Hi,
It was set to 7500 in the original dmrirc file. Now I use a file from
another subject and changed the dcmlist. Hope that works.
Regards
Gerit
On 15 July 2013 20:33, Anastasia Yendiki ayend...@nmr.mgh.harvard.eduwrote:
Hi Gerit - It seems like the nsample variable is empty. Are you by
Hi Doug,
Thanks for your help. I think the most important thing for me was to know that
the vertices are thresholded by default at p .01. So that is good news! I was
just a little worried that the thresholding I see was arbitrary and might even
be inconsistent across subjects.
In that case
Hi Bruce,
I am sorry, I mean, is there a DK atlas on a standard template brain (like MNI
152)? sorry, I don't know how DK atlas works. Is it a probabilistic atlas, or
dependent on the exact folding pattern of the unique individual? (I guess it's
the latter).
I'd like to generate a ROI brain
Hi Daniel
you could use the DK annotation of the fsaverage brain, which I think we
supply. The atlas itself is a compilation of multiple statistics and not
easily visualizable (except for the prior probability I guess).
cheers
Bruce
On Tue, 16 Jul 2013, Yang, Daniel wrote:
Hi Bruce,
I am
Hi, Rune and Zeke
I have posted some time ago my experience with VirtualBox. I also got
similar segfaults. The only way I could run FreeSurfer without problems
was installing CentOS64 on a second hard disk so I have a dual boot
system and skipped VirtualBox. Freesurfer 5.3 also solved some
Hi Bruce,
Thanks so much! So I ran the following and obtained all the DK ROI labels.
mri_annotation2label --subject fsaverage --hemi rh --outdir my_output_dir
Then, I am wondering how I can use the label files. For example, can I overlay
it on a brain in fslview?
The label file has many
Couple of quick things in regards to smoothing prior to calculating the LI. I'm
just trying to use the fsaverage_sym atlas and improve my xhemi registration,
not conduct a thickness asymmetry analysis. Should the smoothing be done before
the xhemi registration? If so, do you have a
Hi Bruce,
Sorry for so many responses. I figured it out that I can visualize it using
tksurfer.
Besides this, can I visualize it in freeview, CARET, or some other tools? My
goal is to display the ROI on a fsaverage inflated surface.
If it can be done in freeview, could you give me some
I think in freeview the syntax would be:
freeview -f lh.inflated:label=lh.your_ROI.label
cheers
Bruce
On Tue, 16 Jul 2013, Yang, Daniel
wrote:
Hi Bruce,
Sorry for so many responses. I figured it out that I can visualize it using
tksurfer.
Besides this, can I visualize it in freeview,
Hi Anastasia,
I have tried both , 3-row and 3-column format and still wrong bvecc and
bval from flip4fsl. Could you please send me a sample of your original
files so I can compare?
On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Amirhossein - Are
Thanks a lot! It works!
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 7/16/13 10:37 AM, Bruce Fischl
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:
I think in freeview the syntax would be:
freeview -f
Hello,
I wanted to inquire if anyone knows of any articles in the literature that
quantify the differences between using FreeSurfer with and without manual
intervention.
Thank you
Liane
--
Liane Hunter
MD/Ph.D Candidate
Albert Einstein College of Medicine
I must have misunderstood the previous emails then. I though you suggested
smoothing the anatomical data prior to registration to avoid the noisy numbers.
Glad that is now cleared up, thank you.
Is there a way to find out how many vertices are on the fsaverage_sym surface?
Thank you again,
Hi Amirhossein - I'm attaching sample files.
a.y
On Tue, 16 Jul 2013, amirhossein manzouri wrote:
Hi Anastasia,
I have tried both , 3-row and 3-column format and still wrong bvecc and bval
from flip4fsl. Could you please send me a sample of your original files so I
can compare?
On Mon,
Hello,
I noticed that when I am checking the subcortical segmentation the
brainmaskdoes not accurately display the
subcortical structures
( ie. the putamen is too small). The segmentation appears to be correct
when I compare it to the original file. Does anyone know why this is the
case?
