I've never heard of tlrc before. What is it?
doug
On 4/17/14 10:43 PM, charujing123 wrote:
Hi FS experts,
I have a ROI mask in tlrc coordinates in *.tlrc file format, which
represents functional activation. Also I have a significant area in
sig.mgh which represents cortical thickness
I was not able to replicate with subjects that I have. Does the same
thing happen if you use the subject as the target instead of using
fsaverage? If so, then upload the subject for me so I can replicate
doug
On 4/11/14 7:30 AM, Sabin Khadka wrote:
Hi all,
I am trying to extract
Dear Freesurfer experts,
I uploaded a .nii.gz file (which can be downloaded from
'http://gate.nmr.mgh.harvard.edu/filedrop2/?p=7pbsgklemux'). I hope you would
be willing to comment on the quality of this scan for use with Freesurfer (you
can find some parameters below; the scan was acquired on
Hi Jelmer
the scan looks quite nice to me. Have you run it through recon-all? That
is the best way to get an idea of how well it will work.
cheers
Bruce
On Fri, 18 Apr
2014, Kok, JG (neuro) wrote:
Dear Freesurfer experts,
I uploaded a .nii.gz file (which can be downloaded from
Hi Bruce,
Many thanks for your reply.
I did run it through recon-all and it seems to give nice results. Still, as I
am just a beginner using Freesurfer, I would greatly appreciate it when you
would have a look at the output which can be downloaded from
Hi doug
I am so sorry for i didnot describe my problem clearly.
tlrc is a Talairach coordinates, whose format is *+tlrc.HEAD and *+tlrc.BRIK.
This coordinate system is used in AFNI(Analysis of Functional MRI).
Thanks doug.
All the best.
Rujing Zha
2014-04-18
charujing123
发件人：Douglas Greve
Hi,
I am not a heavy Freesurfer user and I haven't had good luck figuring this out
through the FreeSurfer documentation and I thought an expert might have a fast
answer. If anyone has an easy solution it would be very much appreciated.
While I use FreeSurfer for automatic segmentation, I don't
We have had some last minute drop outs and there are now 2 spots available
in the upcoming Boston FreeSurfer course (May 5-7th). If you would like to
sign up for these spots, please register here:
https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.8263.cgi
Note that credit card cannot
On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote:
Hi FS community,
I had some questions regarding the mri_segstats command:
1) In the excludeid flag, are the ids the ones shown in the
FreeSurferColorLUT.txt?
Yes
2) In case I would like to measure the mean intensity of the orig file as
There is not a simple function, but you can look at our wiki page on
coordinate systems. There are some examples there on tranforming from
one coordinate to another
doug
On 4/18/14 2:40 PM, John Pyles wrote:
Hi,
I am not a heavy Freesurfer user and I haven't had good luck figuring
this
Hi Doug,
Thanks for the quick reply! In addition:
1) The average intensity measure in the above example does not include the
intensity of the skull, just everything inside, right?
2) Just to be clear on the purpose of including the segmentations in the
command line: The segmentations only
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The research assistant will be responsible for analysis of neuroimaging
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On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
Thanks for the quick reply! In addition:
1) The average intensity measure in the above example does not include the
intensity of the skull, just everything inside, right?
It includes all the structures that are segmented in
Dear experts,
I have a encountered an Error while doing skull-stripping using freesurfer on
my T1 weighted images, using mri_watershed
I am using the following command:
mri_watershed -atlas mprage_RPI.mgz mprage_skullstrip.mgz
and here is the error:
mri_watershed Error:
w=White Matter
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