Hello,
I have run the following successfully, but when I have moved on to other brains I get:
mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader > chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
I am running a Mac Pro with 8GB RAM.
Anthony
Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks!
Anthony
On 2/15/12 1:43 PM, Anthony Dick wrote:
Hello,
I have run the following successfully, but when I have moved on to other brains I get:
mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
I am running a Mac Pro with 8GB RAM.
Anthony
Hi Anthony
sounds like there is something wrong with one of your volumes. Can you ru mri_info on them?
Bruce On Wed, 7 Mar 2012, Anthony Dick wrote:
Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks!
Anthony
On 2/15/12 1:43 PM, Anthony Dick wrote:
Hello,
I have run the following successfully, but when I have moved on to other brains I get:
mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
I am running a Mac Pro with 8GB RAM.
Anthony
Hello Bruce,
Sorry--just getting back to this project. The basic problem is that I am trying to align a cerebellar parcellation with the underlay in tkmedit. I was working on this with Doug, and his suggestion actually worked, and now I can't get it to work again (see thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21209.html). Here is the information you requested.
Anthony
[miles:[PATH]] adick% mri_info chuman_1.mgz Volume information for chuman_1.mgz type: MGH dimensions: 141 x 103 x 87 voxel sizes: 0.8083, 0.9715, 0.8214 type: FLOAT (3) fov: 113.976 dof: 0 xstart: -57.0, xend: 57.0 ystart: -50.0, yend: 50.0 zstart: -35.7, zend: 35.7 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 = 0.9997, y_r = -0.0228, z_r = 0.0103, c_r = 4.4598 : x_a = 0.0237, y_a = 0.9951, z_a = -0.0965, c_a = 15.3835 : x_s = -0.0080, y_s = 0.0967, z_s = 0.9953, c_s = -6.8289
talairach xfm : Orientation : RAS Primary Slice Direction: axial
voxel to ras transform: 0.8081 -0.0222 0.0084 -51.7364 0.0191 0.9666 -0.0793 -32.3006 -0.0065 0.0939 0.8175 -46.7739 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.645035
ras to voxel transform: 1.2367 0.0293 -0.0099 64.4661 -0.0235 1.0243 0.0995 36.5272 0.0125 -0.1175 1.2117 53.5256 0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_info orig.mgz 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: 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 = 6.0377 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 60.9280 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.0000
talairach xfm : /[PATH]/subjects/01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 134.0377 0.0000 0.0000 1.0000 -67.0720 0.0000 -1.0000 0.0000 127.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 134.0377 -0.0000 -0.0000 -1.0000 127.0000 -0.0000 1.0000 -0.0000 67.0720 0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader > chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
On 3/7/12 9:17 AM, Bruce Fischl wrote:
Hi Anthony
sounds like there is something wrong with one of your volumes. Can you ru mri_info on them?
Bruce On Wed, 7 Mar 2012, Anthony Dick wrote:
Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks!
Anthony
On 2/15/12 1:43 PM, Anthony Dick wrote:
Hello,
I have run the following successfully, but when I have moved on to other brains I get:
mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
I am running a Mac Pro with 8GB RAM.
Anthony
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 successfully run mri_convert on chuman_1.mgz, eg mri_convert chuman_1.mgz junk.mgh
doug
On 04/04/2012 12:29 PM, Anthony Dick wrote:
Hello Bruce,
Sorry--just getting back to this project. The basic problem is that I am trying to align a cerebellar parcellation with the underlay in tkmedit. I was working on this with Doug, and his suggestion actually worked, and now I can't get it to work again (see thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21209.html). Here is the information you requested.
