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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
it may be that one of your voxel dimensions (and hence FOV) is wrong if it looks squeezed horizontally. Can you find out what the original data dimensions were?
On Tue, 18 Jun 2013, Ray, Siddharth wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It looks the dimensions are 512x512x256.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, June 18, 2013 12:01 PM To: Ray, Siddharth Cc: Z K; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ERROR! FOV=348.000 > 256
it may be that one of your voxel dimensions (and hence FOV) is wrong if it looks squeezed horizontally. Can you find out what the original data dimensions were?
On Tue, 18 Jun 2013, Ray, Siddharth wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
is that from the analyze? If so, it may be incorrect. 512x512 is a pretty big matrix and would be quite unusual. What are your voxel dimensions? Do you have access to the information from the original acquisitions?
On Tue, 18 Jun 2013, Ray, Siddharth wrote:
It looks the dimensions are 512x512x256.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, June 18, 2013 12:01 PM To: Ray, Siddharth Cc: Z K; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ERROR! FOV=348.000 > 256
it may be that one of your voxel dimensions (and hence FOV) is wrong if it looks squeezed horizontally. Can you find out what the original data dimensions were?
On Tue, 18 Jun 2013, Ray, Siddharth wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Its 512x512x248 voxels and 0.47 x 0.47 x 1.40 mm.
-Siddharth
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, June 18, 2013 12:18 PM To: Ray, Siddharth Cc: Z K; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ERROR! FOV=348.000 > 256
is that from the analyze? If so, it may be incorrect. 512x512 is a pretty big matrix and would be quite unusual. What are your voxel dimensions? Do you have access to the information from the original acquisitions?
On Tue, 18 Jun 2013, Ray, Siddharth wrote:
It looks the dimensions are 512x512x256.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, June 18, 2013 12:01 PM To: Ray, Siddharth Cc: Z K; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ERROR! FOV=348.000 > 256
it may be that one of your voxel dimensions (and hence FOV) is wrong if it looks squeezed horizontally. Can you find out what the original data dimensions were?
On Tue, 18 Jun 2013, Ray, Siddharth wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I see. Can you crop it and still fit the head? I don't think anyone needs 340mm to fit inside a volume On Tue, 18 Jun 2013, Ray, Siddharth wrote:
Its 512x512x248 voxels and 0.47 x 0.47 x 1.40 mm.
-Siddharth
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, June 18, 2013 12:18 PM To: Ray, Siddharth Cc: Z K; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ERROR! FOV=348.000 > 256
is that from the analyze? If so, it may be incorrect. 512x512 is a pretty big matrix and would be quite unusual. What are your voxel dimensions? Do you have access to the information from the original acquisitions?
On Tue, 18 Jun 2013, Ray, Siddharth wrote:
It looks the dimensions are 512x512x256.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, June 18, 2013 12:01 PM To: Ray, Siddharth Cc: Z K; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] ERROR! FOV=348.000 > 256
it may be that one of your voxel dimensions (and hence FOV) is wrong if it looks squeezed horizontally. Can you find out what the original data dimensions were?
On Tue, 18 Jun 2013, Ray, Siddharth wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
wow, why is your FOV so big?
On Tue, 18 Jun 2013, 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Ray, Siddharth -
Z K