[Freesurfer] Categorical covariates with more than two levels on qdec

Subject: Categorical covariates with more than two levels on qdec Categorical covariates with more than two levels on qdec Dear Freesurfer experts, I am doing an analysis on a large data set gathered from eight different imaging centres. In my analysis I would like to covary for

Re: [Freesurfer] bad freesurfer segmentation

Hi Doety yes, that looks pretty bad. Can you tell us about the acquisition? What resolution/field strength/scan type was it? If you upload the subject we will take a look cheers Bruce On Wed, 9 Jul 2014, Doety Prins wrote: Dear freesurfer experts, I experienced some problems with the

Re: [Freesurfer] Freesurfer longitudinal GLM Design question

Hi Sal, it looks like you have everything together then. You can run your QDEC analysis on the long.thickness-rate (or one of the percent change files) to see where the rate is significantly different from zero. Negative rate means thickness decrease. You could also use glmfit with the one

[Freesurfer] combining aseg and seg_edited files for an atlas

Hi Freesurfer forum, I have never used the forum before but I am a long time user of Freesurfer and I am currently working on making a new atlas for the cerebellum. However I am having a problem loading my *seg_edited.mgz* files into the *rebuild_gca_atlas.csh* script. So I renamed my *aseg.mgz*

[Freesurfer] input anatomy orientation

I have run FreeSurfer 5.3 recon-all, getting different stats output, for these cases of anatomy input: (1) mprage DICOM series converted with dcm2nii (2) fslreorient2std (RL PA IS) on the dcm2nii output (3) mprage DICOM series converted with mri_convert Differing example results

[Freesurfer] LGI error

Hi Marie FreeSurfers: I am running the LGI command on a group of brains and I am getting an error message. MATLAB opens up and begins to run when this error appears: M A T L A B (R) Copyright 1984-2011 The MathWorks, Inc.

Re: [Freesurfer] LGI error

Hi Alan, You probably don't have the matlab image processing toolbox installed. Let me know if you can't install it easily. Best, Marie On Jul 9, 2014, at 11:51 AM, Alan Francis alandarkene...@gmail.commailto:alandarkene...@gmail.com wrote: Hi Marie FreeSurfers: I am running the LGI

Re: [Freesurfer] LGI error

Thanks so much Marie. I will check the toolboxes. best, Alan On Wed, Jul 9, 2014 at 2:56 PM, Marie Schaer marie.sch...@unige.ch wrote: Hi Alan, You probably don't have the matlab image processing toolbox installed. Let me know if you can't install it easily. Best, Marie On

[Freesurfer] Tracula -qa flag

Dear Freesurfer experts, I'm trying to run Tracula -prep after sourcing Freesurfer 5.3. The file subjid/dmri/dwi_motion.txt is not included in the output. I then ran: trac-all -qa -c dmrirc and got the error message: flag -qa unrecognized Do you know what could have gone wrong? Do I have to

Re: [Freesurfer] Tracula -qa flag

hi Trang Within the Martinos center you would not need to update but just source a different version. The right one to source is /usr/local/freesurfer/nmr-dev-env Maybe the right approach? Shantanu On Wed, July 9, 2014 4:57 pm, qtngu...@nmr.mgh.harvard.edu wrote: Dear Freesurfer experts,