Re: [Freesurfer] mri_cvs_register : output

[Lilla Zollei]

Hi Elijah,

Yes, it is.

Lilla

On Sun, 20 Mar 2016, Elijah Mak wrote:


Hi Freesurfer Community,

I am running mri_cvs_register for the spatial normalization and it seems to 
work very nicely on my set of DTI data in subjects with substantial atrophy. 

However, I can't seem to find the file 
combined_tocvs_avg35_elreg_afteraseg-norm.m3z, however, I have 
final_CVSmorph_tocvs_avg35.m3z. Is this essentially the same thing?

Thanks for looking into this.

Best Wishes,
Elijah


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Re: [Freesurfer] mixed models and longitudinal streaming

[Martin Reuter]

Hi Angela,

the smooth function seems to be part of the curve fitting toolbox
http://www.mathworks.com/help/curvefit/smooth.html
so either that is missing, or your version is too old.
You can skip the lowess Plot (it is just for initially checking the data).


Make sure your M has the same number of rows as your Y (and as the sID). 
Also make sure you are computing the ni (and sorted M and Y) like this 
(if your first column in M is the time, else specify the column with the 
time as the second parameter):

[M,Y,ni] = sortData(M,1,Y,sID);  # (sorts the data)


Best, Martin



On 03/20/2016 04:38 PM, Angela Favaro wrote:
> Dear Freesurfer experts,
> I need some help with the longitudinal streaming and the use of mixed
> models in matlab.
> I followed all the instructions and tried to use the following
> commands in matlab:
>
> lme_timePlot(M(:,1),Y,ni)
> and this worked well
>
> However, when I tried this:
> lme_lowessPlot(M(:,1),Y,0.70,M(:,2))
>
> matlab gave the following error message:
>
> Undefined function 'smooth' for input arguments of type 'double'.
> Error in lme_lowessPlot (line 49)
>   ybw = smooth(st,dat(ix),bw,'rlowess')
>
> I checked in my version of matlab (R2012b) and the command 'smooth'
> does not exist
>
> Further, when I tried this:
>
> lhstats  = lme_fit_FS(X,[1 2],Y,ni)
>
> Error using  -
> Matrix dimensions must agree.
>
> Error in lme_fit_init (line 42)
>   ri = yi-Xi*Bhat;
>
> Error in lme_fit_FS (line 71)
> [D,phisq] = lme_fit_init(X,Zcols,y,ni);
>
> Looking into the matlab code, I observed that in line 42 there is no
> command.
> and I am sure that matrix dimensions are correct.
>
> So, I have problems in solving these issues... Any help is greatly
> appreciated!
> Is it a problem of Matlab version?
> Thank you!
>
> Angela
>
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>

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] longitudinal data analysis

[John Anderson]

Hi Dr Martin
I want to study the change in cortical thickness overtime in one group of subjects.


I have only one group of subjects who scanned multiple times ( two time points and more)

I followed the pipeline exactly as in wiki.

I want to inquire about  X in this case . Is it supposed to be 1 ( one group)

In wiki they used the follwoing x=[ones(length(M),1) M M(:,1).M*(:2)] how this formulla will be for one group of subjects?

 

 

Bests,
John
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Re: [Freesurfer] longitudinal data analysis

[Martin Reuter]

Hi John,


X is the design matrix. The rows are the total number of time points for 
all subjects, the columns the different parameters of your model.


In the wiki example, the first column is all 1s (intercept) the second 
is the time_from_baseline and other parameters that are in the matrix M 
(M was read from the qdec table file), the last column is the 
interaction between the first and second column in M (so probably time X 
group interaction).


So for you,  you probably have
column of ones, time_from_baseline and potentially other control 
variables (age_at_baseline, gender, scores? IQ.. whatever you want).
Only having 2 columns (ones for the intercept and time for the slope) 
allow you to test
- if whatever you test is different from zero (intercept), usually that 
is the case, as you measure volume or thickness
- if the longitudinal slope is different from zero, usually that is also 
the case, but sometimes you don't have enough power to find that effect.


So that does not really tell you much. For most interesting questions 
you need two groups.


Best, Martin


On 03/21/2016 12:40 PM, John Anderson wrote:

Hi Dr Martin
I want to study the change in cortical thickness overtime in one group 
of subjects.


I have only one group of subjects who scanned multiple times ( two 
time points and more)

I followed the pipeline exactly as in wiki.
I want to inquire about  X in this case . Is it supposed to be 1 ( one 
group)
In wiki they used the follwoing x=[ones(length(M),1) M M(:,1).M*(:2)] 
how this formulla will be for one group of subjects?

Bests,
John


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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] mris_fix_topology with ROI surface

[Ajay Kurani]

Hi Freesurfer experts,
   I wanted to create a Freesurfer surface on some of the aseg ROIs.  I was
able to run mri_tesselate, mris_smooth, mris_inflate and mris_sphere some
of the subcortical volumes for creating a surface.

The mri_sphere had a big chunk that was deleted and so I wanted to run
mris_fix_topology to fix this issue.  In trying to run this command it
appears that mris_fix_topology tries to correct based off of a brain sphere
(which this ROI is clearly not) and therefore it fails.  I plan to then run
subsequent steps such as mris_euler number and mris_remove_intersections

1) Is there any way to fix the topology of this ROI using freesurfer tools
or a way to work around this issue?  Do you feel the sphere is needed for a
small subcortical surface (ie globus pallidus) or is this really more for
complex structures such as cortical surfaces?

2) Is there a recommended set of steps to accomplish creating a surface
from the ROI that is different from what I stated?


Thanks,
Ajay
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Re: [Freesurfer] longitudinal data analysis

[John Anderson]

Dear Dr Martin,

Thanks you very much for your awesome clarification and your kindness!!

Bests,
John 

 


Hi John,


X is the design matrix. The rows are the total number of time points for all subjects, the columns the different parameters of your model.

In the wiki example, the first column is all 1s (intercept) the second is the time_from_baseline and other parameters that are in the matrix M (M was read from the qdec table file), the last column is the interaction between the first and second column in M (so probably time X group interaction).

So for you,  you probably have
column of ones, time_from_baseline and potentially other control variables (age_at_baseline, gender, scores? IQ.. whatever you want).
Only having 2 columns (ones for the intercept and time for the slope) allow you to test
- if whatever you test is different from zero (intercept), usually that is the case, as you measure volume or thickness
- if the longitudinal slope is different from zero, usually that is also the case, but sometimes you don't have enough power to find that effect.

So that does not really tell you much. For most interesting questions you need two groups.

Best, Martin
 

On 03/21/2016 12:40 PM, John Anderson wrote:






Hi Dr Martin
I want to study the change in cortical thickness overtime in one group of subjects.


I have only one group of subjects who scanned multiple times ( two time points and more)

I followed the pipeline exactly as in wiki.

I want to inquire about  X in this case . Is it supposed to be 1 ( one group)

In wiki they used the follwoing x=[ones(length(M),1) M M(:,1).M*(:2)] how this formulla will be for one group of subjects?

 

 

Bests,
John

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[Freesurfer] extracting pial surface area numbers...

[Karl Liu]

Dear FS team,


My question is how I should extract the measure of pial surface area from a
significant cluster after group-analysis. I performed statistical analysis in
QDEC, choosing pial surface area as the measure. I found a significant cluster.
Now I would to extract the surface area of this cluster from each subject, so
that I can plot the group means.  But the
numbers I got from the "cache.th20.neg.y.ocn.dat" file are quite
small (mean centered at ~1). I am wondering how I should get the correct numbers
from each subject.


thank you in advance


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Re: [Freesurfer] mris_fix_topology with ROI surface

[Bruce Fischl]

Hi Ajay

Florent Segonne developed some volumetric topology correction algorithms 
as well as surface-based ones when he was here. Try 
mri_topologycorrection and see how it works for you (although be warned 
that we haven't tried it in ages)


cheers
Bruce


On Mon, 21 Mar 2016, 
Ajay Kurani wrote:



Hi Freesurfer experts,   I wanted to create a Freesurfer surface on some of
the aseg ROIs.  I was able to run mri_tesselate, mris_smooth, mris_inflate
and mris_sphere some of the subcortical volumes for creating a surface.  

