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=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 >>> >>> This message and any attachment are intended solely for the addressee >> and may contain confidential information. If you have received this >> message in error, please send it back to me, and immediately delete > it. >> Please do not use, copy or disclose the information contained in this >> message or in any attachment. Any views or opinions expressed by the >> author of this email do not necessarily reflect the views of the >> University of Nottingham. >>> >>> This message has been checked for viruses but the contents of an >> attachment >>> may still contain software viruses which could damage your computer >> system: >>> you are advised to perform your own checks. Email communications with >> the >>> University of Nottingham may be monitored as permitted by UK >> legislation. >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender > and >> properly >> dispose of the e-mail. >> >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
