Hello,
I am trying to train a cerebellar atlas based on 20 manually parcellated cerebellums. I have run the anatomical through freesurfer. When I try to load the overlay (parcellation) in tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay (the parcellation) are no longer in alignment.
However, loaded in AFNI the underlay and overlay of course align. Is there a quick fix to get them in alignment?
Anthony
Hi Anthony, how are you creating the parcellation? Are you generating it off the orig.mgz? doug
Anthony Dick wrote:
Hello,
I am trying to train a cerebellar atlas based on 20 manually parcellated cerebellums. I have run the anatomical through freesurfer. When I try to load the overlay (parcellation) in tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay (the parcellation) are no longer in alignment.
However, loaded in AFNI the underlay and overlay of course align. Is there a quick fix to get them in alignment?
Anthony
Good question. The parcellation is created outside of Freesurfer (the data were shared from another lab and I don't know which program they used to create the parcellation; of course I can find out if this would be helpful). At any rate, the anatomy and parcellation align when viewed in AFNI.
Anthony
On 1/13/12 2:11 PM, Douglas N Greve wrote:
Hi Anthony, how are you creating the parcellation? Are you generating it off the orig.mgz? doug
Anthony Dick wrote:
Hello,
I am trying to train a cerebellar atlas based on 20 manually parcellated cerebellums. I have run the anatomical through freesurfer. When I try to load the overlay (parcellation) in tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay (the parcellation) are no longer in alignment.
However, loaded in AFNI the underlay and overlay of course align. Is there a quick fix to get them in alignment?
Anthony
Try changing the header information in your parcellation, something like mri_convert yourparcellation.mgh --in_like orig.mgz yourparcellation.new.mgh doug
Anthony Dick wrote:
Good question. The parcellation is created outside of Freesurfer (the data were shared from another lab and I don't know which program they used to create the parcellation; of course I can find out if this would be helpful). At any rate, the anatomy and parcellation align when viewed in AFNI.
Anthony
On 1/13/12 2:11 PM, Douglas N Greve wrote:
Hi Anthony, how are you creating the parcellation? Are you generating it off the orig.mgz? doug
Anthony Dick wrote:
Hello,
I am trying to train a cerebellar atlas based on 20 manually parcellated cerebellums. I have run the anatomical through freesurfer. When I try to load the overlay (parcellation) in tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay (the parcellation) are no longer in alignment.
However, loaded in AFNI the underlay and overlay of course align. Is there a quick fix to get them in alignment?
Anthony
Here is the command, in case I didn't run it right.
adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii reading info from orig.mgz... $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) adick%
An image of the tkmedit output is attached. Thanks for any suggestions.
Anthony
On 1/13/12 2:15 PM, Douglas N Greve wrote:
Try changing the header information in your parcellation, something like mri_convert yourparcellation.mgh --in_like orig.mgz yourparcellation.new.mgh doug
Anthony Dick wrote:
Good question. The parcellation is created outside of Freesurfer (the data were shared from another lab and I don't know which program they used to create the parcellation; of course I can find out if this would be helpful). At any rate, the anatomy and parcellation align when viewed in AFNI.
Anthony
On 1/13/12 2:11 PM, Douglas N Greve wrote:
Hi Anthony, how are you creating the parcellation? Are you generating it off the orig.mgz? doug
Anthony Dick wrote:
Hello,
I am trying to train a cerebellar atlas based on 20 manually parcellated cerebellums. I have run the anatomical through freesurfer. When I try to load the overlay (parcellation) in tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay (the parcellation) are no longer in alignment.
However, loaded in AFNI the underlay and overlay of course align. Is there a quick fix to get them in alignment?
Anthony
What volume was human_1_do_shft.nii created from?
Anthony Dick wrote:
Here is the command, in case I didn't run it right.
adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii reading info from orig.mgz... $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) adick%
An image of the tkmedit output is attached. Thanks for any suggestions.
Anthony
On 1/13/12 2:15 PM, Douglas N Greve wrote:
Try changing the header information in your parcellation, something like mri_convert yourparcellation.mgh --in_like orig.mgz yourparcellation.new.mgh doug
Anthony Dick wrote:
Good question. The parcellation is created outside of Freesurfer (the data were shared from another lab and I don't know which program they used to create the parcellation; of course I can find out if this would be helpful). At any rate, the anatomy and parcellation align when viewed in AFNI.
Anthony
On 1/13/12 2:11 PM, Douglas N Greve wrote:
Hi Anthony, how are you creating the parcellation? Are you generating it off the orig.mgz? doug
Anthony Dick wrote:
Hello,
I am trying to train a cerebellar atlas based on 20 manually parcellated cerebellums. I have run the anatomical through freesurfer. When I try to load the overlay (parcellation) in tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay (the parcellation) are no longer in alignment.
However, loaded in AFNI the underlay and overlay of course align. Is there a quick fix to get them in alignment?
Anthony
It was created from the ahuman_1_do_shft.nii volume, which was what was input to recon-all in Freesurfer. And these volumes (the overlay and underlay) align in other viewers (e.g., AFNI and mricron).
On 1/13/12 2:40 PM, Douglas N Greve wrote:
What volume was human_1_do_shft.nii created from?
Anthony Dick wrote:
Here is the command, in case I didn't run it right.
adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii reading info from orig.mgz... $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) adick%
An image of the tkmedit output is attached. Thanks for any suggestions.
Anthony
On 1/13/12 2:15 PM, Douglas N Greve wrote:
Try changing the header information in your parcellation, something like mri_convert yourparcellation.mgh --in_like orig.mgz yourparcellation.new.mgh doug
Anthony Dick wrote:
Good question. The parcellation is created outside of Freesurfer (the data were shared from another lab and I don't know which program they used to create the parcellation; of course I can find out if this would be helpful). At any rate, the anatomy and parcellation align when viewed in AFNI.
Anthony
On 1/13/12 2:11 PM, Douglas N Greve wrote:
Hi Anthony, how are you creating the parcellation? Are you generating it off the orig.mgz? doug
Anthony Dick wrote:
Hello,
I am trying to train a cerebellar atlas based on 20 manually parcellated cerebellums. I have run the anatomical through freesurfer. When I try to load the overlay (parcellation) in tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay (the parcellation) are no longer in alignment.
However, loaded in AFNI the underlay and overlay of course align. Is there a quick fix to get them in alignment?
Anthony
what does mri_info say about them (and the rawavg.mgz) On Fri, 13 Jan 2012, Anthony Dick wrote:
It was created from the ahuman_1_do_shft.nii volume, which was what was input to recon-all in Freesurfer. And these volumes (the overlay and underlay) align in other viewers (e.g., AFNI and mricron).
On 1/13/12 2:40 PM, Douglas N Greve wrote:
What volume was human_1_do_shft.nii created from?
Anthony Dick wrote:
Here is the command, in case I didn't run it right.
adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii reading info from orig.mgz... $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) adick%
An image of the tkmedit output is attached. Thanks for any suggestions.
