Hi, I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error; -------------[esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gzmri_convert /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $reading from /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc...mincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc[esther@m3012-04 ~]$ --------------------I look up, and the file is at the rith place.... Could you help me..Thanks VP]
Do you have read permission to the file? Also, you can convert straight to mgz, not need to use nii as an intermediate. doug
On 3/15/13 5:13 AM, Valtina Pouegue wrote:
Hi,
I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error;
[esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gz mri_convert /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc... mincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc [esther@m3012-04 ~]$
I look up, and the file is at the rith place.... Could you help me.. Thanks
VP ]
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Valtina
you can convert directly without going through nii. What happens when you run ls -l on that file? Or mri_info?
cheers Bruce
On Fri, 15 Mar 2013, Valtina Pouegue wrote:
Hi,
I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error;
[esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gz mri_convert /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc... mincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc [esther@m3012-04 ~]$
I look up, and the file is at the rith place.... Could you help me.. Thanks
VP]
I get this error-------------esther@m3012-04 ~]$ mri_info $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mncmincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.mnc-------I check in the directory enad the file is right there,
Date: Fri, 15 Mar 2013 09:24:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem
Hi Valtina
you can convert directly without going through nii. What happens when you run ls -l on that file? Or mri_info?
cheers Bruce
On Fri, 15 Mar 2013, Valtina Pouegue wrote:
Hi,
I have a problem of conversion. I would like to convert mnc file to mgz. But I think I shoul first convert mnc to nii then nii to mgz. , so I try the command mri_convert and I have this error;
[esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc Folder1.nii.gz mri_convert /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc... mincRead(): can't find file /home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc [esther@m3012-04 ~]$
I look up, and the file is at the rith place.... Could you help me.. Thanks
VP]
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.
can you run ls -l and mri_info on it? On Fri, 15 Mar 2013, Valtina Pouegue wrote:
I get this error------------- esther@m3012-04 ~]$ mri_info $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc mincRead(): can't find file/home/esther/Freesufer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.m nc -------I check in the directory enad the file is right there,
Date: Fri, 15 Mar 2013 09:24:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem
Hi Valtina
you can convert directly without going through nii. What happens when you run ls -l on that file? Or mri_info?
cheers Bruce
On Fri, 15 Mar 2013, Valtina Pouegue wrote:
Hi,
I have a problem of conversion. I would like to convert mnc file to mgz.
But I think I shoul first convert mnc to nii then
nii to mgz. , so I try the command mri_convert and I have this error;
[esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc
Folder1.nii.gz
mri_convert
/home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from
/home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc...
mincRead(): can't find file
/home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc
[esther@m3012-04 ~]$
I look up, and the file is at the rith place.... Could you help me.. Thanks
VP]
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
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.
Sorry, I am also a beginner in Linux environment. Now it works. I try :-------------esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AAtotal 13892-rwxr--r-- 1 esther esther 14224696 12 mar 23:33 t1_icbm_normal_1mm_pn3_rf20.mnc[esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc-rwxr--r-- 1 esther esther 14224696 12 mar 23:33 /home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.mnc----------------And this ----------Volume information for /home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.mnc type: MINC dimensions: 181 x 217 x 181 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 217.000 dof: 0 xstart: -90.5, xend: 90.5 ystart: -108.5, yend: 108.5 zstart: -90.5, zend: 90.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWNras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.5000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.5000Orientation : RASPrimary Slice Direction: axial voxel to ras transform: 1.0000 0.0000 0.0000 -90.0000 0.0000 1.0000 0.0000 -126.0000 0.0000 0.0000 1.0000 -72.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: 1.0000 -0.0000 -0.0000 90.0000 -0.0000 1.0000 -0.0000 126.0000 -0.0000 -0.0000 1.0000 72.0000 0.0000 0.0000 0.0000 1.0000------------------- which command shoul I use for convert direct from MNC to mgz^ Thanks
Date: Fri, 15 Mar 2013 10:00:04 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem
can you run ls -l and mri_info on it? On Fri, 15 Mar 2013, Valtina Pouegue wrote:
I get this error------------- esther@m3012-04 ~]$ mri_info $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc mincRead(): can't find file/home/esther/Freesufer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20.m nc -------I check in the directory enad the file is right there,
Date: Fri, 15 Mar 2013 09:24:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem
Hi Valtina
you can convert directly without going through nii. What happens when you run ls -l on that file? Or mri_info?
cheers Bruce
On Fri, 15 Mar 2013, Valtina Pouegue wrote:
Hi,
I have a problem of conversion. I would like to convert mnc file to mgz.
