Hi all,
I bit confused about how to create labels from annotation2label command to
create DLPFC. I want make DLPFC label by merging G_frontal_middle.label,
S_frontal_inferior.label and S_frontal_middle.label (available in the 2009
atlas). But I only can get annotation2label to work with the other
Hi,
I just mean that it is not an option in the drop down menu at all? And I
thought it would be?
On Fri, Jul 26, 2013 at 6:19 PM, Douglas Greve wrote:
>
> Hi Linn, what do you mean that you cannot select it? Is it grayed out?
> doug
>
>
>
> On 7/26/13 4:20 AM, Linn Mittlestein wrote:
>
> Dea
yes, if they are surface-based then it is really trivial (just give them to
mris_anatomical_stats with the -l flag)
cheers
Bruce
On Tue, 6 Aug 2013, Yang, Daniel wrote:
Dear FreeSurfer Experts,
Theoretically, if you have a set of functional ROIs, is it possible to
derive the cortical thick
Dear FreeSurfer community,
I've been unable to get my recon-all commands to work, and this appears to be
because my output orientations are wrong.
As input, I am using .nii.gz structural images (from 3 different scanners: a
Siemens Sonata (1.5T), Siemens Trio (3T) GE Signa (1.5T))
Using FSLvie
Dear Freesurfer experts,
I am currently trying to obtain mean thickness values for certain
sub-regions of the cortex. I have previously used this command
asegstats2table --subjects X_* --meas thickness --tablefile aseg_stats.txt
however now (Ive updated to v 5.3) I receive this error
asegsta
Hi Bruce,
Thanks for your reply. Those functional ROIs are volume-based (that is,
generated by spm/fsl/BrainVoyager).
So it seems that I need to generate a label for them in order to use
mris_anatomical_stats -l.
Do you know what I can generate label files based on volumetric functional
ROIs?
Thank you. It worked. I have been running a few brains and they have been
preprocessed successfully. One brain gave me an error message. Can you
please help me address this:
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//BW_104/dmri/xfms/mni2diff.bbr.mat
--ncpts
Apparently my problem is because my .nii.gz files lack any orientation data,
and I'm going to see if I can get the original DICOM data to address this.
Any other tips welcome, otherwise I'll see how far I get with that.
Best,
Amy
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-
Hi Amy
starting with the original dicoms is usually a good idea.
Bruce
On Tue, 6 Aug
2013, Amy Bilderbeck wrote:
Apparently my problem is because my .nii.gz files lack any orientation data,
and I?m going
to see if I can get the original DICOM data to address this.
Any other tips welcome
You're welcome. It seems like it can't find this file:
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data//bin/dmri_train
I can't tell exactly what's going on without looking at your trac-all.log
in its entirety. Can you please send it?
On Tue, 6 Aug 2013, Alan Francis wrote:
T
Hi Freesurfers (Lilla),
I'm running v5.1.0 on a Mac trying to apply a cvs morph via the following
function:
mri_vol2vol --targ cvs_avg35_inMNI152 --m3z
$SUBJECTS_DIR/NC001/cvs_avg35_inMNI152/combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.m3z
--noDefM3zPath --mov $SUBJECTS_DIR/NC001/labels/
Hi Anastasia:
The problem is solved. thanks so much,
Alan
On Tue, Aug 6, 2013 at 11:21 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> You're welcome. It seems like it can't find this file:
> /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_**
> Data//bin/dmri_trai
Use --annotation aparc.a2009s
Run it with --help to see all the options.
doug
On 08/06/2013 08:24 AM, Linn Mittlestein wrote:
> Hi all,
>
> I bit confused about how to create labels from annotation2label
> command to create DLPFC. I want make DLPFC label by merging
> G_frontal_middle.label, S_
That is mostly informative. FSL, which is used to initialize, has
specific standards for the orientation of the data that sometimes
requires the orientation be adjusted.
On 08/06/2013 12:52 PM, Mark Plantz wrote:
> As an update, I noticed that the bbregister output log had an
> interesting war
Hi Cathy, I don't think there ever was a thickness option for
asegstats2table. Are you sure you weren't using aparcstats2table?
doug
On 08/06/2013 09:56 AM, Catherine Bois wrote:
> Dear Freesurfer experts,
>
> I am currently trying to obtain mean thickness values for certain
> sub-regions of the
I see, you're using the old version of tracula (from freesurfer 5.1). In
that version, you had to define the number of low-b images in the
configuration file. I strongly recommend updating to freesurfer 5.3. A lot
of things have improved in tracula since then.
Also, in the future please attach
Thanks, Doug, for the procedure. I'm just wondering how the ROI sampling is
performed.
May I ask three questions?
(a) when you say sample the ROIs from the fMRI space to the "surface", are you
referring to white or pial surface?
