The Neurofunctional Imaging Group (GIN) is a CNRS-CEA joint research unit of
the Bordeaux University (UMR 5296, dir. Bernard Mazoyer) and a core member of
the TRAIL Laboratory of Excellence. The GIN is a multidisciplinary research
unit gathering scientists with initial training in mathematics an
Dear, I lost the toolbar above control panel in the freeview window. How could I reload the toolbar? Thank you for your consideration.Sincerely yours, Youngkook Kim
Youngkook Kim, M.D.Clinical Fellow of Department of Physical Medicine & RehabilitationSeoul
Dear Freesurfers,
I would like to alter the trac-preproc to include an EPI to T2 registration
(diffeomorphic) as I do not have a field map, is there a way of doing this?
I saw that bbregister actually only uses 6 doF.
Thank you very much,
Barbara
___
Fr
Hi Doug,
So I am using a command like this:
epidewarp.fsl --mag ~/MonkeyfMRI/oz_fparc/fieldmap/003/fid_mag.nii --dph
~/MonkeyfMRI/oz_fparc/fieldmap/004/fid_phasediff.nii --exf
~/MonkeyfMRI/oz_fparc/bold/template.nii.gz --exfdw
~/MonkeyfMRI/oz_fparc/bold/b0dc.nii.gz --vsm vsm.nii.gz --tediff 2.46
You will need to reset FreeView’s settings. Make sure freeview is closed, open
a terminal and run the following command:
defaults delete edu.harvard.mgh.nmr.FreeView
Start freeview again.
Best,
Ruopeng
On Sep 12, 2014, at 4:49 AM, 김영국 wrote:
>
> Dear,
>
> I lost the toolbar above control
Hi Doug,
I was able to get the surface connectivity analysis to run successfully for
the L.Cingulate example that you posted online (
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
). For my own analysis, I'm hoping to use my own functionally defined ROIs
instead
Hi Patrick,
no images were attached.
If the skull strip removes any brain, you edit the brainmask and fill
the voxels back (or adjust the watershed parameter if lot's of brain is
missing). In you case it sounds like the brain is not missing from the
brainmask, but the surfaces don't grab all
Hi,
many of you are aware of (yes, even excited about) our social media
presence at
Facebook: http://facebook.com/FreeSurferMRI
Twitter: http://www.twitter.com/FreeSurferMRI
and so we have just added a group on
LinkedIn: https://www.linkedin.com/groups/FreeSurfer-8173404
(it's hard to believe, b
Hi Doug,
I tested this new script on volume data and it did create the file
'sig.masked.mgh', which shows the significance map masked by Monte Carlo
surviving clusters. So, I guess you can update the current file now.
Thanks!
Hamdi
From: freesurfer-b
great, I'll check it in to the source so it will be part of the next version
thanks
doug
On 09/12/2014 10:31 AM, Eryilmaz, Huseyin Hamdi wrote:
> Hi Doug,
>
> I tested this new script on volume data and it did create the file
> 'sig.masked.mgh', which shows the significance map masked by Monte Car
You need to have your ROI as a segmentation in the anatomical
(conformed) space. If it is a label on the surface, you can use
mri_label2vol to turn it into a volume (make sure to use --proj frac 0 1
.1 to fill the ribbon). When you run funcroi-config specify -seg
yourseg.mgz 1 where yourseg.m
Sorry, the b0dc.nii.gz should be the argument of --vsm (no need to use
--exfdw).
On 09/12/2014 08:28 AM, Reza Rajimehr wrote:
> Hi Doug,
>
> So I am using a command like this:
>
> epidewarp.fsl --mag ~/MonkeyfMRI/oz_fparc/fieldmap/003/fid_mag.nii --dph
> ~/MonkeyfMRI/oz_fparc/fieldmap/004/fid_p
Tried...unfortunately it didn't improve
On Thu, Sep 11, 2014 at 4:56 PM, Chris Watson <
christopher.wat...@childrens.harvard.edu> wrote:
> You can try just re-running "trac-prep -prior" and "trac-paths" for the
> L uncinate and no other tracts
>
> On 09/11/2014 02:58 PM, Michele Cavallari wrote
You can run something like
cd $SUBJECTS_DIR/subject
mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f
stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c
label/aparc.annot.ctab subject lh pial
The "Measure Cortex" fields in the output stats/lh.aparc.pial.stats will
be measure
Hi FreeSurfer list members,
I'm working on a white matter hyper-intensity study, and trying to group
the segmented WM labels in lobes based on the wmparc.mgz file made by
recon.
