Re: [Freesurfer] S_intraparietal-and_Parietal_transverse.label

Hi Esther I don't see a volume overlay, just one on the inflated surface. Is that what you mean? If not, can you resend and explain? Bruce On Thu, 2 Jun 2011, Esther Walton wrote: > > Thanks so much for your input. > > Could somebody please answer the second part of the question? > That is, ig

[Freesurfer] Surface Normals in Freesurfer

Hi Bruce et al. I have a quick question about the interpretation of surface normal files and the various ways you can create them with Freesurfer. As far as I know, there are two ways to get the normals information: mris_convert -n lh.inflated lh.inflated.normals2 and mri_surf2surf --s fsavera

Re: [Freesurfer] Surface Normals in Freesurfer

Hi Michael the ascii file is first: vertex_nx vertex_ny vertex_nz ripflag (usually 0) . . . up to # of vertices. Then, for each face: vertex_0 vertex_1 vertex_2 ripflag cheers Bruce On Thu, 2 Jun 2011, Michael Waskom wrote: > Hi Bruce et al. > > I have a quick question about the interp

[Freesurfer] Error: talairach_avi: Command not found.

Hi all, I am running recon-all -autorecon1 -subjid subject and I have been getting an error saying: \n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n talairach_avi: Command not found. And then the program exits with errors. I looked in the transforms directory within my subjec

[Freesurfer] Error in recon-all on seychelles

Hello, I am not able to do a regular recon-all of my data on seychelles-- I am doing the same thing I used to do. We have started moving our data to a different location, however, since this is all new data, I don't see how this could be the problem. I am using freesurfer 4, so I set this var bef

Re: [Freesurfer] Error in recon-all on seychelles

Hi Chindhuri, we'll need to know what the error was that resulted in the non-zero exit status. cheers Bruce On Thu, 2 Jun 2011, Chindhuri Selvadurai wrote: > Hello, > > I am not able to do a regular recon-all of my data on seychelles-- I am > doing the same thing I used to do. We have started m

Re: [Freesurfer] Error in recon-all on seychelles

I'm not sure how to get that information. It does not give me an error message in the terminal. Is there a log I could look at? Is there anything that I need to do prior to the recon-all? > Hi Chindhuri, > > we'll need to know what the error was that resulted in the non-zero exit > status. > > che

Re: [Freesurfer] Error in recon-all on seychelles

http://www.nmr.mgh.harvard.edu/martinos/itgroup/seychelles.html describes the cluster use. It will tell you how to check errors (there are pbsjob files in your folder that contain output and error messages. Best, Martin On Thu, 2011-06-02 at 14:54 -0400, Chindhuri Selvadurai wrote: > I'm not su

[Freesurfer] Error in generating V1 labels

Hi, I used the command: recon-all -s subjid -label-v1 to generate the V1 label for my individual subjects and I did not face any error. When I checked the label directory of the corresponding subjects, I see two new labels named lh.v1.predict.label rh.v1.predict.label but I don't see a

[Freesurfer] combining data from two sessions

Hi all, we have a subject who had to end a run early, and as a result his data is split over two sessions. The two sessions can't be analyzed independently, since some events are missing from each, which causes selxavg3 to fail. Instead, what I've been trying to do is take the timecourses

Re: [Freesurfer] combining data from two sessions

Hi Finn, this is much easier to handle in 5.1. Just put all the runs in the same bold directory and everything should work properly. doug Finnegan Calabro wrote: > Hi all, we have a subject who had to end a run early, and as a result > his data is split over two sessions. The two sessions can

Re: [Freesurfer] recon-all very bad tlrc transform, how to fix?

Hi Jen does the orig.mgz look right in tkmedit? That is, is axial really axial, coronal really coronal, etc...? Bruce On Thu, 2 Jun 2011, Jennifer Evans wrote: > > Hey there, > > I have a very bad Talairach transform failure (from recon-all). The images > from tmedit and tkregister2 are attach

[Freesurfer] Unable to run mris_preproc and load data in qdec

Hello! So, my first problem was that I wasn't able to load my new mgh files into qdec. I tried to follow this procedure: 1. Convert a curv file from you subject into mgh: mri_convert lh.curv lh.curv.mgh 2. Load in the mgh file to matlab lhcurv = MRIread('lh.curv.mgh'); 3. Replace the pix

[Freesurfer] How to refine the recon-all results from old version?

Hi, FSers We have lots of data run based on a previous version (see 5.0). Is there any way to refine them using the FS5.1 pipeline but not to re-run all steps of recon-all? Many thanks! -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn)

Re: [Freesurfer] S_intraparietal-and_Parietal_transverse.label

Hi Bruce, Yes, I mean the one on the inflated surface. I found this view easier to judge how well the label and the nii.gz match. Is that a problem? Thanks, Esther > Date: Thu, 2 Jun 2011 08:36:27 -0400 > From: fis...@nmr.mgh.harvard.edu > To: estherkil...@hotmail.com > CC: freesurfer@nmr.mgh.