Anthony
On 1/13/12 2:15 PM, Douglas N Greve wrote:
Try changing the header information in your parcellation, something like mri_convert yourparcellation.mgh --in_like orig.mgz yourparcellation.new.mgh doug
Anthony Dick wrote:
Good question. The parcellation is created outside of Freesurfer (the data were shared from another lab and I don't know which program they used to create the parcellation; of course I can find out if this would be helpful). At any rate, the anatomy and parcellation align when viewed in AFNI.
Anthony
On 1/13/12 2:11 PM, Douglas N Greve wrote:
Hi Anthony, how are you creating the parcellation? Are you generating it off the orig.mgz? doug
Anthony Dick wrote: > Hello, > > I am trying to train a cerebellar atlas based on 20 manually > parcellated cerebellums. I have run the anatomical through > freesurfer. When I try to load the overlay (parcellation) in > tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay > (the parcellation) are no longer in alignment. > > However, loaded in AFNI the underlay and overlay of course align. > Is there a quick fix to get them in alignment? > > Anthony >
Which volumes align in AFNI? The orig.mgz and ahuman_1_do_shft.nii? I'm guessing not. Try this instead:
mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii
and see if you get alignment. If this does not work, make sure to send us the tkmedit command too. doug
Anthony Dick wrote:
It was created from the ahuman_1_do_shft.nii volume, which was what was input to recon-all in Freesurfer. And these volumes (the overlay and underlay) align in other viewers (e.g., AFNI and mricron).
On 1/13/12 2:40 PM, Douglas N Greve wrote:
What volume was human_1_do_shft.nii created from?
Anthony Dick wrote:
Here is the command, in case I didn't run it right.
adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii reading info from orig.mgz... $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) adick%
An image of the tkmedit output is attached. Thanks for any suggestions.
Anthony
On 1/13/12 2:15 PM, Douglas N Greve wrote:
Try changing the header information in your parcellation, something like mri_convert yourparcellation.mgh --in_like orig.mgz yourparcellation.new.mgh doug
Anthony Dick wrote:
Good question. The parcellation is created outside of Freesurfer (the data were shared from another lab and I don't know which program they used to create the parcellation; of course I can find out if this would be helpful). At any rate, the anatomy and parcellation align when viewed in AFNI.
Anthony
On 1/13/12 2:11 PM, Douglas N Greve wrote:
Hi Anthony, how are you creating the parcellation? Are you generating it off the orig.mgz? doug
Anthony Dick wrote: > Hello, > > I am trying to train a cerebellar atlas based on 20 manually > parcellated cerebellums. I have run the anatomical through > freesurfer. When I try to load the overlay (parcellation) in > tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay > (the parcellation) are no longer in alignment. > > However, loaded in AFNI the underlay and overlay of course > align. Is there a quick fix to get them in alignment? > > Anthony >
I ran mri_info--results at the bottom. I also ran mri_convert, but it did not save an output file (summary below).
The tkmedit command is: tkmedit 01_do orig.mgz, and then File > Load Segmentation to load chuman_1_do_shft.nii
I am attaching images of the alignment in AFNI. It does not align in mricron--I misspoke previously.
adick% mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii reading info from rawavg.mgz... $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
rawavg.mgz: (width, height, depth, frames) = (160, 256, 256, 1) adick%
Volume information for chuman_1_do_shft.nii type: nii dimensions: 145 x 136 x 102 voxel sizes: 0.8083, 0.8083, 0.8083 type: SHORT (4) fov: 117.210 dof: 0 xstart: -58.6, xend: -58.6 ystart: -55.0, yend: -55.0 zstart: -41.2, zend: -41.2 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 = 6.6335 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 59.5238 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -0.5958 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -0.8083 -0.0000 -0.0000 65.2384 -0.0000 -0.8083 -0.0000 114.4912 0.0000 0.0000 0.8083 -41.8213 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.528187
ras to voxel transform: -1.2371 0.0000 0.0000 80.7063 0.0000 -1.2371 0.0000 141.6368 -0.0000 -0.0000 1.2371 51.7371 0.0000 0.0000 0.0000 1.0000
Volume information for orig.nii type: nii 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 = 6.5377 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 60.4280 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.5000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 134.5377 0.0000 0.0000 1.0000 -67.5720 0.0000 -1.0000 0.0000 126.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 134.5377 -0.0000 -0.0000 -1.0000 126.5000 -0.0000 1.0000 -0.0000 67.5720 0.0000 0.0000 0.0000 1.0000
Volume information for rawavg.mgz type: MGH dimensions: 160 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -80.0, xend: 80.0 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 = 6.5377 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 60.4280 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -1.5000
talairach xfm : Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 0.0000 0.0000 1.0000 -129.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 -0.0000 -0.0000 1.0000 129.5000 0.0000 0.0000 0.0000 1.0000
Volume information for ahuman_1_do+orig.BRIK type: brik dimensions: 160 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -80.0, xend: 80.0 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 = 6.5377 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 60.4280 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -1.5000 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 0.0000 0.0000 1.0000 -129.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 -0.0000 -0.0000 1.0000 129.5000 0.0000 0.0000 0.0000 1.0000
On 1/13/12 5:14 PM, Douglas N Greve wrote:
Which volumes align in AFNI? The orig.mgz and ahuman_1_do_shft.nii? I'm guessing not. Try this instead:
mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii
and see if you get alignment. If this does not work, make sure to send us the tkmedit command too. doug
Anthony Dick wrote:
It was created from the ahuman_1_do_shft.nii volume, which was what was input to recon-all in Freesurfer. And these volumes (the overlay and underlay) align in other viewers (e.g., AFNI and mricron).
On 1/13/12 2:40 PM, Douglas N Greve wrote:
What volume was human_1_do_shft.nii created from?
Anthony Dick wrote:
Here is the command, in case I didn't run it right.
adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii reading info from orig.mgz... $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) adick%
An image of the tkmedit output is attached. Thanks for any suggestions.
Anthony
On 1/13/12 2:15 PM, Douglas N Greve wrote:
Try changing the header information in your parcellation, something like mri_convert yourparcellation.mgh --in_like orig.mgz yourparcellation.new.mgh doug
Anthony Dick wrote:
Good question. The parcellation is created outside of Freesurfer (the data were shared from another lab and I don't know which program they used to create the parcellation; of course I can find out if this would be helpful). At any rate, the anatomy and parcellation align when viewed in AFNI.
Anthony
On 1/13/12 2:11 PM, Douglas N Greve wrote: > Hi Anthony, how are you creating the parcellation? Are you > generating it off the orig.mgz? > doug > > Anthony Dick wrote: >> Hello, >> >> I am trying to train a cerebellar atlas based on 20 manually >> parcellated cerebellums. I have run the anatomical through >> freesurfer. When I try to load the overlay (parcellation) in >> tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay >> (the parcellation) are no longer in alignment. >> >> However, loaded in AFNI the underlay and overlay of course >> align. Is there a quick fix to get them in alignment? >> >> Anthony >> >
Hi Anthony, there's something I don't understand here. You said that ahuman_1_do_shft.nii was used as input to to create chuman_1_do_shft.nii, but they have different sizes, so something else is happening along the way, and this is causing the problem. One thing you can try first is to load chuman_1_do_shft.nii as an overlay instead of a segmentation. The segmentations much be in voxel-for-voxel alignment or things will get messed up, so
tkmedit 01_do orig.mgz -overlay chuman_1_do_shft.nii -fthresh .5
If this comes up in alignment, then Ithink I know where to go from there. doug
Anthony Dick wrote:
I ran mri_info--results at the bottom. I also ran mri_convert, but it did not save an output file (summary below).
