[Freesurfer] Not able to find file in gtmseg

[Lee Subin Kristine]

Dear FreeSurfer experts,

Hello,
I am trying to use Freesurfer's (developmental version) PVE correction tool and 
I haveone question.

The data to be PVE-corrected are some preprocessed PET data downloaded from the 
Alzheimer's DIsease Neuroimaging Initiative (ADNI) database. Basiclly, the 
dynamic PET images have been co-registered to one another, averaged, and 
spatially normalized to a common space. Now I am trying to apply PVE-correction.
It seems from your answers here 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html)that
 you run the following commands:
(1) gtmseg
(2) bbregister
(3) mri_gtmpvc
(4) mri_glmfit

When I enter gtmseg --s subject such as below ('Desktop/forFSsubin_2' is 
location of the subject MRI and '019_S_4835_N3m_cub_ACPC.nii' is the filename)

~/Desktop/forFSsubin_2$ gtmseg --s 019_S_4835_N3m_cub_ACPC.nii

I get:

ERROR: cannot find 019_S_4835_N3m_cub_ACPC.nii

I have changed directory to the folder where the subject MRI file is, and I 
have typed the subject's filename correctly, but it keeps saying the subject 
file cannot be found. Any ideas on what is wrong here?


Any help would be appreciated.
Thank you in advance.

Regards,
Subin


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Re: [Freesurfer] Get a given point's ROI

[Bruce Fischl]

you can load it into matlab with load_mgh.m or MRIread.m

cheers
Bruce

On Wed, 29 Jun 2016, 
Yuan Lin wrote:



Hi Bruce,

Thank you for your response. I can show the aparc+aseg.mgz with the 
FreeSurferColorLUT.txt on freeview now. But how can I get the index matrix 
using MATLAB? Is there any command to read .mgz file in MATLAB? Or can I 
convert the .mgz file to .vtk file? Thank you so much.

Best,

Lin

在 2016年6月29日，下午5:56，Bruce Fischl  写道：

Hi Lin

you could look that point up in the subject's aparc+aseg.mgz. This will
give you an index into the file $FREESURFER_HOME/FreeSurferColorLUT.txt

cheers
Bruce
On
Wed, 29 Jun 2016, Yuan Lin wrote:


Dear FreeSurfer experts,

I am a beginner to learn to use FreeSurfer. Now I have a question to be solved. 
I have gotten the reconstruction results of a subject after using the command 
recon-all. How can I know a given point belongs to which region of interest? 
For example, how can I know whether a give point belongs to the superior 
frontal or inferior temporal? Which commands should I use? Thank you so much.

Best,

Lin
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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

[Arkadiy Maksimovskiy]

Thank you for catching this. Really appreciate your help.
- Arkadiiy
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Re: [Freesurfer] Freesurfer Digest, Vol 148, Issue 28

[Arkadiy Maksimovskiy]

Thank you!!
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Re: [Freesurfer] Get a given point's ROI

[Yuan Lin]

Hi Bruce,

Thank you for your response. I can show the aparc+aseg.mgz with the 
FreeSurferColorLUT.txt on freeview now. But how can I get the index matrix 
using MATLAB? Is there any command to read .mgz file in MATLAB? Or can I 
convert the .mgz file to .vtk file? Thank you so much.

Best,

Lin
> 在 2016年6月29日，下午5:56，Bruce Fischl  写道：
> 
> Hi Lin
> 
> you could look that point up in the subject's aparc+aseg.mgz. This will 
> give you an index into the file $FREESURFER_HOME/FreeSurferColorLUT.txt
> 
> cheers
> Bruce
> On 
> Wed, 29 Jun 2016, Yuan Lin wrote:
> 
>> Dear FreeSurfer experts,
>> 
>> I am a beginner to learn to use FreeSurfer. Now I have a question to be 
>> solved. I have gotten the reconstruction results of a subject after using 
>> the command recon-all. How can I know a given point belongs to which region 
>> of interest? For example, how can I know whether a give point belongs to the 
>> superior frontal or inferior temporal? Which commands should I use? Thank 
>> you so much.
>> 
>> Best,
>> 
>> Lin
>> ___
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>> 
>> 
>> 
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[Freesurfer] longitudinal tracula

[Harms, Michael]

Hi,
When running TRACULA with longitudinal data, is it necessary for all scan waves of a given subject to be included in a single dmrirc file?  My initial thought was “no”, that it would be fine to run one scan wave
 per subject per dmrirc file (as long as the “baselist” variable is set appropriately for each scan wave and subject).


