fsl_rigid_register is not as it has in the past. It seems the script isn't writing the correct outvol.* format in the /tmp directory. My command line and output are below.
Thanks,
--Steve
lucy [flash] fsl_rigid_register -r orig.mgh -i flash5.mgh -o flash5_fsl.mgh $Id: fsl_rigid_register,v 1.7 2003/08/21 23:28:03 ebeth Exp $ Mon Aug 29 09:31:13 EDT 2005 flash5_fsl.mgh -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash mri_convert orig.mgh /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img mri_convert orig.mgh /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img reading from orig.mgh... TR=2000.00, TE=3.37, TI=950.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img... Analyze Output Matrix -1.000 -0.000 -0.000 129.806; -0.000 0.000 1.000 -58.312; 0.000 -1.000 -0.000 126.746; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to 'coronal flipped' -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash mri_convert flash5.mgh /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.imgmri_convert flash5.mgh /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.img
reading from flash5.mgh... TR=20.00, TE=1.80, TI=1.80, flip angle=5.00 i_ras = (0.0729938, -0.963132, 0.258938) j_ras = (0.0105586, -0.25887, -0.965855) k_ras = (-0.997276, -0.0732354, 0.00872654) writing to /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.img... Analyze Output Matrix 0.073 0.011 -1.326 76.077; -0.963 -0.259 -0.097 234.646; 0.259 -0.966 0.012 88.186; 0.000 0.000 0.000 1.000; -------------------- No such orientation specified in Analyze7.5. Set orient to 0 Direction cosines for /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash/flash5.mgh are: x_r = 0.0730, y_r = 0.0106, z_r = -0.9973, c_r = 0.6410 x_a = -0.9631, y_a = -0.2589, z_a = -0.0732, c_a = 70.6763 x_s = 0.2589, y_s = -0.9659, z_s = 0.0087, c_s = -2.2521 INFO: set hdr.hist.orient to 'transverse unflipped' -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash tkregister2 --targ orig.mgh --mov flash5.mgh --reg /tmp/fsl_rigid_register.6917/tkregister.dat --fslregout /tmp/fsl_rigid_register.6917/initxfm.fslmat --regheader --noedit --s doesnotmatter target volume orig.mgh movable volume flash5.mgh reg file /tmp/fsl_rigid_register.6917/tkregister.dat LoadVol 0 $Id: tkregister2.c,v 1.30 2004/12/14 19:58:00 greve Exp $ Diagnostic Level -1 INFO: loading target orig.mgh Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable flash5.mgh Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.330 -85.120; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 ---- Input registration matrix (computed) -------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000; subject = doesnotmatter RegMat --------------------------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000; register: file /tmp/fsl_rigid_register.6917/tkregister.dat written Init FSL Mat based on geometry ------------------- -0.07299379 -0.01055863 0.99727648 53.97108841 -0.25893784 0.96585459 -0.00872653 38.25601959 -0.96313190 -0.25886959 -0.07323541 290.63790894 0.00000000 0.00000000 0.00000000 1.00000000 ------------------------------------------------- -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash flirt -in /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.hdr -out /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.hdr -init /tmp/fsl_rigid_register.6917/initxfm.fslmat -omat /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image -------------------------------------- /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash mri_convert /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img flash5_fsl.mgh mri_convert /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img flash5_fsl.mgh reading from /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img... ERROR: analyzeRead(): cannot find any files for /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img
don't have perms to look at the data what computer are you on? what env are you using?
