Hi everybody, I've been having a strange problem running stage1 of recon-all. The process finishes successfully when I select "Process Volume" from the GUI, but fails when I start the stage via terminal command (using the same brain). I would prefer using the terminal command because I've been told it is a more up-to-date version than the GUI command. The command I entered was "recon-all -stage1 -nomorphrgb -subjid test0317bTerm" and it appeared to terminate during intensity normalization. Below is the error log. Thanks.
-Aaron-
on Mar 22 15:09:11 EST 2004 /usr/local/freesurfer_dev/bin/noarch/recon-all -stage1 -nomorphrgb -subjid test0317bTerm /j/freesurfsubj/test0317bTerm subjid test0317bTerm SUBJECTS_DIR /j/freesurfsubj FREESURFER_HOME /usr/local/freesurfer_dev Linux Filesystem 1K-blocks Used Available Use% Mounted on freud:/export/freesurfsubj 74697640 36308304 34594784 52% /j/freesurfsubj --------------------------------------------- MotionCor Mon Mar 22 15:09:12 EST 2004
INFO: no runs were found in /j/freesurfsubj/test0317bTerm/mri/orig/XXX, however, there is a volume in /j/freesurfsubj/test0317bTerm/mri/orig, so I am just going to proceed with that as the input. --------------------------------------------- Talairach Mon Mar 22 15:09:14 EST 2004 /j/freesurfsubj/test0317bTerm/mri talairach2 test0317bTerm INFO: registering test0317bTerm Mon Mar 22 15:09:14 EST 2004 -------------------------------------------- mri_convert orig orig/orig.mnc mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm -------------------------------------------- mri_add_xform_to_header /j/freesurfsubj/test0317bTerm/mri/transforms/talairach.xfm /j/freesurfsubj/test0317bTerm/mri/orig /j/freesurfsubj/test0317bTerm/mri/orig
Mon Mar 22 15:11:14 EST 2004 --------------------------------------------- Nu Intensity Correction Mon Mar 22 15:11:14 EST 2004 mri_convert orig nu/nu0.mnc mri_convert orig nu/nu0.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to nu/nu0.mnc... nu_correct -clobber nu/nu0.mnc nu/nu1.mnc [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:11:32] running: /usr/local/bin/nu_estimate_np_and_em -parzen -log -sharpen 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_21409/ nu/nu0.mnc nu/nu1.imp
Processing:............................................................. .... Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 1 CV of field change: 2.16148e-26 [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:11:45] running: /usr/local/bin/make_template -quiet -shrink 3 nu/nu0.mnc /usr/tmp/nu_correct_21409//template.mnc
Transforming slices:................................................................. .... .................Done 256+0 records in 256+0 records out Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................. .... ........................................................................ .... ........................................................................ .... ...................................Done
nu_correct -clobber nu/nu1.mnc nu/nu2.mnc [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:12:16] running: /usr/local/bin/nu_estimate_np_and_em -parzen -log -sharpen 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_21464/ nu/nu1.mnc nu/nu2.imp
Processing:............................................................. .... Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 1 CV of field change: 3.04238e-26 [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:12:28] running: /usr/local/bin/make_template -quiet -shrink 3 nu/nu1.mnc /usr/tmp/nu_correct_21464//template.mnc
Transforming slices:................................................................. .... .................Done 256+0 records in 256+0 records out Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................. .... ........................................................................ .... ........................................................................ .... ...................................Done
nu_correct -clobber nu/nu2.mnc nu/nu3.mnc [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:12:59] running: /usr/local/bin/nu_estimate_np_and_em -parzen -log -sharpen 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_21517/ nu/nu2.mnc nu/nu3.imp
Processing:............................................................. .... Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 1 CV of field change: 2.0113e-26 [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:13:11] running: /usr/local/bin/make_template -quiet -shrink 3 nu/nu2.mnc /usr/tmp/nu_correct_21517//template.mnc
Transforming slices:................................................................. .... .................Done 256+0 records in 256+0 records out Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................. .... ........................................................................ .... ........................................................................ .... ...................................Done
nu_correct -clobber nu/nu3.mnc nu/nu4.mnc [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:13:43] running: /usr/local/bin/nu_estimate_np_and_em -parzen -log -sharpen 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_21575/ nu/nu3.mnc nu/nu4.imp
Processing:............................................................. .... Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 1 CV of field change: 2.08277e-26 [goldmana@feynman:/j/freesurfsubj/test0317bTerm/mri/] [2004-03-22 15:13:57] running: /usr/local/bin/make_template -quiet -shrink 3 nu/nu3.mnc /usr/tmp/nu_correct_21575//template.mnc
Transforming slices:................................................................. .... .................Done 256+0 records in 256+0 records out Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................. .... ........................................................................ .... ........................................................................ .... ...................................Done
mri_convert nu/nu4.mnc nu mri_convert nu/nu4.mnc nu reading from nu/nu4.mnc... DimSizes: 3, 256, 256, 256, 1 DataType: 1 MINC Linear Transform -1.0000 0.0000 0.0000 123.0000 0.0000 0.0000 1.0000 -122.3080 0.0000 -1.0000 0.0000 139.8577 0.0000 0.0000 0.0000 1.0000 Done reading minc TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to nu... --------------------------------------------- Intensity Normalization Mon Mar 22 15:14:37 EST 2004 /j/freesurfsubj/test0317bTerm/mri mri_normalize orig T1 reading from orig... normalizing image... MRInormalize: could not find any valid peaks No such file or directory mri_normalize: normalization failed No such file or directory ERROR: mri_normalize exited with non-zero status ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on freud:/export/freesurfsubj 74697640 36325824 34577264 52% /j/freesurfsubj ------------------------------------------ recon-all exited with errors at Mon Mar 22 15:14:50 EST 2004