Hi Aarthi,
first of all, sorry for the late reply; you caught me on vacation.
Would you mind trying the following: please unset your DYLD_LIBRARY_PATH
environment variable, and the run the hippocampal subfield module. You can do
that as follows:
In bash:
unset DYLD_LIBRARY_PATH
In (t)csh:
Dear colleagues,
I'm installing Freesurfer-Linux-CentOS4-stable-pub-v5.3.0 on Ubuntu 14.04
LTS (updated) and I managed to make tkmedit run correctly, but when I try
QDEC and Freeview I'm getting this message:
"qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open
shared object
On 9/21/15 9:15 PM, chenhf_uestc wrote:
Hi, Douglas
Thanks for your reply. I have two further questions here. First, I
know that
--grf is gaussian random fields for the volume (not surface). Could
the Monte Carlo simulation such as "--cache 4 neg" be used for
correction on volume? Because
Hello,
This is a known when running freesurfer on Ubuntu systems. The solution is
addressed in the FAQ section on the frresurfer download page:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
pecifically, the solution is to go into you system's lib directory and
create a symlink as
Dear All,
I am also waiting for this PVC correction. If you have/know an other
tool for the PVC, please do not hesitate to share.
Many thanks,
Bahri
On 21/09/15 13:30, Kok, JG (neuro) wrote:
Dear Freesurfer experts,
I would be very interested in using the PVC correction software for
PET
Dear Freesurfer experts,
I would be very interested in using the PVC correction software for PET images,
that will be available within Freesurfer version 6. Would you be able to
estimate a date for the release of the stable release of version 6 (I realize
this may be difficult)? Depending on
Hey Guys,
Sorry if this is a frequently asked question.
Do we have an updated ETA for version 6 of Freesurfer? We are planning on
upgrading our 1024-node cluster and version 6 is a big deal for us.
Best
Pedro Paulo Jr.
-
Pedro
Hi, Douglas
Thanks for your reply. I have two further questions here. First, I know that
--grf is gaussian random fields for the volume (not surface). Could the Monte
Carlo simulation such as "--cache 4 neg" be used for correction on volume?
Because the manual introduces this method for the
I've tried downloading the 6.0 beta from
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/freesurfer-Linux-centos6_x86_64-stable-v6-beta-20150724.tar.gz
but it keeps arriving corrupt. Any suggestions on how to proceed?
Thank you,
--
Chuck Theobald
System Administrator
The
Hi Experts,
I want to do tractography for the cortico spinal tract between two ROIs ( ROI1: precentral gyrus; ROI2: basal ganglia). I created the first ROI using mask form wmparc.mgz. How can I create mask for the basal ganglia ( there is no label for it). Do I need to segmenta the basal ganglia
Hi John
what parts of the basal ganglia do you want? We label
caudate/putamen/pallidum/accumbens separately. You can combine them all
together and get one ROI if you want. They should all be in the wmparc.mgz
cheers
Bruce
On Mon, 21 Sep 2015, John Anderson
wrote:
Hi Experts,
I want to do
Hello FS experts,I would like to understand the results from qdec in a GLM
model with Group (PT/HC), and two covariates (Age, gender).I set up my contrast
as follow:
Group DiffHC PT AgeHC AgePT SexHC SexPT 1 -10 0
0 0
Group x Age effectHC PT AgeHC
Hi all,
I have encountered some strange behavior with mri_deface.
I am working on defacing around 70 scans, and was using the mri_deface program
to do so. To start off with, I ran them using the version of mri_deface from
version 5.3, along with the .gca files included here:
--grf is gaussian random fields for the volume (not surface).
Re: --2spaces, your understanding is correct.
FDR: you can do it in matlab, something like
sig = MRIread('sig.mgh');
p = 10.^-abs(sig.vol)
pthresh = fast_fdrthresh(p,fdr);
ind = find(p < pthresh);
sig.vol(ind) = 0;
You can use the methods from my previous email to do FDR correction,
then load that into tksurfer
On 09/20/2015 10:55 PM, chenhf_uestc wrote:
> Dear Freesurfer experts,
> I use Oracle VM VirtualBox to run Freesurfer software and I want to
> perform FDR correction in TKSurfer. However, I cannot
Is there a file in that folder named something like "MRS_MASK"
On 09/19/2015 06:03 AM, std...@virgilio.it wrote:
> Hi listi,
>
> the following error now occur:
>
> --- matlab output
>
>
> < M A T L A B (R) >
>
> Copyright 1984-2014 The
Yes, it is addressing that question. The contrast should be the same as
your Group Diff below. Although I'm not sure you're using the proper
design. It looks like you are using Sex as a continuous covariate? That
is not correct. It should be discrete. So you should have 4 classes
(HC-M, HC-F,
Once you have covariates you need to decide what "percent difference"
means. Do you want to include the covariates? If so, then you'd use 1 0
0 0 and 0 1 0 0 (although see my warning in my previous email about
using gender as a continuous covariate).
On 09/19/2015 05:55 AM, pablo najt wrote:
>
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