Dear Ruopeng,
I didn't install it myself, but I guess it is a stable one. Are you suggesting
the timecourse option might simply not be available in the stable version?
thanks
fabio
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I don't understand what you are trying to do. Can you elaborate? There
is no way to make optseq produce a sequence where two events always
occur in a certain order
On 6/20/14 4:27 AM, charujing123 wrote:
Hi FS experts,
I try to design the schedule by optseq2. However it is beyond my
abili
Dear All,
when I run recon-all I encounter errro saying that
rh.average.curvature.filled.buckner40.tif file is missing. I found this
file missing in my average folder so if someone can send it as an
attachment or guide me to where I can find it it will be great help.
Many thanks in advance
Venka
Hi All,
I am getting the the following error when I run recon-all -subjid E368
-autorecon1
ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
Here is what talairach_avi.log says
/home/administrator/Desktop/freesurfer/subjects_dir/E368/mri
/usr/local/freesurfer/bin/talairach_avi
--i orig
Hi doug,
Thanks doug.
In our experiment, there are 324s, and TR=2s, two kinds of stimulus. Each one
consisted of 3 components(cue 500ms + fixation 500ms + picture 500ms), and will
be presented with a interval of 1.5s. After stimulus onset, followed by
reaction time. One stimulus will repeat 41
I don't think there is anything wrong with what you have. Is there a
problem? You could shorten it to something like 240sec or so.
On 6/20/14 1:43 PM, charujing123 wrote:
Hi doug,
Th?anks doug.
In our experiment, there are 324s, and TR=2s, two kinds of stimulus.
Each one consisted of 3 com
That is correct. timecourse option is only available in dev version. You can
download it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
You may want to make a backup of your current freeview.bin file.
Ruopeng
On Jun 20, 2014, at 3:25 AM, Bernardoni, Fabio
wrote:
> Dear Ruopeng,
>
Dear Bruce
No, I used QDEC to create label. It should be fsaverage.
Wang Kangcheng
Faculty of Psychology, Southwest University, China
Email: kangchengwang0...@gmail.com / wangkangcheng@163.com
Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China
在 2014年6月19日，下午10:00
We do not have a way to resolve the overlapping problem. That is
something you will have to figure out. You should be able to keep the
colors the same by specifying the entries in the color table
doug
On 6/19/14 3:41 PM, Karen Marie Sandø Ambrosen wrote:
> Dear Freesurfer experts,
>
> I have m
Freesurfer,
We recently gained access to a new GE Discovery MR750w 3.0T GEM
MRI with a 24 channel headcoil. Because this system is located at a nearby
hospital and is used clinically, we do not have a research agreement with GE in
place and, therefore, cannot edit the default pu
On 6/20/14 4:14 PM, charujing123 wrote:
Hi doug,
Thanks doug.
Here are two questions that I am not sure:
1, Each stimulus condition has three elements, i.e. cue fixation and
picture. However it is only picture element that will be analyzed. The
time window of picture will not influence the eff
Hi doug,
Thanks doug.
Here are two questions that I am not sure:
1, Each stimulus condition has three elements, i.e. cue fixation and picture.
However it is only picture element that will be analyzed. The time window of
picture will not influence the efficiency of sequence?
2, After stimulus pres
yes, that's a lovely idea, but it is very, very difficult to get NIH
funding to support such a thing.
cheers
Bruce
On Fri, 20 Jun 2014, Yang, Daniel wrote:
That is great to know!
I personally feel that there should be some sort of autoupdate function or
patch file list in FreeSurfer so that w
weird? I'll need something more specific than that
On 6/20/14 4:57 PM, charujing123 wrote:
Hi doug
Thanks very much. I see. When I add --tnullmin 2 --tnullmax 8, result
looks weird.
===
[psylab16@centos1 ~]$ cat ex1-001.par
0.22.000 1.
[sorry, I may have sent this multiple times, but, because I'm not sure if
it got through because I got several "bounce-back" error messages, I'm
sending it out again...]
Thanks, Doug. I think I've kind of sorted that one out by creating a folder
called "Retinotopy" under freesurfer/subjects/Retino
Sorry, I don't know why it is failing. We don't have a problem with it
and no one else has reported this. Check the location of the FSLDIR env
variable. Or maybe it is a new version of FSL that is not compatible
with the old?
On 6/20/14 5:25 PM, Alan Lee wrote:
[sorry, I may have sent
Thanks Doug. After using stage#1 of the longitudinal 2-stage model to
create cross-sectional measuers of e.g. thickness change from tp1 to tp2
(e.g. thickness-pc1), I then did analyses in QDEC on these measures to see
where in the brain such changes are
- different from zero (within each group)
Hi there,
I am trying to run a monte carlo correction on my average subject, using the
full mri-mcsim run with 1 iterations (and about 200 participants). This is
taking a long time, and the cluster I have access to has a limit of 72 hours
which isn't long enough to finish processing. Is the
Hi Freesurfer List,
Do folks have any recommendations on reducing the amount of space used by
each subject? I looked a bit in the list archives but didn't see any recent
tips.
I had a large potential sample size (n=~750) and didn't know if I would
have the estimated 375GBs processing would requir
Thomas,
Thank you so much for this input. I tried out both the striatum and the
general MNI152 template. For the striatum the match is *SO* much better.
The MNI152 template also looks alright - though it's a little fuzzy.
I'm pretty happy with this now and I'll definitely have more confidence in
the sequences specified by adni are a good resource:
http://www.adni-info.org/scientists/MRIProtocols.aspx
they’re known to work with freesurfer.
N.
On Jun 20, 2014, at 10:13 AM, Sherwood, Matt wrote:
> Freesurfer,
> We recently gained access to a new GE Discovery MR750w 3.0T
Hi,
I was wondering if you happened to know why the origin of the rawavg.mgz
image is slightly different than the origin of my original structural image
that I "recon"ed to obtain processed FreeSurfer data. Am I doing something
wrong or is this expected? Is there an image that FreeSurfer creates t
Hi Shazia
did you only have one input image or did you have two to motion correct
and average? If only one, I thought they were exactly the same. Why do you
think they are different?
Bruce
On Fri, 20 Jun 2014, Shazia Dharssi wrote:
> Hi,
> I was wondering if you happened to know why the origi
Dear list,
Does the OS version, hardware or MatLab version (i.e., 2013a vs. 2014a) impacts
in the results from the LME processing (Bernal-Rusiel et al.), employed after
the Freesurfer 5.1/5.3 longitudinal pipeline?
Regards,
Pedro Rosa.
___
Freesurfer m
Dear All,
I am sorry to post this again. Any help will be greatly appreciated. I am
struck as I am unable to run the recon-all step.
Thanks
Venkat
-- Forwarded message --
From: Venkateswaran Rajagopalan
Date: Fri, Jun 20, 2014 at 5:14 PM
Subject: mpr2mni305 failed, see transform
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