Dear FreeSurfer experts,
we did a FreeSurfer-Analysis of cortical thickness in schizophrenia patients
with motor abnormalities and found significant changes of cortical thickness in
many brain regions. The Qdec p-maps showed many regions with surface size
exceeding 100mm2. We used a 15mm
Dear FreeSurfer experts,
we did a FreeSurfer-Analysis of cortical thickness in schizophrenia patients
with motor abnormalities and found significant changes of cortical thickness in
many brain regions. The Qdec p-maps showed many clusters (regions) with
surface size exceeding 100mm2. We used
Hi,
my name is Martina and I'm a student of biomedical engineering in Rome. I'm doin
g a brain imaging research for my final exam.
I'm using freesurfer for registration and segmentation of brain images instead o
f FSL tools (flirt,bet and fast) and then continue to process the data with FSL.
On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote:
Hi Doug
Strangely, the basic mri_concat command now worked, and so did the full
one. I think I initially had a \ at the end of my command, just after the
file name, which should not have been there; although having tried again
with
Hi Andreas
I don't think it's about the OS (I'm on WInXP SP3, 32 bit, hosting Linux
using Vritualbox), but about the environment variables, even though from
what I could see, I had them all correctly set. I gave up and am just
running this through FSL..
Tudor
On 18 March 2013 11:13, Andreas
Hi freesurfer masters,
so I created the '.licence' file in the freesurfer_home, with the 3 lines
of the mail with licence i recieved.
And when testing up freesurfer, as they say
herehttp://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer,
I receive the
ERROR: FreeSurfer license file
Hello,
I obtained a map of cortical thickness asymmetries after the registration on
the symmetric atlas. But I would to obtain the same map with raw data I mean
just by subtract lh.thickness and rh.thickness. How can I modify the part
#Create a stack of subjects in wiki page ? I have to
Hi Dusan
the one significant confound that you have to worry about is subject
motion being substantially more in your patient population. You might try
rating them for motion blinded to group and see if there is an inbalance.
cheers
Bruce
On Sun, 17 Mar
2013, Dusan Hirjak wrote:
Dear
Hi Martina
we analyze the data in native coordinates not MNI/talairach ones. You can
convert volumes to tal coords using either mri_vol2vol or mri_convert and
the talairach transform found in
$SUBJECTS_DIR/$subject/mri/transforms/talairach.xfm
cheers
Bruce
On Mon, 18 Mar 2013,
Hi Alice, I would check out whether autocorrection of the defects in
that area were done properly. You create a segmentation of the defects
with defect-seg. It might not be in 5.0, so I've attached it. It might
not work properly in 5.0. If so, you'll have to download 5.2 (you can
have two
you will have to use the same stream, just specify one subject when your
mris_preproc
doug
On 03/18/2013 08:06 AM, Sophie Maingault wrote:
Hello,
Iobtained a map of cortical thickness asymmetries after the
registration on the symmetric atlas. But I would to obtain the same
map with raw
We use the MNI305through the (affine) talairach.xfm transform.
doug
On 03/17/2013 11:47 AM, Bruce Fischl wrote:
Hi Longchuan
I'm not sure what space the volume average is constructed in - Doug
would know. Probably talairach, in which case it won't match the
surfaces well. Can you send along
Hi Karen
not the s in /home/karen/freesurfer/.license (that is, .license
not .licence)
cheers
Bruce
p.s. I'll admit I had to look at your email 3 or 4 times before I figured
this out :)
On Mon, 18 Mar 2013, Karen Duarte wrote:
Hi freesurfer masters,so I created the '.licence' file in
The wm-anat-snr script (attached in case you don't have it) is good at
picking out cases with motion-related noise. You get one number for each
subject, and you can then do a statistical comparison between groups on
that one number.
doug
On 03/18/2013 03:06 AM, Dusan Hirjak wrote:
Dear
The values look about right in the table. Your pipeline looks ok,
thought the last step uses fa_FOLDER-NAME.mask.nii instead of the output
of mri_vol2vol (fa_FOLDER-NAME.nii).
