External Email - Use Caution -----Bumping this question up because still could not find a solution ---- -----Any contributions or ideas would be greatly appreciated ---------
I am still having problems with running the high resolution recon-all (on v.6.0 stable). I have tried multiple flags (-hires, -cm, with and without cw256), but they all lead to the same error message, basically saying that the orig.mgz FOV is more than 256 (even when I try to conform the image to 256). (ERROR! FOV=272.000 > 256)/ When I try recon-all.v6.hires, the rawavg.mgz is not able to be created. I have tried on both Ubuntu 14.04 and 16.04, but still get the same results. Has anyone had any success in using the hires option of recon-all? Any input would be appreciated. Best Regards, Kristine Windows 10용 메일<https://secure-web.cisco.com/1vz0y7ktiwgpWkZywU_JLAVpOR5ul0liEjA4FFLMLbnQ1-KFbKVMytwPbC7Ye9f6j2rkjgp38ss3In6sCj6YjtsC5EBtW3QzvDOiLYFj-mYsUy8CualuMlKACK0iEdhqWCHKQGHoR7hmFPDlGRcmErL4NCK9BIYKPQgmszciOc6H5es8kQdb-nqVjqQSxOuhVLhm_IMB8pBUPFqRXy3yMopNtiZ0LJBl3AamEv0RQgp9g_XEw0YRQ2q2cRwjv9hOyPDyIF6kw7-rS4C2mAqHYdQ/https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986>에서 보냄 보낸 사람: Lee Subin Kristine<mailto:subin9...@hotmail.com> 보낸 날짜: Friday, October 30, 2020 9:40 PM 받는 사람: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 제목: recon-all for 0.85 isotropic images error Hello FreeSurfer Developers, I'm trying to run recon-all (v.6) on T1- and T2-weighted images that have 0.85mm^3 isotropic voxels I have entered the command as below, with the T2, T2pial, cm, cw256 flags. recon-all -i $T1_DIR/"oT1_"$subj.nii -T2 $T2_DIR/"oT2_"$subj.nii -T2pial -cm -cw256 -subject $subj"_test" -all However, I keep getting the error as follows. ERROR! FOV=272.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. I'm guessing that conforming to the small voxel size results in a FOV that is out of limit? However, when I check the orig.mgz file it looks fine. (It has an image dimension of 320 x 320 x 320). Even when I include the flag -cw256 as the error message says, I still get the same error message. (Also, I cannot find any documentation about the -cw256flag on the help page). I have pasted the full log below. Thank you for your help. Best regards, Kristine ------------------------------------------------------------- subin@ubuntu:/mnt/hgfs/subindata/MYELIN-QSM/SCRIPT$ ./run_fs_1 INFO: all volumes are conformed to the min voxel size 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 /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW Actual FREESURFER_HOME /usr/local/freesurfer Linux ubuntu 4.15.0-112-generic #113~16.04.1-Ubuntu SMP Fri Jul 10 04:37:08 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/scripts/recon-all.local-copy' -cw256 option is now persistent (remove with -clean-cw256) /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test mri_convert /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz mri_convert.bin /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99998, -0.00515189, -0.00357438) j_ras = (0.00515192, 0.999987, 0) k_ras = (0.00357433, -1.83865e-05, 0.999994) writing to /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Fri Oct 30 05:19:16 PDT 2020 /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test mri_convert --no_scale 1 /mnt/hgfs/subindata/MYELIN-QSM/BRL_T2/oT2_BRL_0004.nii /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/T2raw.mgz mri_convert.bin --no_scale 1 /mnt/hgfs/subindata/MYELIN-QSM/BRL_T2/oT2_BRL_0004.nii /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/T2raw.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/hgfs/subindata/MYELIN-QSM/BRL_T2/oT2_BRL_0004.nii... TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99998, -0.00515189, -0.00357438) j_ras = (0.00515192, 0.999987, 0) k_ras = (0.00357433, -1.83865e-05, 0.999994) writing to /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Fri Oct 30 05:19:23 PDT 2020 Found 1 runs /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/rawavg.mgz /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test mri_convert /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/rawavg.mgz /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig.mgz --conform_min mri_convert.bin /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/rawavg.mgz /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig.mgz --conform_min $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/rawavg.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99998, -0.00515189, -0.00357438) j_ras = (0.00515192, 0.999987, 0) k_ras = (0.00357433, -1.83865e-05, 0.999994) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig.mgz... **************************************** ERROR! FOV=272.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Linux ubuntu 4.15.0-112-generic #113~16.04.1-Ubuntu SMP Fri Jul 10 04:37:08 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BRL_0004_test exited with ERRORS at Fri Oct 30 05:19:38 PDT 2020 For more details, see the log file /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1m-H0Fk8daSywmzBlOTFEUugQarr65jbK_hBFXf5qTHGGyEJmHUJbrUcU9JuAS4wStjJSAx5FheVNzHIeU9yhJyRoWrdUlSTUO7mC83W8NMGr9eDeSo50CUm_PVSlH4YPeNyq0H77zfLLG7qTmSF3DgTd3yvN8Rhkz4N_w6RduG_qaFcgQOqMIDnPgAOCkg_J7PbB5OwO6ejkRlg83mWBPJJNHGaE9JEzp_BX8fDzA5Kk5FybLZvhHgmtkeXlpx4T1DoITnt-Jk7PRPJ3MNHcwg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
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