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 #-------------------------------------------- #@# 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

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mri_motion_correct.fsl logfile is /autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/rawavg.mgz.mri_motion_correct.fsl.log

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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;

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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;

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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

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/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

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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