[Freesurfer] Problem with recon-all on the tutorial data (bert)

Dear Freesurfers, I have had a problem when running recon-all on your tutorial data (bert). Please find following the content of recon-all.log: *$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $* * $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $* *MRISread(../surf/lh.inflat

Re: [Freesurfer] Problem with recon-all on the tutorial data (bert)

Hi Long, have you run out of disk space? Bruce On Tue, 24 Nov 2009, L wrote: > Dear Freesurfers, > > I have had a problem when running recon-all on your tutorial data (bert). > Please find following the content of recon-all.log: > > *$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $* > >

[Freesurfer] Recon-all -long

Dear FS experts Am I right that the input for step 3 in recon-all -long are the already cross-sectionally processed images from step 1 and not the raw images that I used to create these cross-sectionally images? Thanks for clarification Regards Jürgen

[Freesurfer] sup temporal plane 3-D view (Neuroimage 2006)

Dear Freesurfer, I am impressed with 3d-view of the supra temporal lobe in your Neuroimage(2006) paper (fig2). I am also trying to create such 3d view of supra temporal plane. If you could tell me the procedure to create it, that would be greatly appreciated. Thanks. Hiroyuki Oya __

Re: [Freesurfer] sup temporal plane 3-D view (Neuroimage 2006)

Hi Hiroyuki, which 2006 paper do you mean? Bruce On Tue, 24 Nov 2009, Oya, Hiroyuki wrote: > Dear Freesurfer, > > I am impressed with 3d-view of the supra temporal lobe in your > Neuroimage(2006) paper (fig2). > I am also trying to create such 3d view of supra temporal plane. > If you could tell

[Freesurfer] memory error

Hi: I got the following fatal error: CORRECTING DEFECT 61 (vertices=98413, convex hull=24013) Excessive topologic defect encountered: could not allocate 896316630 edges for retessellation Cannot allocate memory Linux image 2.6.28-16-generic #55-Ubuntu SMP Tue Oct 20 19:48:24 UTC 2009 i686 GNU/L

[Freesurfer] memory error 2

Hi: I got the following fatal error: CORRECTING DEFECT 61 (vertices=98413, convex hull=24013) Excessive topologic defect encountered: could not allocate 896316630 edges for retessellation Cannot allocate memory Linux image 2.6.28-16-generic #55-Ubuntu SMP Tue Oct 20 19:48:24 UTC 2009 i686 GNU/

Re: [Freesurfer] memory error 2

Hi Gonzalo, look at the ?h.orig.nofix or ?h.inflated.nofix and see if there is something dramatically wrong (e.g. attached cerebellum or skull). You can also look at the filled.mgz. cheers, Bruce On Tue, 24 Nov 2009, Gonzalo Rojas Costa wrote: > > Hi: > > I got the following fatal error: >

[Freesurfer] qdec.table.dat

Hi, I am trying to run qdec for group analysis of subcortical and cortical volumes. I have all of my data in an excel sheet (subject ID, age, gender, volumes of various structures) and am trying to convert this into a file that will be able to be opened in qdec. I use a Mac, and I have exported

Re: [Freesurfer] qdec.table.dat

I forget to load the specific error message for the qdec.table.dat error. Thanks again for your help. *Loading data table /Volumes/GEcontrols/qdec/qdec.table.dat... QdecDataTable::Load: will attempt to open as Mac text file... Number of columns: 6 fsid column: 1 Number of factors: 5 Number of subj

Re: [Freesurfer] qdec.table.dat

Hi Matt, I believe the problem lies in how excel treats end of line characters (even Excel for Mac). You could use Open-office which will export to a more Unix-friendly format, or you could try using tr (a Unix command-line utility that could change the problematic end of line characters to Unix-c

[Freesurfer] convert/reconstructing with mrdc

Hello, So far I have had no problems running recon-all with .mnc files but could use some guidance converting/reconstructing brains processed with AFNI (MRDC). There are 120 MRDC files in the T1 directory. I believe I need to run mri_convert on these MRDC files but am unsure of what the correct

Re: [Freesurfer] convert/reconstructing with mrdc

These are not the standard .BRIK files? Ziad (ccd) will know. Bruce On Tue, 24 Nov 2009, Jesse Bledsoe wrote: > Hello, > > So far I have had no problems running recon-all with .mnc files but could > use some guidance converting/reconstructing brains processed with AFNI > (MRDC). > > There are 1

Re: [Freesurfer] convert/reconstructing with mrdc

I have T1volume+org.BRIK - should I use those with mri_convert? Thanks again, Jesse On Tue, Nov 24, 2009 at 4:23 PM, Saad, Ziad S. (NIH/NIMH) [E] < sa...@mail.nih.gov> wrote: > mri_convert usually work with BRIK files. > > Alternately, 3dAFNItoNIFTI could turn BRIK files to nifti format > whi

[Freesurfer] talairach failure

Hello All, I ran recon-all on a subject and got the following error talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm # #...@# Talairach Failure Detection Thu Nov 19 16:17:54 EST

[Freesurfer] script to check multiple cases with tksurfer

Hi Folks, I would like to visually check the cortical parcellation for a large number of patients (>200) using tksurfer. Is there a script to which I could submit a list of subject id's and get it to launch tksurfer and display the parcellation data for each subject sequentially ? Thanks Mehul