Re: [Freesurfer] LME Contrasts - Longitudinal Analysis

Hi Pedro, yes, the same is true for LME. Best, Martin On 01/10/2015 04:43 PM, Pedro Rosa - Gmail wrote: Dear Freesurfer List, Reading the Wiki for the GLM procedures, I understood that that covariates that are “0” in the contrast matrix are “regressed out”

[Freesurfer] qdec group analysis error

Hello there, I am trying to run an analysis in qdec with 25 subjects, 1 factor (diagnosis) with three levels (e.g control, diag1, diag2) in order to compare cortical thickness in these diagnostic groups. I am coming across two main errors; 1. The first one I get upon clicking analyze in the

Re: [Freesurfer] LME Contrasts - Longitudinal Analysis

Thanks, Martin! Sent from my iPhone On Jan 14, 2015, at 18:34, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Pedro, yes, the same is true for LME. Best, Martin On 01/10/2015 04:43 PM, Pedro Rosa - Gmail wrote: Dear Freesurfer List, Reading the Wiki for the GLM procedures, I

Re: [Freesurfer] qdec group analysis error

You still cannot use 3 levels. You will have to use the manual stream, ie, use mris_preproc, mri_surf2surf (smoothing), mri_glmfit, and mri_glmfit-sim. See the wiki for more info doug On 01/14/2015 02:14 PM, Hirsch, Gabriella wrote: Hello there, I am trying to run an analysis in qdec with

Re: [Freesurfer] Freeview question: using line profile

I think you need to create 2 sets of way points as iso-lines. You can do that from File - New Point Set and select 'way point'. Then you should be able to use the line profile tool. On 01/14/2015 04:55 PM, Albrecht, Daniel S. wrote: Hello, I'm having trouble using the line profile tool in

Re: [Freesurfer] Freeview question: using line profile

Hi Dan, for the line profile you'd select a few points along one curve (e.g. along the pial surface in a slice) , then along the opposite curve (e.g. along the wm surface) and you can then compute line profiles connecting the two curves (via solution of a poisson equation). the tool samples

[Freesurfer] FREESURFER] ERROR: matrix is ill-conditioned or badly scaled, condno = 164365

HelloI’m trying to do an group analysis using mir_glmfit but I met this error. ERROR: matrix is ill-conditioned or badly scaled, condno = 1652791. my command line wasmri_glmfit --y lh.age_edu.thickness.10b.mgh --fsgd age_edu.fsgd --C C_age.edu.mtx --surf fsaverage lh --cortex --glmdir

[Freesurfer] Freeview question: using line profile

Hello, I'm having trouble using the line profile tool in FreeView. I have a PET image overlaid on an MR image, and would like to view a line profile of a rectangular ROI on the PET image. I assumed that the line profile selection in Tools would be able to do this, but I haven't been able to

Re: [Freesurfer] Freeview question: using line profile

Ok thanks! I was using control points previously, I think that was my problem. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Ruopeng Wang [rpw...@nmr.mgh.harvard.edu] Sent: Wednesday, January 14, 2015 5:11 PM

[Freesurfer] incomplete preprocessing

Hi, How can I execute recon-all on an incomplete preprocessed file in freesurfer. My Pc was accidently shut down during the process. Thank you. Best Regards Naveed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Viewing QDEC results in tksurfer

what is your tksurfer command line? On 01/13/2015 07:12 AM, Worker, Amanda wrote: Hi, Is it possible to view the results of a qdec analysis (correlation with a single continuous group) in tksurfer? I am currently unable to open it and I'm getting an error saying could not open file

Re: [Freesurfer] incomplete preprocessing

Hi Naveed try recon-all -s subject id -make all cheers Bruce On Fri, 16 Jan 2015, Muhammad Naveed Iqbal Qureshi wrote: Hi, How can I execute recon-all on an incomplete preprocessed file in freesurfer. My Pc was accidently shut down during the process.   Thank you.   Best Regards

Re: [Freesurfer] FreeSurferOutputVolume

It works! Thank you soo much~! And I am wondering.the output segmentated ROIsIf I would like to use them as a mask, can a set the all the values 0 to be 1 or it's better for me only consider those voxels with 255(max) intensities? Best, Xiaowei. From:

[Freesurfer] error on mris_compute_lgi

Dear Freesurfer Experts, I am encountering an error when I run recon-all with the -localGI flag or run mris_compute_lgi separately. I recently upgraded Matlab from R2013a to R2014b. I found a prior discussion on replacing SearchProjectionOnPial.m

Re: [Freesurfer] TRACULA mask error

Sorry, I misunderstood. I've attached a screenshot of what I can see, it does look like there is probably a different problem now as both the dtifit_FA.nii.gz and aparc+aseg.bbr.nii are completely off centre. Thanks, Amanda From: