Dear All,
I am looking to hire a postdoc to develop machine learning algorithms for fMRI.
Topics are flexible. Example topics include dynamic functional
connectivity, meta-analysis, neural mass modeling, monkey-human
homologies, mental disorder subtypes, etc.
Other details below.
Regards,
Thoma
Hello JorgeTrying to set up for running Linear Mixed Effects. My design has 3
groups (HC, PT relatives and PT) and therefore I am not using QDEC as suggested
in the tutorial. My first question: Are there any changes from the matlab
commands you suggest in the tutorial if using fsgd rather than Q
Thanks Douglas
Now it's ok.
I checked the OSX version. My OSX version was 10.9.5.
I removed the XQuartz 2.7.7 and installed 2.7.5
I run this command is below
recon-all -all -i
/Volumes/yang/S002_AD1118_20090116/NCKU-0003--1.dcm -s S002_20151005
( remove -sd and -ba_labels)
thank you
Hi Simon,
Since you are using the HCP data, this may be more appropriate for the HCP-Users list.
If you look at the current HCP pipeline code, you'll see that after converting FS surfaces to .surf.gii (using 'mris_convert'), an affine transform is then
applied based on the c_ras contents (
Hi Bruce,
I did check the output recon by using mris_euler_number, all the results of
?h.pial, ?.white and also ?h.inflated returned with: 0 holes. But the
result from lh.inflated.nofix was: 28 holes.
When I load the 3D images of ?h.inflated.nofix in freeview, it appears alot
of holes and also han
Forwarded Message
Subject:OHBM 2016 Call For Council Nominations
Date: Mon, 05 Oct 2015 09:59:50 -0500
From: i...@humanbrainmapping.org
Reply-To: i...@humanbrainmapping.org
To: gr...@nmr.mgh.harvard.edu
Dear OHBM Member:
Why is strong leadership so imp
Dear Ruopeng,
I have the same problem with missing toolbars in freeView, however I am not
successful with command
defaults delete edu.harvard.mgh.nmr.FreeView
The command shows:
defaults delete: couldn't remove non-existent domain
edu.harvard.mgh.nmr.FreeView
My command
defaults domains
Hi Doug,
Thanks for the file, do you happen to have one that is compiled for a 64bit
mac installation of freesurfer?
Cheers!
Cheers,
*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.
Honorary Research Fellow
School of Physics, Facu
Dear freesurfer experts,
I have an issue with -autorecon2-wm stage results (freesurfer v.5.3.0).
Sometimes the ventricles are not fully filled and the white matter is
localized within the remaining gaps. After manually filling the gaps in
the wm.mgz (following the wiki - Fixing Common Geometric
Hi Trinh
the inflated.nofix files are the ones before the topology fixer so they
will always have defects in them
cheers
Bruce
On Mon, 5 Oct 2015, Thục Trinh wrote:
Hi Bruce,
I did check the output recon by using mris_euler_number, all the results of
?h.pial, ?.white and also ?h.inflated ret
What system are your running it on? I found it strange "defaults
domains" only shows one item.
On 10/05/2015 11:23 AM, Antonin Skoch wrote:
Dear Ruopeng,
I have the same problem with missing toolbars in freeView, however I
am not successful with command
defaults delete edu.harvard.mgh.nmr.F
Can you also try
delete ~/Library/Preferences/edu.harvard.mgh.nmr.FreeView.plist
Try that and "defaults delete..." together.
On 10/05/2015 12:16 PM, Ruopeng Wang wrote:
What system are your running it on? I found it strange "defaults
domains" only shows one item.
On 10/05/2015 11:23 AM, Anto
Hello,
We are interested in finding a way to use particular parcellations from
Freesurfer in a separate program. For instance, we are very happy with
the way Freesurfer parcellates the Choroid Plexus and separates the
Cerebellum into white and gray matter regions, and would like to import
thes
Hi Eli
sure, you can use mri_extract_label and specify the output volume as .nii
(or .nii.gz)
cheers
Bruce
On Mon, 5 Oct 2015, Rockers, Elijah D. wrote:
Hello,
We are interested in finding a way to use particular parcellations from
Freesurfer in a separate program. For instance, we are very
Hi Ana
you might need to fix the labeling in the aseg. If you can't get this to
work feel free to upload and we will take a look
cheers
Bruce
On Mon, 5 Oct 2015,
Anastasia Klimovich-Smith wrote:
> Dear freesurfer experts,
>
> I have an issue with -autorecon2-wm stage results (freesurfer v.5.3.
Hi,
I got the following error during my first time running the mri_glmfit command:
mri_glmfit --y Model1_Maltx_ParentEd_Sex_Age_n58-lh-thickness.mgh --fsgd
Model1_Maltx_ParentEd_Sex_Age_n58.fsgd --C Model1_Maltx.mtx --C
Model1_ParentEd.mtx --surf fsaverage lh --glmdir
Model1_Maltx_ParentE
Hi All,
If I use mri_vol2surf to sample the functional volume onto surface, how can I
extract the time series from surface vertices corresponding to certain ROI or
Label which were created by freesurfer.
Thanks!
Yun
___
Freesurfer mailing list
Free
Hi,
I got a problem with recon-all of T1's. The problem is that the
surfaces extent into what is essential noise, see linked images. The
problem is reoccurring in all the subjects I have ran so far, so I was
wondering if there could be a generic fix or if it will be necessary
to fix each recon ind
Hi Mads
my guess is that this is a problem with the MP2RAGE. We don't see this in
the mprage or memprage. Can you look at the PD images in that region? Is
the PD close to 0? Maybe you can threshold it out? That region is usually
very dark on an mprage
cheers
Bruce
On Mon, 5 Oct 2015, Mads Je
Hi and thanks for the fast reply.
Pardon my ignorance, but I am not sure that the PD images are?
thanks,
mads
On 5 October 2015 at 21:59, Bruce Fischl wrote:
> Hi Mads
>
> my guess is that this is a problem with the MP2RAGE. We don't see this in
> the mprage or memprage. Can you look at the PD
I thought mp2rage lets you derive a proton-density (PD) weighted image, but
I could be wrong. I'll cc Andre van der Kouwe who will know
On Mon, 5 Oct 2015, Mads Jensen wrote:
> Hi and thanks for the fast reply.
>
> Pardon my ignorance, but I am not sure that the PD images are?
>
> thanks,
> mad
I think the standard MP2RAGE only generates the T1 image on the scanner.
With the Bloch simulation you can also figure out PD but the online
image analysis doesn't do it.
On 10/05/2015 04:21 PM, Bruce Fischl wrote:
> I thought mp2rage lets you derive a proton-density (PD) weighted image,
> but I
Hi Dusan,
setenv is used when you are using tcsh. since you are using bash, you can run
this command to set your language:
export LANG=en_US.UTF-8
Hope this helps.
Best,
Lee
On Tue, 29 Sep 2015, Dusan Hirjak wrote:
Thank you very much for your suggestion. Now it has worked well.
However,
Hi,
From the following output, how should I proceed?
Thank you very much
Timothy Le
> On Oct 2, 2015, at 11:55 AM, Timothy Quang-Tin Le wrote:
>
> Hi,
> Thank you very much for your response. The output of that command was:
>
> tle7@sni-vcs-gotlib:~$ ls -l /home/tle7/freesurfer/bin/mri_convert
Hi Dusan,
On the RepeatedMeasuresAnova page you sent, the last command doesn't include
the --surface flag. You can try running your command without that part:
mri_glmfit --glmdir lh.rmanova --y lh.thickness.sm15.mgh --fsgd long.table.fsgd
doss --C contrast.mtx --C contrast2.mtx --C mean.mtx
Not sure what it is. Can you send the Xtmp.mat file from the output folder?
On 10/2/15 5:47 PM, Morenikeji Adebayo wrote:
Just following up on this - thanks!
On Sep 29, 2015, at 1:29 PM, Morenikeji Adebayo
mailto:k...@nmr.mgh.harvard.edu>> wrote:
Hi there,
I’m running into difficulty execut
I don't think it is a matlab problem. We call some binaries from inside
matlab, and the problem is with those. It looks like the version of FS
does not match your operating system or that you are missing a library.
Maybe Zeke can help sort it out.
doug
On 10/5/15 2:31 AM, Desiree Thielemann wro
here you go
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol.mac64
On 10/5/15 11:24 AM, Kevin Aquino wrote:
Hi Doug,
Thanks for the file, do you happen to have one that is compiled for a
64bit mac installation of freesurfer?
Cheers!
Cheers,
*Dr Kevin Aquino*
Rese
mri_segstats with the label option. Specify --id 1 and use the --avgwf
output option to get the full time course
On 10/5/15 1:34 PM, Yun Wang wrote:
> Hi All,
>
> If I use mri_vol2surf to sample the functional volume onto surface, how can I
> extract the time series from surface vertices corres
Hi Andrea, can you send the files in their original format (not rtf)?
On 10/5/15 12:58 PM, Gold, Andrea (NIH/NIMH) [F] wrote:
Hi,
I got the following error during my first time running the mri_glmfit
command:
mri_glmfit --y Model1_Maltx_ParentEd_Sex_Age_n58-lh-thickness.mgh
--fsgd Model1_M
Yes, they do. There is also a pcc.nii.gz which is the partial
correlation coefficient.
On 9/30/15 1:14 PM, Jiahe Zhang wrote:
Dear Freesurfer experts,
The freesurfer command 'selxavg3-sess' outputs many files in the
contrast folder in addition to the three documented on the Wiki (ces,
cesvar
It is never good to mix versions, so I would re-do it.
On 9/29/15 1:45 PM, Desiree Thielemann wrote:
> Thanks Doug!
>
> I have another question: We did the fsfast analysis some time ago before
> we updated freesurfer version with fast_selxavg3. Now we want to analyse
> additional persons. Do you t
On 9/29/15 3:36 PM, Martin Tisdall wrote:
> I am trying to produce a scalar overlay from PET data to overlay onto the
> pial surface.
> I have coregistered the pet with T1.mgz and then used the transform from
> mri_info --scanner2tkr to co-localise with orig.mgz.
What does that mean? You'll nee
Yes, my data have been normalized to the MNI space. So, in my case, what should
I do if I want to use the mri_surf2vol function?
Best,
Feng
发件人：Douglas Greve
发送时间：2015-09-29 00:00
主题：Re: [Freesurfer] Question about the volume conversion in freesurfer
收件人："freesurfer"
抄送：
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