-- Forwarded message --
From: Zhen Zonglei
Date: Tue, Nov 1, 2011 at 11:13 AM
Subject: Position available: Postdoc in System and Cognitive Neuroscience -
Beijing Normal University, China
To: FSL - FMRIB's Software Library
Postdoctoral positions are available to stud
Hi, Doug;
Is the bug still in FS5.0.
When I used mri_convert to reorient a 4D BOLD volume. All frames except
the first frame are discarded.
My command: mri_convert --out_orientaiton LAS f.nii.gz flas.nii.gz
Is there a convenient way to reorient the 4D volume to match the MNI
template in FSL ?
gt; think FSL has some tools to re-orient the
>
> doug
>
> Zhen Zonglei wrote:
>
>> Hi, Doug;
>> Is the bug still in FS5.0.
>>
>> When I used mri_convert to reorient a 4D BOLD volume. All frames except
>> the first frame are discarded.
>
I use FEAT from FSL to do the fMRI analysis. But the data were unpacked
with the Freesurfer unpacksdcmdir.
Zonglei Zhen
On Tue, Jan 10, 2012 at 1:49 PM, Douglas Greve wrote:
> what software package are you using to do the fMRI analysis?
> doug
>
>
> On 1/9/12 9:19 PM, Zhe
My raw BOLD data is named func.nii.gz in each run directory. It
preprocess-sess reported the ERROR: could not determine format for
S0001/obj/004/f, even I provide the –i func option.
Is there an easy way to let fsfast process the data not named f.nii.gz ?
The version I used is FS 5.1.
Dear all:
While reconstructing monkey brain with FreeSurfer, in the stage of
autorecon2, I used 'noaseg' option to avoid the segmentation. The command is
as follows:
recon-all -s monkey_040409632 -autorecon2 -noaseg -cc-crs 128 117 123
-pons-crs 128 154 108
However, FreeSurfer finally repor
Dear all:
Recon-all has finished without error in my reconstruction. However, when I
checked recon-all.log, I found three was a error “t4_read:
talsrcimg_to_711-2C_as_mni_average_305_t4 read error”.
What’s this error mean? Does it have some effects on my reconstruction?
Thanks
--
Zonglei Zhen
cording to the MP-RAGE source.
> Generation of a suitable 3T target would not be difficult.
>
> Avi
> ------
> Date: Sun, 19 Apr 2009 22:52:35 +0800
> Subject: Re: [Freesurfer] t4_read error (fwd)
> From: Zhen Zonglei
> To: Avi Snyder
> Cc: fis...@nmr.mgh.harv
gt; and all that data looks good. The most important thing is how your data
> looks. Does it look okay?
>
> I'm not sure why this message is there (Nick?) but I think you can ignore
> it.
> Allison
>
>
>
> On Sat, 18 Apr 2009, Zhen Zonglei wrote:
>
> The l
eSurfer developers may or may not wish to undertake such
> a revision. In any case, it can't happen tomorrow.
>
> Avi
> ---
> >Date: Tue, 21 Apr 2009 12:52:45 +0800
> >Subject: Re: [Frees
omparing the
> subject's QA score to a set of QA scores of known-good talairach
> alignments. The -tal-check flag runs by default in recon-all (in -all
> and -autorecon1), and will error exit if the alignment is below
> threshold.
>
> Nick
>
>
> On Tue, 2009-04-21 at 1
Hi FreeSurfer and FSL Guru:
We have analyzed our Siemens Trio 3T dti data with dt_recon, and hope to
do TBSS and FDT analysis with FSL in the next step. However, we are not very
sure that we can directly use the gradient_mgh_dtiNN.gdt in FSL. To my
understanding, FSL’s default orientation is di
econ2 directly?
My version is FreeSurfer4.3.
Thanks.
Zonglei Zhen
--
Zonglei Zhen, PhD
Assistant Professor of Cognitive Neuroscience
BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive
Neuroscience and Learning, P.R. China
___
Frees
ocessing on
> some young adult populations though.
>
> Nick
>
>
> On Mon, 2009-06-22 at 20:24 +0800, Zhen Zonglei wrote:
> > Hi all:
> > After autorecon1 was done, I corrected the talairach registration
> > manually. Next, I rerun autorecon1 on the data, but tal_che
stream: 1644
In my work, I access our linux sever remotely using VNC from a PC windows
machine. Our Linux system is centos 4.0, and the version of FreeSurfer is
4.30.
Any idea, how to resolve this problem?
Thanks
Zonglei Zhen
--
Zonglei Zhen, PhD
Assistant Professor of Cognitive Neuroscience
Hi Dr. Moore:
I met the same error reported as you posted when I used qdec in our
system. Have you already resolved this probelm ?
If you have the solution to resolve it, please give me some clues.
Thanks
Zonglei Zhen
2009/7/14 Dana W. Moore
> Hi everyone,
>
> I am trying to use qdec for t
Hi, all:
I am a naive user of fs and fsfast. Now, I am trying to do functional
connectivity analysis with fsfast. But, I actually do not know how to do
correlation analysis with a reference time course (a mean time course from a
specific ROI) in fs and fsfast? Can someone give me some cues on this
Hi, all:
When I run mkanalysis-sess -gui, Matlab reported the following error, can
someone help me solve the problem ?
