Hi Dillan - Thank you for your support!
Because the maximum value can sometimes be an outlier, we use the values
of the 99th percentile instead. In the absence of an outlier this would be
very close to the maximum.
Best,
a.y
On Tue, 26 Jul 2016, Newbold, Dillan wrote:
Hi everyone,
I’m h
Hi Barbara - Your hack sounds like the right idea. One option would be to
switch the FA values between the pathstats.byvoxel.txt files in the lh.*
and rh.* output directories, by editing the text files without renaming
the directories.
Hope this helps,
a.y
On Mon, 25 Jul 2016, Barbara Kreilk
Hi Barbara - We're working on a new atlas for TRACULA that will include
the fornix. We've already done the manual labeling for it.
Best,
a.y
On Mon, 25 Jul 2016, Barbara Kreilkamp wrote:
> Dear Anastasia,
>
> As we are analyzing DTI data acquired in patients with epilepsy we are
> especially
Hi Michael - Which build of freesurfer do you use? I can send you the new
version of dmri_paths so you can try it out.
Best,
a.y
On Wed, 20 Jul 2016, Harms, Michael wrote:
Hi Anastasia,
I was wondering what the resolution to this thread was:
http://www.mail-archive.com/freesurfer%40nmr.m
Hi Derek - Good to know things worked out!
a.y
On Tue, 19 Jul 2016, Derek Pisner wrote:
> Hi Anastasia,
>
> I thought I should let you know that this issue has now been resolved. We
> specified the base ID's/ subject ID's incorrectly in the config file! Sorry
> for the confusion. Now our grou
Hi Anri - The problem is in this line:
set cmd = ($cmd --ref $cvstempdir/$cvstemp)
It should be changed to this:
set cmd = ($cmd --ref $cvstempdir/$cvstemp/mri/norm.mgz)
For this to take effect, you need to run "which trac-all" and make the
change in the trac-all fi
Hi Knut Jørgen - Do you get this error only with the dev version of
freesurfer? The command line causing the error is:
bbregister --s 4_test --init-fsl --dti --mov
/home/knutjbj/subjects/4_test/dmri/dwi.nii.gz --reg
/home/knutjbj/subjects/4_test/dmri/xfms/anatorig2diff.bbr.dat --fslmat
/hom
It need to run some additional tests, but I'm almost sure it is solved. The
fixed code will be in the development version very soon, with some other
updates. Stay tuned!
Cheers,
Eugenio
Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
h
Dear All,
I am looking to hire a postdoc with either strong machine learning
background OR system neuroscience background. Prior experience with
fMRI is a plus.
Topics are flexible. Example topics include individual-subject brain
parcellations, relationships between behavior and brain networks,
d
sure, you can do that with mri_vol2surf. Basically the initial surface
and the final (inflated) surface have the same number of vertices, so the
vertex identity is preserved and mri_vol2surf samples values from the
volume onto the surface which can then be displayed on any surface
configuration
Hello,
I was trying the new segmentation module of hippocampal subfields, but I also
encountered the same errors as Pierre reported a week ago:
--
Invalid MEX-file
'/tmp/MCR_103136811
Hi Bruce,
Thanks to your advice, I was able to obtain the surface of the segmented
brain area and its inflated surface using FreeSurfer.
The generated surface however does not contain any texture, which is needed
for further steps in my project.
I am considering to project the texture of the seg
thanks, Doug!
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Mon, Jul 25, 2016 at 11:57 PM, Douglas Greve
wrote:
> We are working pretty hard to get it out but we are still reluctant to set
> a hard date. I think we'll have a beta version in two weeks, bu
Hi,
Yes my original data has 1x1x1mm voxel dimension but I prefer to work with
the upsampled data. I am satisfied with the results I get from Freesurfer
and the results actually look better than the results I get with the 1mm
data, the only problem I have is that the thalamus mask does not keep the
Hi,
Bumping this up for AY.
