Hello all,
I'm attempting to use mri_convert in order to match the slice size and thickness of T2 and PD images to the Freesurfer T1 images, after converting the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/T2/T2_like_norm.nii.gz
And having no problems. However, using the same code for the PD images I'm arriving at a bus error each time (output below). Is there any possible work around for this?
(freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0)
---
bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.nii.gz
mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl 003_S_0907_M00/mri/norm.nii.gz --like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_norm.nii.gz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 003_S_0907_M00/PD/PD.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 2.05103e-10, 0)
j_ras = (-2.05103e-10, -1, 0)
k_ras = (-0, -0, 1)
reading template info from volume 003_S_0907_M00/mri/norm.nii.gz...
INFO: transform src into the like-volume: 003_S_0907_M00/mri/norm.nii.gz
Bus error
if you file drop these volumes we'll take a look Bruce On Wed, 22 Jun 2011, G. William Chapman IV wrote:
Hello all, I'm attempting to use mri_convert in order to match the slice size and thickness of T2 and PD images to the Freesurfer T1 images, after converting the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/T2/T2_like_norm.nii.gz
And having no problems. However, using the same code for the PD images I'm arriving at a bus error each time (output below). Is there any possible work around for this?
(freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0)
bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.nii.gz
mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl 003_S_0907_M00/mri/norm.nii.gz --like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_norm.nii.gz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 003_S_0907_M00/PD/PD.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 2.05103e-10, 0)
j_ras = (-2.05103e-10, -1, 0)
k_ras = (-0, -0, 1)
reading template info from volume 003_S_0907_M00/mri/norm.nii.gz...
INFO: transform src into the like-volume: 003_S_0907_M00/mri/norm.nii.gz
Bus error
The files have been dropped. https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/24787/1/d2a16267...
On Wed, Jun 22, 2011 at 13:21, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
if you file drop these volumes we'll take a look Bruce
On Wed, 22 Jun 2011, G. William Chapman IV wrote:
Hello all,
I'm attempting to use mri_convert in order to match the slice size and thickness of T2 and PD images to the Freesurfer T1 images, after converting the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${**SUBJECT}/T2/T2_like_norm.nii.**gz
And having no problems. However, using the same code for the PD images I'm arriving at a bus error each time (output below). Is there any possible work around for this?
(freesurfer-Darwin-leopard-**i686-stable-pub-v5.0.0)
bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.**nii.gz
mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl 003_S_0907_M00/mri/norm.nii.gz --like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_** norm.nii.gz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from 003_S_0907_M00/PD/PD.nii.gz...
TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 2.05103e-10, 0)
j_ras = (-2.05103e-10, -1, 0)
k_ras = (-0, -0, 1)
reading template info from volume 003_S_0907_M00/mri/norm.nii.**gz...
INFO: transform src into the like-volume: 003_S_0907_M00/mri/norm.nii.gz
Bus error
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/**compliancelinehttp://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.
just took a look. Why is your PD.nii.gz two frames? The problem is reslicing a 2-frame volume but specifying a volume as a template that only has 1 frame. We shouldn't be core dumping, but that's the unusual situation that is causing it.
cheers Bruce On Thu, 23 Jun 2011, G. William Chapman IV wrote:
The files have been dropped.https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/24787/1/d2a16267...
On Wed, Jun 22, 2011 at 13:21, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: if you file drop these volumes we'll take a look Bruce
On Wed, 22 Jun 2011, G. William Chapman IV wrote:
Hello all, I'm attempting to use mri_convert in order to match the slice size and thickness of T2 and PD images to the Freesurfer T1 images, after converting the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using: mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/T2/T2_like_norm.nii.gz And having no problems. However, using the same code for the PD images I'm arriving at a bus error each time (output below). Is there any possible work around for this? (freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0) --- bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.nii.gz mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl 003_S_0907_M00/mri/norm.nii.gz --like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_norm.nii.gz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 003_S_0907_M00/PD/PD.nii.gz... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.05103e-10, 0) j_ras = (-2.05103e-10, -1, 0) k_ras = (-0, -0, 1) reading template info from volume 003_S_0907_M00/mri/norm.nii.gz... INFO: transform src into the like-volume: 003_S_0907_M00/mri/norm.nii.gz Bus errorThe 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.
p.s. also, why are you specifying --like and -rl? On Thu, 23 Jun 2011, G. William Chapman IV wrote:
The files have been dropped.https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/24787/1/d2a16267...