Anthony
[miles:[PATH]] adick% mri_info chuman_1.mgz Volume information for chuman_1.mgz type: MGH dimensions: 141 x 103 x 87 voxel sizes: 0.8083, 0.9715, 0.8214 type: FLOAT (3) fov: 113.976 dof: 0 xstart: -57.0, xend: 57.0 ystart: -50.0, yend: 50.0 zstart: -35.7, zend: 35.7 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 = 0.9997, y_r = -0.0228, z_r = 0.0103, c_r = 4.4598 : x_a = 0.0237, y_a = 0.9951, z_a = -0.0965, c_a = 15.3835 : x_s = -0.0080, y_s = 0.0967, z_s = 0.9953, c_s = -6.8289
talairach xfm : Orientation : RAS Primary Slice Direction: axial
voxel to ras transform: 0.8081 -0.0222 0.0084 -51.7364 0.0191 0.9666 -0.0793 -32.3006 -0.0065 0.0939 0.8175 -46.7739 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.645035
ras to voxel transform: 1.2367 0.0293 -0.0099 64.4661 -0.0235 1.0243 0.0995 36.5272 0.0125 -0.1175 1.2117 53.5256 0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_info orig.mgz 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: 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 = 6.0377 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 60.9280 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.0000
talairach xfm : /[PATH]/subjects/01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 134.0377 0.0000 0.0000 1.0000 -67.0720 0.0000 -1.0000 0.0000 127.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 134.0377 -0.0000 -0.0000 -1.0000 127.0000 -0.0000 1.0000 -0.0000 67.0720 0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
On 3/7/12 9:17 AM, Bruce Fischl wrote:
Hi Anthony
sounds like there is something wrong with one of your volumes. Can you ru mri_info on them?
Bruce On Wed, 7 Mar 2012, Anthony Dick wrote:
Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks!
Anthony
On 2/15/12 1:43 PM, Anthony Dick wrote:
Hello,
I have run the following successfully, but when I have moved on to other brains I get:
mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
I am running a Mac Pro with 8GB RAM.
Anthony
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.
No, but the conversion from the original .nii works...
[miles:[PATH]] adick% mri_convert chuman_1.mgz junk.mgh mri_convert chuman_1.mgz junk.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.mgz... MRIallocIndices: could not allocate 1701979223 elt index array Cannot allocate memory
[miles:[PATH]] adick% mri_convert chuman_1.nii chuman_1_new.mgz mri_convert chuman_1.nii chuman_1_new.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999687, 0.0236858, -0.00800704) j_ras = (-0.0228015, 0.995052, 0.0967044) k_ras = (0.0102579, -0.0964916, 0.995281) writing to chuman_1_new.mgz...
On 4/4/12 4:47 PM, Douglas N Greve wrote:
Can you successfully run mri_convert on chuman_1.mgz, eg mri_convert chuman_1.mgz junk.mgh
doug
On 04/04/2012 12:29 PM, Anthony Dick wrote:
Hello Bruce,
Sorry--just getting back to this project. The basic problem is that I am trying to align a cerebellar parcellation with the underlay in tkmedit. I was working on this with Doug, and his suggestion actually worked, and now I can't get it to work again (see thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21209.html). Here is the information you requested.
Anthony
[miles:[PATH]] adick% mri_info chuman_1.mgz Volume information for chuman_1.mgz type: MGH dimensions: 141 x 103 x 87 voxel sizes: 0.8083, 0.9715, 0.8214 type: FLOAT (3) fov: 113.976 dof: 0 xstart: -57.0, xend: 57.0 ystart: -50.0, yend: 50.0 zstart: -35.7, zend: 35.7 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 = 0.9997, y_r = -0.0228, z_r = 0.0103, c_r = 4.4598 : x_a = 0.0237, y_a = 0.9951, z_a = -0.0965, c_a = 15.3835 : x_s = -0.0080, y_s = 0.0967, z_s = 0.9953, c_s = -6.8289
talairach xfm : Orientation : RAS Primary Slice Direction: axial
voxel to ras transform: 0.8081 -0.0222 0.0084 -51.7364 0.0191 0.9666 -0.0793 -32.3006 -0.0065 0.0939 0.8175 -46.7739 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.645035
ras to voxel transform: 1.2367 0.0293 -0.0099 64.4661 -0.0235 1.0243 0.0995 36.5272 0.0125 -0.1175 1.2117 53.5256 0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_info orig.mgz 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: 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 = 6.0377 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 60.9280 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.0000
talairach xfm : /[PATH]/subjects/01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 134.0377 0.0000 0.0000 1.0000 -67.0720 0.0000 -1.0000 0.0000 127.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 134.0377 -0.0000 -0.0000 -1.0000 127.0000 -0.0000 1.0000 -0.0000 67.0720 0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
On 3/7/12 9:17 AM, Bruce Fischl wrote:
Hi Anthony
sounds like there is something wrong with one of your volumes. Can you ru mri_info on them?
