Hi,
>From https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
"SubCortGray - includes thalamus, caudate, hippocampus, amygdala, accumbens,
ventral DC, substancia nigra (if there). This is a simple voxel count of
structures identified as subcortical GM."
Could you please let me know if "
See if the talairach.lta is any better, eg
cd subject/mri/transforms
tkregister --mov ../nu.mgz --s fsaverage --reg talairach.lta
If so, you can try running make_average_subject with --xform talairach.lta
I've never done this, but it might work :)
On 03/15/2018 01:02 PM, Francesca Strappini
Hello fellow neuroimagers!
The Laboratory for Child Brain Development at the University of Pittsburgh
is looking for a postdoctoral fellow starting this summer or fall. The LCBD
employs multimodal neuroimaging to study child affective development from
infancy to middle childhood. Please see the at
Thank you, Doug!
One monkey has a pretty decent registration while the other one does not
even appear in the window when I try to manually check the registration
with this command line:
tkregister --mgz --s MonkeyCelia --fstal --surf orig
It looks like if there is no brain.
2018-03-15 16:57 GMT+01
I uploaded the datasets to the ftp site, does anyone have further advice
regarding this issue?
Both datasets are for the same subject for a longitudinal concussion study
and fail for different reasons.
matt1 - has "ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 errors" and fails
with "CORRECTING DEF
Dear Kersten,
Thanks a lot, it's really help. I have another question, after I got
results that two group have significant, then how could I get direction?
Thanks,
Lanbo
On Tue, Mar 13, 2018 at 5:40 PM, Diers, Kersten /DZNE wrote:
> Hello,
>
> On Di, 2018-03-13 at 21:48 +0100, lanbo Wang wrote
It sounds like you want to convert your label into a binary mask to use
with mri_fdr. Use mri_label2label, something like
mri_label2label --srclabel your.label --s subject --hemi lh --outmask
your.label.nii.gz
Run with --help to get more info
On 03/14/2018 10:41 PM, Chen Jen-I. wrote:
> This
Check the talairach.xfm registration. It is probably way off. It does
not have to be perfect (esp since they are different species), but the
two subjects should have a similar registration
On 03/14/2018 07:27 PM, Francesca Strappini wrote:
> Both average hemispheres look very bad, they don't ev
Register day 1 to one of the anatomicals with bbregister, call output
day1.lta
Register day 1 to the same anatomical with bbregister, call output day2.lta
mri_concatenate_lta -invert1 day1.ltaday2.lta day2-to-day1.lta
Check:
tkregisterfv --mov day2.nii --targ day1.nii --reg day2-to-day1.lta
A
Hi Freesurfer team & Doug,
Just thought I'd check back in as you had asked! Any thoughts on censoring
resting state volumes for fcseedcorr?
Thanks,
Adam
On Thu, Feb 15, 2018 at 12:57 PM, Douglas N Greve wrote:
> Currently there is no way to do this. But it might not be hard to add.
> If I don'
The command below appears to have run successfully but I get a note that the
'volumesAmygdla.txt' file could not be moved. See message below at the end of
the freesurfer run. I am using 6.0 (Jan. 18, 2017 release).
Is this expected? Jim
--
Hi Neda,
That’s unusual - can you send the output of sourcing the file in a debug shell:
sh -x
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
You’ll probably have to ctrl-c to stop this as well. After running it, can you
also send the ouput of:
env | so
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