Steve Stufflebeam wrote:
fsl_rigid_register is not as it has in the past. It seems the script isn't writing the correct outvol.* format in the /tmp directory. My command line and output are below. Thanks,
--Steve
lucy [flash] fsl_rigid_register -r orig.mgh -i flash5.mgh -o flash5_fsl.mgh $Id: fsl_rigid_register,v 1.7 2003/08/21 23:28:03 ebeth Exp $ Mon Aug 29 09:31:13 EDT 2005 flash5_fsl.mgh
/autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash
mri_convert orig.mgh /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img mri_convert orig.mgh /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img reading from orig.mgh... TR=2000.00, TE=3.37, TI=950.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img... Analyze Output Matrix -1.000 -0.000 -0.000 129.806; -0.000 0.000 1.000 -58.312; 0.000 -1.000 -0.000 126.746; 0.000 0.000 0.000 1.000;
INFO: set hdr.hist.orient to 'coronal flipped'
/autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash
mri_convert flash5.mgh /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.imgmri_convert flash5.mgh /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.img
reading from flash5.mgh... TR=20.00, TE=1.80, TI=1.80, flip angle=5.00 i_ras = (0.0729938, -0.963132, 0.258938) j_ras = (0.0105586, -0.25887, -0.965855) k_ras = (-0.997276, -0.0732354, 0.00872654) writing to /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.img... Analyze Output Matrix 0.073 0.011 -1.326 76.077; -0.963 -0.259 -0.097 234.646; 0.259 -0.966 0.012 88.186; 0.000 0.000 0.000 1.000;
No such orientation specified in Analyze7.5. Set orient to 0 Direction cosines for /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash/flash5.mgh are: x_r = 0.0730, y_r = 0.0106, z_r = -0.9973, c_r = 0.6410 x_a = -0.9631, y_a = -0.2589, z_a = -0.0732, c_a = 70.6763 x_s = 0.2589, y_s = -0.9659, z_s = 0.0087, c_s = -2.2521 INFO: set hdr.hist.orient to 'transverse unflipped'
/autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash
tkregister2 --targ orig.mgh --mov flash5.mgh --reg /tmp/fsl_rigid_register.6917/tkregister.dat --fslregout /tmp/fsl_rigid_register.6917/initxfm.fslmat --regheader --noedit --s doesnotmatter target volume orig.mgh movable volume flash5.mgh reg file /tmp/fsl_rigid_register.6917/tkregister.dat LoadVol 0 $Id: tkregister2.c,v 1.30 2004/12/14 19:58:00 greve Exp $ Diagnostic Level -1 INFO: loading target orig.mgh Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable flash5.mgh Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.330 -85.120; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 ---- Input registration matrix (computed) -------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000;
---- Input registration matrix -------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000; subject = doesnotmatter RegMat --------------------------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000; register: file /tmp/fsl_rigid_register.6917/tkregister.dat written Init FSL Mat based on geometry ------------------- -0.07299379 -0.01055863 0.99727648 53.97108841 -0.25893784 0.96585459 -0.00872653 38.25601959 -0.96313190 -0.25886959 -0.07323541 290.63790894 0.00000000 0.00000000 0.00000000 1.00000000
/autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash
flirt -in /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.hdr -out /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.hdr -init /tmp/fsl_rigid_register.6917/initxfm.fslmat -omat /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image
/autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/mri/flash
mri_convert /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img flash5_fsl.mgh mri_convert /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img flash5_fsl.mgh reading from /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img... ERROR: analyzeRead(): cannot find any files for /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On Aug 29, 2005, at 12:12 PM, Doug Greve wrote:
I can't get to the data. group is megclin, which I'm not in. Also, please make sure to copy the previous emails into each email so that I don't have to go fishing though my inbox to get info from a previous email.
thanks
doug
Ugh, Sorry Doug. My fault. I copied the wrong link for you. I'm on the road and don't have a stable connection, so I"m not myself (I was using my cell phone as a modem which keeps going down).
The link with the proper permissions is in:
/space/linus/7/users/sms/MRI/clin_2356772/mri/flash
All the best,
--Steve
On Aug 29, 2005, at 11:26 AM, Doug Greve wrote:
don't have perms to look at the data what computer are you on? what env are you using?
