Re: [Freesurfer] recon surf folder is missing data

Thank you Bruce and Doug > but remember to delete the IsRunning file > > Bruce Fischl wrote: >> Hi Jake >> >> looks like recon-all stopped in the middle of running. You can see >> this because (1) the recon-all.log file is in the middle of the >> surface deformation, with no error message or termi

Re: [Freesurfer] recon surf folder is missing data

but remember to delete the IsRunning file Bruce Fischl wrote: Hi Jake looks like recon-all stopped in the middle of running. You can see this because (1) the recon-all.log file is in the middle of the surface deformation, with no error message or termination notice, and (2) there is an IsRun

Re: [Freesurfer] recon surf folder is missing data

Hi Jake looks like recon-all stopped in the middle of running. You can see this because (1) the recon-all.log file is in the middle of the surface deformation, with no error message or termination notice, and (2) there is an IsRunning.lh+rh in the scripts dir, meaning FreeSurfer thinks the rec

[Freesurfer] recon surf folder is missing data

Hi All, I was just wondering if anyone has had data missing from the surf directory in the recon folder of a subject, ie- right hemisphere data is missing, or no data at all. Here is the path to a recon where I recently have found missing data: /space/amaebi/35/users/ablood/R01_Botox/R01BTX_

Re: [Freesurfer] Cluster analysis

yes, I'm afraid so Devdutta W wrote: Hi, We are doing cluster analysis on 16 subjects using the following command: /mri_glmfit-sim --glmdir /data/zonda1/freesurfer_subjects_zonda/qdec/rh.area --sim mc-z 5000 2 mc-z.abs.2 --sim-sign abs --overwrite/ / /It has been running for seven days alrea

Re: [Freesurfer] Display-problem

Hi Pål Check this thread out http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07545.html anyway did you do anything to your system which might have overwritten your Nvidia drivers? Re-install the latest drivers for your graphics hardware and try again. Krish On Mar 9, 2009,

[Freesurfer] Cluster analysis

Hi, We are doing cluster analysis on 16 subjects using the following command: *mri_glmfit-sim --glmdir /data/zonda1/freesurfer_subjects_zonda/qdec/rh.area --sim mc-z 5000 2 mc-z.abs.2 --sim-sign abs --overwrite* * *It has been running for seven days already and seems to have output well over 72000

[Freesurfer] ROI definition based on cortical parcellation

Dear freesurfers, comparing patient groups I found volume differences in specific cortical regions (using aparc_stats), which I would now like to compare to the results of a classical VBM. Concerning the whole brain analyses, the VBM did not yield comparable results (what might partly be a mat

Re: [Freesurfer] Destrieux or Desikan/Ron Killiany

Hi Lars There is no atlas more accurate than the other one ; they just differ in anatomical convention. In fact the difference between the 2 nomenclatures comes from the definition of the parcellation: - Rahul used a gyral based atlas : ie a gyrus was defined as running between the bottoms o

RE: [Freesurfer] Destrieux or Desikan/Ron Killiany

any would help, or show the curvature in the background On Tue, 10 Mar 2009, Lars M. Rimol wrote: Hi, I just mapped these on the fsaverage lh.inflated. By images of the folding patterns, do you mean pial or smoothwm images from fsaverage? Or do you mean data from single subjects? LMR

RE: [Freesurfer] Destrieux or Desikan/Ron Killiany

Hi Rahul, Thanks for the input! I'm afraid I don't see how the atlases agree with regard to the medial SFG, since only a tiny portion of the area of interest is in SFG according to the Destriuex annotation (SFG is the uppermost parcellation in the anterior half of the hemisphere in that i

RE: [Freesurfer] Destrieux or Desikan/Ron Killiany

Hi, I just mapped these on the fsaverage lh.inflated. By images of the folding patterns, do you mean pial or smoothwm images from fsaverage? Or do you mean data from single subjects? LMR > Date: Tue, 10 Mar 2009 08:01:31 -0400 > From: fis...@nmr.mgh.harvard.edu > To: lari...@gmail.com >

Re: [Freesurfer] Destrieux or Desikan/Ron Killiany

Hi Lars, >From looking at the images you sent, your area of interest is clearly in the anterior portion of the cingulate gyrus as well as in the medial portion of the superior frontal gyrus (as well as a small portion in the corpus callosum). I think both atlases agree on this quite consistently.

Re: [Freesurfer] Destrieux or Desikan/Ron Killiany

Hi Lars, you need to send images of the folding patterns for Christophe and Rahul to decide. cheers, Bruce On Tue, 10 Mar 2009, Lars M. Rimol wrote: Hi, I have an area of significance on the mesial surface of the hemisphere (please see attached tiffs). I would like to know if it is exclusive