Re: [Freesurfer] intersection of triangles from the reconstructed pial surface

Hi Yasheng, hmmm, there is triangle/triangle intersection code that is supposed to prevent this from happening. Does this happen if you use the native (binary) format? How many faces intersect? Bruce On Mon, 8 Mar 2010 yasheng_c...@med.unc.edu wrote: Hi all, I am using tetgen to constr

Re: [Freesurfer] problem on freesurfer

Xiaoying, You can find information about changing the skull strip thresholds on this wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix The wmparc.mgz has the wm parcellated and labeled according to the closest cortical (gm) region. The aparc+aseg.mgz will show you the gm r

Re: [Freesurfer] Cluster-wise correction error

How many iterations did it finish? It will be in the .csd file. If it is 10k or more, you run just run mri_glmfit with the --no-sim option. doug lordowen wrote: > Dear Freesurfer experts: > > We used QDEC to generate the script for cluster-wise correction. After > 2 days running, we get error me

[Freesurfer] Cluster-wise correction error

Dear Freesurfer experts: We used QDEC to generate the script for cluster-wise correction. After 2 days running, we get error message : ERROR: opening /usr/local/freesurfer/subjects/qdec/group_thickness_age_rh/csd/mc-z.abs.2.69.j001-rh-Avg-Intercept-thickness.csd We checked /csd and find the .c

[Freesurfer] intersection of triangles from the reconstructed pial surface

Hi all, I am using tetgen to construct a tetrahedral mesh with the extracted pial surface in subject 004 from the tutorial datasets.  But I got an error message from tetgen to say that some triangles are intersecting each other.  I am not sure whether anyone has found this before. The file I te

Re: [Freesurfer] --fsl flag in bbregister

What are you trying to do? If you want to init with fsl then use --init-fsl. In newer versions you can have it output a flirt matrix with --fsl. doug Nasim Maleki wrote: > Hello Doug, > > I get an error message when using --fsl flag with bbregister: > > "ERROR: Flag --fsl unrecognized." > > I'm

Re: [Freesurfer] Cortical thickness measurement

That command gives several options as suggestions and a format for typing in the command. Following that format I write- mris_anatomical_stats -a jan lh.pial mris_anatomical_stats -a jan lh tkmedit mris_anatomical_stats -a jan lh tkmedit mris_anatomical_stats -a jan lh pial tkmedit mris_anatomical

[Freesurfer] --fsl flag in bbregister

Hello Doug, I get an error message when using --fsl flag with bbregister: "ERROR: Flag --fsl unrecognized." I'm using: bbregister,v 1.14.2.12 2009/08/07 22:21:00 greve Is this version of the bbregister that I'm using the latest? Thank you, Nasim _

Re: [Freesurfer] Cortical thickness measurement

Use mris_anatomical_stats Janani Dhinakaran wrote: > > Hello all, > > Can anyone tell me the commands I'll need to use to extract and > measure the cortical thickness and volume of certain regions of the brain? > > thanks > -- > I am the Sun, I know no darkness. > ---

Re: [Freesurfer] Error with Talairach Transform during recon-all

Do you have a subject called "tal_before"? Janani Dhinakaran wrote: > > I also checked without the '--surf orig'. Still not found. > > > On 8 March 2010 14:22, Janani Dhinakaran > wrote: > > Here is how I checked if it was done okay > Looks like it wasn't. >

Re: [Freesurfer] Error with Talairach Transform during recon-all

I also checked without the '--surf orig'. Still not found. On 8 March 2010 14:22, Janani Dhinakaran wrote: > Here is how I checked if it was done okay > Looks like it wasn't. > > s0964...@cric-0012:~$ export SUBJECTS_DIR=~/Desktop/Newdata > s0964...@cric-0012:~$ tkregister2 --mgz --s tal_before

[Freesurfer] Cortical thickness measurement

Hello all, Can anyone tell me the commands I'll need to use to extract and measure the cortical thickness and volume of certain regions of the brain? thanks -- I am the Sun, I know no darkness. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Error with Talairach Transform during recon-all

Here is how I checked if it was done okay Looks like it wasn't. s0964...@cric-0012:~$ export SUBJECTS_DIR=~/Desktop/Newdata s0964...@cric-0012:~$ tkregister2 --mgz --s tal_before --fstal --surf orig tkregister_tcl /usr/local/freesurfer/lib/tcl/tkregister2.tcl surfname set to orig INFO: no target v

Re: [Freesurfer] Error with Talairach Transform during recon-all

That is a message from the routine that we use to automatically check the tal transform. Sometimes it is too conservative. You should check the transform manually with tkregister2. If it looks ok, then you can run recon-all with -notal-check. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutor

[Freesurfer] Error with Talairach Transform during recon-all

Any idea what this means and what I can do about it? Mon Mar 8 12:46:58 GMT 2010 talairach_avi done # #...@# Talairach Failure Detection Mon Mar 8 12:46:58 GMT 2010 /home/s0964091/Desktop/Newdata/JS/mri talairach_afd -T 0.005 -xfm transforms/talairac