[Freesurfer] Recon-all -qcache curvature error & recon-all make -all

Hello, I have run several scans using recon-all -all -subjid subject_no -expert expert.opts where my expert.opts file changes the parameters for the mri_normalize step (this works well in my scans). I then had to edit a few of the scans by adding in more white matter and a few control points.

Re: [Freesurfer] Recon-all -qcache curvature error & recon-all make -all

Hello, I emailed last week to ask about an error I was getting. Has anyone had a chance to look into it? Thank you very much. Best wishes, Clare From: Gibbard, Clare Sent: 25 July 2012 16:45 To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject

Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 1

.edu Message-ID: <5018245a.1050...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Subject 20 is definitely out of synch, but the "make all" feature is not catching it. Try re-running this subject with -autorecon3 doug On 07/25/2012 11:45 AM, Gibbar

[Freesurfer] QDEC results

Hello, I went on the FS course in Amsterdam recently. I have run a QDEC analysis to see whether cortical thickness differs between my two groups. I have two questions: 1. I put in the lh_bankssts_thickness as my continuous variable. The display outputs results for whether average thickness

[Freesurfer] Re. QDEC results

Hi Doug, Thanks for your quick response - that all makes sense now. Best wishes, Clare -- Message: 13 Date: Fri, 10 Aug 2012 10:19:43 + From: "Gibbard, Clare" Subject: [Freesurfer] QDEC results To: "freesurfer@nmr.mgh.harvard.e

[Freesurfer] TRACULA - failed corpus callosum forceps major

Hello, I have tried out running TRACULA on 20 subjects. It all seemed to work well except that in 8 of the subjects the corpus callosum forceps major was either missing or was a very small cluster. The same happened for the temporal SLF of 2 subjects. I read previous posts related to this an

Re: [Freesurfer] TRACULA - failed corpus callosum forceps major

hes, Clare ____ From: Gibbard, Clare Sent: 14 September 2012 16:00 To: freesurfer@nmr.mgh.harvard.edu Subject: TRACULA - failed corpus callosum forceps major Hello, I have tried out running TRACULA on 20 subjects. It all seemed to work well except that in 8 of the subjects

Re: [Freesurfer] temporal lobe cut off

s. Let me know if you need any more information. Best wishes, Clare From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 10 January 2012 13:40 To: Gibbard, Clare Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] temporal lobe cut off Hi Cla

[Freesurfer] fsaverage error - too many levels of symbolic links

Hi, I am running recon-all on several scans, but it is exiting with an error. I think the error is occurring because my symbolic link to fsaverage is self-referential. However, the symbolic link is generated automatically during recon-all so I cannot see how to correct it. I have tried delet

Re: [Freesurfer] fsaverage error - too many levels of symbolic links

From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 21 February 2012 18:03 To: Gibbard, Clare Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fsaverage error - too many levels of symbolic links Hi Clare, try moving your SUBJECTS_DIR outside of the