Steve Stufflebeam wrote:
fsl_rigid_register is not as it has in the past. It seems the script isn't writing the correct outvol.* format in the /tmp directory. My command line and output are below. Thanks,
--Steve
lucy [flash] fsl_rigid_register -r orig.mgh -i flash5.mgh -o flash5_fsl.mgh $Id: fsl_rigid_register,v 1.7 2003/08/21 23:28:03 ebeth Exp $ Mon Aug 29 09:31:13 EDT 2005 flash5_fsl.mgh
/autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/ mri/flash mri_convert orig.mgh /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img mri_convert orig.mgh /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img reading from orig.mgh... TR=2000.00, TE=3.37, TI=950.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 0, -1) k_ras = (-0, 1, -0) writing to /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.img... Analyze Output Matrix -1.000 -0.000 -0.000 129.806; -0.000 0.000 1.000 -58.312; 0.000 -1.000 -0.000 126.746; 0.000 0.000 0.000 1.000;
INFO: set hdr.hist.orient to 'coronal flipped'
/autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/ mri/flash mri_convert flash5.mgh /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.imgmri_convert flash5.mgh /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.img reading from flash5.mgh... TR=20.00, TE=1.80, TI=1.80, flip angle=5.00 i_ras = (0.0729938, -0.963132, 0.258938) j_ras = (0.0105586, -0.25887, -0.965855) k_ras = (-0.997276, -0.0732354, 0.00872654) writing to /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.img... Analyze Output Matrix 0.073 0.011 -1.326 76.077; -0.963 -0.259 -0.097 234.646; 0.259 -0.966 0.012 88.186; 0.000 0.000 0.000 1.000;
No such orientation specified in Analyze7.5. Set orient to 0 Direction cosines for /autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/ mri/flash/flash5.mgh are: x_r = 0.0730, y_r = 0.0106, z_r = -0.9973, c_r = 0.6410 x_a = -0.9631, y_a = -0.2589, z_a = -0.0732, c_a = 70.6763 x_s = 0.2589, y_s = -0.9659, z_s = 0.0087, c_s = -2.2521 INFO: set hdr.hist.orient to 'transverse unflipped'
/autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/ mri/flash tkregister2 --targ orig.mgh --mov flash5.mgh --reg /tmp/fsl_rigid_register.6917/tkregister.dat --fslregout /tmp/fsl_rigid_register.6917/initxfm.fslmat --regheader --noedit --s doesnotmatter target volume orig.mgh movable volume flash5.mgh reg file /tmp/fsl_rigid_register.6917/tkregister.dat LoadVol 0 $Id: tkregister2.c,v 1.30 2004/12/14 19:58:00 greve Exp $ Diagnostic Level -1 INFO: loading target orig.mgh Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable flash5.mgh Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.330 -85.120; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 ---- Input registration matrix (computed) -------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000;
---- Input registration matrix -------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000; subject = doesnotmatter RegMat --------------------------- -0.073 0.963 -0.259 -0.000; -0.997 -0.073 0.009 -0.165; -0.011 0.259 0.966 -0.000; 0.000 0.000 0.000 1.000; register: file /tmp/fsl_rigid_register.6917/tkregister.dat written Init FSL Mat based on geometry ------------------- -0.07299379 -0.01055863 0.99727648 53.97108841 -0.25893784 0.96585459 -0.00872653 38.25601959 -0.96313190 -0.25886959 -0.07323541 290.63790894 0.00000000 0.00000000 0.00000000 1.00000000
/autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/ mri/flash flirt -in /tmp/fsl_rigid_register.6917/invol.fsl_rigid_register.hdr -out /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /tmp/fsl_rigid_register.6917/refvol.fsl_rigid_register.hdr -init /tmp/fsl_rigid_register.6917/initxfm.fslmat -omat /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image
/autofs/space/megraid_048/MEG-clin/users/sms/epilepsy/clin_2356772/ mri/flash mri_convert /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img flash5_fsl.mgh mri_convert /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img flash5_fsl.mgh reading from /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img... ERROR: analyzeRead(): cannot find any files for /tmp/fsl_rigid_register.6917/outvol.fsl_rigid_register.img
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Steve Stufflebeam -
Steven Stufflebeam