Bruce On Wed, 7 Mar 2012, Anthony Dick wrote:
Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks!
Anthony
On 2/15/12 1:43 PM, Anthony Dick wrote:
Hello,
I have run the following successfully, but when I have moved on to other brains I get:
mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
I am running a Mac Pro with 8GB RAM.
Anthony
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.
What version are you using? One of our versions had a problem with creating bad mgzs. You probably don't need to convert it to mgz. Can you run mri_label2vol with the original nii and see if it works? doug
On 04/04/2012 04:50 PM, Anthony Dick wrote:
No, but the conversion from the original .nii works...
[miles:[PATH]] adick% mri_convert chuman_1.mgz junk.mgh mri_convert chuman_1.mgz junk.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.mgz... MRIallocIndices: could not allocate 1701979223 elt index array Cannot allocate memory
[miles:[PATH]] adick% mri_convert chuman_1.nii chuman_1_new.mgz mri_convert chuman_1.nii chuman_1_new.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999687, 0.0236858, -0.00800704) j_ras = (-0.0228015, 0.995052, 0.0967044) k_ras = (0.0102579, -0.0964916, 0.995281) writing to chuman_1_new.mgz...
On 4/4/12 4:47 PM, Douglas N Greve wrote:
Can you successfully run mri_convert on chuman_1.mgz, eg mri_convert chuman_1.mgz junk.mgh
doug
On 04/04/2012 12:29 PM, Anthony Dick wrote:
Hello Bruce,
Sorry--just getting back to this project. The basic problem is that I am trying to align a cerebellar parcellation with the underlay in tkmedit. I was working on this with Doug, and his suggestion actually worked, and now I can't get it to work again (see thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21209.html). Here is the information you requested.
Anthony
[miles:[PATH]] adick% mri_info chuman_1.mgz Volume information for chuman_1.mgz type: MGH dimensions: 141 x 103 x 87 voxel sizes: 0.8083, 0.9715, 0.8214 type: FLOAT (3) fov: 113.976 dof: 0 xstart: -57.0, xend: 57.0 ystart: -50.0, yend: 50.0 zstart: -35.7, zend: 35.7 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 = 0.9997, y_r = -0.0228, z_r = 0.0103, c_r = 4.4598 : x_a = 0.0237, y_a = 0.9951, z_a = -0.0965, c_a = 15.3835 : x_s = -0.0080, y_s = 0.0967, z_s = 0.9953, c_s = -6.8289
talairach xfm : Orientation : RAS Primary Slice Direction: axial
voxel to ras transform: 0.8081 -0.0222 0.0084 -51.7364 0.0191 0.9666 -0.0793 -32.3006 -0.0065 0.0939 0.8175 -46.7739 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.645035
ras to voxel transform: 1.2367 0.0293 -0.0099 64.4661 -0.0235 1.0243 0.0995 36.5272 0.0125 -0.1175 1.2117 53.5256 0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_info orig.mgz 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: 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 = 6.0377 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 60.9280 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.0000
talairach xfm : /[PATH]/subjects/01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 134.0377 0.0000 0.0000 1.0000 -67.0720 0.0000 -1.0000 0.0000 127.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 134.0377 -0.0000 -0.0000 -1.0000 127.0000 -0.0000 1.0000 -0.0000 67.0720 0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
On 3/7/12 9:17 AM, Bruce Fischl wrote:
Hi Anthony
sounds like there is something wrong with one of your volumes. Can you ru mri_info on them?
