Thanks Nick and Anil! I tried with the Bert data set in its original
location, and got a different kind of error:
ERROR: talairach_afd::Load_xfm(): could not parse transforms/talairach.xfm
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure
Hello
I'm new to freesurfer, I have some .nii images that i converted to .mgz
via mri_converter in freesurfer and run recon-all on them!
it seems everything is fine and i've got stats in m subjects folders. but
when I try to do tkmedit to visualize images it gives me an error:
Tkmedit couldn't
Hi Sudhin
are you sure that the NaNs don't exist before registration and
extraction? Cany you check? I don't see why anything we would have done
would introduce
them.
cheers
Bruce
On Fri, 22 Feb 2013, Sudhin A. Shah wrote:
Hello
I have run free surfer and co-registered with
Hi Chris, in the color table file, do you have an unkown entryas the
first entry? There should be one or else use --no-unknown.
doug
On 02/16/2013 11:07 PM, Chris McNorgan wrote:
Hi all,
I posted this back in January, and got a direct email reply from
someone on the mailing list, who gave
You will have to merge the labels into an annotation (mris_label2annot),
then the annotation to a segmentation volume (mri_aparc2aseg), then
apply mri_label2vol to the segmentation.
doug
On 02/19/2013 10:45 AM, Vincent Koppelmans wrote:
Hi all,
I am trying to convert Brodmann area 4a and 4p
Hi katie, I'm guessing that you have one event type that only has one
event? If so, you can do what Sebastian suggests, but you won't be able
to look at contrasts related to that condition.
doug
On 02/19/2013 03:24 PM, Katie Bettencourt wrote:
I am having a problem with selxavg3-sess (for FS
Hi Shani, it looks like your commands are right. How are you judging
that the mask is thicker? What is the resolution of the DTI volume? When
you binarize in a coarser space, you'll naturally not get it to line up
with the surface, and the binary mask will naturally be thicker.
doug
On
Hi Greg, the target (--targ) should be a volume, not the name of a
subject (eg, 816/mri/orig.mgz)
doug
On 02/21/2013 02:23 PM, Gregory Kirk wrote:
Greetings lords of freesurfer!
I am having a problem getting a combined cvs warp+bbregister to map an FA
volume
onto a template.
mri_vol2vol
Hi Glen, I think there is some confusion here about what this conversion
is doing and what you want it to do. This conversion simply changes the
way the information is stored, but it is still surface data. SPM/MRIcron
cannot display surface data even if it is in nifti format. It sounds
like
Hi Caspar, youcan do it that way and then extract the average time
course from the residuals. Otherwise, you'd have to do the regression
yourself in matlab.
doug
On 02/22/2013 11:01 AM, Caspar M. Schwiedrzik wrote:
hm, I just realized that I should probably run selxavg3-sess with
-svres and
Dear Gari,
The subfield module uses a different, independent method to segment the
hippocampus, and consistency with ASEG results is not explicitly
enforced. That said, the subfield module is inialialized with the ASEG,
and the results should be pretty close to each other, for the most part.
Have
Hi Sophie, in the output directory there should be several folders, one
for each contrast. One of those contrasts will be your age-slope
contrast. Load the gamma.mgh file to see what the slopes are.
doug
On 02/25/2013 08:42 AM, Sophie Maingault wrote:
Hello,
I used qdec to visualize
Hi Maria, I don't know exactly how they generated it. It might not even
have been using the FS tools. If I were to do it in FS, I would create a
segmentation by thresholding the continuous map into the ranges of F
values I wanted. I would then create an annotation (mris_seg2annot)
where I can
If there are negative values in the lh.area, then something is very
wrong. Can you double check? If they persist, can you upload the subject?
doug
On 02/20/2013 10:18 AM, j janssen wrote:
Hi,
freesurfer-x86_64-redhat-linux-gnu-stable5-20110522
$Id: mris_preproc,v 1.66 2012/12/06 16:06:17
The first cmd (mris_register, or use the surfreg script) will create a
new registration file in subject/surf. Make sure you don't overwrite the
original one (?h.sphere.reg). mris_preproc will just create a single
output file with all of your subjects' thickness data (unless you use
--qcache)
First check the value of the BBR cost function. If it is over .8, then
something is wrong. To check whether it is an LR flip, you can flip the
volume LR and re-run the registration to see if it gets better.
doug
On 02/25/2013 11:19 AM, Sudhin A. Shah wrote:
Hi Doug,
When I initially pulled
Hi Paul, do you still have a problem that needs to be solved?
doug
On 02/18/2013 04:39 PM, Paul Beach wrote:
Thank you for forwarding this.
I realize I need to further clarify my issue as well.
With the help of Doug Greve I've taken hand made ROIs in tksurfer,
repackaged them into a new
Hi Doug,
Is the BBR cost function in anat2exf.register.dat.bbr.init?
mwtp5
3.75
4.00
0.15
9.689088e-01 6.952747e-02 -2.374479e-01 6.737892e+00
2.456762e-01 -1.566831e-01 9.566056e-01 -2.835866e+01
2.930631e-02 -9.851995e-01 -1.688930e-01 1.765446e+01
0 0 0 1
round
Or in
The cost (from .mincost) looks fine. Can you send a pic of the
registration inaccuracy?
doug
On 02/25/2013 11:53 AM, Sudhin A. Shah wrote:
Hi Doug,
Is the BBR cost function in anat2exf.register.dat.bbr.init?
mwtp5
3.75
4.00
0.15
9.689088e-01 6.952747e-02 -2.374479e-01
It does not look bad to me. Why do you think it looks wrong?
