The original data (that I have) was in analyze format.
~Siddharth
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, June 18, 2013 11:58 AM To: Ray, Siddharth Cc: Z K; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR! FOV=348.000 > 256
if they look squeezed horizontally I would guess something is wrong. What was your original data? Do you have dicoms? On Tue, 18 Jun 2013, Ray, Siddharth wrote:
Oooppss my bad, but do you know why exactly this was? FOV > 256?
Also when I open the orig.mgz file the image was squeezed horizontally.
Bruce, I have no idea why the FOV is so big. It just occured for few of my subjects. (from large data sample)
Will try include flag and see.
Thanks Zeke.
-----Original Message----- From: Z K [mailto:zkaufman@nmr.mgh.harvard.edu] Sent: Tuesday, June 18, 2013 11:44 AM To: Ray, Siddharth Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR! FOV=348.000 > 256
Hello Siddharth,
The error message says "Include the flag -cw256 with recon-all!" So I would recommend giving that a try.
-Zeke
On 06/18/2013 12:33 PM, Ray, Siddharth wrote:
Hi all,
I am coming across this error for couple of my subjects:
WARNING ==================++++++++++++++++++++++++=========================== = ===========
The physical sizes are (240.00 mm, 240.00 mm, 347.20 mm), which cannot fit in 256^3 mm^3 volume.
The resulting volume will have 348 slices.
If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).
==================================================+++++++++++++++++++
++++===============
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/sray2/Data/50183/50183/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
Original Data has (0.468746, 0.468746, 1.4) mm size and (512, 512, 248) voxels.
Data is conformed to 1 mm size and 348 voxels for all directions
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /home/sray2/Data/50183/50183/mri/orig.mgz...
ERROR! FOV=348.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
Linux localhost.localdomain 2.6.32-71.el6.x86_64 #1 SMP Wed Sep 1 01:33:01 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 50183 exited with ERRORS at Sat Jun 15 06:02:30 CDT 2013
Do anyone know whats wrong and how can I fix this?
Thanks in advance.
-Siddharth
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