The tkmedit command is: tkmedit 01_do orig.mgz, and then File > Load Segmentation to load chuman_1_do_shft.nii
I am attaching images of the alignment in AFNI. It does not align in mricron--I misspoke previously.
adick% mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii reading info from rawavg.mgz... $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
rawavg.mgz: (width, height, depth, frames) = (160, 256, 256, 1) adick%
Volume information for chuman_1_do_shft.nii type: nii dimensions: 145 x 136 x 102 voxel sizes: 0.8083, 0.8083, 0.8083 type: SHORT (4) fov: 117.210 dof: 0 xstart: -58.6, xend: -58.6 ystart: -55.0, yend: -55.0 zstart: -41.2, zend: -41.2 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 = 6.6335 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 59.5238 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -0.5958 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -0.8083 -0.0000 -0.0000 65.2384 -0.0000 -0.8083 -0.0000 114.4912 0.0000 0.0000 0.8083 -41.8213 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.528187
ras to voxel transform: -1.2371 0.0000 0.0000 80.7063 0.0000 -1.2371 0.0000 141.6368 -0.0000 -0.0000 1.2371 51.7371 0.0000 0.0000 0.0000 1.0000
>
Volume information for orig.nii type: nii dimensions: 256 x 256 x 256voxel 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 = 6.5377 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 60.4280 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.5000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 134.5377 0.0000 0.0000 1.0000 -67.5720 0.0000 -1.0000 0.0000 126.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 134.5377 -0.0000 -0.0000 -1.0000 126.5000 -0.0000 1.0000 -0.0000 67.5720 0.0000 0.0000 0.0000 1.0000
>
Volume information for rawavg.mgz type: MGH dimensions: 160 x 256 x 256voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -80.0, xend: 80.0 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 = 6.5377 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 60.4280 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -1.5000
talairach xfm : Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 0.0000 0.0000 1.0000 -129.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 -0.0000 -0.0000 1.0000 129.5000 0.0000 0.0000 0.0000 1.0000
Volume information for ahuman_1_do+orig.BRIK type: brik dimensions: 160 x 256 x 256voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -80.0, xend: 80.0 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 = 6.5377 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 60.4280 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -1.5000 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 0.0000 0.0000 1.0000 -129.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 -0.0000 -0.0000 1.0000 129.5000 0.0000 0.0000 0.0000 1.0000
On 1/13/12 5:14 PM, Douglas N Greve wrote:
Which volumes align in AFNI? The orig.mgz and ahuman_1_do_shft.nii? I'm guessing not. Try this instead:
mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii
and see if you get alignment. If this does not work, make sure to send us the tkmedit command too. doug
Anthony Dick wrote:
It was created from the ahuman_1_do_shft.nii volume, which was what was input to recon-all in Freesurfer. And these volumes (the overlay and underlay) align in other viewers (e.g., AFNI and mricron).
On 1/13/12 2:40 PM, Douglas N Greve wrote:
What volume was human_1_do_shft.nii created from?
Anthony Dick wrote:
Here is the command, in case I didn't run it right.
adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii reading info from orig.mgz... $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) adick%
An image of the tkmedit output is attached. Thanks for any suggestions.
Anthony
On 1/13/12 2:15 PM, Douglas N Greve wrote:
Try changing the header information in your parcellation, something like mri_convert yourparcellation.mgh --in_like orig.mgz yourparcellation.new.mgh doug
Anthony Dick wrote: > Good question. The parcellation is created outside of Freesurfer > (the data were shared from another lab and I don't know which > program they used to create the parcellation; of course I can > find out if this would be helpful). At any rate, the anatomy and > parcellation align when viewed in AFNI. > > Anthony > > On 1/13/12 2:11 PM, Douglas N Greve wrote: >> Hi Anthony, how are you creating the parcellation? Are you >> generating it off the orig.mgz? >> doug >> >> Anthony Dick wrote: >>> Hello, >>> >>> I am trying to train a cerebellar atlas based on 20 manually >>> parcellated cerebellums. I have run the anatomical through >>> freesurfer. When I try to load the overlay (parcellation) in >>> tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the overlay >>> (the parcellation) are no longer in alignment. >>> >>> However, loaded in AFNI the underlay and overlay of course >>> align. Is there a quick fix to get them in alignment? >>> >>> Anthony >>> >> > >
Hello Doug,
Prof. Diedrichsen kindly shared the original brains he manually parcellated that were used to create his probabilistic atlas (http://www.icn.ucl.ac.uk/motorcontrol/imaging/propatlas.htm; see the 2009 Neuroimage paper). So each brain had an anatomy and a cerebellar parcellation, and these align in AFNI so I assumed there wasn't anything special about the parcellation process. However, I don't know the exact process he used to create them. So you're right, there is likely some intermediate step that I am missing. My goal here is to use them to create a training atlas for Freesurfer, which (if it works) we would like to share with the community. So all of your help here is appreciated!
Here's where I am: The tkmedit command doesn't work (the cerebellum ends up in the same place--see image). Here was the output--is there a way to specify a registration file? Any ideas? Would knowing the intermediate steps help, or is there a way for me to try to troubleshoot this without bugging Prof. Diedrichsen?
adick% tkmedit 01_do orig.mgz -overlay chuman_1_do_shft.nii -fthresh .5 INFO: No registration type specified for overlay, assuming identity. tkmedit: Trying to open ./chuman_1_do_shft.dat Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl
Thanks much for all the help so far,
Anthony
On 1/17/12 12:57 PM, Douglas N Greve wrote:
Hi Anthony, there's something I don't understand here. You said that ahuman_1_do_shft.nii was used as input to to create chuman_1_do_shft.nii, but they have different sizes, so something else is happening along the way, and this is causing the problem. One thing you can try first is to load chuman_1_do_shft.nii as an overlay instead of a segmentation. The segmentations much be in voxel-for-voxel alignment or things will get messed up, so
tkmedit 01_do orig.mgz -overlay chuman_1_do_shft.nii -fthresh .5
If this comes up in alignment, then Ithink I know where to go from there. doug
Anthony Dick wrote:
I ran mri_info--results at the bottom. I also ran mri_convert, but it did not save an output file (summary below).
