer] Desikan-Kilany atlas

I see. You could do what you want by sampling the ?h.aparc.annot into the volume (mri_surf2vol), then mapping into MNI space (mri_vol2vol). Actually, if you do surf2vol from fsaverage I think it's already in MNI coords, but Doug can confirm. The problem is going to be that the mapping won't be

[Freesurfer] Desikan-Kilany atlas

Hi, I want to use the Desikan-Kilany atlas to run some analysis in some regions, however I am very new to freesurfer. What I would like to accomplish is the following: 1) Transform the atlas into MNI152 2mm space 2) Convert the atlas to a binary nifti image (similarly to the way FSL's atlases are

[Freesurfer] fMRI post-doctoral position in Barcelona

The translational neuroimaging team at FIDMAG Research Foundation, located in Barcelona (Spain) is looking for a functional MRI researcher. Description of the job: The FIDMAG Research Foundation is offering a position for a post-doc researcher with solid experience in the field of brain

Re: [Freesurfer] visualize subcortical areas in tksurfer?

Thanks, Bruce!! Daniel On Feb 23, 2015, at 8:23 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Daniel I wouldn't advise this - you will miss most of the activation unless it happens to be right next to where the surface runs adjacent to the structure of interest. For

[Freesurfer] Longitudinal post processing

Hello,   I am trying to make the Two Stage Longitudinal processing and when I give the command to prepare the data with QCACHE.   I've already set up the environment for FREESURFER_HOME, but it keeps appearing the error message:    ERROR: FREESURFER_HOME not defined in environment ERROR 1 :

Re: [Freesurfer] Longitudinal post processing

Your environmental variables need to be set in the environment you use. I don’t think the environment gets carried through when you use “sudo”. That’s why your status messages show things like: Working in SUBJECTS_DIR: /analise// $SUBJECTS_DIR didn’t get interpreted. You can double check by

[Freesurfer] Granger Causality

Dear Freesurfer, I would like to analyze my resting state fMRI data with Granger Causality. Are there any tools available in freesurfer at the moment or are there any being developed? If not, what would be the most effective method to exporting a file containing the time series of the HRF for

Re: [Freesurfer] mris_preproc skips subjects

Hi again, I'm still totally stuck here. Any idea what the problem might be? I tried running mris_preproc with the --s option instead of --fsgd and this apparently works for all subjects that I tried so far. Now, using --fsgd, mris_preproc only processes the first subject in group 2?! All the

[Freesurfer] long_mris_slopes error

Hi FreeSurfer experts,   I am trying to run Longitudinal Two Steps analysis.    In the long_mris_slopes I run the following command:   long_mris_slopes --qdec $SUBJECTS_DIR/qdec/longRRMSP01.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Hi Doug and others, I would like apply (Monte Carlo simulation) cluster correction (as opposed to the implemented vertex-wise FDR correction) on the results from a longitudinal study I analyzed using the LME toolbox. The design is unbalanced (different number of time points, from 1 to 4, per