doug
On 03/17/2013 02:16 AM, Rotem Saar wrote:
Hi all,
I run into somthing that seems odd to me and wanted
Hi Alice,
you might also see what Rahul (ccd) thinks if you send an image.
cheers
Bruce
On Mon, 18
Mar 2013, Alice Burnett wrote:
Hi FreeSurfer experts,
I have been working with a dataset we have run through FreeSurfer 5.0 and am
interested in the medial orbitofrontal
region (Desikan
The Memory and Neuroimaging lab (PI: Scott M. Hayes;
http://www.bu.edu/brainlab/), integrated with the Memory Disorders Research
Center and Neuroimaging Research Center at VA Boston Healthcare System, is
currently accepting applications for a full-time neuroimaging research
assistant to begin in
No, it is not, the target needs to be fsaverage_sym
doug
On 03/18/2013 09:13 AM, Sophie Maingault wrote:
So I do : mris_preproc --target fsaverage --xhemi --hemi lh --paired-diff
--meas thickness --out lh.lh-rh.thickness.sm00.mgh --s t0001 --s t0003 --s
t0009 --s t0027 --s t0031 --s t0033 --s
It is possible, it is just not a good idea because if you map rh to lh
and then compare to lh, the rh will have been interpolated to get it
into the lh. Even if there are no differences between the two, you will
see differences because of the interpolation. Mapping both to
fsaverage_sym means
Hello freesurfer experts,
I am doing some TBM analysis and I am looking for the definition of
Medial temporal lobe. According to the definitions I found out they are
hippocampus+amygdala+brainstem+parahippocampal regions+entorhinal region.
I can get hippocampus and amygdala ROI from aseg.mgz;
Hey Martin,
Thanks for your quick response and all the great work you've done on the
longitudinal pipeline. Replacing the LongQdecTable.py did the trick.
Thanks again,
Chris
On Thu, Mar 14, 2013 at 12:38 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu
wrote:
Hi Chris,
try to
rename the
Hi Mehul,
that should work. Let us know if you have any problems.
Kind regards,
Juan Eugenio Iglesias
On Sat, 2013-03-16 at 14:29 -0700, Mehul Sampat wrote:
Hi Folks,
I had a question about the hippocampus subfield segmentations as
described here :
Hello All,
I am trying to do a cross-subject surface based analysis of data analysed using
FSL. I am following the instructions in the following tutorial link.
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer
Each of my subject data comprises of two runs. My question is
Hi everyone,
I'm a very new fresurfer user and I have to understand the very simple
basis of its use yet.
So I have some maybe stupid questions about that.
I heve to work on cortical thickness, so I suppose I have to complete the
segmentation and then correcting CPs and Pial surface.
The first
Hi Claudia
the first thing to do is run recon-all -all to complete a recon. Then you
look through your data (surfaces overlaid on volumes) and determine if it
is accurate (or accurate enough). If not, then control points are one
possible intervention, and yes you would put them in regions of
yes I'm sorry, I'm new here.
thanks a lot.
claudia
2013/3/18 Bruce Fischl fis...@nmr.mgh.harvard.edu
Hi Claudia
can you cc the list so others can answer? I would view the ?h.pial and
?h.white surfaces over the norm.mgz and see if you think they are accurate.
If not, there are various
Hi
You would probably like to include :
- the parahippocampal gyrus
- the hippocampus
- the amygdala
but not the brain stem
The question is more complex for the entorhinal area since it is a part of the
parahippocampal gyrus. To make things simple :
- the hippocampus lies at the
Hi, Bruce
Thank you for the information. I tried all possible combinations of mris_fill
command line and none of them worked. Also, I loaded my ?h.white in tksurfer
and confirmed that the surface is there. Do you want me to send you the surface
file?
One example I used is this:
mris_fill
Dear FreeSurfer experts,
I have run a longitudinal study considering multiple time points (7
scans/subject on average) with FS 5.1. However, I am interested in the
percent changes between two time points only (between 0 and 6 months
and between 0 and 1 year). Should I run the longitudinal stream
i am trying to computer the LGI local gyrification index with freesurfer. I
have Matlab on my machine.
I got the following error:
recon-all -s freesurfer -localGI
Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Hi Yolanda,
actually it is advantageous if the template is build from more time
points. You don't need to process the images again, just do your
statistical analysis with the time points you are interested in.