On 02/25/2013 12:29 PM, Sudhin A. Shah wrote:
Hi Doug,
Here's an example view... It looks fine to me. See attached..
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Monday,
Paula,
what is the processor type and speed? how much memory do you have on
your system?
Nick
On Mon, 2013-02-25 at 11:50 +0100, Vieweg, Paula /DZNE wrote:
Hi,
I have installed Freesurfer (Leopard version) on Mac Mountain Lion and
tried to use it for a full segmentation (recon-all
Dear all,
I am trying to prepare freesurfer surfaces for probtrackx
fibertracking. I use the pial surfaces to stop fibers from going back
into the white matter. In order to be able to track between
hemispheres, the medial_wall labels have to be removed from these pial
surfaces. I have
Recon is still running. I started the process on 2/21/2013. Its been 4 days.
I ran this command, and viewed the aseg file, and that looks reasonable
tkmedit ./ brainmask.mgz -aux T1.mgz -surfs -aseg
Currently it is at this stage:
Correction of the Topology
Finding true center and radius of
I'd collect highres T1w as well and then refine the 1mm surfaces using that.
Peace,
Matt.
From: SHAHIN NASR sha...@nmr.mgh.harvard.edu
Date: Monday, February 25, 2013 1:39 PM
To: Freesurfer freesurfer@nmr.mgh.harvard.edu, Bruce Fischl
fis...@nmr.mgh.harvard.edu, Doug Greve
You do not need another one unless you think that the brain has changed
in some way between when you collected the anat and the func. Also, if
you are going to acquire a partial field of view (ie, only part of the
brain), make sure you get a full brain acq of something to help in
registration
We always collect a low resolution whole brain mprage structural scan
before the functional scans to help us position our slices. Can I use
that?
You do not need another one unless you think that the brain has changed
in some way between when you collected the anat and the func. Also, if
you
yes
On 02/25/2013 03:23 PM, sha...@nmr.mgh.harvard.edu wrote:
We always collect a low resolution whole brain mprage structural scan
before the functional scans to help us position our slices. Can I use
that?
You do not need another one unless you think that the brain has changed
in some way
try looking at the lh.inflated.nofix or lh.orig.nofix (or rh, whichever
one is running) and see if something is dramatically wrong (like skull
attached to brain, or hemis connected, etc)
On Mon, 25 Feb 2013, Blessy
M wrote:
Recon is still running. I started the process on 2/21/2013. Its
Hi Andries
you could use the cutting tools in tksurfer, although it sounds like this
is something that we might want to make easier to do automatically.
cheers
Bruce
On Mon, 25 Feb 2013, Andries R. Van Der Leij wrote:
Dear all,
I am trying to prepare freesurfer surfaces for probtrackx
Hi FreeSurfer Community,
I am trying to run TRACULA's last step, 'trac-all -path -c
path-to-dmrirc-config-script', and am receiving the error:
Segmentation fault(core dumped)
Moreover, when I look to standard output (terminal), I noticed that the
initial 'dmri_paths' command is incomplete.
Hi Susan - Can you please send your entire trac-all.log? I'll need to see
what else was going on before the error message occurred.
Thanks,
a.y
On Mon, 25 Feb 2013, Susan Kuo wrote:
Hi FreeSurfer Community, I am trying to run TRACULA's last step,
'trac-all -path -c
It looks to me like there was an error at an earlier stage, in the -prior
step, so some of the files that the -path step is looking for are not
correct. Look for img2imgcoord: Command not found. That's a command from
FSL that it can't find. (The 5.2 version of trac-all will not use this any
Hi! It turns out the 3T scans have a lot of susceptibility artifact so it might
not be the registration failing but more of the signal :( Unfortunately I will
just leave out those ROIs for my analysis..
From: freesurfer-boun...@nmr.mgh.harvard.edu
Hi Zeke,
Thank you for the advice. I have Mac OS X Version 10.7.5.
I checked to see if XQuartz is installed and it is. I reinstalled it to be
sure but I'm still running into the same problems. Do you (or does anyone
else) have other ideas about what could be causing this issue?
Thanks,
Daniel
have you rebooted since installing XQuartz? i've found a reboot is
necessary to get Terminal to open up again.
N.
On Mon, 2013-02-25 at 17:07 -0500, Daniel Cole wrote:
Hi Zeke,
Thank you for the advice. I have Mac OS X Version 10.7.5.
I checked to see if XQuartz is installed and it is. I
Hi FreeSurfer experts,
We are dealing with a sample of children MRI and we want to introduce our
own templates into the pipeline instead of the MNI/tailarach.
Any advice or guidance you can provide on how to go about doing this would
be much appreciate it.
Thanks,
Kev
Hi Kev
for what purpose? If it's just for talairaching, Avi (ccd) is the person
to ask
cheers
Bruce
On Mon, 25 Feb 2013, Schumman Resonance wrote:
Hi FreeSurfer experts,
We are dealing with a sample of children MRI and we want to introduce our
own templates into the pipeline instead of the
Dear Freesurfers,
I tried to install freesurfer on amazon EC2 as instructed on the wiki page.
Everything went well except that mri_* tools like mri_convert doesn't work.
When calling it, it returns nothing.\
I also tried to make another Centos instance and install freesurfer manuall,
but the
I would like to play with both normalization and registration steps, and
contrast results.
Thanks,
Kev
On Mon, Feb 25, 2013 at 6:03 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
Hi Kev
for what purpose? If it's just for talairaching, Avi (ccd) is the person
to ask
cheers
Bruce
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