Hello, I've been following the Ex-Vivo Recon instructions https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) with an MPRAGE scan of a formalin-fixated brain. With considerable manual editing, I've been able to produce convincing white and pial surfaces, but I am having trouble getting a good parcellation. The labels are reversed from anterior to posterior (e.g., superior parietal lobule area is labelled as middle frontal gyrus). I am assuming this has to do with problems with the surface registration. Also, when viewing the surfaces in Freeview, they appear pretty dark (perhaps similar to https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.html), although the correspondence between red/green and gyri and sulci appears to be correct. Might this be part of the problem?
Any advice would be much appreciated! If you'd like to take a look at the files, please let me know what and where to upload.
Thanks very much for your help.
Best regards, John Plass
Hi John
does it come up in the correct orientation in freeview? If you didn't scan it in the orientation that a person would have been lying in the scanner, you will need to reorient the data so that we know what e.g. anterior is
cheers Bruce
On Tue, 26 Jan 2016, John Plass wrote:
Hello, I've been following the Ex-Vivo Recon instructions https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) with an MPRAGE scan of a formalin-fixated brain. With considerable manual editing, I've been able to produce convincing white and pial surfaces, but I am having trouble getting a good parcellation. The labels are reversed from anterior to posterior (e.g., superior parietal lobule area is labelled as middle frontal gyrus). I am assuming this has to do with problems with the surface registration. Also, when viewing the surfaces in Freeview, they appear pretty dark (perhaps similar tohttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm l), although the correspondence between red/green and gyri and sulci appears to be correct. Might this be part of the problem?
Any advice would be much appreciated! If you'd like to take a look at the files, please let me know what and where to upload.
Thanks very much for your help.
Best regards, John Plass
Hi Bruce, Thanks for your reply. The orientation is correct in freeview, although, digging further, I see that that it is misoriented when I view it in tkregister2. I ran tkregister --mgz --s {subID} --fstal --surf orig, and the orig volume is shown oriented correctly, but the orig surface appears to have some of the dimensions swapped. Any idea why this might be?
Thanks for your help!
John
On Tuesday, January 26, 2016, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi John
does it come up in the correct orientation in freeview? If you didn't scan it in the orientation that a person would have been lying in the scanner, you will need to reorient the data so that we know what e.g. anterior is
cheers Bruce
On Tue, 26 Jan 2016, John Plass wrote:
Hello, I've been following the Ex-Vivo Recon instructions https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) with an MPRAGE
scan
of a formalin-fixated brain. With considerable manual editing, I've been able to produce convincing white and pial surfaces, but I am having
trouble
getting a good parcellation. The labels are reversed from anterior to posterior (e.g., superior parietal lobule area is labelled as middle
frontal
gyrus). I am assuming this has to do with problems with the surface registration. Also, when viewing the surfaces in Freeview, they appear pretty dark (perhaps similar tohttps://
mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm
l), although the correspondence between red/green and gyri and sulci
appears
to be correct. Might this be part of the problem?
Any advice would be much appreciated! If you'd like to take a look at the files, please let me know what and where to upload.
Thanks very much for your help.
Best regards, John Plass
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu javascript:; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
I don't know how that could have happened. Is the geometry of the exvivo input oriented correctly? Ie, if you load the orig.mgz into freeview or tkmedit, is sag actually sagital, etc?
On 01/26/2016 06:08 PM, John Plass wrote:
Hi Bruce, Thanks for your reply. The orientation is correct in freeview, although, digging further, I see that that it is misoriented when I view it in tkregister2. I ran tkregister --mgz --s {subID} --fstal --surf orig, and the orig volume is shown oriented correctly, but the orig surface appears to have some of the dimensions swapped. Any idea why this might be?
Thanks for your help!
