Dave,

In the mri/orig dir of that subject, the 002.mgz looks like a regular T1 anatomical, but 001.mgz is some other kind of scan. So probably the import went wrong. Try going back to the original dicoms to identify the proper two anatomicals.

Confirm they are ok by using tkmedit:

tkmedit -f 001.mgz -aux 002.mgz

Nick

On Tue, 2009-05-05 at 12:23 -0400, Dave Brohawn wrote:

Hello,

My bugr info is at the bottom, if needed:

I was doing a recon-all on one of our subjects, and I received this error message:

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ERROR! FOV=320.000 > 256 Include the flag -cw256 with recon-all!

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I pasted this error message into the archives, and saw Nick had asked someone with a similar problem to check the FOV of their subject to see if it was greater than 256 via mri_info orig.mgz.

Our subject, FB0011055B, has an FOV of 320, and dimensions 320 X 320 X 320. This is unusual because we opened the same set protocol as we usually do and did not make any adjustments to the FOV or slice parameters.

Most of our subject's orig.mgz info looks like this -

Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2200.00 msec, TE: 1.54 msec, TI: 1100.00 msec, flip angle: 7.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -0.7146 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 24.6542 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -26.7758

talairach xfm : /autofs/space/seymour_001/users/folate_subjects/FB0011053B/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 0.0000 0.0000 127.2854 0.0000 0.0000 1.0000 -103.3458 0.0000 -1.0000 0.0000 101.2242 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 0.0000 0.0000 127.2854 -0.0000 -0.0000 -1.0000 101.2242 -0.0000 1.0000 -0.0000 103.3458 0.0000 0.0000 0.0000 1.0000

This subject's is different, and it looks like this:

Volume information for orig.mgz type: MGH dimensions: 320 x 320 x 320 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 320.000 dof: 0 xstart: -160.0, xend: 160.0 ystart: -160.0, yend: 160.0 zstart: -160.0, zend: 160.0 TR: 2200.00 msec, TE: 1.54 msec, TI: 1100.00 msec, flip angle: 7.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.2500 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000

talairach xfm : Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 0.0000 0.0000 158.7500 0.0000 0.0000 1.0000 -160.0000 0.0000 -1.0000 0.0000 160.0000 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 0.0000 0.0000 158.7500 -0.0000 -0.0000 -1.0000 160.0000 -0.0000 1.0000 -0.0000 160.0000 0.0000 0.0000 0.0000 1.0000

Any ideas as to why this would happen?

Also, what does this -cw256 flag do and will it fix the issue?

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ERROR! FOV=320.000 > 256 Include the flag -cw256 with recon-all!

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Thank you,

Dave Brohawn

FREESURFER_HOME: /usr/local/freesurfer/stable4

Build stamp: freesurfer-Linux-centos4-stable-v4.3.0-20090503

RedHat release: CentOS release 5.2 (Final)

Kernel info: Linux 2.6.18-92.1.22.el5 i686

NMR Center info (/space/freesurfer exists):

machine: seymour

SUBJECTS_DIR: /space/seymour/1/users/folate_subjects

PWD: /space/seymour/1/users/folate_subjects

ssh seymour setenv SUBJECTS_DIR /space/seymour/1/users/folate_subjects cd /space/seymour/1/users/folate_subjects

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