Hi Jessica
it depends which ones you mean. Thalamus we label in the aseg.mgz, although for some reason the CMA called it "thalamus proper" so that is the index you should use (10 instead of 9 for left). What other labels do you mean?
Bruce
On Wed, 29 Nov 2017, Jessica Huang wrote:
Hi Bruce,
Ah! I found these regions (ex. the thalamus) in the FreeSurferColorLUT.txt
lookup table but otherwise not in each subject's aseg/apar/label dir. Would
you have any suggestions for how to extract a timecourse for the thalamus or
the hippocampus? Did I miss a step? I have labels for the following regions
for all subjects:
BA1
BA2
BA3a
BA3b
BA4a
BA4p
BA6
BA44
BA45
cortex
entorhinal
medial wall
MT
perirhinal
ribbon
V1
V2
As a correction, I misclassified in my initial email - I do have the label
for BA6.
Thank you for your insight!!
Best,
Jessica
On Wed, Nov 29, 2017 at 10:01 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
Hi Jessica
not sure I understand, but I don't think so. If we didn't label
it in the aseg/aparc/label dir then how would you find it? Or do
you mean manually draw it? That is possible.
Bruce
On Wed, 29 Nov 2017, Jessica Huang wrote:
Hi Freesurfer Experts,
Can I extract time courses for regions without labels in
the subject/mri folder?
Thank you for your insight!
Best,
Jessica
On Tue, Nov 28, 2017 at 5:51 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu> wrote:
You will need to create a segmentation volume in the
subject/mri folder.
For BA6, you can use lh.BA6_exvivo.thresh.label to
create this volume.
Use mri_label2vol. Run it with --help to get
examples. You can use
example #4 just with the single label above (for the
output use a mgz
file instead of img). When you are done, you should
have a binary volume
at 1mm3 with the lh BA6 -- view this to make sure it
is right. Then use
fcseed-config to configure this seed, specifying
-segid 1 and -seg
NameOfSeg.mgz
where NameOfSeg.mgz is the output of the
mri_label2vol above
On 11/28/2017 05:44 PM, Jessica Huang wrote:
> Hi Freesurfer Experts,
>
> I've been looking to extract the timecourses of a
couple regions of
> interest from fMRI data that's be registered
against anatomical data.
>
> I've used commands such as recon-all and
preproc-sess on all subjects.
>
> I've already used command fcseed-sess to extract
timecourses from many
> regions in the default parcellations/
segmentations transferred
> through previous commands. I've also used
fcseed-sess for regions that
> were labelled in each subject's anatomical labels
folder. I'm still
> curious how to extract the timecourses for other
ROIs not in the
> default parcellations/ segmentations. For example,
with reference to
> the lookup table FreeSurferColorLUT.txt, how do I
access the
> timecourse of:
> #9 Left-Thalamus 0 118 14 0
> Thank you for any insight. Is there some folder I
could look in or
> specific subject files that might help?
> Thank you again!
> Jessica
>
> p.s. for more examples of timecourses I have/
don't have access to
> already:
>
> In the default segmentation, I know how to extract
these:
> - 1007 ctx-lh-fusiform
>
> In the labels folder of each subject, I know how
to extract these:
> - 400 V1
>
> Unsure how to extract these because they're not
found in each of my
> subjects:
> - 406 BA6
>
> --
> Harvard College Class of 2020
> A.B. Candidate in Computer Science
> jessicalihuang.com <http://jessicalihuang.com>
> 1 (516) 343-4850
>
>
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