Bruce On Wed, 7 Mar 2012, Anthony Dick wrote:
Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks!
Anthony
On 2/15/12 1:43 PM, Anthony Dick wrote:
Hello,
I have run the following successfully, but when I have moved on to other brains I get:
mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
I am running a Mac Pro with 8GB RAM.
Anthony
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.
Hello--was wondering if you guys have any ideas. I am a bit stumped. Thanks for the help!
Anthony
On 4/4/12 4:50 PM, Anthony Dick wrote:
No, but the conversion from the original .nii works...
[miles:[PATH]] adick% mri_convert chuman_1.mgz junk.mgh mri_convert chuman_1.mgz junk.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.mgz... MRIallocIndices: could not allocate 1701979223 elt index array Cannot allocate memory
[miles:[PATH]] adick% mri_convert chuman_1.nii chuman_1_new.mgz mri_convert chuman_1.nii chuman_1_new.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999687, 0.0236858, -0.00800704) j_ras = (-0.0228015, 0.995052, 0.0967044) k_ras = (0.0102579, -0.0964916, 0.995281) writing to chuman_1_new.mgz...
On 4/4/12 4:47 PM, Douglas N Greve wrote:
Can you successfully run mri_convert on chuman_1.mgz, eg mri_convert chuman_1.mgz junk.mgh
doug
On 04/04/2012 12:29 PM, Anthony Dick wrote:
Hello Bruce,
Sorry--just getting back to this project. The basic problem is that I am trying to align a cerebellar parcellation with the underlay in tkmedit. I was working on this with Doug, and his suggestion actually worked, and now I can't get it to work again (see thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21209.html).
Here is the information you requested.
Anthony
[miles:[PATH]] adick% mri_info chuman_1.mgz Volume information for chuman_1.mgz type: MGH dimensions: 141 x 103 x 87 voxel sizes: 0.8083, 0.9715, 0.8214 type: FLOAT (3) fov: 113.976 dof: 0 xstart: -57.0, xend: 57.0 ystart: -50.0, yend: 50.0 zstart: -35.7, zend: 35.7 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 = 0.9997, y_r = -0.0228, z_r = 0.0103, c_r = 4.4598 : x_a = 0.0237, y_a = 0.9951, z_a = -0.0965, c_a = 15.3835 : x_s = -0.0080, y_s = 0.0967, z_s = 0.9953, c_s = -6.8289
talairach xfm : Orientation : RAS Primary Slice Direction: axial
voxel to ras transform: 0.8081 -0.0222 0.0084 -51.7364 0.0191 0.9666 -0.0793 -32.3006 -0.0065 0.0939 0.8175 -46.7739 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.645035
ras to voxel transform: 1.2367 0.0293 -0.0099 64.4661 -0.0235 1.0243 0.0995 36.5272 0.0125 -0.1175 1.2117 53.5256 0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_info orig.mgz 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: 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 = 6.0377 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 60.9280 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.0000
talairach xfm : /[PATH]/subjects/01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 134.0377 0.0000 0.0000 1.0000 -67.0720 0.0000 -1.0000 0.0000 127.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 134.0377 -0.0000 -0.0000 -1.0000 127.0000 -0.0000 1.0000 -0.0000 67.0720 0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
On 3/7/12 9:17 AM, Bruce Fischl wrote:
Hi Anthony
sounds like there is something wrong with one of your volumes. Can you ru mri_info on them?
Bruce On Wed, 7 Mar 2012, Anthony Dick wrote:
Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks!
Anthony
On 2/15/12 1:43 PM, Anthony Dick wrote:
Hello,
I have run the following successfully, but when I have moved on to other brains I get:
mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
I am running a Mac Pro with 8GB RAM.
Anthony
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 upload chuman_1.nii to our file drop?
On 04/06/2012 11:30 AM, Anthony Dick wrote:
Hello--was wondering if you guys have any ideas. I am a bit stumped. Thanks for the help!