The tkmedit command is: tkmedit 01_do orig.mgz, and then File > Load Segmentation to load chuman_1_do_shft.nii
I am attaching images of the alignment in AFNI. It does not align in mricron--I misspoke previously.
adick% mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii reading info from rawavg.mgz... $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
rawavg.mgz: (width, height, depth, frames) = (160, 256, 256, 1) adick%
>
Volume information for chuman_1_do_shft.nii type: nii dimensions: 145 x 136 x 102 voxel sizes: 0.8083, 0.8083, 0.8083 type: SHORT (4) fov: 117.210 dof: 0 xstart: -58.6, xend: -58.6 ystart: -55.0, yend: -55.0 zstart: -41.2, zend: -41.2 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 = 6.6335 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 59.5238 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -0.5958 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -0.8083 -0.0000 -0.0000 65.2384 -0.0000 -0.8083 -0.0000 114.4912 0.0000 0.0000 0.8083 -41.8213 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.528187
ras to voxel transform: -1.2371 0.0000 0.0000 80.7063 0.0000 -1.2371 0.0000 141.6368 -0.0000 -0.0000 1.2371 51.7371 0.0000 0.0000 0.0000 1.0000
>>
Volume information for orig.nii type: nii dimensions: 256 x 256 x 256voxel 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 = 6.5377 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 60.4280 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.5000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 134.5377 0.0000 0.0000 1.0000 -67.5720 0.0000 -1.0000 0.0000 126.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 134.5377 -0.0000 -0.0000 -1.0000 126.5000 -0.0000 1.0000 -0.0000 67.5720 0.0000 0.0000 0.0000 1.0000
>>
Volume information for rawavg.mgz type: MGH dimensions: 160 x 256 x 256voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -80.0, xend: 80.0 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 = 6.5377 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 60.4280 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -1.5000
talairach xfm : Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 0.0000 0.0000 1.0000 -129.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 -0.0000 -0.0000 1.0000 129.5000 0.0000 0.0000 0.0000 1.0000
Volume information for ahuman_1_do+orig.BRIK type: brik dimensions: 160 x 256 x 256voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -80.0, xend: 80.0 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 = 6.5377 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 60.4280 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -1.5000 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 0.0000 0.0000 1.0000 -129.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 -0.0000 -0.0000 1.0000 129.5000 0.0000 0.0000 0.0000 1.0000
On 1/13/12 5:14 PM, Douglas N Greve wrote:
Which volumes align in AFNI? The orig.mgz and ahuman_1_do_shft.nii? I'm guessing not. Try this instead:
mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii
and see if you get alignment. If this does not work, make sure to send us the tkmedit command too. doug
Anthony Dick wrote:
It was created from the ahuman_1_do_shft.nii volume, which was what was input to recon-all in Freesurfer. And these volumes (the overlay and underlay) align in other viewers (e.g., AFNI and mricron).
On 1/13/12 2:40 PM, Douglas N Greve wrote:
What volume was human_1_do_shft.nii created from?
Anthony Dick wrote:
Here is the command, in case I didn't run it right.
adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like orig.mgz chuman_1_do_shft_new.nii reading info from orig.mgz... $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) adick%
An image of the tkmedit output is attached. Thanks for any suggestions.
Anthony
On 1/13/12 2:15 PM, Douglas N Greve wrote: > Try changing the header information in your parcellation, > something like > mri_convert yourparcellation.mgh --in_like orig.mgz > yourparcellation.new.mgh > doug > > Anthony Dick wrote: >> Good question. The parcellation is created outside of >> Freesurfer (the data were shared from another lab and I don't >> know which program they used to create the parcellation; of >> course I can find out if this would be helpful). At any rate, >> the anatomy and parcellation align when viewed in AFNI. >> >> Anthony >> >> On 1/13/12 2:11 PM, Douglas N Greve wrote: >>> Hi Anthony, how are you creating the parcellation? Are you >>> generating it off the orig.mgz? >>> doug >>> >>> Anthony Dick wrote: >>>> Hello, >>>> >>>> I am trying to train a cerebellar atlas based on 20 manually >>>> parcellated cerebellums. I have run the anatomical through >>>> freesurfer. When I try to load the overlay (parcellation) in >>>> tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the >>>> overlay (the parcellation) are no longer in alignment. >>>> >>>> However, loaded in AFNI the underlay and overlay of course >>>> align. Is there a quick fix to get them in alignment? >>>> >>>> Anthony >>>> >>> >> >> >
What are the two things that align in AFNI? doug
Anthony Dick wrote:
Hello Doug,
Prof. Diedrichsen kindly shared the original brains he manually parcellated that were used to create his probabilistic atlas (http://www.icn.ucl.ac.uk/motorcontrol/imaging/propatlas.htm; see the 2009 Neuroimage paper). So each brain had an anatomy and a cerebellar parcellation, and these align in AFNI so I assumed there wasn't anything special about the parcellation process. However, I don't know the exact process he used to create them. So you're right, there is likely some intermediate step that I am missing. My goal here is to use them to create a training atlas for Freesurfer, which (if it works) we would like to share with the community. So all of your help here is appreciated!
Here's where I am: The tkmedit command doesn't work (the cerebellum ends up in the same place--see image). Here was the output--is there a way to specify a registration file? Any ideas? Would knowing the intermediate steps help, or is there a way for me to try to troubleshoot this without bugging Prof. Diedrichsen?
adick% tkmedit 01_do orig.mgz -overlay chuman_1_do_shft.nii -fthresh .5 INFO: No registration type specified for overlay, assuming identity. tkmedit: Trying to open ./chuman_1_do_shft.dat Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl
Thanks much for all the help so far,
Anthony
On 1/17/12 12:57 PM, Douglas N Greve wrote:
Hi Anthony, there's something I don't understand here. You said that ahuman_1_do_shft.nii was used as input to to create chuman_1_do_shft.nii, but they have different sizes, so something else is happening along the way, and this is causing the problem. One thing you can try first is to load chuman_1_do_shft.nii as an overlay instead of a segmentation. The segmentations much be in voxel-for-voxel alignment or things will get messed up, so
tkmedit 01_do orig.mgz -overlay chuman_1_do_shft.nii -fthresh .5
If this comes up in alignment, then Ithink I know where to go from there. doug
Anthony Dick wrote:
I ran mri_info--results at the bottom. I also ran mri_convert, but it did not save an output file (summary below).
The tkmedit command is: tkmedit 01_do orig.mgz, and then File > Load Segmentation to load chuman_1_do_shft.nii
I am attaching images of the alignment in AFNI. It does not align in mricron--I misspoke previously.