But I think I shoul first convert mnc to nii then
nii to mgz. , so I try the command mri_convert and I have this error;
[esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc
Folder1.nii.gz
mri_convert
/home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from
/home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc...
mincRead(): can't find file
/home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc
[esther@m3012-04 ~]$
I look up, and the file is at the rith place.... Could you help me.. Thanks
VP]
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
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 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.
just:
mri_convert <full path to minc file> volume.mgz
cheers Bruce
On Fri, 15 Mar 2013, Valtina Pouegue wrote:
Sorry, I am also a beginner in Linux environment. Now it works. I try :
esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA total 13892 -rwxr--r-- 1 esther esther 14224696 12 mar 23:33 t1_icbm_normal_1mm_pn3_rf20.mnc [esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc -rwxr--r-- 1 esther esther 14224696 12 mar 23:33/home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20. mnc
And this
Volume information for/home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20. mnc type: MINC dimensions: 181 x 217 x 181 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 217.000 dof: 0 xstart: -90.5, xend: 90.5 ystart: -108.5, yend: 108.5 zstart: -90.5, zend: 90.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.5000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.5000 Orientation : RAS Primary Slice Direction: axial
voxel to ras transform: 1.0000 0.0000 0.0000 -90.0000 0.0000 1.0000 0.0000 -126.0000 0.0000 0.0000 1.0000 -72.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: 1.0000 -0.0000 -0.0000 90.0000 -0.0000 1.0000 -0.0000 126.0000 -0.0000 -0.0000 1.0000 72.0000 0.0000 0.0000 0.0000 1.0000
which command shoul I use for convert direct from MNC to mgz^
Thanks
Date: Fri, 15 Mar 2013 10:00:04 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem
can you run ls -l and mri_info on it? On Fri, 15 Mar 2013, Valtina Pouegue wrote:
I get this error------------- esther@m3012-04 ~]$ mri_info $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc mincRead(): can't find file/home/esther/Freesufer/freesurfer/subjects/AA/t
1_icbm_normal_1mm_pn3_rf20.m
nc -------I check in the directory enad the file is right there,
Date: Fri, 15 Mar 2013 09:24:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem
Hi Valtina
you can convert directly without going through nii. What happens when yo
u
run ls -l on that file? Or mri_info?
cheers Bruce
On Fri, 15 Mar 2013, Valtina Pouegue wrote:
Hi,
I have a problem of conversion. I would like to convert mnc file to mg
z.
But I think I shoul first convert mnc to nii then
nii to mgz. , so I try the command mri_convert and I have this error;
[esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc
Folder1.nii.gz
mri_convert
/home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from
/home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc...
mincRead(): can't find file
/home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc
[esther@m3012-04 ~]$
I look up, and the file is at the rith place.... Could you help me.. Thanks
VP]
The information in this e-mail is intended only for the person to whom i
t
is
addressed. If you believe this e-mail was sent to you in error and the
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you i
n
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 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.
Thanks a lot!
Date: Fri, 15 Mar 2013 13:09:41 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem
just:
mri_convert <full path to minc file> volume.mgz
cheers Bruce
On Fri, 15 Mar 2013, Valtina Pouegue wrote:
Sorry, I am also a beginner in Linux environment. Now it works. I try :
esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA total 13892 -rwxr--r-- 1 esther esther 14224696 12 mar 23:33 t1_icbm_normal_1mm_pn3_rf20.mnc [esther@m3012-04 ~]$ ls -l $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc -rwxr--r-- 1 esther esther 14224696 12 mar 23:33/home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20. mnc
And this
Volume information for/home/esther/Freesurfer/freesurfer/subjects/AA/t1_icbm_normal_1mm_pn3_rf20. mnc type: MINC dimensions: 181 x 217 x 181 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 217.000 dof: 0 xstart: -90.5, xend: 90.5 ystart: -108.5, yend: 108.5 zstart: -90.5, zend: 90.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.5000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.5000 Orientation : RAS Primary Slice Direction: axial
voxel to ras transform: 1.0000 0.0000 0.0000 -90.0000 0.0000 1.0000 0.0000 -126.0000 0.0000 0.0000 1.0000 -72.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: 1.0000 -0.0000 -0.0000 90.0000 -0.0000 1.0000 -0.0000 126.0000 -0.0000 -0.0000 1.0000 72.0000 0.0000 0.0000 0.0000 1.0000
which command shoul I use for convert direct from MNC to mgz^
Thanks
Date: Fri, 15 Mar 2013 10:00:04 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem
can you run ls -l and mri_info on it? On Fri, 15 Mar 2013, Valtina Pouegue wrote:
I get this error------------- esther@m3012-04 ~]$ mri_info $SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc mincRead(): can't find file/home/esther/Freesufer/freesurfer/subjects/AA/t
1_icbm_normal_1mm_pn3_rf20.m
nc -------I check in the directory enad the file is right there,
Date: Fri, 15 Mar 2013 09:24:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_convert problem
Hi Valtina
you can convert directly without going through nii. What happens when yo
u
run ls -l on that file? Or mri_info?
cheers Bruce
On Fri, 15 Mar 2013, Valtina Pouegue wrote:
Hi,
I have a problem of conversion. I would like to convert mnc file to mg
z.
But I think I shoul first convert mnc to nii then
nii to mgz. , so I try the command mri_convert and I have this error;
[esther@m3012-04 ~]$ mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc
Folder1.nii.gz
mri_convert
/home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc Folder1.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from
/home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc...
mincRead(): can't find file
/home/esther/Freesufer/freesurfer/subjects/Patient1/fichierMnc.mnc
[esther@m3012-04 ~]$
I look up, and the file is at the rith place.... Could you help me.. Thanks
VP]
The information in this e-mail is intended only for the person to whom i
t
is
addressed. If you believe this e-mail was sent to you in error and the
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you i
n
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 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 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 -
Douglas Greve -
Valtina Pouegue