The problem is that one volume (001.mgz) has 158 slices, while the other volume (002.mgz) has 160 slices. Originating volumes all need to be the same size.
I'll add an error-check to print a message if there is a mismatch. If you really want to use these two volumes, then you could run mri_convert --conform to convert each to 256x256x256 and use those as your originating volumes. On Thu, 2006-03-23 at 12:30 -0500, Daniel Goldenholz wrote: > Hi > > I emailed a little while ago about this, but I haven't heard any > solutions yet. As a check, I re-ran recon-all again this morning on a > local machine. Still crashing. Here is the output: > > > > recon-all -s $SUBJECT -motioncor > > INFO: SUBJECTS_DIR is /autofs/space/megraid_043/seder/freesurfer > Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0_x86_64/dev > -rw-rw-r-- 1 dwakeman megclin 27336 Mar 10 18:01 > /autofs/space/megraid_043/seder/freesurfer/nmr00069/scripts/recon-all.log > Linux rerun 2.6.9-22.0.2.106.unsupportedsmp #1 SMP Fri Jan 20 04:48:30 > CST 2006 x86_64 x86_64 x86_64 GNU/Linux > #-------------------------------------------- > [EMAIL PROTECTED] MotionCor Thu Mar 23 11:37:22 EST 2006 > Found 2 runs > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz > #----------------------------------------------- > /autofs/space/megraid_043/seder/freesurfer/nmr00069 > > mri_motion_correct.fsl -o > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/rawavg.mgz -wild > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz > > tmpdir is > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962 > -------------------------------------------------------------- > mri_motion_correct.fsl logfile is > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/rawavg.mgz.mri_motion_correct.fsl.log > -------------------------------------------------------------- > ----------------------------------------- > Converting > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz > Thu Mar 23 11:37:32 EST 2006 > /autofs/space/megraid_043/seder/freesurfer/nmr00069 > mri_convert > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img > > -odt float > reading from > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/001.mgz... > TR=2000.00, TE=3.25, TI=950.00, flip angle=7.00 > i_ras = (-0, -1, -5.55112e-17) > j_ras = (-0.0401318, -0, -0.999194) > k_ras = (-0.999194, -0, 0.0401318) > changing data type from 4 to 3 (noscale = 0)... > writing to > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img... > Analyze Output Matrix > -0.000 -0.040 -0.999 91.684; > -1.000 -0.000 -0.000 129.675; > -0.000 -0.999 0.040 117.569; > 0.000 0.000 0.000 1.000; > -------------------- > INFO: set hdr.hist.orient to -1 > ----------------------------------------- > Converting > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz > Thu Mar 23 11:37:37 EST 2006 > /autofs/space/megraid_043/seder/freesurfer/nmr00069 > mri_convert > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img > > -odt float > reading from > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/orig/002.mgz... > TR=2000.00, TE=3.25, TI=950.00, flip angle=7.00 > i_ras = (-0, -1, -5.55112e-17) > j_ras = (-0.0401318, -0, -0.999194) > k_ras = (-0.999194, -0, 0.0401318) > changing data type from 4 to 3 (noscale = 0)... > writing to > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img... > Analyze Output Matrix > -0.000 -0.040 -0.999 91.684; > -1.000 -0.000 -0.000 129.675; > -0.000 -0.999 0.040 117.569; > 0.000 0.000 0.000 1.000; > -------------------- > INFO: set hdr.hist.orient to -1 > ----------------------------------------- > Motion Correcting > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img > Thu Mar 23 11:37:43 EST 2006 > /autofs/space/megraid_043/seder/freesurfer/nmr00069 > fsl_rigid_register -maxangle 90 -r > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img > > -i > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img > > -o > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img > > -tmpdir > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962 > > -cleanup > \n\n > $Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $ > Thu Mar 23 11:37:43 EST 2006 > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img > Reference is analyze, not converting > Input is analyze, not converting > Output is analyze, not converting > -------------------------------------- > /autofs/space/megraid_043/seder/freesurfer/nmr00069 > calling eval flirt -in > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.hdr > > -out > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.hdr > > -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 > 90 -interp trilinear -dof 6 -ref > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.hdr > > -omat > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.fslmat > WARNING: Both reference and input images have an sform matrix set > The output image will use the sform from the reference image > > Started at Thu Mar 23 11:37:43 EST 2006 > Ended at Thu Mar 23 11:43:33 EST 2006 > > fsl_rigid_register Done > > To check results, run: > tkmedit -f > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img > > -aux > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img > > mv > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/resampled.img > > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img > ----------------------------------------- > Averaging > Thu Mar 23 11:43:33 EST 2006 > /autofs/space/megraid_043/seder/freesurfer/nmr00069 > inhibiting isotropic volume interpolation > 1 of 2: reading > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-1.img... > 2 of 2: reading > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img... > INFO: analyzeRead(): min = 0, max = 1543 > ERROR: premature end of file > ERROR: Success (0) > frame = 0, slice = 158, k=158, row = 0 > nread = 0, nexpected = 256 > fname = > height = 256 > width = 256 > depth = 160 > nframe = 1 > imnr0 = 1 > imnr1 = 160 > xnum = 256 > ynum = 256 > fov = 256.000000 > thick = 1.000000 > xstart = -128.000000 > xend = 128.000000 > ystart = -128.000000 > yend = 128.000000 > zstart = -80.000000 > zend = 80.000000 > type = 3 > xsize = 1.000000 > ysize = 1.000000 > zsize = 1.000000 > x ras = 0.000000 -1.000000 -0.000000 > y ras = -0.040132 0.000000 -0.999194 > z ras = -0.999194 0.000000 0.040132 > c ras = 5.572693 0.674698 -8.076317 > det(xyz_ras) = -1.000000 > ras_good_flag = 1 > brightness = 1 > subject_name = > path_to_t1 = > fname_format = > analyzeRead2(): error reading from file > /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img > mri_average: > MRIread(/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img) > > failed > Linux rerun 2.6.9-22.0.2.106.unsupportedsmp #1 SMP Fri Jan 20 04:48:30 > CST 2006 x86_64 x86_64 x86_64 GNU/Linux > > recon-all exited with ERRORS at Thu Mar 23 11:43:38 EST 2006 > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
