Hi Bruce, The control points are now saved. It looks like I need to save them at least 3 times. I think tkmedit interface does not respond from the first time.
Many thanks Ali -----Original Message----- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Tuesday, September 07, 2010 2:22 AM To: Ali Radaideh Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] control points you need to visualize it in tkmedit. As for the control points, we haven't seen that happen. Can you try saving a couple and seeing if the file changes? cheers Bruce On Tue, 7 Sep 2010, Ali Radaideh wrote: > Hi Bruce > > That is strange. I have just repeated adding control points and save > them in tkmedit (file>save control points) but when I cat the > control.dat it shows nothing as before. > > Regarding talairach.xfm, > > MNI Transform File > % tkregister2 > > Transform_Type = Linear; > Linear_Transform = > 1.08922994 0.00106384 -0.03315430 2.06818056 > 0.05027838 1.18083215 -0.06254977 -14.10989380 > 0.06858014 -0.25201771 1.33514297 -10.44485474 ; > > Does this look ok? > > Ali > > -----Original Message----- > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Sent: Tuesday, September 07, 2010 1:30 AM > To: Ali Radaideh > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] control points > > 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. 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