But looking at the ‘trac-all’ script, I see


if ($#baselist == 0) then
#--->>> A single time point for each subject
…
else
#--->>> Multiple time points for each subject
…


So, I’m wondering why different sections in the code would be necessary if in fact it is ok to process a single scan wave per dmrirc file.


thanks,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu




 



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Re: [Freesurfer] Get a given point's ROI

[Bruce Fischl]

Hi Lin

you could look that point up in the subject's aparc+aseg.mgz. This will 
give you an index into the file $FREESURFER_HOME/FreeSurferColorLUT.txt

cheers
Bruce
On 
Wed, 29 Jun 2016, Yuan Lin wrote:

> Dear FreeSurfer experts,
>
> I am a beginner to learn to use FreeSurfer. Now I have a question to be 
> solved. I have gotten the reconstruction results of a subject after using the 
> command recon-all. How can I know a given point belongs to which region of 
> interest? For example, how can I know whether a give point belongs to the 
> superior frontal or inferior temporal? Which commands should I use? Thank you 
> so much.
>
> Best,
>
> Lin
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] Get a given point's ROI

[Yuan Lin]

Dear FreeSurfer experts,

I am a beginner to learn to use FreeSurfer. Now I have a question to be solved. 
I have gotten the reconstruction results of a subject after using the command 
recon-all. How can I know a given point belongs to which region of interest? 
For example, how can I know whether a give point belongs to the superior 
frontal or inferior temporal? Which commands should I use? Thank you so much.

Best,

Lin
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[Freesurfer] Announcement: fsurf, a command line tool for running freesurfer on the Open Science Grid

[Krieger, Donald N.]

Dear FreeSurfer community,

The Open Science Grid (http://www.opensciencegrid.org) is a federation of 
university and laboratory HPC facilities which share computing capacity to 
support science.
We have developed a command line tool "fsurf" you can use from your laptop or 
desktop computer to submit scans for FreeSurfer processing on these clusters.
In the initial release it is capable of executing "recon-all -all -i 
SubjectName.mgz" using FreeSurfer 5.3.

No allocation is required.
We only request that you cite the OSG in publications that benefit from its use.
Instructions for getting started are found here: 
http://bit.ly/freesurferopensciencegrid.

Please post questions and problems to OSG user support at 
user-supp...@opensciencegrid.org.
We hope you find it useful.

Best regards,

The OSG fsurf support team

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Re: [Freesurfer] No intensity command

[Sabrina Yu]

Hi Bruce, 

Thank you for your reply. I am looking at differences in WM intensity, but am 
concerned that the intensity normalization will reduce tissue differences in 
addition to addressing inhomogeneity from the MRI. The WM is normalized to an 
average of 110, but is there any way to keep the variable intensity values for 
the WM? 

Thanks
Sabrina


> On Jun 29, 2016, at 2:51 PM, Bruce Fischl  wrote:
> 
> Hi Sabrina
> 
> what are you trying to accomplish? This is unlikely to work well (if at all), 
> as we depend on the normalization
> 
> cheers
> Bruce
> On Wed, 29 Jun 2016, Sabrina Yu wrote:
> 
>> Hello, 
>> I have a question about taking out the intensity normalization commands in
>> recon-all. I want to eliminate all normalization steps so that the WM will
>> not be set at an average of 110. Using the ReconAllDevTable
>> (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable), I took out all
>> command flags related to intensity normalization. Are these commands
>> correct? 
>> 1) I copied orig.mgz to generate nu.mgz, T1.mgz, norm.mgz. 
>> 2) recon-all -i <.nii file> -motioncor -talairach -skullstrip -s SUBJECT
>> 3) recon-all -skullstrip -s SUBJECT
>> 4) recon-all -gcareg -careg -calabel -maskbfs -segmentation -fill
>> -tessellate -smooth1 -inflate1 -qsphere -fix -white -smooth2 -inflate2 -s
>> SUBJECT
>> 5) recon-all -autorecon3 -s SUBJECT
>> I hope that my question makes sense. Thank you in advance for your time. 
>> Sabrina
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Re: [Freesurfer] No intensity command

[Bruce Fischl]

Hi Sabrina

what are you trying to accomplish? This is unlikely to work well (if at 
all), as we depend on the normalization


cheers
Bruce
On Wed, 29 Jun 2016, Sabrina Yu 
wrote:



Hello, 

I have a question about taking out the intensity normalization commands in
recon-all. I want to eliminate all normalization steps so that the WM will
not be set at an average of 110. Using the ReconAllDevTable
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable), I took out all
command flags related to intensity normalization. Are these commands
correct? 

