I agree with Bruce. You can use MRIread.m to read in the data.
Regarding the other question: first you need to combine the posteriors of all the subfields into a single posterior for the whole hippocampus. You can do that like this:
mri_concat posterior_fimbria.mgz posterior_CA1.mgz ... --sum --o posteriorWholeHippocampus.mgz
Then you can threshold the posterior at probability 0.5 to obtain a binary hippocampal mask:
mri_binarize --i posteriorWholeHippocampus.mgz --min 127 --o binaryHippocampalMask.mgz
Finally, you can generate a surface by tesselating the mask:
mri_tesselate binaryHippocampalMask.mgz 1 surfaceFile
You can visualize the output with
freeview -v posteriorWholeHippocampus.mgz -f surfaceFile
Cheers,
/Eugenio
On Thu, 2013-04-18 at 11:22 -0400, Bruce Fischl wrote:
Hi Marcos
I would do it in matlab. Compute the spatial eigenvectors then divide the hippocampus up along the primary eigenvector
cheers Bruce On Thu, 18 Apr 2013, Marcos Martins da Silva wrote:
Thank you for your answer, Juan.
Yes, I want a surface of the whole hippocampus and I thought I had just obtained that using freeview and adding all hippo-subfield files. That resulted in the screenshot I previously attached. I just do not know how I can save the resultant surface.
After I checked "show as isosurface in 3D view" the low and high threshold controls appeared. The default threshold values on Freeview for low was 127.5 and high was 255. When I played with these controls, the size of the surfaces changed on 3D view. That is why I made the second question. I was trying to select the correct values for low and high threshoulds so I get an image consistent with the volume values we get after running kvlQuantifyPosteriorProbabilityImages. After setting the correct values I would like to save the work as a surface so I could load the whole surface instead of loading each individual subfield file. But I did not find a "save as surface" option. So I used the screenshot tool to "save" the work. This way I could at least show you what I got but I thought it was not the best way to do it.
Relating to the last question about generating a new segmentation (anterior, body and posterior), you said I could use simple geometric rules to get it. Could you tell me where I can find instructions about how to do it?
Sorry, I am afraid I am a novice here and my questions are the best proof of this, so I would like to thank you for all your patience.
Em Qua, 2013-04-17 às 21:19 -0400, Juan Eugenio Iglesias escreveu: Dear Marcos,
1- How do I save the combined 3D view I got as a surface?
Do you want a surface of the whole hippocampus? In that case I would suggest adding up the probability volumes from all the subfields and thresholding the resulting volume.
2-I know the hippo-subifields .mgz files are probability maps and if I guess right kvlQuantifyPosteriorProbabilityImages read these files to count how many voxels you have in each subfield. I also guess it count only the voxels with reasonable high probability to be part of each subfield. If so, what is the minimum value between 1 and 255 the program use to decide if a particular voxel is valid?
The estimates of the volumes are based on soft probabilities, so all voxels with non-zero probability contribute towards the estimate. For instance, a voxel with value 255 contributes to the volume 255 times as much as a voxel with a value of 1.
3- Is it possible to merge hippo-subfield .mgz files data and to generate a different segmentation like anterior (anterior quarter), body (the2 intermediate quarters) and posterior (posterior quarter).
There are currently no scripts in FreeSurfer to generate such a partition. But you could always take a mask of the whole hippocampus (either from aseg.mgz of from the combination of all the subfields, like I mentioned in 1) and define some simple geometric rules to create it.
Kind regards,
Eugenio
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