adick% mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii reading info from rawavg.mgz... $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
rawavg.mgz: (width, height, depth, frames) = (160, 256, 256, 1) adick%
>>
Volume information for chuman_1_do_shft.nii type: nii dimensions: 145 x 136 x 102 voxel sizes: 0.8083, 0.8083, 0.8083 type: SHORT (4) fov: 117.210 dof: 0 xstart: -58.6, xend: -58.6 ystart: -55.0, yend: -55.0 zstart: -41.2, zend: -41.2 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 = 6.6335 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 59.5238 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -0.5958 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -0.8083 -0.0000 -0.0000 65.2384 -0.0000 -0.8083 -0.0000 114.4912 0.0000 0.0000 0.8083 -41.8213 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.528187
ras to voxel transform: -1.2371 0.0000 0.0000 80.7063 0.0000 -1.2371 0.0000 141.6368 -0.0000 -0.0000 1.2371 51.7371 0.0000 0.0000 0.0000 1.0000
>>>
Volume information for orig.nii type: nii dimensions: 256 x 256 x 256voxel 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 = 6.5377 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 60.4280 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.5000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 134.5377 0.0000 0.0000 1.0000 -67.5720 0.0000 -1.0000 0.0000 126.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 134.5377 -0.0000 -0.0000 -1.0000 126.5000 -0.0000 1.0000 -0.0000 67.5720 0.0000 0.0000 0.0000 1.0000
>>>
Volume information for rawavg.mgz type: MGH dimensions: 160 x 256 x 256voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -80.0, xend: 80.0 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 = 6.5377 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 60.4280 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -1.5000
talairach xfm : Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 0.0000 0.0000 1.0000 -129.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 -0.0000 -0.0000 1.0000 129.5000 0.0000 0.0000 0.0000 1.0000
>
Volume information for ahuman_1_do+orig.BRIK type: brik dimensions: 160 x 256 x 256voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -80.0, xend: 80.0 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 = 6.5377 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 60.4280 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -1.5000 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 0.0000 0.0000 1.0000 -129.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 -0.0000 -0.0000 1.0000 129.5000 0.0000 0.0000 0.0000 1.0000
On 1/13/12 5:14 PM, Douglas N Greve wrote:
Which volumes align in AFNI? The orig.mgz and ahuman_1_do_shft.nii? I'm guessing not. Try this instead:
mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii
and see if you get alignment. If this does not work, make sure to send us the tkmedit command too. doug
Anthony Dick wrote:
It was created from the ahuman_1_do_shft.nii volume, which was what was input to recon-all in Freesurfer. And these volumes (the overlay and underlay) align in other viewers (e.g., AFNI and mricron).
On 1/13/12 2:40 PM, Douglas N Greve wrote:
What volume was human_1_do_shft.nii created from?
Anthony Dick wrote: > Here is the command, in case I didn't run it right. > > adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz > chuman_1_do_shft_new.nii > mri_convert chuman_1_do_shft.nii --in_like orig.mgz > chuman_1_do_shft_new.nii > reading info from orig.mgz... > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from chuman_1_do_shft.nii... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > volume sizes do not match > > chuman_1_do_shft.nii: (width, height, depth, frames) = (145, > 136, 102, 1) > > orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) > adick% > > > An image of the tkmedit output is attached. Thanks for any > suggestions. > > Anthony > > > On 1/13/12 2:15 PM, Douglas N Greve wrote: >> Try changing the header information in your parcellation, >> something like >> mri_convert yourparcellation.mgh --in_like orig.mgz >> yourparcellation.new.mgh >> doug >> >> Anthony Dick wrote: >>> Good question. The parcellation is created outside of >>> Freesurfer (the data were shared from another lab and I don't >>> know which program they used to create the parcellation; of >>> course I can find out if this would be helpful). At any rate, >>> the anatomy and parcellation align when viewed in AFNI. >>> >>> Anthony >>> >>> On 1/13/12 2:11 PM, Douglas N Greve wrote: >>>> Hi Anthony, how are you creating the parcellation? Are you >>>> generating it off the orig.mgz? >>>> doug >>>> >>>> Anthony Dick wrote: >>>>> Hello, >>>>> >>>>> I am trying to train a cerebellar atlas based on 20 manually >>>>> parcellated cerebellums. I have run the anatomical through >>>>> freesurfer. When I try to load the overlay (parcellation) in >>>>> tkmedit, the underlay (e.g., orig.mgz, T1.mgz) and the >>>>> overlay (the parcellation) are no longer in alignment. >>>>> >>>>> However, loaded in AFNI the underlay and overlay of course >>>>> align. Is there a quick fix to get them in alignment? >>>>> >>>>> Anthony >>>>> >>>> >>> >>> >> > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry Doug--it seems I misspoke.
The following works, as you predicted, and these are the files that align in AFNI (had to convert chuman_1_do to .mgz):
adick% tkmedit 01_do orig.mgz -overlay chuman_1_do.mgz -fthresh .5 INFO: No registration type specified for overlay, assuming identity. tkmedit: Trying to open ./chuman_1_do.dat Reading /Applications/freesurfer/tktools/tkm_common.tcl Reading /Applications/freesurfer/tktools/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/tktools/tkUtils.tcl
Loading the same file as a segmentation does not. This might give you some different ideas.
Anthony
On 1/26/12 11:36 AM, Douglas N Greve wrote:
What are the two things that align in AFNI? doug
Anthony Dick wrote:
Hello Doug,
Prof. Diedrichsen kindly shared the original brains he manually parcellated that were used to create his probabilistic atlas (http://www.icn.ucl.ac.uk/motorcontrol/imaging/propatlas.htm; see the 2009 Neuroimage paper). So each brain had an anatomy and a cerebellar parcellation, and these align in AFNI so I assumed there wasn't anything special about the parcellation process. However, I don't know the exact process he used to create them. So you're right, there is likely some intermediate step that I am missing. My goal here is to use them to create a training atlas for Freesurfer, which (if it works) we would like to share with the community. So all of your help here is appreciated!
Here's where I am: The tkmedit command doesn't work (the cerebellum ends up in the same place--see image). Here was the output--is there a way to specify a registration file? Any ideas? Would knowing the intermediate steps help, or is there a way for me to try to troubleshoot this without bugging Prof. Diedrichsen?
adick% tkmedit 01_do orig.mgz -overlay chuman_1_do_shft.nii -fthresh .5 INFO: No registration type specified for overlay, assuming identity. tkmedit: Trying to open ./chuman_1_do_shft.dat Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl
Thanks much for all the help so far,
Anthony
On 1/17/12 12:57 PM, Douglas N Greve wrote:
Hi Anthony, there's something I don't understand here. You said that ahuman_1_do_shft.nii was used as input to to create chuman_1_do_shft.nii, but they have different sizes, so something else is happening along the way, and this is causing the problem. One thing you can try first is to load chuman_1_do_shft.nii as an overlay instead of a segmentation. The segmentations much be in voxel-for-voxel alignment or things will get messed up, so
tkmedit 01_do orig.mgz -overlay chuman_1_do_shft.nii -fthresh .5
If this comes up in alignment, then Ithink I know where to go from there. doug
Anthony Dick wrote:
I ran mri_info--results at the bottom. I also ran mri_convert, but it did not save an output file (summary below).
