I'm actually curious about this as well!
Best,
Panos
> Hi Doug, still wondering about this - thanks!
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara
> Johanna [smakar...@mgh.harvard.
Dear all,
mri_cc does not seem to be working properly to parcellate corpus callosum.
As per one of the previous posts, there is a bug in the current release of
mri_cc. However, the link provided in the same thread for an updated
version of mri_cc is no longer existent. Our cluster runs on 64bit Ub
Thanks Doug, this worked. Misconfigured my nuisance regressor seeds. Matrix
still has 47 columns, but it seems to be appropriately designed.
Best,
Jared
Message: 2
Date: Thu, 26 May 2016 12:14:27 -0400
From: Douglas N Greve
Subject: Re: [Freesurfer] Connectivity design ill-conditioned
To:
Hi all,
I created a custom template using a few subjects and have two tif. files
for lh and rh.
I am trying to create a cortical/surface atlas from scratch. My
understanding is that I must use mris_ca_train.
mris_ca_train [options] [subject2
...]
the canonsurf is mentioned to be lh,sphere,
Hello All,
I am currently using Freesurfer version 5.1 and when I run the recon-all
command I get the following warning message: Use of ?PATTERN? without
explicit operator is deprecated at
/usr/local/freesurfer/mni/bin/sharpen_volume line 153. Recon-all continues
to run and finishes completely wit
That it is a warning and can be ignored.
-Zeke
On 05/27/2016 12:27 PM, Tamara Tavares wrote:
> Hello All,
>
> I am currently using Freesurfer version 5.1 and when I run the recon-all
> command I get the following warning message: Use of ?PATTERN? without
> explicit operator is deprecated at
> /us
Hi all,
As a process a subject through recon-all I get the brainmask.mgz, norm.mgz
too bright. the white matter turns out to be 150 or higher.
instead of normalization and normalization2 I tried to do mri_normalize
-gentle which helps a bit but when I run autorecon2-wm it just makes it
very brigh
Hello,
I would like to extract white matter volume from both anterior and posterior
limb of the internal capsule, but the wmparc lists these regions as
‘unsegmented white matter’. They appear in the ColorTableLUT as regions
155-158, but do not actually appear in any of the outputted parcellatio
Hello FS experts,
I am running a command "fcseed-sess -s S01 -cfg abc.config" to get *.dat
file for further analysis. I used the same steps to calculate FC for 40
subjects, all steps run fine with 38 subjects but for 2 subjects I am
getting an error: Segmentation fault: Core dumped.
I checked the
Hello Anastasia,
sorry for few information and let me tell you command and error log.
Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
Error log: Loading output reference volume from
/Applications/freesurfer/subjects/cvs_avg35
corRead(): can't open file
/Applications/f
Hi, Doug:
Right now, I got the result that I excepted for FS and SurfStat, still a small
question for FS:
I just got one hemisphere for my result,
with ' --2spaces'
/cluster_wise_correction_for_multiple_comparisons.sh: line 26: --2spaces:
command not found
with '--bonferroni 2'
./cluster_wise_cor
Hi Douglas,
Can I ask another question relating to an issue I ran into already a year ago?
My lGI data were very smooth at the time (after smoothing for 10mm). I decided
to use the unsmoothed data, since the fwmh is in the order of 10 then
(according to the fwhm.dat file). My results are valid
Hi Marja
what ROI do you mean? We generate lots of them, and tabulate the
thickness within each one. Look for example in id>/stats/aparc.stats
cheers
Bruce
On Fri, 27 May 2016, Marja Caverlé wrote:
Hi all,
So I ran a recon-all -all on one of my subjects, and it completed without
errors (acc
Hm. It either doesn't recognize the --no-y flag (no matter at which position)
or it doesn't recognize the --mczsim flag.
- Ursprüngliche Mail -
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 26. Mai 2016 18:58:39
Betreff: Re: [Freesurfer] glmdir question
Dear FreeSurfer experts,
I would like to correlate my thickness data with behavioral measures. Can I do
that with glmfit? If so, could you explain how to specify the contrast for that?
My fsgd file looks like this:
GroupDescriptorFile 1
Class 1male plus blue
Class 1female plus red
Class 2male
Hi Bruce,
Thanks, that indeed includes most of the roi's I want to include. What if
there are some area's that are not in that list? Is there a way of adding
areas?
Best,
Marja
On Fri, May 27, 2016 at 10:26 PM, Bruce Fischl
wrote:
> Hi Marja
>
> what ROI do you mean? We generate lots of them,
it depends what they are. You can look in the other stats files to see if
they are there (we include a couple of cortical parcellations). If they
aren't, you can draw them yourself on fsaverage and map them to all your
subjects using our spherical transform
cheers
Bruce
On Fri, 27 May 2016, Ma
Hi Bruce,
Thanks for the fast response! I indeed found them in other stats files.
What is the difference between these files? I assume they are based on
different atlases? I saw that there are some slight differences between the
numbers in different files for the same structures, so how do I know
yes, they are based on different atlases. You can look at the original
papers (Rahul Desikan's is one and Christophe Destriuex's is the other)
to see the differences. Or you can load the various .annot files in
freeview on the inflated surface to see them visually
cheers
Bruce
On Fri, 27 May 2
Hi Anri - I do not know what command line you ran and what your
configuration file looks like, so it is very hard for me to suggest
solutions.
Best,
a.y
On Fri, 27 May 2016, Anri WATANABE wrote:
Hi Anastasia,
Thank you for your answer.
There aren't stats/*.path.mean.txt files and terminal
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