For some reason, when I run that command, I get the following output:
Input volume is : seg_mov Output volume is : seg_mov_2
There are no errors, but when I check "mri_info" of the output file, the TR, TE, etc. values are still non-zero. Any ideas what could cause that to happen?
Thanks!
MP
On Mon, Aug 5, 2013 at 11:35 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
yes, I think so
On Mon, 5 Aug 2013, Mark Plantz wrote:
thank you. Would the command simply be something like this: mri_modify
-tr 0 -te 0 -ti 0 -fa 0 <input.mgz> <output.mgz> ?
On Thu, Aug 1, 2013 at 1:41 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Mark
the formatting got messed up so I can't parse your table. You canget around this using mri_modify, and just setting everything to 0. As for the effects, look at the images and see what you think.
cheers Bruce On Thu, 1 Aug 2013, Mark Plantz wrote: Hello freesurfers, I currently have a series of images with variousTR,TE,TI,FA values. I would like to use mri_ca_train to create a .gca atlas based on these segmented volumes. Unfortunately, they all have slightly different control parameters (TR,TE,TI,FA). Is there any way around this problem, or would it be best to break the subjects into multiple groups with the same control parameters?
Here are the various parameters: [each row is a subject] TR TE TI flip angle 9.38 3.86 450 12 9.34 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.34 3.86 450 12 9.44 3.87 450 12 9.39 3.86 450 12 2065.98 7.61 886.92 90 9.45 3.89 450 12 9.41 3.87 450 12 9.41 3.87 450 12 9.42 3.91 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.44 3.86 450 12 9.44 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.34 3.86 450 12 9.34 3.86 450 12 9.39 3.86 450 12 1900 2.6 900 9 1900 2.6 900 9 1900 2.6 900 9 9.41 3.87 450 12 9.41 3.87 450 12 9.41 3.87 450 12 1900 2.6 900 9 9.41 3.87 450 12 1900 2.6 900 9 1900 2.6 900 9 Thank you in advance. -MarkThe 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.
can you send us the full command line and screen output of what you ran? On Mon, 5 Aug 2013, Mark Plantz wrote:
For some reason, when I run that command, I get the following output: Input volume is : seg_mov Output volume is : seg_mov_2
There are no errors, but when I check "mri_info" of the output file, the TR, TE, etc. values are still non-zero. Any ideas what could cause that to happen?
Thanks!
MP
On Mon, Aug 5, 2013 at 11:35 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: yes, I think so On Mon, 5 Aug 2013, Mark Plantz wrote:
thank you. Would the command simply be something like this: mri_modify -tr 0 -te 0 -ti 0 -fa 0 <input.mgz> <output.mgz> ? On Thu, Aug 1, 2013 at 1:41 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Mark the formatting got messed up so I can't parse your table. You can get around this using mri_modify, and just setting everything to 0. As for the effects, look at the images and see what you think. cheers Bruce On Thu, 1 Aug 2013, Mark Plantz wrote: Hello freesurfers, I currently have a series of images with various TR,TE,TI,FA values. I would like to use mri_ca_train to create a .gca atlas based on these segmented volumes. Unfortunately, they all have slightly different control parameters (TR,TE,TI,FA). Is there any way around this problem, or would it be best to break the subjects into multiple groups with the same control parameters? Here are the various parameters: [each row is a subject] TR TE TI flip angle 9.38 3.86 450 12 9.34 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.34 3.86 450 12 9.44 3.87 450 12 9.39 3.86 450 12 2065.98 7.61 886.92 90 9.45 3.89 450 12 9.41 3.87 450 12 9.41 3.87 450 12 9.42 3.91 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.44 3.86 450 12 9.44 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.34 3.86 450 12 9.34 3.86 450 12 9.39 3.86 450 12 1900 2.6 900 9 1900 2.6 900 9 1900 2.6 900 9 9.41 3.87 450 12 9.41 3.87 450 12 9.41 3.87 450 12 1900 2.6 900 9 9.41 3.87 450 12 1900 2.6 900 9 1900 2.6 900 9 Thank you in advance. -Mark 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.