The tkmedit command is: tkmedit 01_do orig.mgz, and then File > Load Segmentation to load chuman_1_do_shft.nii
I am attaching images of the alignment in AFNI. It does not align in mricron--I misspoke previously.
adick% mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii reading info from rawavg.mgz... $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
rawavg.mgz: (width, height, depth, frames) = (160, 256, 256, 1) adick%
>>>
Volume information for chuman_1_do_shft.nii type: nii dimensions: 145 x 136 x 102 voxel sizes: 0.8083, 0.8083, 0.8083 type: SHORT (4) fov: 117.210 dof: 0 xstart: -58.6, xend: -58.6 ystart: -55.0, yend: -55.0 zstart: -41.2, zend: -41.2 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 = 6.6335 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 59.5238 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -0.5958 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -0.8083 -0.0000 -0.0000 65.2384 -0.0000 -0.8083 -0.0000 114.4912 0.0000 0.0000 0.8083 -41.8213 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.528187
ras to voxel transform: -1.2371 0.0000 0.0000 80.7063 0.0000 -1.2371 0.0000 141.6368 -0.0000 -0.0000 1.2371 51.7371 0.0000 0.0000 0.0000 1.0000
>>>>
Volume information for orig.nii type: nii dimensions: 256 x 256 x 256voxel 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 = 6.5377 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 60.4280 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.5000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 134.5377 0.0000 0.0000 1.0000 -67.5720 0.0000 -1.0000 0.0000 126.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 134.5377 -0.0000 -0.0000 -1.0000 126.5000 -0.0000 1.0000 -0.0000 67.5720 0.0000 0.0000 0.0000 1.0000
>>>>
Volume information for rawavg.mgz type: MGH dimensions: 160 x 256 x 256voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -80.0, xend: 80.0 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 = 6.5377 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 60.4280 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -1.5000
talairach xfm : Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 0.0000 0.0000 1.0000 -129.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 -0.0000 -0.0000 1.0000 129.5000 0.0000 0.0000 0.0000 1.0000
>>
Volume information for ahuman_1_do+orig.BRIK type: brik dimensions: 160 x 256 x 256voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -80.0, xend: 80.0 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 = 6.5377 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 60.4280 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -1.5000 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 0.0000 0.0000 1.0000 -129.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 -0.0000 -0.0000 1.0000 129.5000 0.0000 0.0000 0.0000 1.0000
On 1/13/12 5:14 PM, Douglas N Greve wrote:
Which volumes align in AFNI? The orig.mgz and ahuman_1_do_shft.nii? I'm guessing not. Try this instead:
mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii
and see if you get alignment. If this does not work, make sure to send us the tkmedit command too. doug
Anthony Dick wrote:
It was created from the ahuman_1_do_shft.nii volume, which was what was input to recon-all in Freesurfer. And these volumes (the overlay and underlay) align in other viewers (e.g., AFNI and mricron).
On 1/13/12 2:40 PM, Douglas N Greve wrote: > What volume was human_1_do_shft.nii created from? > > Anthony Dick wrote: >> Here is the command, in case I didn't run it right. >> >> adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz >> chuman_1_do_shft_new.nii >> mri_convert chuman_1_do_shft.nii --in_like orig.mgz >> chuman_1_do_shft_new.nii >> reading info from orig.mgz... >> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >> reading from chuman_1_do_shft.nii... >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >> volume sizes do not match >> >> chuman_1_do_shft.nii: (width, height, depth, frames) = (145, >> 136, 102, 1) >> >> orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) >> adick% >> >> >> An image of the tkmedit output is attached. Thanks for any >> suggestions. >> >> Anthony >> >> >> On 1/13/12 2:15 PM, Douglas N Greve wrote: >>> Try changing the header information in your parcellation, >>> something like >>> mri_convert yourparcellation.mgh --in_like orig.mgz >>> yourparcellation.new.mgh >>> doug >>> >>> Anthony Dick wrote: >>>> Good question. The parcellation is created outside of >>>> Freesurfer (the data were shared from another lab and I don't >>>> know which program they used to create the parcellation; of >>>> course I can find out if this would be helpful). At any rate, >>>> the anatomy and parcellation align when viewed in AFNI. >>>> >>>> Anthony >>>> >>>> On 1/13/12 2:11 PM, Douglas N Greve wrote: >>>>> Hi Anthony, how are you creating the parcellation? Are you >>>>> generating it off the orig.mgz? >>>>> doug >>>>> >>>>> Anthony Dick wrote: >>>>>> Hello, >>>>>> >>>>>> I am trying to train a cerebellar atlas based on 20 >>>>>> manually parcellated cerebellums. I have run the anatomical >>>>>> through freesurfer. When I try to load the overlay >>>>>> (parcellation) in tkmedit, the underlay (e.g., orig.mgz, >>>>>> T1.mgz) and the overlay (the parcellation) are no longer in >>>>>> alignment. >>>>>> >>>>>> However, loaded in AFNI the underlay and overlay of course >>>>>> align. Is there a quick fix to get them in alignment? >>>>>> >>>>>> Anthony >>>>>> >>>>> >>>> >>>> >>> >> >> >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
OK, try running mri_label2vol --seg chuman_1_do.mgz --temp orig.mgz --regheader chuman_1_do.mgz --o chuman_1_do.conf.mgz Then load chuman_1_do.conf.mgz as a segmentation. doug
Anthony Dick wrote:
Sorry Doug--it seems I misspoke.
The following works, as you predicted, and these are the files that align in AFNI (had to convert chuman_1_do to .mgz):
adick% tkmedit 01_do orig.mgz -overlay chuman_1_do.mgz -fthresh .5 INFO: No registration type specified for overlay, assuming identity. tkmedit: Trying to open ./chuman_1_do.dat Reading /Applications/freesurfer/tktools/tkm_common.tcl Reading /Applications/freesurfer/tktools/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/tktools/tkUtils.tcl
Loading the same file as a segmentation does not. This might give you some different ideas.
Anthony
On 1/26/12 11:36 AM, Douglas N Greve wrote:
What are the two things that align in AFNI? doug
Anthony Dick wrote:
Hello Doug,
Prof. Diedrichsen kindly shared the original brains he manually parcellated that were used to create his probabilistic atlas (http://www.icn.ucl.ac.uk/motorcontrol/imaging/propatlas.htm; see the 2009 Neuroimage paper). So each brain had an anatomy and a cerebellar parcellation, and these align in AFNI so I assumed there wasn't anything special about the parcellation process. However, I don't know the exact process he used to create them. So you're right, there is likely some intermediate step that I am missing. My goal here is to use them to create a training atlas for Freesurfer, which (if it works) we would like to share with the community. So all of your help here is appreciated!
Here's where I am: The tkmedit command doesn't work (the cerebellum ends up in the same place--see image). Here was the output--is there a way to specify a registration file? Any ideas? Would knowing the intermediate steps help, or is there a way for me to try to troubleshoot this without bugging Prof. Diedrichsen?
adick% tkmedit 01_do orig.mgz -overlay chuman_1_do_shft.nii -fthresh .5 INFO: No registration type specified for overlay, assuming identity. tkmedit: Trying to open ./chuman_1_do_shft.dat Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl
Thanks much for all the help so far,
Anthony
On 1/17/12 12:57 PM, Douglas N Greve wrote:
Hi Anthony, there's something I don't understand here. You said that ahuman_1_do_shft.nii was used as input to to create chuman_1_do_shft.nii, but they have different sizes, so something else is happening along the way, and this is causing the problem. One thing you can try first is to load chuman_1_do_shft.nii as an overlay instead of a segmentation. The segmentations much be in voxel-for-voxel alignment or things will get messed up, so
tkmedit 01_do orig.mgz -overlay chuman_1_do_shft.nii -fthresh .5
If this comes up in alignment, then Ithink I know where to go from there. doug
Anthony Dick wrote:
I ran mri_info--results at the bottom. I also ran mri_convert, but it did not save an output file (summary below).
