Hi Freesurfers,
I am new to this software and i am trying to learn how to use it.
I have two questions:
1) if I do recon-all on a group of 20 subject, and I am primarily
interested in a few regions (In my case - amygdala, insula and anterior
cingulate cortex), do I have to edit all the datasets
Looks like you don't have
> /home/virtualuser/freesurfer/subjects/lh.EC_average
You will need to download it
Cheers
Bruce
On Dec 20, 2012, at 12:32 AM, Linda Zhang wrote:
> Hi Bruce,
>
> This is what I get:
>
> FreeSurfer:~/freesurfer/lindadata> ls -l
> drwxr-sr-x 42 virtualuser virtualuser
Thanks Bruce, from where? Should I download the other directories I seem to
be missing as well?
On 20 Dec 2012 21:26, "Bruce Fischl" wrote:
> Looks like you don't have
>
> /home/virtualuser/freesurfer/subjects/lh.EC_average
>
>
> You will need to download it
> Cheers
> Bruce
>
> On Dec 20, 2012,
Hi Jenny
1) yes, they are usually fine, but you *always* should look at the regions you
are hoping to make biological statements about.
2) mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.rawavg.nii
Wold convert the aseg. Not that they are already in the original RAS space,
just a differen
Which other ones? Grab a whole new distribution, unpack it somewhere and either
use it or move the dirs you need where you want them. Or wait a few weeks for
5.2
Bruce
On Dec 20, 2012, at 8:29 AM, Linda Zhang wrote:
> Thanks Bruce, from where? Should I download the other directories I seem to
Hi Gabriel
Colin27 I believe has been reconned, and if not you can just run it and use our
standard tools for mapping. The others you can use the talairach.xfm for, but
it won't be terribly accurate. You can't use our training and labeling unless
you have the original datasets that went into the
Hi Mojdeh
Have you checked out Koen van Leemput's hippocampal fled segmentation that you
can run through recon-all? It might do what you want automatically.
Cheers
Bruce
On Dec 19, 2012, at 4:07 PM, Mojdeh Zamyadi wrote:
> Hi there,
>
> Sorry, if my question is confusing. This is what I want
Hi Greg
What version are you using and what acquisition? There are some expert options
you could try like editing one volume and using it as an example for all
further intensity estimations
Cheers
Bruce
On Dec 18, 2012, at 5:40 PM, Gregory Kirk wrote:
>
> Hi,
>
> tried to use control poin
> Dear FreeSurfer group
> I am new to free surfer and have dificulties running fs-fast analysis for
> the first time
> I use freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on ubuntu but ran
> the same commands for the same data on a NMR computer (nmr-stable5.0-env)
> which gave the same error
>
Hello,
I would like to download and install the software described at
http://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping
Your email address is listed on this website.
I cannot find a download link.
We would like to use this with Freesurfer.
Do you know where I can download this softwa
Is it not included in your freesurfer installation?
To check:
After sourcing Freesurfer type
which grad_unwarp
HTH
Dan
On Thu, Dec 20, 2012 at 9:42 AM, John Drozd wrote:
> Hello,
>
> I would like to download and install the software described at
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/Gra
Hi-
Our Unix system was recently updated and I am now unable to use SPM 8 from
/autofs/space/grover_001 or from /autofs/space/bert_002. I get the following
message:
Initialising SPM...Error using fileparts
Too many output arguments.
Error in cfg_util>local_initapps (line 1217)
[p n e v] =
Hi Yuval,
while I have no real clue about your specific issues, it reminds e of an issue
we had in the past. We had used some condition names that start with a number
instead of a letter (e.g. "90degree") and the parsing code choked on that, as
it uses the first character of a field and tries t
Thanks Dan.
It is already installed with Freesurfer as you say:
[jdrozd@trumpet bin]$ pwd
/trumpet/downloads/FreeSurfer/freesurfer/bin
[jdrozd@trumpet bin]$ ./grad_unwarp
USAGE: grad_unwarp
-i infile : dcmdir or dcmfile or mghfile
-s seriesno : dicom series - needed only if invoking -i
Hi Doug,
I am trying to run a Monte Carlo simulation on functional data constrained to a
label. Looking at a previous post -
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-November/016290.html
- I see that your advice is to 1) constrain when running mri_glmfit, then 2)
use mri_glm
Hi Bryon - I was able to reconstruct the forceps major in your subject
after tweaking some of the 7 control points for the initialization. I'm
attaching the text file with the corrected control points - just drop it
in dlabel/diff and rerun the path reconstruction (don't use reinit,
though!)
Hi Arman - I changed one of your 5 controls points for the forceps major
to make sure that the initial path is well within the white matter,
following the approach I described to Bryon in my previous email. I'm
attaching the edited text file, please save it in the dlabel/diff/
directory of yo
Hi Prerona - As I've mentioned to others, you can ignore the "Degenerate
spline segment" message.
I can't tell what you mean by "only traced a part of the trac". Can you
see the rest of it when you play with the threshold? Are you
reconstructing only the ILF? If not, do the other pathways lo
Hi Prerona - I think this is explained in the archives on the same thread
as the bedpostx upgrade issue. If you run bedpostx outside of trac-all,
you should create dmri/data.nii.gz as a symbolic link to dmri/dwi.nii.gz
and dmri/nodif_brain_mask.nii.gz as a symbolic link to whichever brain
mas
Hi Yaniv - What results did you anticipate and what results did you get?
a.y
On Thu, 20 Dec 2012, Yaniv Kaufman wrote:
> Dear Freesurfers,
>
> I am not very experienced with Freesurfer and would like to construct a
> Diffusion Tensor Image. I have the .bvecs, .bvals and .img files which I
> b
Hi Ping - The total number of paths that were sampled doesn't enter the
picture. Of these sampled paths, some get rejected and some get accepted.
The latter are added up to get an estimate of the posterior probability
distribution of the path (that's path.pd.nii.gz). You can normalize to a
tot
Hi Maia - It would still be probabilistic global tracrography, you'd just
run it without anatomical priors since you don't have any prior knowledge
of what areas your pathway goes through.
For each subject you'd need to define the two end ROIs of the pathway and
(this is the trickier part) an
Hi everyone,
does anyone on the FS mailing list have any good recommendations for
litterature on anorexia nervosa / eating disorders / starvation and brain
morphometry ?
I am especially interested in any study using FreeSurfer software.
Thank you very much in advance,
- Jenny Mercolini
___
Thank you for correcting this. This in fact works. Alternatively after
re-running the pipeline with reinit=1 for so many times, as it tried
different initialization each time I managed to get the tract.
All the best,
-Arman
On Fri, Dec 21, 2012 at 12:56 AM, Anastasia Yendiki <
ayend...@nmr.mgh.h
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