No worries about that.
I have created some manual cortical labels in freesurfer using tksurfer. The .labels file containing the vertices of the cortical labels does not correspond to the labels of the pial surface even though they were drawn on the pial. I noticed however, that they do correspond to the lh.base.mgh and rh.base.mgh file that was created with an older version of freesurfer. These files contain coordinates and their corresponding label in the look up table. My guess is that the base file is an intermediate surface between the white and gray. The question is why do the vertices in the manual labels not correspond to the those in the pial surface? Alternatively, since the lh.base.mgh and rh.base.mgh are no longer apart of the recon-all process is there another name in to which it is called?
The command to make the cortical label is: mri_label2vol--label labelname.label --temp brainmask.mgz --o labelname.nii.gz --identity --proj frac 0 1 .1 --subject subject_id --hemi lh
The command(s) to make the base file an ascii file is: mri_annotation2label --subject # --hemi *h --seg #/surf/*h.base.mgh --outdir junk mris_convert -c *h.base.mgh #/surf/*h.white #/surf/*h.base.asc
Thank you, Tina Jeon
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, April 02, 2012 12:50 PM To: Tina Jeon; Freesurfer@nmr.mgh.harvard.edu Subject: Re: Freesurfer base file question
Hi Tina, sorry no one got to your first email. Sometimes emails do fall through the cracks, so always feel free to repost. It is not clear to me what command you are running or what you are trying to do. Can you supply more detail? doug
On 04/02/2012 11:55 AM, Tina Jeon wrote:
Hi Doug could you please answer these questions that I posted on the listserv. Your help would be much appreciated to an upcoming project on cortical development. Thank you.
I noticed that the newest version of freesurfer does not output a
?h.base.mgh file, which contains vertices, but no triangular meshes and corresponding gyral labels from the color look up table.
Question:
1). Why does my cortical labels created using tksurfer correspond to the vertices in the base.mgh file and not the pial surface that I drew the surface on?
2). Is there a file in place of the ?h.base.mgh file in the newer version of freesurfer? i.e. called a different name?
My goal is to figure out which surface aligns with my manually created cortical labels for visualization.
I am running version FSv5.0.0 on Centos4_x86_64 bit.
Many thanks,
Tina Jeon
--
UT Southwestern Medical Center The future of medicine, today.
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