But I found that there's a large part of "unsegmented WM" near ventricles,
and wonder if such labels are consistently a
Thanks, Zeke. OK, that makes sense about the static vs. dynamic linking
information. Good to know about the usage of UPX in case we need to
'decompress' at some point and use 'ldd' and get specific library dependency
information.
The list of binaries/scripts came via the FTP download site her
On 09/12/2014 11:32 AM, Gurney, Jenny wrote:
> Thanks, Zeke. OK, that makes sense about the static vs. dynamic linking
> information. Good to know about the usage of UPX in case we need to
> 'decompress' at some point and use 'ldd' and get specific library dependency
> information.
>
> The li
Hello,
Yeah I would ignore the contents of that ftp site and simply go with
whatever the contents are on the Release Notes page. The 3 files you
have listed make sense based on my quick glance of that page.
And yes, I would simply overlay those files on top of the originals.
Although it may be
Hi,
I'm processing 3T data with 60 direction vectors and 2 images with b-val =
0. Trac-all -prep has been failing at the command:
> mri_convert --frame 0 31
/dmri/dwi.nii.gz /dmri/lowb.nii.gz
> mri_convert: extra argument ("/dmri/lowb.nii.gz")
> type mri_convert -u for usage
Since --frame seems
Dear all,
I am trying to make work Qdec on my system ubuntu 12.04.
freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
After I have loaded my qdec.table.dat and renamed the analysis folder ,
when I then try to create the "stats tables", I get an error and it blocks
at 20% of the waiting bar.
Dat
Hi Markus,
maybe for some weird reason it uses the subjects_dir from the
environment variable instead of the qdec file (that would probably be a
bug). If that's the case, try setting the subject dir on the command
line before starting qdec:
setenv SUBJECTS_DIR ~/Documents/ARNAUD/
(or the full
Hi Martin!
Thanks!
Yes, indeed typing in the command
export SUBJECTS_DIR= before starting qdec solved the first
problem... there are others to follow...
When now writing the table stats file:
Data table loading completed successfully.
SUBJECTS_DIR is '~/Documents/ARNAUD/'
mkdir -p /home/user/D
Hi Doug,
My issue is I am not intending to use a labeled segmented ROI. My main goal
is to calculate the connectivity strength between two binarized ROIs that
are functionally defined. Can fcseed-config accept non Freesurfer segmented
ROIs?
Thanks,
JIahe
On Fri, Sep 12, 2014 at 11:08 AM, Douglas
Dear Martin,
Actually, I found that it doesn't like the ~/ for /home/username
When replacing the first line in the qdec.table.dat
SUBJECTS_DIR=/home/username/...
and also export the SUBJECTS_DIR in the terminal with the foll path, it
works nicley!
Thanks again!
Markus
2014-09-12 22:06 GMT+02:0
Hey everyone,
i have tried to run the trac-all command (Tracula), but it returned an error (bvecs and bvals don't have the same number of entries).
I'm using the latest freesurfer and Tracula update.
I have attached the corresponding bvecs and bvals files. If the log file is necessary i
Hi Bruce,
I was wondering if there is info somewhere about what each of those 7 MIN_
and MAX_ variables control regarding the positioning of the white and pial
surfaces?
thanks,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neurosci
Have a look at mris_make_surfaces.c, this is how I learned about most of
this stuff as the code is pretty well commented (and Bruce telling me
things).
Peace,
Matt.
On 9/12/14, 11:01 PM, "Harms, Michael" wrote:
>
>Hi Bruce,
>I was wondering if there is info somewhere about what each of those 7
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