Dear Bruce,
Thanks for your precious promt.
All the best.
2013-11-22
Rujing Zha
发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu
发送时间：2013-11-21 22:42
主题：Re: [Freesurfer] recon-all Process Flow
收件人：Rujing Zhacharujing...@163.com
抄送：freesurferfreesurfer@nmr.mgh.harvard.edu
Hi Rujing
sure, you
Dear FreeSurfers,
Is it possible to compare left and right cortical thickness patterns,
vertex-wise?
Thanks
Heidi
Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Maybe do an interhemispheric comparison?
On Fri, November 22, 2013 8:24 am, Jacobs H (NP) wrote:
Dear FreeSurfers,
Is it possible to compare left and right cortical thickness patterns,
vertex-wise?
Thanks
Heidi
Dr. Heidi Jacobs
Postdoc
Hi Doug,
Thanks for your reply. I have the problem even if I use MRIread and MRIwrite.
But I have done a little more digging following your suggestions. Basically,
there are differences in the output of mri_vol2surf (that I should have spotted
earlier), as well as differences in the header
Dear Experts,
When re-running the complete recon-all stream after numeral manual edits
almost all the files in the mri folder are overwritten (apart from the
brain.finalsurfs.manedit.mgz,
brainmask.gcuts.mgz and mdi_nu_correct.mni.log.bak). The control points and
the changes of the brainmask are
Hi Rongxiang,
looks good. You seemed to need a lot of different types of edits though,
usually you don't really need to edit much.
Surfaces in the base should be as accurate as possible, so you should
fix topological defects there.
Best, Martin
On 11/14/2013 11:24 PM, Rongxiang Tang wrote:
Hi Knut,
yes you can. Make sure that you create all base (subject templates) and
long runs with 5.3 and don't mix that with 5.1.
Best, Martin
On 11/19/2013 09:19 AM, Knut J Bjuland wrote:
Hi,
we have finished cross sectional scanworkups in Freesurfer 5.1 and
gone through qa. Can we use
Hi freesurfers,
Anyone know what the scale bar in TkSurfer represents? From past threads I
gathered that it represent 1 cm on the human brain. However, the size of
the bar displayed gets smaller as I scale the brain up which does not make
sense if the bar is supposed to represent a constant
I think it is 1cm. I noticed that it gets smaller on the first zoom, but
then it gets bigger after that. When I zoom in 3 or 4 times, I can
measure the distance from end to end by looking at the xyz of the
vertices at the ends, and it comes out to 10mm
doug
On 11/22/2013 12:10 PM, Cesar
Hi Cesar
what do you mean by scale the brain up?
Bruce
On Fri, 22 Nov 2013, Cesar
Echavarria wrote:
Hi freesurfers,
Anyone know what the scale bar in TkSurfer represents? From past threads I
gathered that it represent 1 cm on the human brain. However, the size of the
bar displayed gets
I meant zoom in on the brain. I guess I'll take Doug's approach and
estimate the scale of the bar with the xyz coordinates.
Cesar
On Fri, Nov 22, 2013 at 12:16 PM, Bruce Fischl
fis...@nmr.mgh.harvard.eduwrote:
Hi Cesar
what do you mean by scale the brain up?
Bruce
On Fri, 22 Nov 2013,
Actually, Doug can you tell me how to get the xyz coordinates on Tksurfer
so I can figure out the length of the bar as you did?
Thanks
Cesar
On Fri, Nov 22, 2013 at 12:19 PM, Cesar Echavarria
cechavarri...@gmail.comwrote:
I meant zoom in on the brain. I guess I'll take Doug's approach and
Just click on a point and look at the vertex RAS. At zoom=1, you have to
translate the surface over to the scale bar. At zoom=1 I got about 10mm,
but it did seem to change when I zoomed in.
doug
On 11/22/2013 12:23 PM, Cesar Echavarria wrote:
Actually, Doug can you tell me how to get the
Hi All-
We have a longitudinal study that is ongoing and we have already processed most
of our scans to date with Freesurfer 5.1. We would like to upgrade our software
to 5.3. Is there a way to bring the already reconstructed scans forward to
Freesurfer 5.3 without starting over from scratch?
Hi all,
I can't find any explanation of how to perform an affine registration with
mdi_robust_register. Could someone please explain?
Thanks,
Nathaniel
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mri_robust_register --help
You would need to use the --affine flag.
Lilla
On Fri, 22 Nov 2013, Nathaniel Reynolds wrote:
Hi all,
I can't find any explanation of how to perform an affine registration with
mdi_robust_register. Could someone please explain?
Thanks,
Nathaniel
Hi
You should do cat -n
$RAW_DATA/Bled_Jean_Jacques/TENSEUR_50_directions_ASSET_10/20121113_141004COMA201210s010a1001.bvec
and cat -n set bvalfile =
$RAW_DATA/Bled_Jean_Jacques/TENSEUR_50_directions_ASSET_10/20121113_141004COMA201210s010a1001.bval
to look for empty lines. Trac-all -prep -c
Hi again,
Does anybody know about a function called mri_mi?
I have someone else's script that seems to utilize it, but I can't seem to
access it myself.
Thanks,
Nathaniel
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It is not checked in as of now to the FS distribution. I can send it to
you.
On Fri, 22 Nov 2013, Nathaniel Reynolds wrote:
Hi again,
Does anybody know about a function called mri_mi?
I have someone else's script that seems to utilize it, but I can't seem to
access it myself.
Thanks,
Hi Freesurfers,
I am working with fsfast, and interested in doing a 2nd-level fixed effects
analysis over a number of subjects. However, the volumes I'm using aren't in a
standard freesurfer space (native, talraich, etc.). They are nx1x1 volumes
containing results from n ROIs. While I got
Dear FreeSurfer group/Dr. Reuter,
My questions are in regards to the LONG stream.
My version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
1) Error message
During the creation of the BASE, I get the following error in the beginning of
the recon:
WARNING: Image geometries differ across
Dear FreeSurfer group/Dr. Reuter,
My questions are in regards to the LONG stream.
My version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
1) Error message
During the creation of the BASE, I get the following error in the beginning of
the recon:
WARNING: Image geometries differ across
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