External Email - Use Caution Dear Falk,
Thank you for your input! I have just tried without the T2 image as well, but it still output the same error. My original image size was 224*320*320 (voxel size 0.85*0.85*0.85), and the produced orig.mgz was 320*320*320 (voxel size 0.85*0.85*0.85). I eventually found a solution however, just a while ago. When I first resized the original image to the 256*256*256 myself (using mri_convert -oni 256 -onj 256 -onk 256 option), and then entered the resized image to recon-all (rather than entering the raw 224*320*320 image and having recon-all resize it), it finally runs. There is no direct explanation of the -oni -onj -onk flags on the FreeSurfer wiki page, but it seems like the flags change the image dimension only, which is what I needed in this case. I had tried the --crop flag too, but it resulted in some undesired overcropping of the images, so I found -oni etc to be better. Best, Kristine Windows 10용 메일<https://secure-web.cisco.com/1u3jPH_6TBD5qur5eLvSvI9DkZ9A0Cp4j4PpUvbotxRsYu1VbG1AwDR5ZSU1BkLSgbYw9kclbd1wD38kOt_Ces6Iwx4coQa8R13cdJadX81bOnDoqTg_LP8ukNnJeYA2EsMtGPWQR0VWmukoAAgQD8K-4Xf12dN7f-OkrlVtTeSkaM9QW4KEqWqar1QdrypZZY_T_Z262LzzycCuoQHf7ThQmnAT506u5fS_1gyEwY5WpJPCol_JpLk_ZN1DtYxS5f-R_nZGq-cHb_VbkzO-UaA/https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986>에서 보냄 보낸 사람: falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de> 보낸 날짜: 2020년 11월 18일 수요일 오후 4:52 받는 사람: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>; Lee Subin Kristine<mailto:subin9...@hotmail.com> 제목: AW: recon-all for 0.85 isotropic images error (bump) Dear Kristine, I haven't had any issues processing high resolution data with version 6 or 7 using either the -cm or -hires flag. However, I never used the -cw 256 flag as my FoV was never greater than 256. Could you post the size of the created files? Especially orig.mgz with and without using the cw256 flag? Have you tried to not include the T2 volume? Just an educated guess, but maybe cropping of the FoV is done on the T1 only and, therefore, results in the error you are facing due to the additional contrasts. Best, Falk ________________________________ Von: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Lee Subin Kristine <subin9...@hotmail.com> Gesendet: Montag, 16. November 2020 18:56:55 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] recon-all for 0.85 isotropic images error (bump) 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/13ctVtS4YP4Lclat7s3Ykq_mJDR2UHlE7uT-HCz2YJaV7dfzRWDuMPFXcdf_1anOudk7waAYoi2o-QQ0Gq3LwDNCxkVdtxkh8D6MptbW0nNMDneNZn7MHtq9rUAySUwvfzXKO264ktPjBXHRsStvFHJC7sdU8xTgil8zQdgE3mWe4lG0JR2Gy75indwcrlKOIXwK-qruG8vxisfw2tIpO939xR4tr5cRHz8-NOSgqvGNWpMHajOlClEMhFzSYw6M5u-LkcTl705bZJwXGD8X2-A/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1vz0y7ktiwgpWkZywU_JLAVpOR5ul0liEjA4FFLMLbnQ1-KFbKVMytwPbC7Ye9f6j2rkjgp38ss3In6sCj6YjtsC5EBtW3QzvDOiLYFj-mYsUy8CualuMlKACK0iEdhqWCHKQGHoR7hmFPDlGRcmErL4NCK9BIYKPQgmszciOc6H5es8kQdb-nqVjqQSxOuhVLhm_IMB8pBUPFqRXy3yMopNtiZ0LJBl3AamEv0RQgp9g_XEw0YRQ2q2cRwjv9hOyPDyIF6kw7-rS4C2mAqHYdQ%252Fhttps%25253A%25252F%25252Fgo.microsoft.com%25252Ffwlink%25252F%25253FLinkId%25253D550986%26data%3D04%257C01%257C%257C3df16ccbdbb54bf690dd08d88b96dd24%257C84df9e7fe9f640afb435aaaaaaaaaaaa%257C1%257C0%257C637412827354961416%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D1%252B7YmGqwxzgvPdczHVn1WDw8UINUYuGqXPglIzlrqIo%253D%26reserved%3D0>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 https://secure-web.cisco.com/1h_p3jRoYe96MYPTestwUD0cYBCiLkAfyXoQJFTJUJYXnuN_oC4p3zlUkFdnC5PahFyxMaIeC9vRzzotj16ZXYFT_sUvBCVAXzX5-Vq8FwhMWv6Y4IQ-rCyZ4UPoFVCzSd7ojMBkpaLp-JpS-O5CAwLglb-vTe9X3k3aQb-UfbTjtxF31nd8_2BKkanYyXnTUD0eEKiiXmjHJehIckbo9lihMIf0HR9XbqvXTBPoAwYuaITMuKdMwi5ThUnSGV-nhJe-R82N8GjmopaJxPInrcA/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FBugReporting%26data%3D04%257C01%257C%257C3df16ccbdbb54bf690dd08d88b96dd24%257C84df9e7fe9f640afb435aaaaaaaaaaaa%257C1%257C0%257C637412827354961416%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DqazmezZW5QhCkdFaxe0aK1o2EknnDI3%252FY0bW66%252Fhplc%253D%26reserved%3D0
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