Command and output:
dhcp-165-124-23-213:Desktop IngvalsonLab$ mri_modify -tr 0 -te 0 -ti 0 -fa 0 seg.mgz seg_new.mgz Input volume is : seg.mgz Output volume is : seg_new.mgz dhcp-165-124-23-213:Desktop IngvalsonLab$
Then, I checked the mri_info for each of the files (input and output)
- *input info (seg.mgz):*
Volume information for seg.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2065.98 msec, TE: 7.61 msec, TI: 886.92 msec, flip angle: 90.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = 4.4739 : x_a = -0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 6.3212 : x_s = 0.0000, y_s = -1.0000, z_s = -0.0000, c_s = 2.7581
talairach xfm : /Applications/freesurfer/subjects/CMH-7263/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 -0.0000 0.0000 132.4739 -0.0000 0.0000 1.0000 -121.6788 0.0000 -1.0000 -0.0000 130.7581 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 132.4739 -0.0000 -0.0000 -1.0000 130.7581 -0.0000 1.0000 -0.0000 121.6788 0.0000 0.0000 0.0000 1.0000
- *info for output (seg_new.mgz)*
Volume information for seg_new.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2065.98 msec, TE: 7.61 msec, TI: 886.92 msec, flip angle: 90.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = 4.4739 : x_a = -0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 6.3212 : x_s = 0.0000, y_s = -1.0000, z_s = -0.0000, c_s = 2.7581
talairach xfm : /Applications/freesurfer/subjects/CMH-7263/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 -0.0000 0.0000 132.4739 -0.0000 0.0000 1.0000 -121.6788 0.0000 -1.0000 -0.0000 130.7581 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 132.4739 -0.0000 -0.0000 -1.0000 130.7581 -0.0000 1.0000 -0.0000 121.6788 0.0000 0.0000 0.0000 1.0000
On Mon, Aug 5, 2013 at 11:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
can you send us the full command line and screen output of what you ran?
On Mon, 5 Aug 2013, Mark Plantz wrote:
For some reason, when I run that command, I get the following output:
Input volume is : seg_mov Output volume is : seg_mov_2
There are no errors, but when I check "mri_info" of the output file, the TR, TE, etc. values are still non-zero. Any ideas what could cause that to happen?
Thanks!
MP
On Mon, Aug 5, 2013 at 11:35 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: yes, I think so On Mon, 5 Aug 2013, Mark Plantz wrote:
thank you. Would the command simply be something like this:mri_modify -tr 0 -te 0 -ti 0 -fa 0 <input.mgz> <output.mgz> ?
On Thu, Aug 1, 2013 at 1:41 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Mark
the formatting got messed up so I can't parse yourtable. You can get around this using mri_modify, and just setting everything to 0. As for the effects, look at the images and see what you think.
cheers Bruce On Thu, 1 Aug 2013, Mark Plantz wrote: Hello freesurfers, I currently have a series of images withvarious TR,TE,TI,FA values. I would like to use mri_ca_train to create a .gca atlas based on these segmented volumes. Unfortunately, they all have slightly different control parameters (TR,TE,TI,FA). Is there any way around this problem, or would it be best to break the subjects into multiple groups with the same control parameters?
Here are the various parameters: [each row is asubject]
TR TE TI flip angle 9.38 3.86 450 12 9.34 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.34 3.86 450 12 9.44 3.87 450 12 9.39 3.86 450 12 2065.98 7.61 886.92 90 9.45 3.89 450 12 9.41 3.87 450 12 9.41 3.87 450 12 9.42 3.91 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.44 3.86 450 12 9.44 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.34 3.86 450 12 9.34 3.86 450 12 9.39 3.86 450 12 1900 2.6 900 9 1900 2.6 900 9 1900 2.6 900 9 9.41 3.87 450 12 9.41 3.87 450 12 9.41 3.87 450 12 1900 2.6 900 9 9.41 3.87 450 12 1900 2.6 900 9 1900 2.6 900 9 Thank you in advance. -Mark The information in this e-mail is intended only for theperson 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.