Thanks very much.
Zonglei Zhen
>mkanalysis-sess -gui
Font specified in font.properties not found [-*-standard symbols
l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
Fon
Hi all:
I have installed fsl with freesurfer 4.0.1, but some errors were reported
when I run fsl:
> source new_fs.csh
Setting up Enviroment for NewFreeSurfer && new_subjects
freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1
Setting up environment for FreeSurfer/FS-FAST (and FS
Dear FS and fsfast expert:
We want to know the effect of some external regressors such as the reaction
time of every trial. We found that external regressor can be integrated into
the GLM model with mkanalysis-sess's 'extreg' option, but we did not find
the way to do comparison of these external r
Hi，all:
I have some questions related to the command of mri_surfcluster (and
mri_volcluster). The help of this command says cwsig option can give the
cluster-wise sig-map, but vwsig option will give vertex-wise sig-map. What
is the exact meaning of these options?
Does every voxel in one specifi
Hi,all:
I have some questions related to the command of mri_surfcluster (and
mri_volcluster). The help of this command says cwsig option can give the
cluster-wise sig-map, but vwsig option will give vertex-wise sig-map. What
is the exact meaning of these options?
Does every voxel in one specifi
Dear, Dr. Greve:
I hope I don't bother you too much. But I'm wondering about how to analyze
mixed blocked/event related design with FSFAST. In our experiment, we have
two blocked conditions and three event-related conditions in every block. We
are not sure how to write the parfiles and construct t
gt; starts att=0, lasts 2 sec
> 5 22 1 > starts at t=5, lasts 2 sec
> 7 2 2 1 ---> starts at t=7, lasts 2 sec
>
> The last col of 1s just means that the event weight is one (probably what
> you want).
>
> doug
>
>
> Zhen Zonglei wrote:
>
&
nii -it siemens_dicom
>
> dt_recon --i dwi.nii --s chenGN1995 --o dti_analysis
>
> doug
>
>
> Zhen Zonglei wrote:
>
> Dear, Dr. Greve:
>
> Thanks for your help. Today, when we tried to run the new function of FS
> in DTI analysis, we got stuck again. The dt_
Dear, Dr. Greve:
Sorry for bothering you again. Can you explain us what is function of
selxavg-jk-sess? We have searched its information in FS wiki and mailing
list many times, but nothing is found. Now we want to do leave-one(run)-out
feature selection, we hope this command can help us, but not
?Please help us.
Thanks in advance.
Zonglei Zhen
2008/4/6, Zhen Zonglei <[EMAIL PROTECTED]>:
>
> Dear, Dr. Greve:
>Sorry for bothering you again. Can you explain us what is function of
> selxavg-jk-sess? We have searched its information in FS wiki and mailing
> list ma
e details on this command, especially, its computational process and
> output?Please help us.
>
> Thanks in advance.
>
> Zonglei Zhen
>
>
>
> 2008/4/6, Zhen Zonglei <[EMAIL PROTECTED]>:
> >
> > Dear, Dr. Greve:
> >Sorry for bothering you again.
Hi all
When I run selxavg3-sess with a sessid which contain more than six
subjects, the procedure report some error as following:
Error in ==> fast_selxavg3 at 270
>> >> >> ??? /matlab2006b/toolbox/matlab/iofun/tempname.m: Too many files
open.
>> >> >> >>
/nfs/h1/r1/jliu/new_soft_test/freesurfer/f
024 or more. If its
> a small number, you can increase by:
>
> unlimit descriptors
>
> Nick
>
>
> On Thu, 2008-04-17 at 11:16 +0800, Zhen Zonglei wrote:
> > Hi all
> > When I run selxavg3-sess with a sessid which contain more than six
> > subjects, the proced
But after I run unlimit descriptors, the number of descriptors is still
1024.
Wjat is wrong?
2008/4/17, Zhen Zonglei <[EMAIL PROTECTED]>:
>
> Thanks,Nick.
>
> The limit descriptors our system is 1024. Is not enough for six subjects(
> six run per subject)?
>
>
Hi all:
When I run selxavg3-sess on a analysis with 'fmc' as 'funcstem', the
program report the following error,
but when I did the same analysis on the same data with 'fmcsm6' as
'funcstem', the program could run successfully.
our data was preprocessed with the command 'preproc-sess -sf cm_ses
Dear fs/fsfast user:
Would you please tell me how to do F test in fsfast? For example, I have 4
conditions, and want to test the 4x4 contrast matrix [1 0 0 0; 0 1 0 0; 0 0
1 0;0 0 0 1] with a F test. How should I use mkcontrast-sess or other
commands to construct the contrast matrix and do F test?
Oh, I see. Thanks very much.
Zonglei Zhen
2008/7/29 Doug Greve <[EMAIL PROTECTED]>
> mkcontrast-sess -a 1 -a 2 -a 3 -a 4 -c 0 -nosumconds
>
> should do it
>
> doug
>
> Zhen Zonglei wrote:
>
> Dear fs/fsfast user:
> Would you please tell me how to do F t
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