1) I copied orig.mgz to generate nu.mgz, T1.mgz, norm.mgz. 
2) recon-all -i <.nii file> -motioncor -talairach -skullstrip -s SUBJECT
3) recon-all -skullstrip -s SUBJECT
4) recon-all -gcareg -careg -calabel -maskbfs -segmentation -fill
-tessellate -smooth1 -inflate1 -qsphere -fix -white -smooth2 -inflate2 -s
SUBJECT
5) recon-all -autorecon3 -s SUBJECT

I hope that my question makes sense. Thank you in advance for your time. 

Sabrina

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[Freesurfer] No intensity command

[Sabrina Yu]

Hello, 

I have a question about taking out the intensity normalization commands in 
recon-all. I want to eliminate all normalization steps so that the WM will not 
be set at an average of 110. Using the ReconAllDevTable 
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable 
), I took out all 
command flags related to intensity normalization. Are these commands correct? 

1) I copied orig.mgz to generate nu.mgz, T1.mgz, norm.mgz. 
2) recon-all -i <.nii file> -motioncor -talairach -skullstrip -s SUBJECT
3) recon-all -skullstrip -s SUBJECT
4) recon-all -gcareg -careg -calabel -maskbfs -segmentation -fill -tessellate 
-smooth1 -inflate1 -qsphere -fix -white -smooth2 -inflate2 -s SUBJECT
5) recon-all -autorecon3 -s SUBJECT

I hope that my question makes sense. Thank you in advance for your time. 

Sabrina___
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Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

Hi Bruce

I simply use

mri_vol2surf --mov spam.mnc --output overlayspam.mgz --regheader subject
--hemi lh --surf pial

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 29, 2016 at 1:23 PM, Bruce Fischl 
wrote:

> how do you create the overlay?
> On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
>
> Hi Bruce
>>
>> To create the spam I used minctools:
>>
>>  mincaverage  input.mnc output.mnc
>>
>> I blurred the spam using
>>
>> mincblur input.mnc output.mnc -fwhm 3
>>
>> When I open the spams using minc software, the % shown is from about
>> 10-40%
>> (i.e. the max overlap). For some reason when I create an overlay from this
>> it displays the % from 1-255.
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Trisanna
>>
>>   what commands did you use to generate the volumetric probability
>>   map?
>>
>>   Bruce
>>
>>
>>
>>   On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> Hi Bruce
>> So, when I take a probability map formed using
>> linear volumetric
>> registration with minc tools and saved as .mnc and
>> convert it to an
>> overlay.mgz and open it in Freeview, the probability
>> seems to be out of 255
>> (See the image attached). This is different from my
>> Freesurfer generated
>> probability maps where I use -p in the mri_average
>> command.
>>
>> Is there a way to change these probability values
>> that are displaying from
>> 1-255?
>>
>> many thanks
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 27, 2016 at 10:28 AM, Bruce Fischl
>> 
>> wrote:
>>   Hi Trisanna
>>
>>   we need more information if you want us to
>> help you. What does
>>   "very odd mean"? If you do it in .mgz do you
>> get a different
>>   answer than in .mnc? If so, why not just
>> compute them in .mgz
>>   and convert to .mnc at the end?
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Mon, 27 Jun 2016, Trisanna Sprung-Much
>> wrote:
>>
>> any ideas?
>> Thanks!
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 22, 2016 at 10:22 PM,
>> Trisanna
>> Sprung-Much
>> 
>> wrote:
>>   thanks Bruce - I had found that
>> option for my
>> fsaverage maps and
>>   it worked.
>> What about if I am importing probability
>> maps formed
>> as .mnc and
>> creating overlays from them? The
>> percentages seem to
>> be very odd for
>> min and max threshold.
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 22, 2016 at 9:32 PM, Bruce
>> Fischl
>>  wrote:
>>   Hi Trisanna
>>
>>   if you are using mri_average you
>> can give it
>> -p as the
>>   first argument and it will compute
>> a percent
>> at the end
>>   Bruce
>>   On Wed, 22 Jun 2016, Trisanna
>> Sprung-Much
>> wrote:
>>
>>   Hi Bruce
>>
>>   Is there is a way to set the
>> probability of an
>>   overlay between 0 and 1?
>>   Would this have to be done when
>> creating the
>> overlay
>>   using mri_vol2surf?
>>
>>   thanks
>>
>>  

[Freesurfer] Motion values during structural run

[Rodriguez-Thompson, Anais]

Hi Freesurfer Experts,

Is there a way to calculate average displacement during a T1_MEMPRAGE scan 
(similar to using fmcpr.nii to calculate avg displacement during functional 
runs)? 

