Re: [Freesurfer] Error message

Hi Jürgen, a defect with 48000 vertices is huge (1/3 of the cortex). Check to make sure that the skull and cerebellum aren't attached to the filled volume and that the hemispheres are properly separated. cheers, Bruce On Wed, 11 Feb 2009, Jürgen Hänggi wrote: Dear FS experts I tried to re

[Freesurfer] How to show only some parcellations

Dear FS experts Is there any possibility to show only some and not all of the parcellations of the lh.aparc.a2005s.annot annotation file? We have looked for in the archives but did not find any answer Thanks Regards Jürgen

Re: [Freesurfer] How to show only some parcellations

Hi Juergen, we supply matlab scripts for reading and writing the annot files, so it should be easy enough to do - just set all the ones that you don't care about to 0. cheers, Bruce On Wed, 11 Feb 2009, Jürgen Hänggi wrote: Dear FS experts Is there any possibility to show only some and no

[Freesurfer] freeglut ERROR

Hi, In tksurfer, when I have loaded an overlay and then try to add a color bar, I get this error message: freeglut ERROR: Function called without first calling 'glutInit' I'm using freeglut v 2.4.0. I don't know if this is caused by a bug in freeglut (I think it's the latest version). Anyone kno

[Freesurfer] exited with errors

Hello all, I have recently been running some scans with very few defects, but have been encountering a particular error message on occasion when I try to run it through autorecon2 and autorecon3 after a bit of manual correction. The error output is: MRI_fill: could not read segmentation from

Re: [Freesurfer] How to show only some parcellations

you can also use mris_annotation2label to convert the annotation to a label, then use mri_label2annot to recombine only the ones you want Bruce Fischl wrote: Hi Juergen, we supply matlab scripts for reading and writing the annot files, so it should be easy enough to do - just set all the ones

Re: [Freesurfer] freeglut ERROR

Which freesurfer version are you using? The recent builds are built against a local glut lib, so it shouldn't be using the system glut lib. On Wed, 2009-02-11 at 15:06 +0100, Lars M. Rimol wrote: > Hi, > In tksurfer, when I have loaded an overlay and then try to add a color > bar, I get this err

Re: [Freesurfer] exited with errors

What version of freesurfer are you using now and what version was used to process the data? I suspect mixed versions were used. You can rerun with the -clean-aseg flag to start again. On Wed, 2009-02-11 at 10:43 -0500, Dankner, Nathan (NIH/NIMH) [F] wrote: > Hello all, > > I have recently been

RE: [Freesurfer] exited with errors

Yes, the versions are different. I am not sure of the exact version numbers, but I believe they are the 2 most recent releases. Do I need to run the scans from autorecon1 with the clean-aseg command, or can I run them from later processing steps? Thanks for your help, Nathan -Original

RE: [Freesurfer] exited with errors

they can be started from the -autorecon2 stage (also include - autorecon3). On Wed, 2009-02-11 at 12:05 -0500, Dankner, Nathan (NIH/NIMH) [F] wrote: > Yes, the versions are different. I am not sure of the exact version numbers, > but I believe they are the 2 most recent releases. Do I need to

RE: [Freesurfer] mri_label2label error

Hi there, I'm trying to copy the dlpfc label I've made using mri_label2label , but keep getting the following error. I've tried putting in paths in the command line, but haven't been able to rectify the problem. I was wondering if this might be a permission issue with the freesurfer folders. Any h

Re: [Freesurfer] mri_label2label error

Are the labels in the subjects' 'label' directories? If not, then this is usually fixed by putting the full path to the labels. Can you double check that that failed? Prapti Gautam wrote: Hi there, I'm trying to copy the dlpfc label I've made using mri_label2label , but keep getting the foll

RE: [Freesurfer] mri_label2label error

Yes, the labels are in the subjects' label directories; putting the full path to the labels solved the problem. Thank you, Prapti -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thursday, 12 February 2009 8:39 AM To: Prapti Gautam Cc: Nick Schmansky; Fr

RE: [Freesurfer] exited with errors

I attempted to re-run using the -clean-aseg flag, but this time got an error which said: ERROR: cannot find [subject path]/mri/aseg.mgz Is the underlying problem that I used two different versions? Should I sync up the two versions (one is on a server and one is on my desktop) in order to avo

[Freesurfer] new eTIV calculation

If you make use of the estimated Total Intracranial Volume (eTIV) calculation found in the aseg.stats file of your subject data, then you should be aware that we have recently found a more accurate way to make this calculation. We have found that using the talairach.xfm transform instead of the ta

Re: [Freesurfer] topological defect

this is probably stuff labeled as choroid in the aseg.mgz and won't matter (it's not near cortex in any case). cheers, Bruce On Wed, 11 Feb 2009, Dankner, Nathan (NIH/NIMH) [F] wrote: Hello, In many of the surfaces that I have made, a frequent error seems to center around the ventricles.