Oh, I see. It checks against zero to see if things are specified. I'll fix that, but in the meantime why don't yo uset everything to 1 instead of 0 On Mon, 5 Aug 2013, Mark Plantz wrote:
Command and output:
dhcp-165-124-23-213:Desktop IngvalsonLab$ mri_modify -tr 0 -te 0 -ti 0 -fa 0 seg.mgz seg_new.mgz Input volume is : seg.mgz Output volume is : seg_new.mgz dhcp-165-124-23-213:Desktop IngvalsonLab$
Then, I checked the mri_info for each of the files (input and output)
- input info (seg.mgz):
Volume information for seg.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2065.98 msec, TE: 7.61 msec, TI: 886.92 msec, flip angle: 90.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = 4.4739 : x_a = -0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 6.3212 : x_s = 0.0000, y_s = -1.0000, z_s = -0.0000, c_s = 2.7581
talairach xfm : /Applications/freesurfer/subjects/CMH-7263/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 -0.0000 0.0000 132.4739 -0.0000 0.0000 1.0000 -121.6788 0.0000 -1.0000 -0.0000 130.7581 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 132.4739 -0.0000 -0.0000 -1.0000 130.7581 -0.0000 1.0000 -0.0000 121.6788 0.0000 0.0000 0.0000 1.0000
- info for output (seg_new.mgz)
Volume information for seg_new.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2065.98 msec, TE: 7.61 msec, TI: 886.92 msec, flip angle: 90.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = 4.4739 : x_a = -0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 6.3212 : x_s = 0.0000, y_s = -1.0000, z_s = -0.0000, c_s = 2.7581
talairach xfm : /Applications/freesurfer/subjects/CMH-7263/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 -0.0000 0.0000 132.4739 -0.0000 0.0000 1.0000 -121.6788 0.0000 -1.0000 -0.0000 130.7581 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 132.4739 -0.0000 -0.0000 -1.0000 130.7581 -0.0000 1.0000 -0.0000 121.6788 0.0000 0.0000 0.0000 1.0000
On Mon, Aug 5, 2013 at 11:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: can you send us the full command line and screen output of what you ran? On Mon, 5 Aug 2013, Mark Plantz wrote:
For some reason, when I run that command, I get the following output: Input volume is : seg_mov Output volume is : seg_mov_2 There are no errors, but when I check "mri_info" of the output file, the TR, TE, etc. values are still non-zero. Any ideas what could cause that to happen? Thanks! MP On Mon, Aug 5, 2013 at 11:35 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: yes, I think so On Mon, 5 Aug 2013, Mark Plantz wrote: thank you. Would the command simply be something like this: mri_modify -tr 0 -te 0 -ti 0 -fa 0 <input.mgz> <output.mgz> ? On Thu, Aug 1, 2013 at 1:41 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Mark the formatting got messed up so I can't parse your table. You can get around this using mri_modify, and just setting everything to 0. As for the effects, look at the images and see what you think. cheers Bruce On Thu, 1 Aug 2013, Mark Plantz wrote: Hello freesurfers, I currently have a series of images with various TR,TE,TI,FA values. I would like to use mri_ca_train to create a .gca atlas based on these segmented volumes. Unfortunately, they all have slightly different control parameters (TR,TE,TI,FA). Is there any way around this problem, or would it be best to break the subjects into multiple groups with the same control parameters? Here are the various parameters: [each row is a subject] TR TE TI flip angle 9.38 3.86 450 12 9.34 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.34 3.86 450 12 9.44 3.87 450 12 9.39 3.86 450 12 2065.98 7.61 886.92 90 9.45 3.89 450 12 9.41 3.87 450 12 9.41 3.87 450 12 9.42 3.91 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.44 3.86 450 12 9.44 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.38 3.86 450 12 9.34 3.86 450 12 9.34 3.86 450 12 9.39 3.86 450 12 1900 2.6 900 9 1900 2.6 900 9 1900 2.6 900 9 9.41 3.87 450 12 9.41 3.87 450 12 9.41 3.87 450 12 1900 2.6 900 9 9.41 3.87 450 12 1900 2.6 900 9 1900 2.6 900 9 Thank you in advance. -Mark 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 -
Mark Plantz