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-----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
보낸 사람: Lee Subin Kristinemailto:subin9126@hotmail.com 보낸 날짜: Friday, October 30, 2020 9:40 PM 받는 사람: freesurfer@nmr.mgh.harvard.edumailto: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_hBFXf5qTHGGyEJ...