I have installed freesurfer V5 on my system (ubuntu 12.4) and there is no FSL
in this path /usr/local/freesurfer. I think FSL has not been installed ad I
want to install FSL compeletly in ubuntu there are two questions:
1. Should I write any command in terminal before doing anything else? I
Hello Bruce,
The I am a little confused with the results of the recon-all command? Does the
recon-all -help explain the file placement?
Isaiah
On Jul 30, 2014, at 6:21 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Isaiah
remove the space. It should be:
recon-all
cheers
Hi Mahsa, freesurfer does not come with FSL installed. I would suggest
you go to the FSL web site and follow their installation instructions.
As I remember, it is pretty easy.
doug
On 7/31/14 8:53 AM, mahsa abadian wrote:
I have installed freesurfer V5 on my system (ubuntu 12.4) and there
thanks for your reply
Sent from my iPad
On Jul 31, 2014, at 17:57, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:
Hi Mahsa, freesurfer does not come with FSL installed. I would suggest you go
to the FSL web site and follow their installation instructions. As I
remember, it is pretty
Thanks again for the pointer, Bruce.
You wrote:
... mri_convert -rl rawavg.mgz input vol output vol
which does produce an output volume from which I now need to extract RAS voxel
coordinates.
A pointer to a keyboard command would be most welcome.
Of interest is the difference between the
Hello,
I am trying to convert my significant cluster from qdec into a .gii file, and I
have a couple of questions.
My mri_convert is not working, but it is my first time using it so I may be
missing something, but it just keeps opening up the usage and gives no errors.
mris_convert --annot
The XQuartz upgrade from v2.7.5 to v2.7.6 broke some of the FreeSurfer
GUIs. Please reinstall XQuartz v2.7.5. It can be downloaded from this page:
http://xquartz.macosforge.org/trac/wiki/Releases
-Zeke
On 07/30/2014 10:54 PM, wang kangcheng wrote:
Dear experts
when I use the tkedit, it
Hi Stefano
do you have the perirhinal labels? If not, I'll attach them. Just copy them
into the fsaverage/label dir and you should be all set.
cheers
Bruce
On Thu, 31 Jul 2014, std...@virgilio.it
wrote:
Hi list,
during recon-all, I have this error in three subjects (some months ago I
Hi Doug,
For the functional runs, it's the same task during each run, so the volumes
shouldn't be changing.
Ben
Benjamin Brent, M.D., M.S.
Massachusetts Mental Health Center
75 Fenwood Road, Room 618
Boston, MA 02115
617-754-1262
This message is intended for the use of the person(s) to whom
the format of what?
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you,
I will go there now. But regarding the output of freesurfer, the format will
be .ccd?
On Jul 30, 2014, at 7:23 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Isaiah
you might check out MNE from Matti
The new version uses 2, 41, 77, 251-255, but you should look through
$FREESURFER_HOME/FreeSurferColorLUT.txt to get the ROIs you want
On 07/30/2014 06:39 PM, Alshikho, Mohamad J. wrote:
Thank you Doug,
Do you mean an error in the script that running this command line ?! kindly
what is
Check out this page
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
This might also be useful
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 07/30/2014 08:12 PM, Krieger, Donald N. wrote:
Thanks for the helpful responses to the previous questions, Bruce.
It’s
I don't know about the gii question, but the labels can be created with
mri_annotation2label specifying fsaverage as the subject
doug
On 07/31/2014 09:41 AM, Tara Ann Miskovich wrote:
Hello,
I am trying to convert my significant cluster from qdec into a .gii file, and
I have a couple of
should not be or do you know for sure because you checked it?
doug
On 07/31/2014 10:42 AM, bbr...@bidmc.harvard.edu wrote:
Hi Doug,
For the functional runs, it's the same task during each run, so the volumes
shouldn't be changing.
Ben
Benjamin Brent, M.D., M.S.
Massachusetts Mental
Hello Doug,
Ideally, I am trying to take subject tstat maps from FsFast (stable3
environment) and register these native structural space maps to the
MNI152_2mm standard brain.
The t_000.bfloat file is what was generated relative to my contrast that
was set up in FsFast stable3. There are a
The files after recon-all
On Jul 31, 2014, at 7:10 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
the format of what?
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Thank you,
I will go there now. But regarding the output of freesurfer, the format will
be .ccd?
On Jul 30, 2014, at
Use the version from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mni152reg
Copy it into $FREESURFER_HOME/bin
doug
On 07/30/2014 05:14 PM, Fan, Qiuyun wrote:
Hi Freesurfer experts,
I was trying to align T1 image to MNI space by running 'mni152reg --s
subject',
there are many, many files in many different formats (e.g. volumes in
.mgz format, surfaces in our internal format, labels, parcellations,
etc...)