The tkmedit command is: tkmedit 01_do orig.mgz, and then File > Load Segmentation to load chuman_1_do_shft.nii
I am attaching images of the alignment in AFNI. It does not align in mricron--I misspoke previously.
adick% mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii reading info from rawavg.mgz... $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
rawavg.mgz: (width, height, depth, frames) = (160, 256, 256, 1) adick%
>>>>
Volume information for chuman_1_do_shft.nii type: nii dimensions: 145 x 136 x 102 voxel sizes: 0.8083, 0.8083, 0.8083 type: SHORT (4) fov: 117.210 dof: 0 xstart: -58.6, xend: -58.6 ystart: -55.0, yend: -55.0 zstart: -41.2, zend: -41.2 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 = 6.6335 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 59.5238 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -0.5958 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -0.8083 -0.0000 -0.0000 65.2384 -0.0000 -0.8083 -0.0000 114.4912 0.0000 0.0000 0.8083 -41.8213 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.528187
ras to voxel transform: -1.2371 0.0000 0.0000 80.7063 0.0000 -1.2371 0.0000 141.6368 -0.0000 -0.0000 1.2371 51.7371 0.0000 0.0000 0.0000 1.0000
>>>>>
Volume information for orig.nii type: nii dimensions: 256 x 256 x 256voxel 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 = 6.5377 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 60.4280 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.5000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 134.5377 0.0000 0.0000 1.0000 -67.5720 0.0000 -1.0000 0.0000 126.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 134.5377 -0.0000 -0.0000 -1.0000 126.5000 -0.0000 1.0000 -0.0000 67.5720 0.0000 0.0000 0.0000 1.0000
>>>>>
Volume information for rawavg.mgz type: MGH dimensions: 160 x 256 x 256voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -80.0, xend: 80.0 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 = 6.5377 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 60.4280 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -1.5000
talairach xfm : Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 0.0000 0.0000 1.0000 -129.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 -0.0000 -0.0000 1.0000 129.5000 0.0000 0.0000 0.0000 1.0000
>>>
Volume information for ahuman_1_do+orig.BRIK type: brik dimensions: 160 x 256 x 256voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -80.0, xend: 80.0 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 = 6.5377 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 60.4280 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -1.5000 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 0.0000 0.0000 1.0000 -129.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 -0.0000 -0.0000 1.0000 129.5000 0.0000 0.0000 0.0000 1.0000
On 1/13/12 5:14 PM, Douglas N Greve wrote:
Which volumes align in AFNI? The orig.mgz and ahuman_1_do_shft.nii? I'm guessing not. Try this instead:
mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii
and see if you get alignment. If this does not work, make sure to send us the tkmedit command too. doug
Anthony Dick wrote: > It was created from the ahuman_1_do_shft.nii volume, which was > what was input to recon-all in Freesurfer. And these volumes > (the overlay and underlay) align in other viewers (e.g., AFNI > and mricron). > > On 1/13/12 2:40 PM, Douglas N Greve wrote: >> What volume was human_1_do_shft.nii created from? >> >> Anthony Dick wrote: >>> Here is the command, in case I didn't run it right. >>> >>> adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz >>> chuman_1_do_shft_new.nii >>> mri_convert chuman_1_do_shft.nii --in_like orig.mgz >>> chuman_1_do_shft_new.nii >>> reading info from orig.mgz... >>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >>> reading from chuman_1_do_shft.nii... >>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >>> volume sizes do not match >>> >>> chuman_1_do_shft.nii: (width, height, depth, frames) = (145, >>> 136, 102, 1) >>> >>> orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) >>> adick% >>> >>> >>> An image of the tkmedit output is attached. Thanks for any >>> suggestions. >>> >>> Anthony >>> >>> >>> On 1/13/12 2:15 PM, Douglas N Greve wrote: >>>> Try changing the header information in your parcellation, >>>> something like >>>> mri_convert yourparcellation.mgh --in_like orig.mgz >>>> yourparcellation.new.mgh >>>> doug >>>> >>>> Anthony Dick wrote: >>>>> Good question. The parcellation is created outside of >>>>> Freesurfer (the data were shared from another lab and I >>>>> don't know which program they used to create the >>>>> parcellation; of course I can find out if this would be >>>>> helpful). At any rate, the anatomy and parcellation align >>>>> when viewed in AFNI. >>>>> >>>>> Anthony >>>>> >>>>> On 1/13/12 2:11 PM, Douglas N Greve wrote: >>>>>> Hi Anthony, how are you creating the parcellation? Are you >>>>>> generating it off the orig.mgz? >>>>>> doug >>>>>> >>>>>> Anthony Dick wrote: >>>>>>> Hello, >>>>>>> >>>>>>> I am trying to train a cerebellar atlas based on 20 >>>>>>> manually parcellated cerebellums. I have run the >>>>>>> anatomical through freesurfer. When I try to load the >>>>>>> overlay (parcellation) in tkmedit, the underlay (e.g., >>>>>>> orig.mgz, T1.mgz) and the overlay (the parcellation) are >>>>>>> no longer in alignment. >>>>>>> >>>>>>> However, loaded in AFNI the underlay and overlay of course >>>>>>> align. Is there a quick fix to get them in alignment? >>>>>>> >>>>>>> Anthony >>>>>>> >>>>>> >>>>> >>>>> >>>> >>> >>> >> > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That did the trick! Thanks very much!
Anthony
On 1/26/12 12:31 PM, Douglas N Greve wrote:
OK, try running mri_label2vol --seg chuman_1_do.mgz --temp orig.mgz --regheader chuman_1_do.mgz --o chuman_1_do.conf.mgz Then load chuman_1_do.conf.mgz as a segmentation. doug
Anthony Dick wrote:
Sorry Doug--it seems I misspoke.
The following works, as you predicted, and these are the files that align in AFNI (had to convert chuman_1_do to .mgz):
adick% tkmedit 01_do orig.mgz -overlay chuman_1_do.mgz -fthresh .5 INFO: No registration type specified for overlay, assuming identity. tkmedit: Trying to open ./chuman_1_do.dat Reading /Applications/freesurfer/tktools/tkm_common.tcl Reading /Applications/freesurfer/tktools/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/tktools/tkUtils.tcl
Loading the same file as a segmentation does not. This might give you some different ideas.
Anthony
On 1/26/12 11:36 AM, Douglas N Greve wrote:
What are the two things that align in AFNI? doug
Anthony Dick wrote:
Hello Doug,
Prof. Diedrichsen kindly shared the original brains he manually parcellated that were used to create his probabilistic atlas (http://www.icn.ucl.ac.uk/motorcontrol/imaging/propatlas.htm; see the 2009 Neuroimage paper). So each brain had an anatomy and a cerebellar parcellation, and these align in AFNI so I assumed there wasn't anything special about the parcellation process. However, I don't know the exact process he used to create them. So you're right, there is likely some intermediate step that I am missing. My goal here is to use them to create a training atlas for Freesurfer, which (if it works) we would like to share with the community. So all of your help here is appreciated!