The mri_sphere had a big chunk that was deleted and so I wanted to run
mris_fix_topology to fix this issue.  In trying to run this command it
appears that mris_fix_topology tries to correct based off of a brain sphere
(which this ROI is clearly not) and therefore it fails.  I plan to then run
subsequent steps such as mris_euler number and mris_remove_intersections  

1) Is there any way to fix the topology of this ROI using freesurfer tools
or a way to work around this issue?  Do you feel the sphere is needed for a
small subcortical surface (ie globus pallidus) or is this really more for
complex structures such as cortical surfaces?   

2) Is there a recommended set of steps to accomplish creating a surface from
the ROI that is different from what I stated?


Thanks,
Ajay

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[Freesurfer] Create a surface overlay with statistic results using AAL ROI

[carolina.mr]

Hi all,
 
I have some statistical results for AAL 90 coordinates (correlation coefficients from network measurements x clinical data).
 
I would like to create an overlay to visualize in FreeSurfer standard (fsaverage) space, showing the areas with positive and negative correlations (and the scale / power of correlation, i.e. beta-value, for each area).
 
Is it possible using FreeSurfer tools? If it is possible, how should I produce a .txt file to be read in FreeSurfer.
 
Kind regards,
Carolina 
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[Freesurfer] Postdoctoral Position in Infant Brain MRI Analysis

[gangli]

Postdoctoral research associate positions are available at the Infant Brain
Mapping Lab in the Department of Radiology and Biomedical Research Imaging
Center (BRIC) at the University of North Carolina at Chapel Hill. Our
current focuses are to better understand the dynamic and critical early
brain development in health and disease, via multimodal neuroimaging
analysis. The successful candidate will support our efforts either in
advancing neuroimaging analysis technologies or in neuroscience
applications. We are seeking highly motivated individuals who have
extensive research experience in neuroimaging analysis (e.g., structural,
diffusion or functional MRI) and demonstrated academic excellence,
including publications in first-class journals and conferences. The
candidate for Postdoctoral Research Associate should have a Ph.D. (or
equivalent) in Neuroscience, Computer Science, Applied
Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, or
related fields. Good command of programming tools including Matlab, C/C++,
Linux, and scripting are necessary to carry out the research work in this
group.


The successful candidate will be part of a diverse group including
neuroscientists, radiologists, psychologists, physicists, biostatistician,
and computer scientists, and will build upon the group's extensive
foundation on neuroimaging analysis. If interested, please email resume to
Dr. Gang Li (gang...@med.unc.edu).
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Re: [Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

[Francis Tyson Thomas]

Hi Richard,

The first part was smooth. I got it done pretty quickly (installing CUDA
and setting it up!). However for the freesurfer portion I have two
questions,

1. Bruce mentioned in another email thread that v6 beta should be out in a
week or so after testing is completed. Should I wait for that version,
assuming I get the source code for v6 when I download it as per the
instructions on the freesurfer page.

2. Also, would I have to compile and build all modules (mri_em_registe,
mri_ca_register etc or can I limit to just these two when I build it again.

I'm not very well versed with the second part and so if you could explain a
little more it will be good.

Thanks,
Tyson

On Mon, Mar 7, 2016 at 6:38 PM, R Edgar  wrote:

