Hi Barbara and FS-community,
I tried everything you suggested, but unfortunately the same error still
occurs. Have you found a solution yet?
Thanks for your help
Best regards,
Robby
Robby De Pauw, drs.
Ghent University
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan
Dear Bruce,
thank you very much for the quick reply. The aim of our study is to investigate
the correspondence of cortical thickness and measures of functional
connectivity (e.g. from ICA) on a vertex-based within-subject level. However,
we are not sure how to implement this in freesurfer,
Deal all
I have some problem with my fsaverage folder.
can i re-download this folder??
or do I need to download the whole freesurfer package again?
my freesurfer version is '
freesurfer-i386-apple-darwin11.4.2-stable5-20130514'.
Thank you.
Sincerely Wang
Dear FS team,
I have structural data from a training study involving different tDCS
groups. I would like to define ROIs (masks) in MNI space corresponding to
the approximate cortical area underlying the tDCS electrodes, which were
placed on F3F4 for one group and on P3P4 in another group (10-20
Hi Lorenzo
Doug is the person to answer most of these questions, but yes, you want
to sample your raw fMRI data onto the surface, then analyze there so you
can take advantage of things like surface-based smoothing. There is no need
for an inverse matrix to transform back, just the output of
Hi Tudor
I guess the easiest thing to do would be to read the surface and the
electrode coords into matlab and just do an exhaustive search for the
vertex that has the closest MNI coord to each electrode.
cheers
Bruce
On Thu, 4 Sep 2014,
Tudor Popescu wrote:
Dear FS team,
I have
Hi,
Have you ran fieldsign-sess after your selxavg3-sess?
On Thu, Sep 4, 2014 at 8:35 AM, Francesca Strappini
francescastrapp...@gmail.com wrote:
Dear all,
I'm trying to display the fieldsign map. I used standard
rotating-wedge and expanding-ring paradigm, and I followed the steps
Yes, this was the command line
fieldsign-sess -a rtopy.LG.lh -s SUBJ02 -patch lh.full.flat.patch.3d -fwhm 0
Thanks!
Francesca
2014-09-04 15:52 GMT+03:00 SHAHIN NASR sha...@nmr.mgh.harvard.edu:
Hi,
Have you ran fieldsign-sess after your selxavg3-sess?
On Thu, Sep 4, 2014 at 8:35 AM,
The Center for Mind Brain and the Department of Psychology at the University
of California, Davis, invite applications for a tenure-track position in Mind
Brain Sciences. The appointment will be at the Assistant Professor level.
Applications are sought from scholars who have strong and
If you sym link the already finished bedpostx directory to
$SUBJECT/dmri.bedpostX, you should be able to run trac-all -prep and
trac-all -path without any issues (adjusting the config that comes with
tracula)
On 09/03/2014 05:04 PM, Katherine Damme wrote:
Hello Freesurfer Community!
I have
Hi Peggy,
1. All anatomical volumes used in the last update of longitudinal tracula
are in the same space as the *.long.* freesurfer volumes, i.e., the
within-subject base template.
2. There are no changes to the bedpostx step.
2a. The brain mask should be the same across all steps of
Hi Robby - The option to specify a different gradient table for each scan
(with bveclist) was introduced more recently. See:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates
The version that you're using doesn't recognize bveclist.
Hope this helps,
a.y
On Tue, 26 Aug 2014,
Hello,
I am using FreeSurfer version 5.3.0 in 64bit desktop,
I got these errors at the begining of recon-all but the reconstruction is
not stop, keep on going with lots of invalid=96777.
pass 1 of 1
setting smoothness coefficient to 0.039
blurring
Hi Dan,
Thanks. While I agree that all kinds of GPUs might be sufficient as far as
the hardware and FS computations go, the drivers in fact make a major
difference for visualizations. For my card the proprietary NVIDIA drivers
turned out to be 10-20 times faster than the CentOS 6.5 Noveau
That is expected output, No need to worry about it.
-Zeke
On 09/04/2014 04:06 PM, Pom Sailasuta wrote:
Hello,
I am using FreeSurfer version 5.3.0 in 64bit desktop,
I got these errors at the begining of recon-all but the reconstruction
is not stop, keep on going with lots of invalid=96777.
Hi Eileen - In b0plist you can give files that contain either 2 phase maps
(a volume with 2 frames), or the difference of 2 phase maps (a volume with
only 1 frame). Depending on whether the volume that you specified has 2 or
1 frame, trac-all will assume which of the above you're giving it.
Hi Tommi,
That is true, but it is also the most extreme comparison possible. A
crude estimate of the ranking of drivers would be:
NVIDIA Intel (these are open source by default) AMD radeon (open
source amd) Nouveau (open source nvidia)
While both NVIDIA and AMD hardware are of similar speed
Hi Matt,
Did you try the -c option described in the function's help?
