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=9758
iterations
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:fis...@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-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@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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