John
On Tuesday, January 26, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi John does it come up in the correct orientation in freeview? If you didn't scan it in the orientation that a person would have been lying in the scanner, you will need to reorient the data so that we know what e.g. anterior is cheers Bruce On Tue, 26 Jan 2016, John Plass wrote: > Hello, > I've been following the Ex-Vivo Recon instructions > https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) with an MPRAGE scan > of a formalin-fixated brain. With considerable manual editing, I've been > able to produce convincing white and pial surfaces, but I am having trouble > getting a good parcellation. The labels are reversed from anterior to > posterior (e.g., superior parietal lobule area is labelled as middle frontal > gyrus). I am assuming this has to do with problems with the surface > registration. Also, when viewing the surfaces in Freeview, they appear > pretty dark (perhaps similar tohttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm <http://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm> > l), although the correspondence between red/green and gyri and sulci appears > to be correct. Might this be part of the problem? > > Any advice would be much appreciated! If you'd like to take a look at the > files, please let me know what and where to upload. > > Thanks very much for your help. > > Best regards, > John Plass > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <javascript:;> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.--
John Plass Ph.D. Candidate Visual Perception, Neuroscience, and Cognition Lab Northwestern University
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, The geometry of the input is correct in both freeview and tkmedit, and the outlines of the white and pial surfaces align well with with volume in freeview. Looking at the headers, I'm wondering if my initial transform of the image into the proper coordinates might be the problem. The DICOM wasn't oriented correctly at first, so I converted to nifti, and ran "mri_convert -c -iid 0 -1 0 -ijd 0 0 -1 -ikd 1 0 0 mprage.nii.gz mprage.mgz", which produced a conformed image with the correct orientation in freeview. Is there a chance that a problem here could produce the problems later down the pipeline? For example, I see now that mprage.nii.gz's header correctly lists the primary slice direction as axial, whereas the reoriented mprage.mgz incorrectly lists it as coronal. Also, orientation was originally listed as RAS, but changed to LIA after conversion. Is there a chance that this is affecting the later surface registration?
Thanks so much for any help you can provide. I've attached mri_info output for the nifti and mgz files below.
Best regards, John
mri_info mprage.nii.gz Volume information for mprage.nii.gz type: nii dimensions: 199 x 152 x 183 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 199.000 dof: 0 xstart: -99.5, xend: 99.5 ystart: -76.0, yend: 76.0 zstart: -91.5, zend: 91.5 TR: 8.42 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0.7324, y_r = 0.0361, z_r = 0.6799, c_r = 1.7748 : x_a = -0.0157, y_a = 0.9992, z_a = -0.0361, c_a = 25.8853 : x_s = -0.6807, y_s = 0.0157, z_s = 0.7324, c_s = -8.5852 Orientation : RAS Primary Slice Direction: axial
voxel to ras transform: 0.7324 0.0361 0.6799 -136.0543 -0.0157 0.9992 -0.0361 -45.1875 -0.6807 0.0157 0.7324 -9.0720 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.999997
ras to voxel transform: 0.7324 -0.0157 -0.6807 92.7637 0.0361 0.9992 0.0157 50.2057 0.6799 -0.0361 0.7324 97.5155 0.0000 0.0000 0.0000 1.0000
______
mri_info mprage.mgz Volume information for mprage.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 8.42 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 = 1.7748 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 25.8853 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -8.5852
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 129.7748 0.0000 0.0000 1.0000 -102.1147 0.0000 -1.0000 0.0000 119.4148 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 129.7748 -0.0000 -0.0000 -1.0000 119.4148 -0.0000 1.0000 -0.0000 102.1147 0.0000 0.0000 0.0000 1.0000
--- John Plass Ph.D. Candidate Visual Perception, Neuroscience, and Cognition Lab Northwestern University
On Wed, Jan 27, 2016 at 1:43 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
I don't know how that could have happened. Is the geometry of the exvivo input oriented correctly? Ie, if you load the orig.mgz into freeview or tkmedit, is sag actually sagital, etc?
On 01/26/2016 06:08 PM, John Plass wrote:
Hi Bruce, Thanks for your reply. The orientation is correct in freeview, although, digging further, I see that that it is misoriented when I view it in tkregister2. I ran tkregister --mgz --s {subID} --fstal --surf orig, and the orig volume is shown oriented correctly, but the orig surface appears to have some of the dimensions swapped. Any idea why this might be?
Thanks for your help!
John
On Tuesday, January 26, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi John does it come up in the correct orientation in freeview? If you didn't scan it in the orientation that a person would have been lying in the scanner, you will need to reorient the data so that we know what e.g. anterior is cheers Bruce On Tue, 26 Jan 2016, John Plass wrote: > Hello, > I've been following the Ex-Vivo Recon instructions > https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) with an MPRAGE scan > of a formalin-fixated brain. With considerable manual editing, I've been > able to produce convincing white and pial surfaces, but I am having trouble > getting a good parcellation. The labels are reversed from anterior to > posterior (e.g., superior parietal lobule area is labelled as middle frontal > gyrus). I am assuming this has to do with problems with the surface > registration. Also, when viewing the surfaces in Freeview, they appear > pretty dark (perhaps similar tohttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm
<http://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm
> l), although the correspondence between red/green and gyri and sulci appears > to be correct. Might this be part of the problem? > > Any advice would be much appreciated! If you'd like to take a look at the > files, please let me know what and where to upload. > > Thanks very much for your help. > > Best regards, > John Plass > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <javascript:;> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.--
John Plass Ph.D. Candidate Visual Perception, Neuroscience, and Cognition Lab Northwestern University
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think if they look ok in freeview and tkmedit, then they are probably ok. Can you tar up and upload the data set to me?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 01/27/2016 06:05 PM, John Plass wrote:
Hi Doug, The geometry of the input is correct in both freeview and tkmedit, and the outlines of the white and pial surfaces align well with with volume in freeview. Looking at the headers, I'm wondering if my initial transform of the image into the proper coordinates might be the problem. The DICOM wasn't oriented correctly at first, so I converted to nifti, and ran "mri_convert -c -iid 0 -1 0 -ijd 0 0 -1 -ikd 1 0 0 mprage.nii.gz mprage.mgz", which produced a conformed image with the correct orientation in freeview. Is there a chance that a problem here could produce the problems later down the pipeline? For example, I see now that mprage.nii.gz's header correctly lists the primary slice direction as axial, whereas the reoriented mprage.mgz incorrectly lists it as coronal. Also, orientation was originally listed as RAS, but changed to LIA after conversion. Is there a chance that this is affecting the later surface registration?