Thank you,

Anais Rodriguez-Thompson
Clinical Research Coordinator
Brain Genomics Laboratory
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Phone: (617) 643-3215
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Re: [Freesurfer] Hippocampal Subfields Segmentation

[Iglesias, Eugenio]

I could finally look into this. It is indeed weird. The CTF is indeed embedded 
in the executable…
Zeke/Nick, can you shed some light on this?
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 27 Jun 2016, at 15:43, Iglesias, Eugenio 
> wrote:

Hi Pierre,
Due to some technical problems, it might take me a couple of days to figure out 
what’s going on.  But it definitely sounds funny that it is asking for the CTF, 
since this is supposed to be embedded in the executable… I’ll get back to you 
as soon as possible.
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 27 Jun 2016, at 15:32, pierre deman 
> wrote:

I tried that. but didn't work.

Cheers,
Pierre

On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio 
> wrote:
Hi everyone,
you need to install the Matlab 2012b runtime as explained in the wiki:
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime
Cheers,
Eugenio



Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 27 Jun 2016, at 15:16, pierre deman 
> wrote:

Hello,

I have similar problem. "
"Error:Cannot find CTF archive
/autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf"
the file is here but when I try to execute it, it's always missing some library 
(libmwi18n.so for example, it was missing others before that I added on my 
computer, but it never ends)
I am on ubuntu 14.04.
I thought that the problem is linked to the matlab runtime. I installed the 
2012b. I tried newer version. installed again the 2012b.

Regards,
Pierre


On Mon, Jun 27, 2016 at 4:05 PM, Permesh Dhillon 
> 
wrote:
Hello FreeSurfer Developers,

I’m having issues with the hippocampal subfields segmentation using OS X 
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp: 
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting 
an error message : Error:CTF file 
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' 
failed to open for 'Read' access. Error message: 'Open a zip file for 
read/modify failed.’

The segmented hippocampal files as described on free surfer wiki cannot be 
found under the subject ‘mri’ folder.
I understand other users have complained of a similar issue within the last 
week.

I’d ve grateful if you could assist me with the issue above.

Many thanks
Permesh

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Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

how do you create the overlay?
On Wed, 29 Jun 2016, Trisanna Sprung-Much 
wrote:



Hi Bruce

To create the spam I used minctools:

 mincaverage  input.mnc output.mnc 

I blurred the spam using

mincblur input.mnc output.mnc -fwhm 3 

When I open the spams using minc software, the % shown is from about 10-40%
(i.e. the max overlap). For some reason when I create an overlay from this
it displays the % from 1-255.

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl 
wrote:
  Hi Trisanna

  what commands did you use to generate the volumetric probability
  map?

  Bruce



  On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:

Hi Bruce
So, when I take a probability map formed using
linear volumetric
registration with minc tools and saved as .mnc and
convert it to an
overlay.mgz and open it in Freeview, the probability
seems to be out of 255
(See the image attached). This is different from my
Freesurfer generated
probability maps where I use -p in the mri_average
command.

Is there a way to change these probability values
that are displaying from
1-255?

many thanks

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 27, 2016 at 10:28 AM, Bruce Fischl

wrote:
      Hi Trisanna

      we need more information if you want us to
help you. What does
      "very odd mean"? If you do it in .mgz do you
get a different
      answer than in .mnc? If so, why not just
compute them in .mgz
      and convert to .mnc at the end?

      cheers
      Bruce


      On Mon, 27 Jun 2016, Trisanna Sprung-Much
wrote:

            any ideas?
            Thanks!

            Trisanna

            --
            Ph.D. CandidateMcGill University
            Integrated Program in Neuroscience
            Psychology


            On Wed, Jun 22, 2016 at 10:22 PM,
Trisanna
            Sprung-Much
            
wrote:
                  thanks Bruce - I had found that
option for my
            fsaverage maps and
                  it worked.
            What about if I am importing probability
maps formed
            as .mnc and
            creating overlays from them? The
percentages seem to
            be very odd for
            min and max threshold.