On Wed, Jun 22, 2011 at 13:21, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: if you file drop these volumes we'll take a look Bruce
On Wed, 22 Jun 2011, G. William Chapman IV wrote:
Hello all, I'm attempting to use mri_convert in order to match the slice size and thickness of T2 and PD images to the Freesurfer T1 images, after converting the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using: mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/T2/T2_like_norm.nii.gz And having no problems. However, using the same code for the PD images I'm arriving at a bus error each time (output below). Is there any possible work around for this? (freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0) --- bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.nii.gz mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl 003_S_0907_M00/mri/norm.nii.gz --like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_norm.nii.gz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 003_S_0907_M00/PD/PD.nii.gz... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.05103e-10, 0) j_ras = (-2.05103e-10, -1, 0) k_ras = (-0, -0, 1) reading template info from volume 003_S_0907_M00/mri/norm.nii.gz... INFO: transform src into the like-volume: 003_S_0907_M00/mri/norm.nii.gz Bus errorThe 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.
I'm not sure why the PD would be two frames -- the files were downloaded as dcm from the ADNI database. After looking through them though, there was a repeat of the slices, so I removed the second frame. Seems to have solved the problem, as the reslice is working now.
On Thu, Jun 23, 2011 at 09:28, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
p.s. also, why are you specifying --like and -rl?
On Thu, 23 Jun 2011, G. William Chapman IV wrote:
The files have been dropped.https://www.nmr.mgh.**
harvard.edu/facility/filedrop/**showgroup/24787/1/** d2a16267b417faa9da6f7cff3c3622**8ahttps://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/24787/1/d2a16267b417faa9da6f7cff3c36228a
On Wed, Jun 22, 2011 at 13:21, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: if you file drop these volumes we'll take a look Bruce
On Wed, 22 Jun 2011, G. William Chapman IV wrote:
Hello all, I'm attempting to use mri_convert in order to match the slice sizeand thickness of T2 and PD images to the Freesurfer T1 images, after converting the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz--like ${SUBJECT}/mri/norm.nii.gz ${**SUBJECT}/T2/T2_like_norm.nii.**gz
And having no problems. However, using the same code for the PDimages I'm arriving at a bus error each time (output below). Is there any possible work around for this?
(freesurfer-Darwin-leopard-**i686-stable-pub-v5.0.0) --- bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.** nii.gz
mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl003_S_0907_M00/mri/norm.nii.gz --like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_** norm.nii.gz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 003_S_0907_M00/PD/PD.nii.gz... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.05103e-10, 0) j_ras = (-2.05103e-10, -1, 0) k_ras = (-0, -0, 1) reading template info from volume 003_S_0907_M00/mri/norm.nii.**gz...
INFO: transform src into the like-volume:003_S_0907_M00/mri/norm.nii.gz
Bus errorThe 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/**compliancelinehttp://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.
glad to hear it Bruce On Thu, 23 Jun 2011, G. William Chapman IV wrote:
I'm not sure why the PD would be two frames -- the files were downloaded as dcm from the ADNI database. After looking through them though, there was a repeat of the slices, so I removed the second frame. Seems to have solved the problem, as the reslice is working now.
On Thu, Jun 23, 2011 at 09:28, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: p.s. also, why are you specifying --like and -rl?
On Thu, 23 Jun 2011, G. William Chapman IV wrote:
The files have beendropped.https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/24787/1 /d2a16267b417faa9da6f7cff3c36228a On Wed, Jun 22, 2011 at 13:21, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: if you file drop these volumes we'll take a look Bruce On Wed, 22 Jun 2011, G. William Chapman IV wrote: Hello all, I'm attempting to use mri_convert in order to match the slice size and thickness of T2 and PD images to the Freesurfer T1 images, after converting the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using: mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/T2/T2_like_norm.nii.gz And having no problems. However, using the same code for the PD images I'm arriving at a bus error each time (output below). Is there any possible work around for this? (freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0) --- bash-3.2$ mri_convert ${SUBJECT}/PD/PD.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz --like ${SUBJECT}/mri/norm.nii.gz ${SUBJECT}/PD/PD_like_norm.nii.gz mri_convert 003_S_0907_M00/PD/PD.nii.gz -rl 003_S_0907_M00/mri/norm.nii.gz --like 003_S_0907_M00/mri/norm.nii.gz 003_S_0907_M00/PD/PD_like_norm.nii.gz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 003_S_0907_M00/PD/PD.nii.gz... TR=3000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.05103e-10, 0) j_ras = (-2.05103e-10, -1, 0) k_ras = (-0, -0, 1) reading template info from volume 003_S_0907_M00/mri/norm.nii.gz... INFO: transform src into the like-volume: 003_S_0907_M00/mri/norm.nii.gz Bus error 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@nmr.mgh.harvard.edu
-
Bruce Fischl -
G. William Chapman IV