Anthony
On 4/4/12 4:50 PM, Anthony Dick wrote:
No, but the conversion from the original .nii works...
[miles:[PATH]] adick% mri_convert chuman_1.mgz junk.mgh mri_convert chuman_1.mgz junk.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.mgz... MRIallocIndices: could not allocate 1701979223 elt index array Cannot allocate memory
[miles:[PATH]] adick% mri_convert chuman_1.nii chuman_1_new.mgz mri_convert chuman_1.nii chuman_1_new.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999687, 0.0236858, -0.00800704) j_ras = (-0.0228015, 0.995052, 0.0967044) k_ras = (0.0102579, -0.0964916, 0.995281) writing to chuman_1_new.mgz...
On 4/4/12 4:47 PM, Douglas N Greve wrote:
Can you successfully run mri_convert on chuman_1.mgz, eg mri_convert chuman_1.mgz junk.mgh
doug
On 04/04/2012 12:29 PM, Anthony Dick wrote:
Hello Bruce,
Sorry--just getting back to this project. The basic problem is that I am trying to align a cerebellar parcellation with the underlay in tkmedit. I was working on this with Doug, and his suggestion actually worked, and now I can't get it to work again (see thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21209.html).
Here is the information you requested.
Anthony
[miles:[PATH]] adick% mri_info chuman_1.mgz Volume information for chuman_1.mgz type: MGH dimensions: 141 x 103 x 87 voxel sizes: 0.8083, 0.9715, 0.8214 type: FLOAT (3) fov: 113.976 dof: 0 xstart: -57.0, xend: 57.0 ystart: -50.0, yend: 50.0 zstart: -35.7, zend: 35.7 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 = 0.9997, y_r = -0.0228, z_r = 0.0103, c_r = 4.4598 : x_a = 0.0237, y_a = 0.9951, z_a = -0.0965, c_a = 15.3835 : x_s = -0.0080, y_s = 0.0967, z_s = 0.9953, c_s = -6.8289
talairach xfm : Orientation : RAS Primary Slice Direction: axial
voxel to ras transform: 0.8081 -0.0222 0.0084 -51.7364 0.0191 0.9666 -0.0793 -32.3006 -0.0065 0.0939 0.8175 -46.7739 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.645035
ras to voxel transform: 1.2367 0.0293 -0.0099 64.4661 -0.0235 1.0243 0.0995 36.5272 0.0125 -0.1175 1.2117 53.5256 0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_info orig.mgz 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: 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 = 6.0377 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 60.9280 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.0000
talairach xfm : /[PATH]/subjects/01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 134.0377 0.0000 0.0000 1.0000 -67.0720 0.0000 -1.0000 0.0000 127.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 134.0377 -0.0000 -0.0000 -1.0000 127.0000 -0.0000 1.0000 -0.0000 67.0720 0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
On 3/7/12 9:17 AM, Bruce Fischl wrote:
Hi Anthony
sounds like there is something wrong with one of your volumes. Can you ru mri_info on them?
Bruce On Wed, 7 Mar 2012, Anthony Dick wrote:
Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks!
Anthony
On 2/15/12 1:43 PM, Anthony Dick wrote: > Hello, > > I have run the following successfully, but when I have moved on to > other > brains I get: > > mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> > chuman_1.mgz --o chuman_1.conf.mgz > MRIalloc: could not allocate 975187978 frame > > Cannot allocate memory > > I am running a Mac Pro with 8GB RAM. > > Anthony >
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 you email me the .mgz I'll fix it.
On Fri, 6 Apr 2012, Anthony Dick wrote:
Hello--was wondering if you guys have any ideas. I am a bit stumped. Thanks for the help!
Anthony
On 4/4/12 4:50 PM, Anthony Dick wrote:
No, but the conversion from the original .nii works...