> On 7 March 2016 at 11:25, Francis Tyson Thomas
>  wrote:
>
> > That information was a lot helpful. At this point I'm currently trying to
> > reduce the recon-all processing time as much as possible and for this
> reason
> > I was looking to get the -use-gpu flag working. I'm currently running a
> > freesurfer v6 beta version on Ubuntu 14.04.4. With regard to the graphic
> > card it is a dual K2200 configuration (I guess they are running in sli
> > configuration - although I'm not completely sure).
> >
> > When you mentioned you compiled everything, I believe you were referring
> to
> > compiling CUDA 7.5 for Ubuntu 14.04. Because after seeing the link -
> > https://developer.nvidia.com/cuda-gpus
> > -  we settled for CUDA 5 since it was the compatible version mentioned
> for
> > K2200. Does that mean CUDA 7.5 is backwards compatible with a slight
> > tinkering and can be used with freesurfer 6.0 ?
>
> I think that you might have misunderstood the NVIDIA page.
>
> It lists the K2200 as a Compute Capability 5 GPU (just like my K1200).
> The Compute Capability refers to the hardware:
>
> http://docs.nvidia.com/cuda/cuda-c-programming-guide/index.html#compute-capabilities
> Compute capability 5 is also called "Maxwell," while the work I did on
> Freesurfer was around the time of Compute Capability 2, known as
> Fermi. In CPU terms, GPU compute capabilities are a bit like Ivy
> Bridge vs Sandy Bridge (although I think that GPU features vary more
> than the CPU ones).
>
> In order to program the GPU, you need the NVIDIA CUDA Toolkit, which
> contains the required compiler (nvcc). The current version of this is
> 7.5. I installed it by following the instructions on NVIDIA's website:
> http://docs.nvidia.com/cuda/index.html
> This was quite straightforward (certainly moreso than it was five or
> six years ago, when you could never be sure that your X11.conf would
> survive).
>
> Either with the toolkit, or as a separate install, you can get a lot
> of examples from NVIDIA. I'd suggest grabbing those, and making sure
> that you can compile them. The "DeviceQuery" one will probe your PCIe
> bus, and report what GPUs it finds.
>
> > I however tried to setup CUDA 5 following the instructions in the link -
> > http://www.unixmen.com/how-to-install-cuda-5-0-toolkit-in-ubuntu/ -
> however,
> > I'm not able to get it running. I keep getting the following error
> "Unable
> > to acquire CUDA device". Does this sound familiar ?
>
> I suspect (although I wasn't following things at the time) that the
> Toolkit v5 was before Maxwell cards were released. If so, then it
> wouldn't know what to do with the GPUs.
>
> For the record, since I was writing the CUDA bits so long ago (for the
> volume side of things - I didn't do the surface accelerations), they
> only use Fermi features. For this reason, you'll want to make sure
> that you have --enable-fermi-gpu when you run configure (and make sure
> that it's picking out your CUDA installation - I had to tweak the
> configure script for this).
>
> > If you can share some more information in setting this up it will be
> great
> > since the amount of time recon-all takes is quite too long for running
> > multiple datasets. Most importantly we are concerned about the
> hippocampal
> > segmentation in freesurfer 6 rather than recon-all and so speeding this
> up
> > would be extremely helpful.
>
> I don't know if those portions benefit from CUDA acceleration at this
> time. I focused on mri_em_register and mri_ca_register. Even if other
> programs (which ones are they?) can be linked against some of the
> accelerated routines, there is no guarantee of speed up - the time to
> shuffle data to and from the GPU is typically greater than the speedup
> of any one routine.
>
> Hope this helps,
>
> Richard
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>
>
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Re: [Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

[R Edgar]

On 21 March 2016 at 19:59, Francis Tyson Thomas
 wrote:

> The first part was smooth. I got it done pretty quickly (installing CUDA and
> setting it up!). However for the freesurfer portion I have two questions,
>
> 1. Bruce mentioned in another email thread that v6 beta should be out in a
> week or so after testing is completed. Should I wait for that version,
> assuming I get the source code for v6 when I download it as per the
> instructions on the freesurfer page.

Which version of the source code do you have access to? I'm using the
read-only git repository of the main development trunk, sending
patches back to Zeke, which he puts into CVS. I'm not sure which of
those are making it over to v6.

> 2. Also, would I have to compile and build all modules (mri_em_registe,
> mri_ca_register etc or can I limit to just these two when I build it again.

