17 Oct
2012
17 Oct
'12
4:52 p.m.
Hello again,
Thanks for all the information Bruce.
Is it not possible to back-project the regions defined in the 2D surface-based spherical coordinate system onto the mean_intensity.nii image? As those regions in the 2D surface-based coordinate system would have been initially defined on a 3D volume(s) and transformed (inflated) to the 2D spherical surface?
Daniel
---------- Forwarded message ---------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: 2012/10/11 Subject: Re: [Freesurfer] cortical parcellation question To: Daniel Ferreira daniferp@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu
Hi Daniel,
no, sorry. The gca is not a cortical atlas. Those labels are stored in the .gcas file and aren't in the same space (in fact, they are in a surface-based spherical coordinate system and not in the volume at all, so not easily combinable).
Bruce
On Thu, 11 Oct 2012, Daniel Ferreira wrote:
Thanks for the detailed information.
The mean intensity image (mean_intensity.nii) generated from frame #1 is almost exactly what I need. This image has all the sub-cortical regions assigned a discrete integer number (i.e. all the voxels in the left cerebelllar grey matter = 8 and right = 47). However the whole of the neocortex is defined as left (intensity = 3) and right (intensity = 42) only, there are no cortical sub-divisions.
Is it possible to have the individual neocortical regions assigned a discrete integer number; (obviously not one already assigned to the other regions in the mean_intensity.nii image)? For example all inferior temporal voxels = 9; middle temporal voxels = 10; superior temporal voxels = 11. So each of the regions defined in the "colortable_desikan_killiany.**txt" file found in the FREESURFER_HOME/average/ directory are also defined in the mean_intensity.nii image?
Thanks
2012/10/6 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Daniel
it's in .gca format, and includes information that wouldn't fit in a nifti file (e.g. markov relationships). You can use mri_convert to extract some of the basic info though (e.g. the most likely class at each location and the mean intensity of the most likely class) using mri_convert. For example: mri_convert $FREESURFER_HOME/average/RB_**all_2008-03-26.gca#0 ./labels.nii mri_convert $FREESURFER_HOME/average/RB_**all_2008-03-26.gca#1 ./mean_intensity.nii where the #<n> syntax mean extract the nth frame from the 4D gca volume. Frame 0 is the most likely label and frame 1 is the mean intensity. Note however that there is lots more info in the .gca that this doesn't capture such as the MRF parameters I mentioned above, class variances, other class probabilities, etc.... cheers Bruce On Thu, 4 Oct 2012, Daniel Ferreira wrote: Thanks Bruce, When you say the atlas itself is included in the Freesurfer distribution, do you mean there is a 3D version of it available in the download? Also, I am not looking for the individual subjects' images, I just want a copy of the final atlas as a 3D image in analyze/nifti format. (i.e. in the same format as the Harvard-Oxford atlas that is downloaded with FSL). Thanks a lot. Daniel Ferreira 2012/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Daniel, 1. Do you mean the atlas or the parcellation of your subjects? We cannot distribute the individual subjects in the atlas as the data was collected under an IRB long ago that didn't include this. The atlas itself (summary statistics derived from those subjects) is included in the FreeSurfer distribution. 2. The subcortical areas are the same, but not the cortical ones. That cortical parcellation is quite coarse, and while we did implement it we were never given permission to distribute the automated version, so it is not part of FreeSurfer. The boundaries that we define are thus different than that one (and since the Harvard-Oxford one is based on volumetric labeling of folding patterns we found that it contained a bunch of errors in which e.g. the wrong side of a sulcus was labeled) cheers Bruce On Wed, 3 Oct 2012, Daniel Ferreira wrote: Dear experts, I have a couple of questions regarding the cortical parcellation atlas that is used in Freesurfer: 1) I would like to know if it is possible to obtain the Desikan-Killiany atlas in 3D analyze/nifti format. With each region of the brain assigned a discrete integer number (for example the all of the voxels of the left inferior temporal lobe have an intensity = 1, or the whole of the left hippocampus = 2). 2) Are the Harvard-Oxford cortical and subcortical atlases that can be downloaded with FSL the same as the cortical parcellation atlas that is used in Freesurfer? (i.e. are the neuroanatomical boundaries the same; does the left inferior temporal cortex in the Freesurfer cortical parcellation = the left inferior temporal cortex in the Harvard-Oxford atlas downloaded with FSL) Many thanks Daniel Ferreira 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<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.
17 Oct
17 Oct
5 p.m.
New subject: cortical parcellation question
there is no volume associate with them any longer. As a short-cut I think Doug ran the aparc on fsaverage, so you could try sampling it into the volume (or just using the aparc+aseg.mgz that is distributed with fsaverage)
cheers Bruce
On Wed, 17 Oct 2012, Daniel Ferreira wrote:
Hello again,
Thanks for all the information Bruce. Is it not possible to back-project the regions defined in the 2D surface-based spherical coordinate system onto the mean_intensity.nii image? As those regions in the 2D surface-based coordinate system would have been initially defined on a 3D volume(s) and transformed (inflated) to the 2D spherical surface?