[miles:[PATH]] adick% mri_convert chuman_1.mgz junk.mgh mri_convert chuman_1.mgz junk.mgh $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.mgz... MRIallocIndices: could not allocate 1701979223 elt index array Cannot allocate memory
[miles:[PATH]] adick% mri_convert chuman_1.nii chuman_1_new.mgz mri_convert chuman_1.nii chuman_1_new.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.999687, 0.0236858, -0.00800704) j_ras = (-0.0228015, 0.995052, 0.0967044) k_ras = (0.0102579, -0.0964916, 0.995281) writing to chuman_1_new.mgz...
On 4/4/12 4:47 PM, Douglas N Greve wrote:
Can you successfully run mri_convert on chuman_1.mgz, eg mri_convert chuman_1.mgz junk.mgh
doug
On 04/04/2012 12:29 PM, Anthony Dick wrote:
Hello Bruce,
Sorry--just getting back to this project. The basic problem is that I am trying to align a cerebellar parcellation with the underlay in tkmedit. I was working on this with Doug, and his suggestion actually worked, and now I can't get it to work again (see thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21209.html).
Here is the information you requested.
Anthony
[miles:[PATH]] adick% mri_info chuman_1.mgz Volume information for chuman_1.mgz type: MGH dimensions: 141 x 103 x 87 voxel sizes: 0.8083, 0.9715, 0.8214 type: FLOAT (3) fov: 113.976 dof: 0 xstart: -57.0, xend: 57.0 ystart: -50.0, yend: 50.0 zstart: -35.7, zend: 35.7 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 = 0.9997, y_r = -0.0228, z_r = 0.0103, c_r = 4.4598 : x_a = 0.0237, y_a = 0.9951, z_a = -0.0965, c_a = 15.3835 : x_s = -0.0080, y_s = 0.0967, z_s = 0.9953, c_s = -6.8289
talairach xfm : Orientation : RAS Primary Slice Direction: axial
voxel to ras transform: 0.8081 -0.0222 0.0084 -51.7364 0.0191 0.9666 -0.0793 -32.3006 -0.0065 0.0939 0.8175 -46.7739 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.645035
ras to voxel transform: 1.2367 0.0293 -0.0099 64.4661 -0.0235 1.0243 0.0995 36.5272 0.0125 -0.1175 1.2117 53.5256 0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_info orig.mgz 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: 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 = 6.0377 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 60.9280 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.0000
talairach xfm : /[PATH]/subjects/01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 134.0377 0.0000 0.0000 1.0000 -67.0720 0.0000 -1.0000 0.0000 127.0000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 134.0377 -0.0000 -0.0000 -1.0000 127.0000 -0.0000 1.0000 -0.0000 67.0720 0.0000 0.0000 0.0000 1.0000
[miles:[PATH]] adick% mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
On 3/7/12 9:17 AM, Bruce Fischl wrote:
Hi Anthony
sounds like there is something wrong with one of your volumes. Can you ru mri_info on them?
Bruce On Wed, 7 Mar 2012, Anthony Dick wrote:
Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks!
Anthony
On 2/15/12 1:43 PM, Anthony Dick wrote: > Hello, > > I have run the following successfully, but when I have moved on to > other > brains I get: > > mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> > chuman_1.mgz --o chuman_1.conf.mgz > MRIalloc: could not allocate 975187978 frame > > Cannot allocate memory > > I am running a Mac Pro with 8GB RAM. > > Anthony >
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.
Hi Anthony, what's in chuman_1.mgz? How many labels? doug
Anthony Dick wrote:
Hello--I am giving this message a bump. Please let me know if there are any suggestions. Thanks!
Anthony
On 2/15/12 1:43 PM, Anthony Dick wrote:
Hello,
I have run the following successfully, but when I have moved on to other brains I get:
mri_label2vol --seg chuman_1.mgz --temp orig.mgz --regheader> chuman_1.mgz --o chuman_1.conf.mgz MRIalloc: could not allocate 975187978 frame
Cannot allocate memory
I am running a Mac Pro with 8GB RAM.
Anthony
freesurfer@nmr.mgh.harvard.edu
-
Anthony Dick -
Bruce Fischl -
Douglas N Greve