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
The files after recon-all
On Jul 31, 2014, at 7:10 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
Yes, how do i view the files and where can I find where every has been placed
On Jul 31, 2014, at 8:26 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
there are many, many files in many different formats (e.g. volumes in
.mgz format, surfaces in our internal format, labels,
Hi Isaiah
you should go through the tutorials on our website - they detail all this
information
cheers
Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Yes, how do i view the files and where can I find where every has been placed
On Jul 31, 2014, at 8:26 AM, Bruce Fischl
Hi Doug et al,
I'm trying to run an analysis in QDEC and continue to get an error that says
that the QDEC GLM design creates 0 factors.
I'm attaching my data table here as well as the output of QDEC. I've tried
deleting all variables in my data file other than one and testing just that
Hello All,
I have some questions related to the qdec analysis I have run.
1. On running the qdec I see that FWHM is an input which changes cluster
definition significantly. How would I choose the right FWHM for the
analysis and can it be related to any imaging parameters?
2. Secondly, on
Thanks
Sent from my iPhone
On Jul 31, 2014, at 10:47 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Isaiah
you should go through the tutorials on our website - they detail all this
information
cheers
Bruce
On Thu, 31 Jul 2014, Isaiah C. Smith wrote:
Yes, how do i
The title has been FedEx for overnight. Please let me know after getting it.
Xiaomin
From: Thomas, Adam (NIH/NIMH) [E]mailto:ad...@nih.gov
Sent: 7/30/2014 6:36 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu; FSL
- FMRIB's Software
I all!
I have the same problem in about 15% of MRI scans, all made with the same
scanning protocol (T1 MPRAGE in a SIEMENS Avanto 1,5 T) during the
recon-all -all process.
I can't recognize any difference between those scans which work correctly
and those not.
I have never found the same error on
Try this:
First, compute the registration between the bold and the 152
mri_matrix_multiply -im bold/register.dat -iim
mri/transforms/reg.mni152.2mm.dat -om bold-to-mni152.reg.dat
Check the reg
tkregister2 --mov bold.bhdr --reg bold-to-mni152.reg.dat --targ
What gets printed out to the terminal? Can you load it through the
interface?
On 07/31/2014 11:37 AM, Caspar M. Schwiedrzik wrote:
Hi Talia, this is a Problem with x11 forwarding. Everything works fine
if you use VNC instead.
Caspar
On Thursday, July 31, 2014, Talia Raney
What version of FS are you using? When I load that file in 5.3 qdec, it
creates several discrete classes, see below
doug
40 1179 c 17.514000 0.944336 f 12.00 14.00 0.00
-7.50 0.452381 1565300.00 15300.00
41 1180 c 17.330600 0.760936 f 1.00 0.00 0.00
The normalization is done using non-linear surface-based (2D)
registration to align the curvature patterns. See Bruce Fischl's 1999
HBM paper on spherical morphing
doug
On 07/27/2014 09:05 AM, Christoph Abé wrote:
Hello together,
I have a question regarding the -qcache command, which in
Hi Doug,
I'm using 5.3.
This error was generated when I had more variables in the model, so I used the
option within qdec to remove variables from the data table to see if that had
any effect (i.e., deleted everything except one categorical variable). Still
got the error you see below.
Are you sure you are using orig.mgz when you run mri_vol2vol and not
something like rawavg.mgz? You don't need to spec orig.mgz explicitly
(it will use that by default)
doug
On 07/21/2014 04:51 PM, Jon Wieser wrote:
hi freesurfer experts
I am compiling the FA segment stats for several
That command will work. There's no need to include the mask. Also, I
would add --seg-erode 2 which will erode each segmentation by 2 voxel
(1mm3) to make sure you avoid partial voluming. That feature might not
be available in 5.3, but I can get you a version that does if not
doug
On
HI doug,
thanks for getting back to me. I was able to solve the problem on my own.
thanks again
Jon
From: freesurfer-boun...@nmr.mgh.harvard.edu
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve
gr...@nmr.mgh.harvard.edu
Sent: Thursday,
Dear All,
I wonder if there are any functions that can calculate the grey matter density
of the vertices or in the ROI manner? I figured out that Freesurfer can give
the thickness, area, volume, curv, but I can not find grey matter density
anywhere.
Thanks for any advice!
Qiongmin
Thank you very much. I solve it using the method.
Wang Kangcheng
From: Z K
Date: 2014-07-31 22:00
To: Freesurfer support list
CC: kangchengwang0808
Subject: Re: [Freesurfer] tkmedit error
The XQuartz upgrade from v2.7.5 to v2.7.6 broke some of the FreeSurfer
GUIs. Please reinstall XQuartz
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