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 wrote:
> 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,
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 same
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 th
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
___
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.
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
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
[freesu
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 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 ', and am receiving th
Hi FreeSurfer Community,
I am trying to run TRACULA's last step, 'trac-all -path -c
', 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. The terminal shows that the
com
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
>
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 b
It may be that there is a lot of T2* decay around the edge of the brain.
See slide 13 from this presentation:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fs.multimodal-integration.ppt
To check your data, turn off the intensity normalization by clicking in
the image window and
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 so
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
> y
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
I'd collect highres T1w as well and then refine the 1mm surfaces using that.
Peace,
Matt.
From: SHAHIN NASR
Date: Monday, February 25, 2013 1:39 PM
To: Freesurfer , Bruce Fischl
, Doug Greve
Subject: [Freesurfer] High resolution fMRI and resolution of anatomical
scans
Hi,
We are plann
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 Spher
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 difficulties
Here is the last subject - coronal view.. This is where I started
scaling/stretching :(
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sudhin A. Shah
[sut2...@med.cornell.edu]
Sent: Monday, February 25,
Hi,
We are planning to collect high resolution *functional* MRI for a group
of subjects with voxel size smaller than 1 mm. For these subjects, we
already have reconstructed *anatomical *scans with 1 mm voxel size. The
question is, do we need to re-collect *anatomical* scans for these subjects
w
Hi Maria,
We followed the steps laid out by Winkler here:
http://brainder.org/2011/07/05/freesurfer-brains-in-arbitrary-colours/
It's actually quite easy, especially if you are are using parcellations as
ROIs (which looks like what the authors did) and not vertex generated
ROIs. You would have t
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
Sorry - this doesn't look bad. Still I cannot extract values for the ROI label
2013..
On Feb 25, 2013, at 12:43 PM, "Douglas N Greve"
wrote:
>
> 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 ex
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, F
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 6
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 anat2exf.re
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
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 pulle
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)
d
Hi Linn, I'm not sure what you mean. Can you point me to the wiki page
where you are getting these instructions?
doug
On 02/20/2013 11:31 AM, Linn Mittlestein wrote:
> Dear Freesurfer experts,
>
> I have a question about qdec...as it is supposed to be doing whole
> brain cortical analyses, how
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:
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 c
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 cor
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 y
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
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 wha
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_vol
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 02/21/
No, each condition has at least 3 instances of it in each run. The runs
are all set up exactly the same, just the order changes, so there is
nothing different about the runs that work than the runs that fail, and
again, all of these runs worked fine with the exact same paradigm files and
set up, b
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
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
you can use mri_surf2surf, using the XYZ (--sval-xyz) as input, applying
a transformation --reg, and spec XYZ as an output (--tval-xyz). You will
need a registration matrix to map it from the surf coordinates to
whatever coordinates slicer uses.
doug
On 02/19/2013 06:05 AM, Efrat Kliper wrote:
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
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 Ehsan
what is the command you ran? And what is your SUBJECTS_DIR env variable
set to when you run it?
cheers
Bruce
On Mon, 25 Feb 2013, Ehsan Tadayon wrote:
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
Hello,
I used qdec to visualize correlation between cortical thickness and age.
With tksurfer, when I load the file sig.mgh I can see the p-value for each
vertex (log10 pvalue) but I would like to load a file which show the value
of the slope, I mean the change of thickness with age. Which file
Hi Stefano,
You dont need to-- the thickness measures are created by the mris_preproc
command with the --meas thickness flag and the file is saved in $PWD
Hth,
Shantanu
On Mon, February 25, 2013 6:03 am, std...@virgilio.it wrote:
> Dear fs users,
> I do not understand from tutorial if I should s
Hi,
I am calculating hippocampus volumes with 5.2 in CentOS 4.
I compare volumes (the same apply for lh and for rh) when calculating as:
> Left.Hippocampus value in 1mm3 from aseg.stats
> I use the method kvlQuantifyHippocampalSubfieldSegmentations.sh and
obtain the nonPartialVolumeStatsLeft.txt,
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
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
Dear fs users,
I do not understand from tutorial if I should specify in
mris_preproc --fsgd file.fsgd \--target fsaverage --hemi lh \
--meas thickness \
--target fsaverage --hemi lh \ --o lh.thickness.mgh
the .thickness directory for each subject after --meas thickness. If yes, h
Hi,
I have installed Freesurfer (Leopard version) on Mac Mountain Lion and tried to
use it for a full segmentation (recon-all -all).
On my own files I get a problem with Talairach, the program aborts and I get
the recommendation to try it with -notal–check.
I have done this and Freesurfer has si
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