Hi Ali,
that means that there are 0 control points stored in the file. For the 2nd error have you checked the talairach.xfm?
cheers Bruce
On Tue, 7 Sep 2010, Ali Radaideh wrote:
Hi Bruce,
Catting the file shows something like
cat control.dat info numpoints 0 useRealRAS 0
The version of freesurfer is
freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0
Unfortunately, I repeated hat you suggested in your previous email (-make all) to another subject but failed at some point although this subject's data have been proceed month ago successfully ( the data from the first subject still running), the error is:
second estimation of the COG coord: x=129,y=120, z=120, r=9758iterations GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 22554 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 1548 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = 1656 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=33 , nb = 9459 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 9819 OTHER CSF_MIN=0, CSF_intensity=18, CSF_MAX=39 , nb = 72 mri_watershed Error: GLOBAL region of the brain empty ! Linux comp13 2.6.22.17-0.1-default #1 SMP 2008/02/10 20:01:04 UTC x86_64 x86_64 x86_64 GNU/Linu x
recon-all exited with ERRORS at Mon Sep 6 15:03:10 BST 2010
Thanks Ali
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, September 06, 2010 3:30 PM To: Ali Radaideh Subject: RE: [Freesurfer] control points
Hi Ali,
can you post your responses to the list? Try catting that file to see what's in it. Also, what version are you running?
cheers Bruce
On Mon, 6 Sep 2010, Ali Radaideh wrote:
Hi Bruce,
control.dat file is there (size=75).
Actually I finished running this subject before and checked that.
Now I am running the recon-all with -make all flag as you suggested
and
it is working fine.
But not sure if 'reading 0 control points' means that there will be no improvement after running the recon-all !!
Thanks Ali
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, September 06, 2010 2:03 PM To: Ali Radaideh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] control points
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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