Hi Ali,

the control points are saved in the subject's directory under

<subject id>/tmp/control.dat

does that file exist? It also looks like you hadn't finished running this subject previously. Try running -make all in recon-alll which will rerun only what it needs to.

cheers Bruce

On Mon, 6 Sep 2010, Ali Radaideh wrote:

Dear Freesurfer experts,

One more question for today please. I have edited the wm in tkmedit and saved the control points then ran

Recon-all -autorecon2-cp -autorecon3 -s mySubjectName

But unfortunately I got the following message after 5min of running. I tried to use a different subject but I got the same message again.

It was displaying a message that it is 'reading 0 control points'. Is this message related to the error below?

mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz

logging cutting plane coordinates to ../scripts/ponscc.cut.log...

INFO: Using transforms/talairach.lta and its offset for Talairach volume ...

using segmentation aseg.auto_noCCseg.mgz...

reading input volume...done.

searching for cutting planes...voxel to talairach voxel transform

1.047 0.006 0.067 -14.718;

0.005 1.161 0.015 -27.233;

-0.083 -0.006 1.022 -2.059;

0.000 0.000 0.000 1.000;

mri_fill: could not read segmentation from aseg.auto_noCCseg.mgz

reading segmented volume aseg.auto_noCCseg.mgz...

ERROR: cannot find /data_local/ali/freesurfer/subjects/ali1/mri/aseg.auto_noCCseg.mgz

No such file or directory

Linux comp07 2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC x86_64 x86_64 x86_64 GNU /Linux

recon-all exited with ERRORS at Mon Sep 6 13:00:12 BST 2010

Many thanks

Ali

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