Also, if
Hi Liane
the brainmask is not for subcortical segmentation - use the norm.mgz if
you want to visualize subcortical structures
cheers
Bruce
On Tue, 16 Jul 2013, Liane
Hunter wrote:
Hello,
I noticed that when I am checking the subcortical segmentation the brainmask
does not accurately
I don't know of any, though I'm doing such a study right now.
doug
On 07/16/2013 11:00 AM, Liane Hunter wrote:
Hello,
I wanted to inquire if anyone knows of any articles in the literature
that quantify the differences between using FreeSurfer with and
without manual intervention.
Thank
I think Xiao Han or Jorge Jovicich did a reliability study and found no
detectable inter-rater effects, but I can't remember if they published it.
Maybe Jorge will chime in?
cheers
Bruce
On Tue, 16 Jul 2013, Douglas N Greve wrote:
I don't know of any, though I'm doing such a study right now.
Hello,
I have a quick question about talairach transform. I know that
FreeSurfer previously used mritotal to create the linear talairach
transform. You could check the final objective function value in the
mritotal.log file. I think the ideal value was in the ballpark of 0.06.
Is there a
Dear Freesurfer Users,
I have opened up the X.mat file from the analysis. I think that the
button regressor is the third column in the file, but I am not 100%
sure. Do you know which column the button regressor is? Below is the
background info to this question.
I am trying to regress out the
I support what Marcos found. Freesurfer does not work on CentOS in
VirtualBox because of the 3D error in the VirtualBox driver for graphics
under CentOS. I solved the problem by using Vmware player instead. It seems
more mature in the 3D driver.
If others would like to use freesurfer on a
-- Forwarded message --
From: Bruce Fischl fis...@nmr.mgh.harvard.edu
Date: Tue, Jul 16, 2013 at 12:44 PM
Subject: Re: [Freesurfer] subcortical segmentation
To: Liane Hunter liane.hun...@med.einstein.yu.edu
Hi Liane
can you cc the list so others can answer? You will get better
Hi Louis,
Thanks again for your help!
In addition, I was wondering: Would it be ok to follow the exact same
procedure/pipeline (that is the mri_robust template command, followed by the
mri_convert and mri_add_xform_to_header commands) if I only have one movable
volume (for the
On 07/12/2013 12:15 PM, Dorian P. wrote:
Dear list,
We are buying a computer dedicated mostly to Freesurfer. Initially we
thought an I7 3770k a bit overclocked (about 4.5ghz) should be a good
choice. However, I noticed that Freesurfer seem better tuned to use
CUDA. Many of the messages I
the QC on the T1 data gives no obvious clue. We edit the brainmask when
there are surface issues
However, we have not quantified this data yet - a closer look may indeed
tell us more.
Thanks
Gerit
On 16 July 2013 20:52, Pfuhl, Gerit gerit.pf...@uniklinikum-dresden.dewrote:
Hi Christine
why don't you upload the subject and we'll take a look
cheers
Bruce
On Tue, 16 Jul 2013,
Christine Smith wrote:
I have a subject for whom we have had consistent difficulties within
freesurfer. The difficulties existed for a single scan from 2008 and also
for a pair of scans
Dear FreeSurfer Experts,
I am interested in a specific ROI in the DK atlas, and I know that I can use
tkregister2 to obtain a register.dat, and then mri_annotation2label +
mri_label2vol to convert the annotation of the ROI to an .nii.gz.
However, it seems that the end product is in the TAL
Hi,
I'd like to use freesurfer to determine the center of gravity of an ROI
from a functional overlay in surface space. I've tried looking for some
sequence of commands to do this with no luck. Any suggestions? Thanks in
advance for your help.
All the best,
Tyler
use
$FREESURFER_HOME/average/mni152.register.dat
doug
On 7/16/13 8:36 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,
I am interested in a specific ROI in the DK atlas, and I know that I
can use tkregister2 to obtain a register.dat, and then
mri_annotation2label + mri_label2vol to
Tyler, you can use mri_surfcluster with the (hidden) --centroid option
doug
On 7/16/13 8:39 PM, Tyler Manning wrote:
Hi,
I'd like to use freesurfer to determine the center of gravity of an
ROI from a functional overlay in surface space. I've tried looking for
some sequence of commands to
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