Hello FreeSurfer Support, My name is Sucika Perumalla and I hope you can please help me with troubleshooting recon-all. I’m getting multiple frames errors when trying to run recon-all with my dicoms even after extracting the multiple frames. I was wondering if you can please help resolve this issue. Please refer to the attachment with my recon-all log.
Thanks _____________________________ Sucika Perumalla Clinical Research Assistant I Department of Neurology, Division of Movement Disorders Brigham and Women’s Hospital 60 Fenwood Road, Boston, MA 02115 sperumal...@bwh.harvard.edu<mailto:sperumal...@bwh.harvard.edu> | 508-414-2601
Last login: Tue Feb 20 11:15:44 on ttys001 sucikaperumalla@PHS027570 ~ % export FREESURFER_HOME="/Applications/freesurfer/7.4.1" source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/7.4.1 FSFAST_HOME /Applications/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects MNI_DIR /Applications/freesurfer/7.4.1/mni sucikaperumalla@PHS027570 ~ % export DATA=/Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769 sucikaperumalla@PHS027570 ~ % cd $DATA sucikaperumalla@PHS027570 E36409769 % recon-all -s JO1 -i /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm -all -qcache fs-check-version --s JO1 --o /var/folders/j5/20t8sd891y5_z4_q07d5b2km0000gr/T//tmp.wTf2uk Tue Feb 20 11:25:01 EST 2024 setenv SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects cd /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769 /Applications/freesurfer/7.4.1/bin/fs-check-version --s JO1 --o /var/folders/j5/20t8sd891y5_z4_q07d5b2km0000gr/T//tmp.wTf2uk -rwxrwxrwx 1 root wheel 18565 Jun 14 2023 /Applications/freesurfer/7.4.1/bin/fs-check-version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin PHS027570 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:53:18 PST 2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6000 arm64 pid 4595 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /Applications/freesurfer/7.4.1/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Applications/freesurfer/7.4.1/subjects Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 Darwin PHS027570 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:53:18 PST 2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6000 arm64 /Applications/freesurfer/7.4.1/subjects/JO1 \n mri_convert /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz reading from /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm dcmdir = /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE Found 384 DICOM file(s) load Image /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855821.dcm, size 114688 Warning: Unable to determine slice direction: please check whether slices are flipped Warning: Unable to determine slice direction: please check whether slices are flipped Convert 384 DICOM (224x256x192x2) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms WARNING: MRIsetRas2VoxFromMatrix(): voxels sizes are inconsistent (0.976562,0.976562) (0.976562,0.976562) (1,0) This is probably due to shear in the vox2ras matrix Input Vox2RAS ------ -0.97656 0.00000 -0.00000 105.30721; -0.00000 -0.97656 -0.00000 122.96610; 0.00000 0.00000 0.00000 -113.12712; 0.00000 0.00000 0.00000 0.00000; TR=2000.00, TE=3.03, TI=1100.00, flip angle=15.00 i_ras = (-1, -4.897e-12, 0) j_ras = (4.897e-12, -1, 0) k_ras = (nan, nan, nan) writing to /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Feb 20 11:25:45 EST 2024 Found 1 runs /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz has 2 frames Darwin PHS027570 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:53:18 PST 2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6000 arm64 recon-all -s JO1 exited with ERRORS at Tue Feb 20 11:25:46 EST 2024 For more details, see the log file /Applications/freesurfer/7.4.1/subjects/JO1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting sucikaperumalla@PHS027570 E36409769 % recon-all -s JO1 -i /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm -all -qcache fs-check-version --s JO1 --o /var/folders/j5/20t8sd891y5_z4_q07d5b2km0000gr/T//tmp.cSlXa6 Tue Feb 20 14:02:08 EST 2024 setenv SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects cd /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769 /Applications/freesurfer/7.4.1/bin/fs-check-version --s JO1 --o /var/folders/j5/20t8sd891y5_z4_q07d5b2km0000gr/T//tmp.cSlXa6 -rwxrwxrwx 1 root wheel 18565 Jun 14 2023 /Applications/freesurfer/7.4.1/bin/fs-check-version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin PHS027570 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:53:18 PST 2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6000 arm64 pid 29759 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /Applications/freesurfer/7.4.1/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Applications/freesurfer/7.4.1/subjects Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 Darwin PHS027570 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:53:18 PST 2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6000 arm64 /Applications/freesurfer/7.4.1/subjects/JO1 \n mri_convert /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz reading from /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm... mriio.cpp: starting DICOMRead3() Starting DICOMRead3() dcmfile = /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855840.dcm dcmdir = /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE Found 384 DICOM file(s) load Image /Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855821.dcm, size 114688 Warning: Unable to determine slice direction: please check whether slices are flipped Warning: Unable to determine slice direction: please check whether slices are flipped Convert 384 DICOM (224x256x192x2) DICOM row order preserved: may appear upside down in tools that ignore spatial transforms WARNING: MRIsetRas2VoxFromMatrix(): voxels sizes are inconsistent (0.976562,0.976562) (0.976562,0.976562) (1,0) This is probably due to shear in the vox2ras matrix Input Vox2RAS ------ -0.97656 0.00000 -0.00000 105.30721; -0.00000 -0.97656 -0.00000 122.96610; 0.00000 0.00000 0.00000 -113.12712; 0.00000 0.00000 0.00000 0.00000; TR=2000.00, TE=3.03, TI=1100.00, flip angle=15.00 i_ras = (-1, -4.897e-12, 0) j_ras = (4.897e-12, -1, 0) k_ras = (nan, nan, nan) writing to /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Feb 20 14:02:18 EST 2024 Found 1 runs /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz has 2 frames Darwin PHS027570 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:53:18 PST 2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6000 arm64 recon-all -s JO1 exited with ERRORS at Tue Feb 20 14:02:18 EST 2024 For more details, see the log file /Applications/freesurfer/7.4.1/subjects/JO1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting sucikaperumalla@PHS027570 E36409769 % cd $SUBJECTS_DIR/JO1/mri/orig sucikaperumalla@PHS027570 orig % mv 001.mgz 001.multiframe.mgz mri_convert -nth 0 001.multiframe.mgz 001.mgz mri_convert -nth 0 001.multiframe.mgz 001.mgz reading from 001.multiframe.mgz... TR=2000.00, TE=3.03, TI=1100.00, flip angle=15.00 i_ras = (-1, -4.897e-12, 0) j_ras = (4.897e-12, -1, 0) k_ras = (nan, nan, nan) writing to 001.mgz... sucikaperumalla@PHS027570 orig % recon-all -s JO1 -all -qcache fs-check-version --s JO1 --o /var/folders/j5/20t8sd891y5_z4_q07d5b2km0000gr/T//tmp.7H0bnm Tue Feb 20 14:04:32 EST 2024 setenv SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects cd /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig /Applications/freesurfer/7.4.1/bin/fs-check-version --s JO1 --o /var/folders/j5/20t8sd891y5_z4_q07d5b2km0000gr/T//tmp.7H0bnm -rwxrwxrwx 1 root wheel 18565 Jun 14 2023 /Applications/freesurfer/7.4.1/bin/fs-check-version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin PHS027570 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:53:18 PST 2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6000 arm64 pid 30166 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 bstampfile exists /Applications/freesurfer/7.4.1/subjects/JO1/scripts/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Applications/freesurfer/7.4.1/subjects Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 -rw-rw-r-- 1 sucikaperumalla wheel 30589 Feb 20 14:02 /Applications/freesurfer/7.4.1/subjects/JO1/scripts/recon-all.log Darwin PHS027570 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:53:18 PST 2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6000 arm64 #-------------------------------------------- #@# MotionCor Tue Feb 20 14:04:34 EST 2024 Found 1 runs /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. usage: sleep seconds \n cp /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig/001.mgz /Applications/freesurfer/7.4.1/subjects/JO1/mri/rawavg.mgz \n \n mri_info /Applications/freesurfer/7.4.1/subjects/JO1/mri/rawavg.mgz \n rawavg.mgz ======================================== Volume information for /Applications/freesurfer/7.4.1/subjects/JO1/mri/rawavg.mgz type: MGH dimensions: 224 x 256 x 192 voxel sizes: 0.976562, 0.976562, 1.000000 type: SHORT (4) fov: 250.000 dof: 1 xstart: -109.4, xend: 109.4 ystart: -125.0, yend: 125.0 zstart: -96.0, zend: 96.0 TR: 2000.00 msec, TE: 3.03 msec, TI: 1100.00 msec, flip angle: 15.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = nan, c_r = nan : x_a = -0.0000, y_a = -1.0000, z_a = nan, c_a = nan : x_s = 0.0000, y_s = 0.0000, z_s = nan, c_s = nan talairach xfm : Orientation : LPI Primary Slice Direction: axial voxel to ras transform: -0.9766 0.0000 nan nan -0.0000 -0.9766 nan nan 0.0000 0.0000 nan nan 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant nan ras to voxel transform: error: mat = NULL! /Applications/freesurfer/7.4.1/subjects/JO1 \n mri_convert /Applications/freesurfer/7.4.1/subjects/JO1/mri/rawavg.mgz /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig.mgz --conform \n mri_convert /Applications/freesurfer/7.4.1/subjects/JO1/mri/rawavg.mgz /Applications/freesurfer/7.4.1/subjects/JO1/mri/orig.mgz --conform reading from /Applications/freesurfer/7.4.1/subjects/JO1/mri/rawavg.mgz... TR=2000.00, TE=3.03, TI=1100.00, flip angle=15.00 i_ras = (-1, -4.897e-12, 0) j_ras = (4.897e-12, -1, 0) k_ras = (nan, nan, nan) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 943 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation error: MRIresample(): error inverting matrix; determinant is nan, matrix is: -0.97656 0.00000 nan nan; -0.00000 -0.97656 nan nan; 0.00000 0.00000 nan nan; 0.00000 0.00000 0.00000 1.00000; Darwin PHS027570 23.2.0 Darwin Kernel Version 23.2.0: Wed Nov 15 21:53:18 PST 2023; root:xnu-10002.61.3~2/RELEASE_ARM64_T6000 arm64 recon-all -s JO1 exited with ERRORS at Tue Feb 20 14:04:36 EST 2024 For more details, see the log file /Applications/freesurfer/7.4.1/subjects/JO1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting sucikaperumalla@PHS027570 orig %
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