Here's where I am: The tkmedit command doesn't work (the cerebellum ends up in the same place--see image). Here was the output--is there a way to specify a registration file? Any ideas? Would knowing the intermediate steps help, or is there a way for me to try to troubleshoot this without bugging Prof. Diedrichsen?
adick% tkmedit 01_do orig.mgz -overlay chuman_1_do_shft.nii -fthresh .5 INFO: No registration type specified for overlay, assuming identity. tkmedit: Trying to open ./chuman_1_do_shft.dat Reading /Applications/freesurfer/lib/tcl/tkm_common.tcl Reading /Applications/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /Applications/freesurfer/lib/tcl/tkUtils.tcl
Thanks much for all the help so far,
Anthony
On 1/17/12 12:57 PM, Douglas N Greve wrote:
Hi Anthony, there's something I don't understand here. You said that ahuman_1_do_shft.nii was used as input to to create chuman_1_do_shft.nii, but they have different sizes, so something else is happening along the way, and this is causing the problem. One thing you can try first is to load chuman_1_do_shft.nii as an overlay instead of a segmentation. The segmentations much be in voxel-for-voxel alignment or things will get messed up, so
tkmedit 01_do orig.mgz -overlay chuman_1_do_shft.nii -fthresh .5
If this comes up in alignment, then Ithink I know where to go from there. doug
Anthony Dick wrote:
I ran mri_info--results at the bottom. I also ran mri_convert, but it did not save an output file (summary below).
The tkmedit command is: tkmedit 01_do orig.mgz, and then File > Load Segmentation to load chuman_1_do_shft.nii
I am attaching images of the alignment in AFNI. It does not align in mricron--I misspoke previously.
adick% mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz chuman_1_do_shft_new.nii reading info from rawavg.mgz... $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from chuman_1_do_shft.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 volume sizes do not match
chuman_1_do_shft.nii: (width, height, depth, frames) = (145, 136, 102, 1)
rawavg.mgz: (width, height, depth, frames) = (160, 256, 256, 1) adick%
>>>>> Volume information for chuman_1_do_shft.nii type: nii dimensions: 145 x 136 x 102 voxel sizes: 0.8083, 0.8083, 0.8083 type: SHORT (4) fov: 117.210 dof: 0 xstart: -58.6, xend: -58.6 ystart: -55.0, yend: -55.0 zstart: -41.2, zend: -41.2 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 = 6.6335 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = 59.5238 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -0.5958 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -0.8083 -0.0000 -0.0000 65.2384 -0.0000 -0.8083 -0.0000 114.4912 0.0000 0.0000 0.8083 -41.8213 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.528187
ras to voxel transform: -1.2371 0.0000 0.0000 80.7063 0.0000 -1.2371 0.0000 141.6368 -0.0000 -0.0000 1.2371 51.7371 0.0000 0.0000 0.0000 1.0000
>>>>>> Volume information for orig.nii type: nii 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 = 6.5377 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 60.4280 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -1.5000 Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 134.5377 0.0000 0.0000 1.0000 -67.5720 0.0000 -1.0000 0.0000 126.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 134.5377 -0.0000 -0.0000 -1.0000 126.5000 -0.0000 1.0000 -0.0000 67.5720 0.0000 0.0000 0.0000 1.0000
>>>>>> Volume information for rawavg.mgz type: MGH dimensions: 160 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -80.0, xend: 80.0 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 = 6.5377 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 60.4280 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -1.5000
talairach xfm : Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 0.0000 0.0000 1.0000 -129.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 -0.0000 -0.0000 1.0000 129.5000 0.0000 0.0000 0.0000 1.0000
>>>> Volume information for ahuman_1_do+orig.BRIK type: brik dimensions: 160 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 256.000 dof: 0 xstart: -80.0, xend: 80.0 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 = 6.5377 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 60.4280 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -1.5000 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 0.0000 0.0000 1.0000 -129.5000 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 1
ras to voxel transform: -1.0000 0.0000 0.0000 86.5377 0.0000 -1.0000 0.0000 188.4280 -0.0000 -0.0000 1.0000 129.5000 0.0000 0.0000 0.0000 1.0000
On 1/13/12 5:14 PM, Douglas N Greve wrote: > Which volumes align in AFNI? The orig.mgz and > ahuman_1_do_shft.nii? I'm guessing not. Try this instead: > > mri_convert chuman_1_do_shft.nii --in_like rawavg.mgz > chuman_1_do_shft_new.nii > > and see if you get alignment. If this does not work, make sure > to send us the tkmedit command too. > doug > > Anthony Dick wrote: >> It was created from the ahuman_1_do_shft.nii volume, which was >> what was input to recon-all in Freesurfer. And these volumes >> (the overlay and underlay) align in other viewers (e.g., AFNI >> and mricron). >> >> On 1/13/12 2:40 PM, Douglas N Greve wrote: >>> What volume was human_1_do_shft.nii created from? >>> >>> Anthony Dick wrote: >>>> Here is the command, in case I didn't run it right. >>>> >>>> adick% mri_convert chuman_1_do_shft.nii --in_like orig.mgz >>>> chuman_1_do_shft_new.nii >>>> mri_convert chuman_1_do_shft.nii --in_like orig.mgz >>>> chuman_1_do_shft_new.nii >>>> reading info from orig.mgz... >>>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >>>> reading from chuman_1_do_shft.nii... >>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >>>> volume sizes do not match >>>> >>>> chuman_1_do_shft.nii: (width, height, depth, frames) = (145, >>>> 136, 102, 1) >>>> >>>> orig.mgz: (width, height, depth, frames) = (256, 256, 256, 1) >>>> adick% >>>> >>>> >>>> An image of the tkmedit output is attached. Thanks for any >>>> suggestions. >>>> >>>> Anthony >>>> >>>> >>>> On 1/13/12 2:15 PM, Douglas N Greve wrote: >>>>> Try changing the header information in your parcellation, >>>>> something like >>>>> mri_convert yourparcellation.mgh --in_like orig.mgz >>>>> yourparcellation.new.mgh >>>>> doug >>>>> >>>>> Anthony Dick wrote: >>>>>> Good question. The parcellation is created outside of >>>>>> Freesurfer (the data were shared from another lab and I >>>>>> don't know which program they used to create the >>>>>> parcellation; of course I can find out if this would be >>>>>> helpful). At any rate, the anatomy and parcellation align >>>>>> when viewed in AFNI. >>>>>> >>>>>> Anthony >>>>>> >>>>>> On 1/13/12 2:11 PM, Douglas N Greve wrote: >>>>>>> Hi Anthony, how are you creating the parcellation? Are you >>>>>>> generating it off the orig.mgz? >>>>>>> doug >>>>>>> >>>>>>> Anthony Dick wrote: >>>>>>>> Hello, >>>>>>>> >>>>>>>> I am trying to train a cerebellar atlas based on 20 >>>>>>>> manually parcellated cerebellums. I have run the >>>>>>>> anatomical through freesurfer. When I try to load the >>>>>>>> overlay (parcellation) in tkmedit, the underlay (e.g., >>>>>>>> orig.mgz, T1.mgz) and the overlay (the parcellation) are >>>>>>>> no longer in alignment. >>>>>>>> >>>>>>>> However, loaded in AFNI the underlay and overlay of >>>>>>>> course align. Is there a quick fix to get them in alignment? >>>>>>>> >>>>>>>> Anthony >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> >>> >> >> >
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