We have a bunch of jobs we want to send to our cluster, and we are wondering if we need a revised version of dmri_paths to properly handle single time points in the TRACULA longitudinal stream.
thanks,
-MH
--
Michael Harms, Ph.D.
sorry, I'm confused about what you are trying to do. Can you start from the
beginning and explain? If the data you have is 1mm but upsampled by
the scanner there is really nothing to be gained by processing the
upsampled data and it will waste lots of time
cheers
Bruce
On Mon, 25 Jul 2016,
D
Hi everyone,
I’m having a little trouble understanding the exact meaning of the 20% default
threshold used in the freeview -tv option and dmri_pathstats --pthr. I’ve seen
multiple threads where Anastasia said that it is 20% of the maximum value in
the probability distribution—which corresponds
Here's my design matrix
1.000 0.000 -0.960 0.000 -0.170 0.000 1.860 0.000 1.970
0.000 2.010 0.000 2.140 0.000;
1.000 0.000 0.170 0.000 0.290 0.000 -0.560 0.000 -0.400
0.000 0.110 0.000 -0.260 0.000;
1.000 0.000 -0.050 0.000 0.750 0.000 -0.700
I added normalizing and demeaning code like you suggested in my fsgd file
and perform the GLM analysis (mri_glmfit). However, my covariates were only
demeaned (DeMeanFlag 1) but they were not normalized (ReScaleFlag 1). Hence
I received this error from freesurfer. I have attached my fsgd files and
what do you mean it did not work? can you be more specific?
On 07/26/2016 12:21 PM, miracle ozzoude wrote:
> Hello Doug,
> The ReScaleFlag 1 command did not work. Only the demean command.
> Paul
>
>
> On Mon, Jul 25, 2016 at 6:17 PM, Douglas Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
Does this wiki page help?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 07/25/2016 04:22 PM, Dorsa Haji Ghaffari wrote:
> Yes I created it using the higher resolution and I think it looks
> fine. I attached the aseg.mgz. Is there any way to create the thalamus
> mask with the
Hello Doug,
The ReScaleFlag 1 command did not work. Only the demean command.
Paul
On Mon, Jul 25, 2016 at 6:17 PM, Douglas Greve
wrote:
> Actually, I checked the code and found that I had already put a flag in
> there to do this (I'm so clever). Add
>
> ReScaleFlag 1
>
> in addition to
>
> DeMe
Can you resend the design matrix?
On 07/26/2016 11:46 AM, miracle ozzoude wrote:
> Hello Doug,
> Sure. Here are my new fsgd file and new contrast matrix ( matrix is
> the same as the old one).
> Best,
> Paul
> GroupDescriptorFile 1
> Title MOT
> Class Group1
> Class Group2
> Variables Age Educat
Hello Doug,
Sure. Here are my new fsgd file and new contrast matrix ( matrix is the
same as the old one).
Best,
Paul
GroupDescriptorFile 1
Title MOT
Class Group1
Class Group2
Variables Age Education Firstscore Secondscore Thirdscore Averagescore
Input 01053p/fsdir Group1 -0.96 -0.17 1.86 1.97 2.01
The -log10(p) is signed by the sign of the contrast, so to get back to
the p value you must compute 10^-abs(sig).
On 7/26/16 10:42 AM, Caroline Beelen wrote:
Dear FS team,
I tried to run GLM-analysis using aparc stats files. At first I
created these files for a few subjects of interest (e.g
Dear FS team,
I tried to run GLM-analysis using aparc stats files. At first I created these
files for a few subjects of interest (e.g. aparc_rh_thickness_stats.txt) and
checked whether they looked ok, which they did (values were pretty similar).
Then I used the following command (for example):
Dear FS team,
I tried to run GLM-analysis using aparc stats files. At first I created these
files for a few subjects of interest (e.g. aparc_rh_thickness_stats.txt) and
checked whether they looked ok, which they did (values were pretty similar).
Then I used the following command (for example):
Dear Douglas,
Thank you for your input. Additional background information to answer your
question (why not register the anatomical to the DTI):
Freesurfer segmentation was done in a previous project and used the native
space T1 scans. For this DTI project, I would like to use the Freesurfer
se
Hi Bruce,
thanks. Keep up the fantastic work!
Best,
Falk
-Ursprüngliche Nachricht-
Von: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Gesendet: Donnerstag, 21. Juli 2016 16:44
An: Falk Lüsebrink
Cc: Freesurfer support list
Betreff: Re: AW: AW: AW: [Freesurfer] mri_ca_label with high
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