(b) Let's say, the functional activation is halfway inside a cert
On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve wrote:
> mri/hippsubfieldseg.mgz
Thank you Doug. Just to clarify the code you suggested earlier, should
"mri/hippsubfieldseg.mgz"
be replaced with each of the specific hipposubfields:
posterior_Left-Cerebral-Cortex.mgz
posterior_Left-Cerebral-Whit
oh, sorry, you are right. I had thought that they generated a single
file with the segmentations. In this case, you will need to threshold at
some value of the posterior probability. Alternatively, you could
generate a segmentation file by selecting the seg at a voxel that has
the highest post
Hi Doug,
I realize now that I was unclear of the function
of kvlQuantifyHippocampalSubfieldSegmentations.sh
It creates a summary file of volumes for the left and right subfields as
volumeStats_X.txt (where x is left or right). It writes the files into the
mri subdirectory. Is there a scripted way
I can add that after running "kvlQuantifyHippocampalSubfield
Segmentations.sh" I cannot find the nonPartialVolumeStatsLeft.txt
and nonPartialVolumeStatsRigt.txt files mentioned on the tutorial page:
http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation
I only have the volumeStats_
What happens if you load the output of bbregister?
On 08/06/2013 03:30 PM, Mark Plantz wrote:
> The output of bbregister is actually fine. It seems like the inversion
> happens after mri_label2vol is run. I am currently viewing in
> FreeView, but the tkmedit command is:
>
> tkmedit CMH-8169 001
Hi Doug,
Turns out the kvlQuantifyHippocampalSubfieldSegmentations.sh was crashing
before it got a chance to write the summary files. It crashed after trying
to go into fsaverage/mri. I edited the file to specifically only go into my
current study folders (they all have a common prefix), and then
Hi Doug,
So the program to be used is mri_vol2surf, correct? Is there any other program
that might be related?
Thanks,
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 8/6/13 2:55 PM, "Douglas N Greve"
mailto:gr...@nmr.mgh.ha
I think I gave you the wrong command line for mri_label2vol. Try added
--invertmtx to the command line. Sorry for the wild goose chase.
doug
On 08/06/2013 04:00 PM, Mark Plantz wrote:
> The bbregister output looks like a typical intensity volume [attached].
>
> Out of curiosity, I ran mri_
Dear Doug,
thank you very much for your advice. I re-ran the contrast to look at
age-area differences between the two slopes. There were no significant
differences after monte carlo simulation so I changed the mriglmfit script
to doss, as you suggested (but left the .fsgd file as is).However when
Hello!
I want to know if there are any change in the files of the folder *fsaverage
* in the different versions of freesurfer. Specifically, I'm interested in
know if the files lh.pial_avg and rh.pial_avg are the same in the versions
v4.5.0 and v5.3.0
Many thanks in advance,
Best,
--
Francisco
Hi Franciso,
I think that we made some small mods to the spherical registration in that
time to make it more robust, so things probably did change
cheers
Bruce
On Tue, 6 Aug 2013, Fco. Javier Román wrote:
Hello!
I want to know if there are any change in the files of the folder fsaverage
in
Hi Bruce, thanks so much!!
Do you know some web (or maybe you cant send to me) to obtained the files
of the version 4.5.0?
Thanks!!
FJ
2013/8/6 Bruce Fischl
> Hi Franciso,
>
> I think that we made some small mods to the spherical registration in that
> time to make it more robust, so things
Hello,
I am measuring the changes of subcortical volumes in a longitudinal
study, so I took the volumes from longitudinal subjects
(/name.long.base/). Now we need to perform the correction using the eTIV
parameter, but the eTIV for longitudinal subjects for all time points is
the same (/i//.e
Hi Daniel,
You need to specify the full path to the target volume, the subject id
is not sufficient. It should be somthing like this:
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/norm.mgz
Lilla
On Tue, 6 Aug 2013, Barron, Daniel S wrote:
> Hi Freesurfers (Lilla),
>
> I'm running v5.1.0 o
-- Forwarded message --
From: Bruce Fischl
Date: 2013/8/5
Subject: Re: [Freesurfer] How to transfer a reconstructed pial surface file
into a 256*256*256 matlab matrix file?
To: Yunxin Wang
Cc: freesurfer@nmr.mgh.harvard.edu
Hi Yunxin
the surface lives in a continuum and is 2D.
-- Forwarded message --
From: Yunxin Wang
Date: 2013/8/6
Subject: Re: [Freesurfer] How to transfer a reconstructed pial surface file
into a 256*256*256 matlab matrix file?
To: Bruce Fischl
Hi Bruce,
Thanks for your response. Actually I want to use the fast marching toolbox
to f
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