Hi Stephanie Do you know why you have multiple frames? You can always extract a frame via:
cd $SUBJECTS_DIR/$subject/mri/orig mv 001.mgz 001.multiframe.mgz mri_convert -nth 0 001.multiframe.mgz 001.mgz assuming you know that frame 0 is the correct one. You might have to do this for 002 also, after which you can just run recon-all without the -i cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Hsieh, Stephanie Sent: Monday, December 14, 2020 9:16 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Multiple Frames Error Hi FreeSurfer Developers, I am trying to process a few MPRAGE sequences (different sessions), so I can edit the scans. And I am having trouble reconning the .mgz files. I have looked into why my job terminated early and I have attached the message below. The error states that 'input(s) cannot have multiple frames'. And I then looked into the mri_info, which I have also attached below, and based off of some similar questions I found in the archive, my dimensions seem to be incorrect for freesurfer to process. My dimensions are 240 x 256 x 176 x 2, and I believe they should be 240 x 256 x 176 in order for it to work. How do I go about fixing my dimensions? Does it have to do with how I unpacked the DICOMS? I have not run into this issue before so I would love to learn what caused this error. Thanks in advance, Stephanie Early termination error: Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /autofs/cluster/brutha/FS6 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Linux compute-0-85.nmr.mgh.harvard.edu<http://compute-0-85.nmr.mgh.harvard.edu/>3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux '/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/recon-all' -> '/autofs/cluster/brutha/FS6/SCD_021_BL/scripts/recon-all.local-copy' /autofs/cluster/brutha/FS6/SCD_021_BL mri_convert /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz mri_convert.bin /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz... TR=2300.00, TE=2.95, TI=900.00, flip angle=9.00 i_ras = (0.108201, -0.990984, 0.079018) j_ras = (0.0145467, -0.0778978, -0.996855) k_ras = (-0.994023, -0.10901, -0.00598659) writing to /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz... /autofs/cluster/brutha/FS6/SCD_021_BL mri_convert /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz mri_convert.bin /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz... TR=2300.00, TE=2.95, TI=900.00, flip angle=9.00 i_ras = (0.108201, -0.990984, 0.079018) j_ras = (0.0145467, -0.0778978, -0.996855) k_ras = (-0.994023, -0.10901, -0.00598659) writing to /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz... #-------------------------------------------- #@# MotionCor Thu Dec 10 21:00:24 EST 2020 Found 2 runs /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz has 2 frames Linux compute-0-85.nmr.mgh.harvard.edu<http://compute-0-85.nmr.mgh.harvard.edu/>3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SCD_021_BL exited with ERRORS at Thu Dec 10 21:00:25 EST 2020 mri_info on the session I am trying to run: Volume information for SCD_021_BL-1.mgz type: MGH dimensions: 240 x 256 x 176 x 2 voxel sizes: 1.054688, 1.054688, 1.200000 type: SHORT (4) fov: 270.000 dof: 0 xstart: -126.6, xend: 126.6 ystart: -135.0, yend: 135.0 zstart: -105.6, zend: 105.6 TR: 2300.00 msec, TE: 2.95 msec, TI: 900.00 msec, flip angle: 9.00 degrees nframes: 2 PhEncDir: ROW FieldStrength: 3.000000 ras xform present xform info: x_r = 0.1082, y_r = 0.0145, z_r = -0.9940, c_r = 9.2070 : x_a = -0.9910, y_a = -0.0779, z_a = -0.1090, c_a = 36.6058 : x_s = 0.0790, y_s = -0.9969, z_s = -0.0060, c_s = -29.9521 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: 0.1141 0.0153 -1.1928 98.5179 -1.0452 -0.0822 -0.1308 184.0548<tel:184.0548> 0.0833 -1.0514 -0.0072 95.2548 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1.33484 ras to voxel transform: 0.1026 -0.9396 0.0749 155.6942<tel:155.6942> 0.0138 -0.0739 -0.9452 102.2669<tel:102.2669> -0.8284 -0.0908 -0.0050 98.8026 -0.0000 -0.0000 -0.0000 1.0000 Volume information for SCD_021_BL-2.mgz type: MGH dimensions: 240 x 256 x 176 x 2 voxel sizes: 1.054688, 1.054688, 1.200000 type: SHORT (4) fov: 270.000 dof: 0 xstart: -126.6, xend: 126.6 ystart: -135.0, yend: 135.0 zstart: -105.6, zend: 105.6 TR: 2300.00 msec, TE: 2.95 msec, TI: 900.00 msec, flip angle: 9.00 degrees nframes: 2 PhEncDir: ROW FieldStrength: 3.000000 ras xform present xform info: x_r = 0.1082, y_r = 0.0145, z_r = -0.9940, c_r = 9.2070 : x_a = -0.9910, y_a = -0.0779, z_a = -0.1090, c_a = 36.6058 : x_s = 0.0790, y_s = -0.9969, z_s = -0.0060, c_s = -29.9521 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: 0.1141 0.0153 -1.1928 98.5179 -1.0452 -0.0822 -0.1308 184.0548<tel:184.0548> 0.0833 -1.0514 -0.0072 95.2548 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1.33484 ras to voxel transform: 0.1026 -0.9396 0.0749 155.6942<tel:155.6942> 0.0138 -0.0739 -0.9452 102.2669<tel:102.2669> -0.8284 -0.0908 -0.0050 98.8026 -0.0000 -0.0000 -0.0000 1.0000
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