HTH
D
On Thu, Sep 4, 2014 at 3:30 PM, Sherwood, Matt matt.sherw...@wright.edu wrote:
Bruce,
Thanks for the pointer. What is happening is we would like to combine
the skin/skull/CSF volumes with that of the cortical
Hi Michelle - Your column-formatted gradient table (original_columns.bvec)
shows up as having only 2 rows in unix (e.g. with the cat command). That's
sometimes the case for text files saved from Excel or other non-unix
applications. When I open your file in TextEdit on a mac and then
Hi Barbara - If your version is the same as Robby's, then you're trying to
use an option (different gradient table for each scan) that was added in a
tracula update. Older versions only allowed a single gradient table for
all scans. See:
Hi Barbara and Anastasia,
thanks to your suggestions and help I was able to run the pre-processing
step of tracula.
I was using FreeSurfer 5.3, but didn't download any update. That's probably
why the row configuration was not working. Anyway, I used the column
configuration after manual correction
Hi Michelle - Based on your recon-all.log, your SUBJECTS_DIR that contains
the freesurfer recon of your subject is /PHShome/my738/FSout. But based on
you trac-all.log, you're using:
SUBJECTS_DIR /Users/michele/Desktop/tracula/sages_diff_test_tracula
So tracula cannot find the freesurfer
Hi Michelle - Try replacing this line:
setenv
/Users/michele/Desktop/tracula/sages_diff_test_tracula/SD40_1/FSout_P0401_e20130813_s002_Cor7minMDEFT_T1_b
with:
setenv SUBJECTS_DIR /PHShome/my738/FSout
(Or whatever the location of your freesurfer recons is.)
a.y
On Wed, 3 Sep 2014,
Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the
seed-to-diffusion transformation would be the MNI-to-diffusion
transformation.
a.y
On Wed, 3 Sep 2014, Emily Louise Belleau wrote:
Hello,
I did all of my DTI preprocessing through tracula. I now am using FSL
Hi Kate - There is an example configuration file for tracula in your
freesurfer distribution ($FREESURFER_HOME/bin/dmrirc.example). The same
file is also here:
http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
If you attach your configuration file and the log file
(scripts/trac-all.log), we can
Thanks Anastasia. I figured out the right path, and I'm now running the 2nd
step of tracula pipeline on that case.
There was a problem with subdirectories (my fault).
And also the missing 'SUBJECTS_DIR' syntax in the setenv command, as both
you and Barbara pointed out.
Thanks again for your help
Hi Anastasia,
Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat file
in the dmri folder and placed it into FSL's probtractx, I developed a track
that was in the wrong area of the brain, so I am thinking there is something
wrong happening with the transformation to
Certainly you can, and it's a good idea for troubleshooting this. In FSL
you can do it with:
flirt -in your_label_in_MNI_space.nii.gz -out your_label_in_diff_space.nii.gz
-ref dmri/lowb.nii.gz -applyxfm -init dmri/xfms/mni2diff.bbr.mat -interp
nearestneighbour
Then you can overlay the
Hi Pom
how long has it run? What you are seeing is probably normal. Let it run
to completion and see how things look
cheers
Bruce
On Thu, 4 Sep 2014, Pom Sailasuta
wrote:
Hello,
I am using FreeSurfer version 5.3.0 in 64bit desktop,
I got these errors at the begining of recon-all but
Hello,
I am having some troubles using QDEC to analyze the cortical thickness changes
in my
group study and I was hoping someone may be able to give me a hand. The steps I
have done are as follows:
I am working on a study looking at 40 subjects scanned at two time points (base
and 6
Hi,
I was having similar errors as Michele Cavallari regarding error reading
/path/to/subject/dmri/dwi_frame, but I'm not sure it's related to my bvecs
file. I did try reconfiguring my bvecs file into columns instead of row just in
case, but that didn't solve the problem. It really just looks
Hello,
Now I have a subject data,including 156 dicom images(MR0001~MR0156),amd
they were converted into a .nii.gz file(eg.CON_T1_01.nii.gz) .I am
wondering whether they are the same :
recon-all -i MR1.dcm -s con01 -all
recon-all -i CON_T1_01.nii.gz -s con01 -all
Many Regards.
Xin-Fa Shi.
Yes, it should be
Bruce
On Sep 4, 2014, at 10:24 PM, Xinfa Shi shixinfa2014...@gmail.com wrote:
Hello,
Now I have a subject data,including 156 dicom images(MR0001~MR0156),amd they
were converted into a .nii.gz file(eg.CON_T1_01.nii.gz) .I am wondering
whether they are the same :
Hi Taylor,
first, in your description you mention 'base and 6 month'. Better call it
'baseline' or 'first and second time points at 0 and 6 months' in order to not
confuse the first time point with the 'base' = within-subject template created
as the second step. I think you did not confuse it,
Hi Martin
Yes I that definitely clears things up, thanks very much for the help.
As for the QCAHCE we did use the long_mris_slopes described in the tutorial you
linked in your email. Just to confirm I believe I should be using the
mri_glmfit -osgm model for my one sample group mean
Hi Ludy - If your gradient table is formatted in 3 rows you need to
either:
1. Convert it to 3 columns so you can use it with the 5.3 version of
tracula, which requires the gradient table to be formatted in columns
OR
2. Download the tracula update that can use gradient tables formatted in
Hi Taylor,
You can do the glmfit osgm on whatever you like (rate, percentchange pc1, or
symm. percent change spc). I recommend SPC. The 2stage model page shows an
example of glmfit with osgm flag and explains how to stack your data first.
Best Martin
Sent via my smartphone, please excuse
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