But: why restrict the statistics to a subset of the data? If you are
interested in
Hi Jon,
It looks like the matlab path is not set on your machine. Can you set the $PATH
environment variable to include the path to the matlab functions as well? You
can try to launch the command getmatlab, if you get the answer that matlab is
not installed, it means that the $PATH
Hi Joy-Loi,
so you have 2 time points? the first with a single scan, the second with
two within-session scans that you want to average? I don't understand
exactly what you are trying to do. To test differences in reliability
you'd have to scan a bunch of subjects twice in a session and then
Hi Ashley
I think including them would potentially bias your results if for example
more of your scans with T2s were controls or some such.
cheers
Bruce
On Mon, 18 Mar 2013,
Ashley Shurick wrote:
Hi all,
I have a similar question: My T2 scans are similar to Nicola's -
approximately .86 x
Hi Mariam, combine the runs ina gfeat analysis, then follow the
instructions in section 1.2 of
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat
doug
On 03/18/2013 10:53 AM, Mariam Sood wrote:
Hello All,
I am trying to do a cross-subject surface based analysis of data
Hi Akio
what was your full command line?
cheers
Bruce
On Mon, 18 Mar 2013, A. Yamamoto wrote:
Hi,
After upgrading to FreeSurfer 5.2.0, the command with -subcortseg flag
exited with the following error.
MRISread(/usr/local/freesurfer/5.2.0/dist/subjects/test/surf/lh.white):
could not
Hi Jon,
I guess you don't have the image processing toolbox installed with matlab?
fspecial is a matlab function comprised in this toolbox… I am afraid that lGI
with not run without it.
Marie
On Mar 18, 2013, at 12:03 PM, Jon Wieser wie...@uwm.edu
wrote:
I added the matlab bin directory
Hi all,
I have a similar question: My T2 scans are similar to Nicola's -
approximately .86 x .86 x 4.5mm. However, about 60/168 subjects don't have
T2 scans. Would you recommend including the T2's for the subjects who have
them, or excluding the T2 scans altogether?
Thank you in advance for your
Hi list,
I'm noting that registration of DWI and T1 images for some subject is wrong (in
the .mincost the first value is netx to 1.1).
Before recall new recon-all, trace-all .. what do you advise me?
Stefano
___
Freesurfer mailing list
Three things:
1. Make sure they are the same subject
2. Make sure they are not left-right reversed
3. Most likely it is that the initial registration failed. This is done
with FSL. There are a couple of options:
a. If the anat and dti were collected within the same session, you
can try
I installed virtualbox 4.2.8 and CentOS6 (kernel
2.6.32-358.2.1.el6.x86_64). Got tkmedit and tksurfer working on CentOS VM.
Recon-all starts and run for sometime but stop with errors a bit later. On
bright side I noticed freeview works great both on centos VM and on Fedora
18. At your site, I
Dear FreeSurfer Experts,
I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161 subjects,
and I'm interested in rh_superior_temporal_sulcus_thickness in particular.
Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in 5.2.0.
They are significantly different,
Hi Bruce,
Here are command lines I used:
recon-all -s test -i ./sample-001.mgz -i ./sample-002.mgz -autorecon1
recon-all -s test -subcortseg
The error occurred in the final process, i.e. calculation of stats on the
automatic segmentation.
Thanks,
Akio
2013/3/19 Bruce Fischl
I concur. I have seen similar results in primary visual cortex from ~40
subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to 1.9 in
V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3.
Ritobrato Datta, Ph.D.
Post Doctoral Researcher
Department of Neurology
University
Do the surfaces look correct in these regions? You might post some
screenshots of subjects who have a big difference between 5.1 and 5.2 with
the 5.1 and 5.2 white and pial surfaces on volume slices that highlight
the difference. Without this kind of info, its hard to know which was
more
Hi Freesurfer experts,
I'm hoping you can help me understand how to interpret interactions in
clusters identified in whole brain analysis using glmfit and glmfit-sim.
Below I describe what I've done and what I'd like to be able to do. Any
suggestions would be most appreciated!
- I have two
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