Hi Judit,
all the edits will be kept, so that shouldn't be a problem. It's hard to diagnose the wm segmentation without looking at a volume, but if they are really hyperintense you may need to manually fill them in in the wm.mgz. As for mri_cc, you should use aseg.auto_noCCseg.mgz instead of aseg.mgz via:
mri_cc -aseg auto_noCCseg ...
what is PLIC? The fornix should be non-zero after running this command.
cheers, Bruce
On Mon, 20 Jul 2009, Judit Haasz wrote:
Bruce Fischl wrote:
Hi Judit,
the fornix is labeled in the aseg, not the parcellation, although this is not the default). If you rerun mri_cc with the -fornix option it will write a volume named mri/fornix.mgz with the fornix in it.
cheers, Bruce
On Wed, 1 Jul 2009, Judit Haasz wrote:
Hi,
We are trying to extract certain regions from FreeSurfer segmentation. There are couple of regions which are not found in the output files. We are currently searching for the regions in 13 output files. The regions are the following: right fornix (508), left fornix (558), right PLIC (158), left PLIC (157) and the starting, way and end points for cingulum and CST.
Could you let us know in which file would we be able to find these regions? Is it possible that some regions are empty?
Thank you for your help
Judit Haasz _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce and all,
I tried using the command as you suggested, but i get the following message:
mri_cc -fornix STROKE_3T including fornix in segmentation reading aseg from /Applications/freesurfer//subjects/STROKE_3T/mri/aseg.mgz mri_cc: volume /Applications/freesurfer//subjects/STROKE_3T/mri/aseg.mgz already has CC in it
Apart from that I encountered two more problems. Our subject group consists of 115 healthy elderly people. Some of the subjects` scan exhibit intensified white matter lesion which results in inaccurate pial surface reconstruction, that is pial surface penentrates into the white matter. Is there any way we could overcome this problem and obtain a more reliable segmentation? My next question refers to the problem of different FreeSurfer versions. We have data from 2005 and 2009. The ones from 2005 were processed by FreeSurfer ver 3.01. Now we are using FreeSurfer 4.3.0 with a separate mri_normalize program, that we received from you since a systematic error in the segmentation process was present. We are planning to compare the two datasets. We are aware of the fact that we have to rerun all subjects from 2005 with the version we are currently using. I am just wondering if there is a way to keep our previous wm and pial surface edits. As far as i know, edits can be kept if FreeSurfer is run from autorecon2. Would it be an option for us even though, mri_normalize is involved in autorecon1.
I really appreciate your help
Judit Haasz