Hi all
Could anyone help me with extracting the wmparc volume stats in accordance
with Destrieux atlas?
As it stands now the segmentations corresponding to whitematter beneath
Destrieux 2009 parcellations are returned empty when called for
Many thanks
Lena
\_
Le
Hello,
The initial command to recon-all:
recon-all -i $FREESURFER_HOME/subjects/PPG1156/1156MPRage.nii.gz -autorecon1
-autorecon2 -subjid MGZ
exited with errors during SubCort Seg. At this point, I am attempting to
obtain subcortical segmentation only (aseg.mgz, wm.mgz, aseg.stats), but
would li
Dear Freesurfer users,
I am wondering how are the volumes calculated from stats such aseg.stat. When
I export the aseg and do a voxel count and multiple the volume per voxel, my
total volume is different from that is given by the stats. For example, the
hippocampal volume given by aseg.stats
yes, we do a partial volume correction of the volumes, accounting for the
fraction of the structure in each border voxel.
cheers
Bruce
On Mon, 15 Feb 2010, Hui J
Yu wrote:
> Dear Freesurfer users,
>
> I am wondering how are the volumes calculated from stats such aseg.stat.
> When I export the
Hi Julie,
can you send us the last couple of hundred or so lines of the
recon-all.log? You can generate this with tail -n 200 recon-all.log
cheers,
Bruce
On Mon, 15
Feb 2010, Julie McEntee wrote:
> Hello,
>
> The initial command to recon-all:
>
> recon-all -i $FREESURFER_HOME/subjects/PPG115
Thank you for the quick response. If you do a partial volume correction, I
would think the volumes from freesurfer would be less than simply counting all
voxels, but it seems to be the opposite. Any thoughts?
- Original Message -
From: Bruce Fischl
Date: Monday, February 15, 2010 10:4
it's not necssarily less, as voxels that are not labeled part of the
structure may contain some volume as well (e.g. ventricular voxels
containing some hippocampus)
On Mon, 15 Feb 2010, Hui J Yu wrote:
> Thank you for the quick response. If you do a partial volume correction, I
> would think t
Hi Bruce,
Here is the last part of the recon-all.log:
#...@# SubCort Seg Mon Feb 15 01:13:58 EST 2010
\n mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z
/Applications/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
\n
renormalizing sequences with structure al
Hi,
Sorry to resend this email, but I tried all the solutions listed on the
help page but they don't work. My graphics card is an Intel Mobile 4
Series Chipset Integrated Graphics Controller. How do I update the
drivers?
Jon
> have you tried updating your video drivers? Freeview doesn't curre
Hi Julie,
do you have write access to the file
aseg.auto_noCCseg.label_intensities.txt
in the subject's mri dir? Is there enough disk space free?
cheers
Bruce
On Mon, 15 Feb 2010, Julie McEntee
wrote:
> Hi Bruce,
>
> Here is the last part of the recon-all.log:
>
> #...@# SubCort Seg Mon Feb
Yes & Yes- over 100 GB
On 2/15/10 11:25 AM, "Bruce Fischl" wrote:
> Hi Julie,
>
> do you have write access to the file
>
> aseg.auto_noCCseg.label_intensities.txt
>
> in the subject's mri dir? Is there enough disk space free?
>
> cheers
> Bruce
>
> On Mon, 15 Feb 2010, Julie McEntee
> wro
Hi:
How can I get the volume of each lobe ?.. each hemisphere ?...
Sincerely,
Gonzalo Rojas Costa
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I wanted to avoid using recon-all because it generally takes so much
time, but from your message it sounds like it will only redo the tasks
that need redoing. Is that correct?
Thanks,
-Alessandro
On Sat, Feb 13, 2010 at 4:28 PM, Bruce Fischl
wrote:
> Hi Alessandro,
>
> usually that means that t
Hi:
There exist any tool that could show me the structures that differ between
each hemisphere more than a given percentage (volume) ?...
Sincerely,
Gonzalo Rojas Costa
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Hi:
There exist any tool that could show me the structures that differ between
each hemisphere more than a given percentage (volume) ?... For example: the
hippocampus...
Sincerely,
Gonzalo Rojas Costa
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yes, that's what -make all will do (it checks timestamps to see what needs
to be rerun)
On Mon, 15 Feb 2010, Alessandro D.
Gagliardi wrote:
I wanted to avoid using recon-all because it generally takes so much
time, but from your message it sounds like it will only redo the tasks
that need re
Hi, there,
I am using the rebuild_gca_atlas.csh to build our own subcortical atals now,
and met a problem at the second step which is
# Train using ONE_SUBJECT, the command line is:
mri_ca_train -prior_spacing 2 -node_spacing 8 -mask brain.mgz -parc_dir
seg_edited.mgz -xform talairach_man.xf
Hi Guang,
these are some checks we put in to catch common errors in the manual
segmentations. In this cause it means we found a Left_Caudate label on
the right side of the brain. Did you check any of those voxels to see
whether they were wrong? Or maybe your talairach is incorrect? If you
spec
Hi,
I'm completely new to FreeSurfer, and I'd like to get some guide to
surface-based inter-subject registration in analyzing some fMRI data.
I have an anatomical image (e.g. t1-spgr or mprage) and functional
images (e.g. epi) in NIFTI or ANALYZE format for each subject. In each
subject's native
1. Yes, recon-all is needed. We can read nifti and analyze, but please
avoid using analyze if you can as it doesn't keep track of the
direction cosines.
2. recon-all will run mris_register. You can run bbregister to register
your anatomicals to your functionals.
3. You an run mri_vol2surf to s
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