Daniel
---------- Forwarded message ---------- From: Bruce Fischl <fischl@nmr.mgh.harvard.edu> Date: 2012/10/11 Subject: Re: [Freesurfer] cortical parcellation question To: Daniel Ferreira <daniferp@gmail.com> Cc: freesurfer@nmr.mgh.harvard.edu Hi Daniel, no, sorry. The gca is not a cortical atlas. Those labels are stored in the .gcas file and aren't in the same space (in fact, they are in a surface-based spherical coordinate system and not in the volume at all, so not easily combinable). Bruce On Thu, 11 Oct 2012, Daniel Ferreira wrote: Thanks for the detailed information. The mean intensity image (mean_intensity.nii) generated from frame #1 is almost exactly what I need. This image has all the sub-cortical regions assigned a discrete integer number (i.e. all the voxels in the left cerebelllar grey matter = 8 and right = 47). However the whole of the neocortex is defined as left (intensity = 3) and right (intensity = 42) only, there are no cortical sub-divisions. Is it possible to have the individual neocortical regions assigned a discrete integer number; (obviously not one already assigned to the other regions in the mean_intensity.nii image)? For example all inferior temporal voxels = 9; middle temporal voxels = 10; superior temporal voxels = 11. So each of the regions defined in the "colortable_desikan_killiany.txt" file found in the FREESURFER_HOME/average/ directory are also defined in the mean_intensity.nii image? Thanks 2012/10/6 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Daniel it's in .gca format, and includes information that wouldn't fit in a nifti file (e.g. markov relationships). You can use mri_convert to extract some of the basic info though (e.g. the most likely class at each location and the mean intensity of the most likely class) using mri_convert. For example: mri_convert $FREESURFER_HOME/average/RB_all_2008-03-26.gca#0 ./labels.nii mri_convert $FREESURFER_HOME/average/RB_all_2008-03-26.gca#1 ./mean_intensity.nii where the #<n> syntax mean extract the nth frame from the 4D gca volume. Frame 0 is the most likely label and frame 1 is the mean intensity. Note however that there is lots more info in the .gca that this doesn't capture such as the MRF parameters I mentioned above, class variances, other class probabilities, etc.... cheers Bruce On Thu, 4 Oct 2012, Daniel Ferreira wrote: Thanks Bruce, When you say the atlas itself is included in the Freesurfer distribution, do you mean there is a 3D version of it available in the download? Also, I am not looking for the individual subjects' images, I just want a copy of the final atlas as a 3D image in analyze/nifti format. (i.e. in the same format as the Harvard-Oxford atlas that is downloaded with FSL). Thanks a lot. Daniel Ferreira 2012/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Daniel, 1. Do you mean the atlas or the parcellation of your subjects? We cannot distribute the individual subjects in the atlas as the data was collected under an IRB long ago that didn't include this. The atlas itself (summary statistics derived from those subjects) is included in the FreeSurfer distribution. 2. The subcortical areas are the same, but not the cortical ones. That cortical parcellation is quite coarse, and while we did implement it we were never given permission to distribute the automated version, so it is not part of FreeSurfer. The boundaries that we define are thus different than that one (and since the Harvard-Oxford one is based on volumetric labeling of folding patterns we found that it contained a bunch of errors in which e.g. the wrong side of a sulcus was labeled) cheers Bruce On Wed, 3 Oct 2012, Daniel Ferreira wrote: Dear experts, I have a couple of questions regarding the cortical parcellation atlas that is used in Freesurfer: 1) I would like to know if it is possible to obtain the Desikan-Killiany atlas in 3D analyze/nifti format. With each region of the brain assigned a discrete integer number (for example the all of the voxels of the left inferior temporal lobe have an intensity = 1, or the whole of the left hippocampus = 2). 2) Are the Harvard-Oxford cortical and subcortical atlases that can be downloaded with FSL the same as the cortical parcellation atlas that is used in Freesurfer? (i.e. are the neuroanatomical boundaries the same; does the left inferior temporal cortex in the Freesurfer cortical parcellation = the left inferior temporal cortex in the Harvard-Oxford atlas downloaded with FSL) Many thanks Daniel Ferreira 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.
30 Oct
30 Oct
5:44 a.m.
New subject: cortical parcellation question
Thanks for all the information given. We finally have managed to solve it thanks to your comments.
Cheers
Daniel
2012/10/17 Bruce Fischl fischl@nmr.mgh.harvard.edu
there is no volume associate with them any longer. As a short-cut I think Doug ran the aparc on fsaverage, so you could try sampling it into the volume (or just using the aparc+aseg.mgz that is distributed with fsaverage)
cheers Bruce
On Wed, 17 Oct 2012, Daniel Ferreira wrote:
Hello again,
Thanks for all the information Bruce. Is it not possible to back-project the regions defined in the 2D surface-based spherical coordinate system onto the mean_intensity.nii image? As those regions in the 2D surface-based coordinate system would have been initially defined on a 3D volume(s) and transformed (inflated) to the 2D spherical surface?
Daniel
---------- Forwarded message ---------- From: Bruce Fischl <fischl@nmr.mgh.harvard.edu> Date: 2012/10/11 Subject: Re: [Freesurfer] cortical parcellation question To: Daniel Ferreira <daniferp@gmail.com> Cc: freesurfer@nmr.mgh.harvard.edu Hi Daniel, no, sorry. The gca is not a cortical atlas. Those labels are stored in the .gcas file and aren't in the same space (in fact, they are in a surface-based spherical coordinate system and not in the volume at all, so not easily combinable). Bruce On Thu, 11 Oct 2012, Daniel Ferreira wrote: Thanks for the detailed information. The mean intensity image (mean_intensity.nii) generated from frame #1 is almost exactly what I need. This image has all the sub-cortical regions assigned a discrete integer number (i.e. all the voxels in the left cerebelllar grey matter = 8 and right = 47). However the whole of the neocortex is defined as left (intensity = 3) and right (intensity = 42) only, there are no cortical sub-divisions. Is it possible to have the individual neocortical regions assigned a discrete integer number; (obviously not one already assigned to the other regions in the mean_intensity.nii image)? For example all inferior temporal voxels = 9; middle temporal voxels = 10; superior temporal voxels = 11. So each of the regions defined in the "colortable_desikan_killiany.**txt" file found in the FREESURFER_HOME/average/ directory are also defined in the mean_intensity.nii image? Thanks 2012/10/6 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Daniel it's in .gca format, and includes information that wouldn't fit in a nifti file (e.g. markov relationships). You can use mri_convert to extract some of the basic info though (e.g. the most likely class at each location and the mean intensity of the most likely class) using mri_convert. For example: mri_convert $FREESURFER_HOME/average/RB_**all_2008-03-26.gca#0 ./labels.nii mri_convert $FREESURFER_HOME/average/RB_**all_2008-03-26.gca#1 ./mean_intensity.nii where the #<n> syntax mean extract the nth frame from the 4D gca volume. Frame 0 is the most likely label and frame 1 is the mean intensity. Note however that there is lots more info in the .gca that this doesn't capture such as the MRF parameters I mentioned above, class variances, other class probabilities, etc.... cheers Bruce On Thu, 4 Oct 2012, Daniel Ferreira wrote: Thanks Bruce, When you say the atlas itself is included in the Freesurfer distribution, do you mean there is a 3D version of it available in the download? Also, I am not looking for the individual subjects' images, I just want a copy of the final atlas as a 3D image in analyze/nifti format. (i.e. in the same format as the Harvard-Oxford atlas that is downloaded with FSL). Thanks a lot. Daniel Ferreira 2012/10/3 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Daniel, 1. Do you mean the atlas or the parcellation of your subjects? We cannot distribute the individual subjects in the atlas as the data was collected under an IRB long ago that didn't include this. The atlas itself (summary statistics derived from those subjects) is included in the FreeSurfer distribution. 2. The subcortical areas are the same, but not the cortical ones. That cortical parcellation is quite coarse, and while we did implement it we were never given permission to distribute the automated version, so it is not part of FreeSurfer. The boundaries that we define are thus different than that one (and since the Harvard-Oxford one is based on volumetric labeling of folding patterns we found that it contained a bunch of errors in which e.g. the wrong side of a sulcus was labeled) cheers Bruce On Wed, 3 Oct 2012, Daniel Ferreira wrote: Dear experts, I have a couple of questions regarding the cortical parcellation atlas that is used in Freesurfer: 1) I would like to know if it is possible to obtain the Desikan-Killiany atlas in 3D analyze/nifti format. With each region of the brain assigned a discrete integer number (for example the all of the voxels of the left inferior temporal lobe have an intensity = 1, or the whole of the left hippocampus = 2). 2) Are the Harvard-Oxford cortical and subcortical atlases that can be downloaded with FSL the same as the cortical parcellation atlas that is used in Freesurfer? (i.e. are the neuroanatomical boundaries the same; does the left inferior temporal cortex in the Freesurfer cortical parcellation = the left inferior temporal cortex in the Harvard-Oxford atlas downloaded with FSL) Many thanks Daniel Ferreira 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<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.
4963
Age (days ago)
4976
Last active (days ago)
freesurfer@nmr.mgh.harvard.edu
2 comments
2 participants
participants (2)
-
Bruce Fischl -
Daniel Ferreira