I imagine you'll have to run configure again. When you do, the key
options you want are:
 --enable-fermi-gpu --with-cuda="/usr/local/cuda"
Note that on my machine:
[rge21@cudastation ~]$ which nvcc
/usr/local/cuda-7.5/bin/nvcc
[rge21@cudastation ~]$ ls -alF /usr/local/cuda
lrwxrwxrwx. 1 root root 8 Jan  9 16:30 /usr/local/cuda -> cuda-7.5/
So if your CUDA installation went somewhere else, you'll have to
adjust that --with-cuda path.

Then when you compile, make sure the nvcc being used really is the one
you've set (things will likely fail horribly if this isn't the case).
If it isn't, you'll have to look in the configure file for:

#
# Nvidia CUDA enabling

CUDA_DIR=""
with_cuda=""

and then comment out
# with_cuda=""
or it will override the directory you set on the command line.

Let me know if you need further help,

Richard
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Re: [Freesurfer] epidewarp.fsl for FSL 5.x

[Bharadwaj, Pradyumna - (prad)]

Hi Doug,

Could you please upload epidewarp.fsl for FSL 5.x once again. 

Thanks!
-Prad

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Tuesday, March 1, 2016 12:39 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] epidewarp.fsl for FSL 5.x

try now

On 03/01/2016 02:16 PM, Versace, Amelia wrote:
>
> Hi,
>
> I am having the same issue.
>
> Can you please upload the updated version of epidewarp.fsl  for FSL 5.x.
>
> Thanks a lot, Amelia
>
> *From:*freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas
> Greve
> *Sent:* Wednesday, February 10, 2016 10:58 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] epidewarp.fsl for FSL 5.x
>
> what is your command line? I think there is a rescaling in which it
> expcts the phase to be 0-2048 (or 4096) as this is how it comes of the
> (siemens) scanner. Could that be the problem?
>
> On 2/10/16 10:40 PM, Joseph Dien wrote:
>
> I ran into the same issue:
>
> FSLVersion 5.0.4
>
> FSLVerMaj 5
>
> FSL Version is 5.0.4, must be 3.X or 4.X
>
> I downloaded the epidewarp.fsl script from the suggested ftp site
> and replaced the existing script.  It did indeed fix the version
> incompatibility with FSL 5.x.
>
> I ran into a new problem where it was aborting.  After some
> trouble shooting and looking over the documentation, I realized
> that —-epi is a required input without which the script crashes
> (or is it supposed to be optional but there is a bug in the script?).
>
> After including it, it ran much further but then aborted with the
> following error:
>
> ERROR: input phase image exceeds allowable phase range.
>
> Allowable range is 6.283 radians.  Image range is: 12.5633 radians.
>
> This is consistent with the documentation.  I’m not sure why the
> phase image exceeds the range though.
>
> It ran without problems with SPM’s FieldMap Toolbox and it is from
> a standard Siemen’s scanner sequence (two magnitude files and one
> phase difference file).
>
> Do I just divide the values by two with something like fslmaths
> since it seems to have exactly double the required range?
>
> Joe
>
> On Nov 26, 2014, at 21:36, Douglas Greve
> mailto:gr...@nmr.mgh.harvard.edu>>
> wrote:
>
>
> It is there again. I don't know what the status if it  is in
> terms of the version. Try it and let me know
> doug
>
> On 11/25/14 4:34 PM, Morgan Hough wrote:
>
> Hi Doug,
>
> Could you put the epidewarp.fsl script back on your ftp
> site? I don’t see it at the link in the archives:
>
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
>
> BTW, is the script updated in some way for 5.x or can I
> can the old script just be changed to accept 5.x version
> numbers.
>
> Cheers,
>
> -Morgan
>
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>
> Joseph Dien, PhD
>
> Senior Research Scientist
>
> Maryland Neuroimaging Center
>
> University of Maryland, College Park
>
> E-mail: jdie...@mac.com 
> Cell Phone: 202-297-8117
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Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Regarding: Freesurfer 6.0 dev version

[Dr Sampada Sinha]

Dear freesurfer experts,

I am trying to do hippocampal subfields segmentation on Mac. I will greatly
appreciate if freesurfer 6.0 version link is forwarded to me.

With thanks and regards,

Sampada
Pre-doctoral student
KGMU, Lucknow
India
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