Re: [Freesurfer] Recon for Rhesus Macaque

Hi Rafael, > On Feb 1, 2016, at 21:18 , Casas, Rafael (NIH/CC/DRD) [F] > wrote: > > Thanks Sabastian! I received the new version of the scripts. > > So I can run 01.05 as the first step and just modify the locations and names > of my files? As you have not

[Freesurfer] recon_checker error

Opensuse 11.4 : Freesurfer 5.3 :QAtools_v1.1 I am trying to generate QC data from data generated using Freesurfer ver 5.3 and I'm getting the following error " Checking if all files exist...PASSED Checking actual file order...FAILED (read

Re: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values

By default, the projection is done using nearest neighbor "interpolation", so there is no averaging. Is this what you mean? On 02/01/2016 09:53 AM, Gardumi Anna (PSYCHOLOGY) wrote: > > Dear FreeSurfer expert, > > I would like to project my maps from the “original” functional space > (2.5mm iso,

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

Try removing the mean from your covariate On 01/30/2016 01:31 PM, Nabin Koirala wrote: > Dear Freesurfer forum, > > 'I am trying to run qdec analysis for a group of subjects to see if > correlation exists but I am getting this error only for this > particular set of data but could not figure

Re: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values

Thank you for your reply. I am then a bit confused because I thought each surface value was the result of a two-step procedure: 1) sampling of the values along the normal to the surface at the points specified by the option --projfrac-avg min max del; with such values computed according the

[Freesurfer] Recon for Rhesus Macaque

Hello, I'm wondering what is the first step in reconstruction when working with rhesus macaque. script 01.05 requires files to be in mgh format initially ? I understand that the recon-all scipt is not setp to work with monkey data [cid:image003.jpg@01D15CF6.FFDB5710] Thanks, Rafael

Re: [Freesurfer] Longitudinal analysis--mass univariate {Disarmed}

Dear Dr Martin , Thanks a lot for your kindness and your great answers!! Please I have one more question regarding the design matrix: If I use my design matrix for LME depending on the exampels mentioned in FS wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples Is this correct?    

[Freesurfer] mri_vol2surf Averaging with exclusion of specific values

Dear FreeSurfer expert, I would like to project my maps from the "original" functional space (2.5mm iso, same format as COPE images from FSL) to inflated FreeSurfer surfaces (created from 1.0mm MPRAGE image with recon-all pipeline) excluding voxels with a specific value (e.g. 0) from the