-----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 메일에서 보냄

보낸 사람: Lee Subin Kristine
보낸 날짜: Friday, October 30, 2020 9:40 PM
받는 사람: 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://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting