Thanks for all the information given. We finally have managed to solve it thanks to your comments.
Cheers Daniel 2012/10/17 Bruce Fischl <fis...@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 <fis...@nmr.mgh.harvard.edu> >> Date: 2012/10/11 >> Subject: Re: [Freesurfer] cortical parcellation question >> To: Daniel Ferreira <danif...@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 <fis...@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 >> <fis...@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. 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