Thanks so much for any help you can provide. I've attached mri_info output for the nifti and mgz files below.
Best regards, John
mri_info mprage.nii.gz Volume information for mprage.nii.gz type: nii dimensions: 199 x 152 x 183 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 199.000 dof: 0 xstart: -99.5, xend: 99.5 ystart: -76.0, yend: 76.0 zstart: -91.5, zend: 91.5 TR: 8.42 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0.7324, y_r = 0.0361, z_r = 0.6799, c_r = 1.7748 : x_a = -0.0157, y_a = 0.9992, z_a = -0.0361, c_a = 25.8853 : x_s = -0.6807, y_s = 0.0157, z_s = 0.7324, c_s = -8.5852 Orientation : RAS Primary Slice Direction: axial
voxel to ras transform: 0.7324 0.0361 0.6799 -136.0543 -0.0157 0.9992 -0.0361 -45.1875 -0.6807 0.0157 0.7324 -9.0720 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.999997
ras to voxel transform: 0.7324 -0.0157 -0.6807 92.7637 0.0361 0.9992 0.0157 50.2057 0.6799 -0.0361 0.7324 97.5155 0.0000 0.0000 0.0000 1.0000
mri_info mprage.mgz Volume information for mprage.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 8.42 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 = 1.7748 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 25.8853 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -8.5852
talairach xfm : Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 129.7748 0.0000 0.0000 1.0000 -102.1147 0.0000 -1.0000 0.0000 119.4148 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 129.7748 -0.0000 -0.0000 -1.0000 119.4148 -0.0000 1.0000 -0.0000 102.1147 0.0000 0.0000 0.0000 1.0000
John Plass Ph.D. Candidate Visual Perception, Neuroscience, and Cognition Lab Northwestern University
On Wed, Jan 27, 2016 at 1:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I don't know how that could have happened. Is the geometry of the exvivo input oriented correctly? Ie, if you load the orig.mgz into freeview or tkmedit, is sag actually sagital, etc? On 01/26/2016 06:08 PM, John Plass wrote: > Hi Bruce, > Thanks for your reply. The orientation is correct in freeview, > although, digging further, I see that that it is misoriented when I > view it in tkregister2. I ran tkregister --mgz --s {subID} --fstal > --surf orig, and the orig volume is shown oriented correctly, but the > orig surface appears to have some of the dimensions swapped. Any idea > why this might be? > > Thanks for your help! > > John > > On Tuesday, January 26, 2016, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > Hi John > > does it come up in the correct orientation in freeview? If you didn't > scan it in the orientation that a person would have been lying in the > scanner, you will need to reorient the data so that we know what e.g. > anterior is > > cheers > Bruce > > On Tue, 26 Jan 2016, John Plass wrote: > > > Hello, > > I've been following the Ex-Vivo Recon instructions > > https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon) with an > MPRAGE scan > > of a formalin-fixated brain. With considerable manual editing, > I've been > > able to produce convincing white and pial surfaces, but I am > having trouble > > getting a good parcellation. The labels are reversed from > anterior to > > posterior (e.g., superior parietal lobule area is labelled as > middle frontal > > gyrus). I am assuming this has to do with problems with the surface > > registration. Also, when viewing the surfaces in Freeview, they > appear > > pretty dark (perhaps similar > tohttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm <http://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm> > <http://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-June/018689.htm> > > l), although the correspondence between red/green and gyri and > sulci appears > > to be correct. Might this be part of the problem? > > > > Any advice would be much appreciated! If you'd like to take a > look at the > > files, please let me know what and where to upload. > > > > Thanks very much for your help. > > > > Best regards, > > John Plass > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <javascript:;> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > -- > > --- > John Plass > Ph.D. Candidate > Visual Perception, Neuroscience, and Cognition Lab > Northwestern University > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
John Plass