I am having some trouble running recon-all.
one thing I have observed: Freesurfer keeps searching in the /mri folder instead of the /mri/orig folder, for example, in order to run tkmedit I had to type the command as follows: tkmedit 2332 orig/orig.mgz and I had to copy the orig.mgz file from the /mri/orig folder to the /mri folder in order to run recon-all, otherwise I would get an error during the 'Nu Intensity Correction' step. Is this what it is supposed to do?
I still get an error during the mri_normalize step (see below- the error is all the way at the end)
Do you know what I might be missing? Thanks, Sasha
[wolosin@localhost mri]# recon-all -subjid 2332 -autorecon1 -mgz INFO: SUBJECTS_DIR is /home/wolosin/subjects ######################################## program versions used $Id: recon-all-nmr,v 1.72 2005/07/12 15:56:32 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ minctracc.c $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### Using mgz format --------------------------------------------- MotionCor Thu Sep 8 16:34:35 EDT 2005
INFO: no runs were found in /home/wolosin/subjects/2332/mri, however, there is a volume /home/wolosin/subjects/2332/mri/rawavg.mgz, so I am just going to proceed with that as the input. --------------------------------------------- Nu Intensity Correction Thu Sep 8 16:34:38 EDT 2005 mri_convert orig.mgz nu0.mnc mri_convert orig.mgz nu0.mnc reading from orig.mgz... TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 34:41] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpe n 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_ 1646/ nu0.mnc nu1.imp
Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 22 CV of field change: 0.00094628 [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 34:58] running: /usr/pubsw/packages/mni/current/bin/make_template -quiet -shrink 3 nu0.mnc /us r/tmp/nu_correct_1646//template.mnc
Transforming slices:............................................................ ..........................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done nu_correct -clobber nu1.mnc nu2.mnc [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:01] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpe n 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_ 1951/ nu1.mnc nu2.imp
Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 12 CV of field change: 0.000947063 [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:10] running: /usr/pubsw/packages/mni/current/bin/make_template -quiet -shrink 3 nu1.mnc /us r/tmp/nu_correct_1951//template.mnc
Transforming slices:............................................................ ..........................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done nu_correct -clobber nu2.mnc nu3.mnc [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:13] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpe n 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_ 2142/ nu2.mnc nu3.imp
Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 9 CV of field change: 0.000974347 [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:20] running: /usr/pubsw/packages/mni/current/bin/make_template -quiet -shrink 3 nu2.mnc /us r/tmp/nu_correct_2142//template.mnc
Transforming slices:............................................................ ..........................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done nu_correct -clobber nu3.mnc nu4.mnc [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:23] running: /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpe n 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_ 2295/ nu3.mnc nu4.imp
Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 8 CV of field change: 0.000890052 [wolosin@localhost.localdomain:/home/wolosin/subjects/2332/mri/] [2005-09-08 16: 35:30] running: /usr/pubsw/packages/mni/current/bin/make_template -quiet -shrink 3 nu3.mnc /us r/tmp/nu_correct_2295//template.mnc
Transforming slices:............................................................ ..........................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:............................................................ ................................................................................ ................................................................................ ....................................Done mri_convert nu4.mnc nu.mgz mri_convert nu4.mnc nu.mgz reading from nu4.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to nu.mgz... --------------------------------------------- Talairach Thu Sep 8 16:35:36 EDT 2005 /home/wolosin/subjects/2332/mri talairach2 2332 .mgz INFO: registering 2332 Thu Sep 8 16:35:36 EDT 2005 -------------------------------------------- mri_convert nu.mgz nu.mnc mri_convert nu.mgz nu.mnc reading from nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to nu.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -protocol icbm nu.mnc transforms/talairach.xfm -------------------------------------------- mri_add_xform_to_header /home/wolosin/subjects/2332/mri/transforms/talairach.xfm /home/wolosin/subjects/2332/mri/orig.mgz /home/wolosin/subjects/2332/mri/orig.m gz INFO: extension is mgz Thu Sep 8 16:36:16 EDT 2005 --------------------------------------------- Intensity Normalization Thu Sep 8 16:36:16 EDT 2005 /home/wolosin/subjects/2332/mri mri_normalize nu.mgz T1.mgz reading from nu.mgz... normalizing image... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 Segmentation fault ERROR: mri_normalize exited with non-zero status recon-all exited with errors at Thu Sep 8 16:37:02 EDT 2005
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270
Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.