            Trisanna

            --
            Ph.D. CandidateMcGill University
            Integrated Program in Neuroscience
            Psychology


            On Wed, Jun 22, 2016 at 9:32 PM, Bruce
Fischl
             wrote:
                  Hi Trisanna

                  if you are using mri_average you
can give it
            -p as the
                  first argument and it will compute
a percent
            at the end
                  Bruce
                  On Wed, 22 Jun 2016, Trisanna
Sprung-Much
            wrote:

                  Hi Bruce

                  Is there is a way to set the
probability of an
                  overlay between 0 and 1?
                  Would this have to be done when
creating the
            overlay
                  using mri_vol2surf?

                  thanks

                  Trisanna

                  --
                  Ph.D. CandidateMcGill University
                  Integrated Program in Neuroscience
                  Psychology


                  On Mon, Jun 20, 2016 at 12:11 PM,
Bruce Fischl
                  
                  wrote:
                        Hi Trisanna

                        the binaries that take
mandatory
            command-line
                  arguments (i.e.
                        without a -- or - in 

Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

Hi Bruce

To create the spam I used minctools:

 mincaverage  input.mnc output.mnc

I blurred the spam using

mincblur input.mnc output.mnc -fwhm 3

When I open the spams using minc software, the % shown is from about 10-40%
(i.e. the max overlap). For some reason when I create an overlay from this
it displays the % from 1-255.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> what commands did you use to generate the volumetric probability map?
>
> Bruce
>
>
>
> On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
>
> Hi Bruce
>> So, when I take a probability map formed using linear volumetric
>> registration with minc tools and saved as .mnc and convert it to an
>> overlay.mgz and open it in Freeview, the probability seems to be out of
>> 255
>> (See the image attached). This is different from my Freesurfer generated
>> probability maps where I use -p in the mri_average command.
>>
>> Is there a way to change these probability values that are displaying from
>> 1-255?
>>
>> many thanks
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 27, 2016 at 10:28 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Trisanna
>>
>>   we need more information if you want us to help you. What does
>>   "very odd mean"? If you do it in .mgz do you get a different
>>   answer than in .mnc? If so, why not just compute them in .mgz
>>   and convert to .mnc at the end?
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Mon, 27 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> any ideas?
>> Thanks!
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 22, 2016 at 10:22 PM, Trisanna
>> Sprung-Much
>>  wrote:
>>   thanks Bruce - I had found that option for my
>> fsaverage maps and
>>   it worked.
>> What about if I am importing probability maps formed
>> as .mnc and
>> creating overlays from them? The percentages seem to
>> be very odd for
>> min and max threshold.
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl
>>  wrote:
>>   Hi Trisanna
>>
>>   if you are using mri_average you can give it
>> -p as the
>>   first argument and it will compute a percent
>> at the end
>>   Bruce
>>   On Wed, 22 Jun 2016, Trisanna Sprung-Much
>> wrote:
>>
>>   Hi Bruce
>>
>>   Is there is a way to set the probability of an
>>   overlay between 0 and 1?
>>   Would this have to be done when creating the
>> overlay
>>   using mri_vol2surf?
>>
>>   thanks
>>
>>   Trisanna
>>
>>   --
>>   Ph.D. CandidateMcGill University
>>   Integrated Program in Neuroscience
>>   Psychology
>>
>>
>>   On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl
>>   
>>   wrote:
>> Hi Trisanna
>>
>> the binaries that take mandatory
>> command-line
>>   arguments (i.e.
>> without a -- or - in front of them)
>> require
>>   all options to be
>> given before the mandatory arguments
>>
>> cheers
>> Bruce
>>
>> On Mon, 20 Jun 2016, Trisanna
>> Sprung-Much
>>   wrote:
>>
>>   thanks, Bruce. Yes in the end
>> through
>>   trial and
>>   error I tried "mri_average
>> -noconform
>>   input output"
>>   and it worked. I was
>>   surprised that I had to put the
>>   -noconform first as
>>   normally one can put the argument
>>   anywhere in the
>>   command.
>>
>>   Best
>>
>>   Trisanna
>>
>>   --
>>

[Freesurfer] Tracula : ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi everyone,

I’m reposting my problem if someone could help me I would really appreciate it.

I have some problems trying to run TRACULA on some DWI data. It is a mosaic 
Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and 
bval files.
Then I run the trac-all -prep -c command and I get the following error :

WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header
has this file been anonymized?
ERROR: cannot unpack mosiacs without ASCII header

I tried to unpack the mosaics with gdcmtar, but I got the same error.

P.S : DTIFIT works on FSL (FDT) but gives a poor quality in the reconstruction 
not as the one expected with Tracula.

Thank you in advance for your help,

Ismail

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Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

Hi Trisanna

what commands did you use to generate the volumetric probability map?

Bruce



On 
Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:



Hi Bruce
So, when I take a probability map formed using linear volumetric
registration with minc tools and saved as .mnc and convert it to an
overlay.mgz and open it in Freeview, the probability seems to be out of 255
(See the image attached). This is different from my Freesurfer generated
probability maps where I use -p in the mri_average command.

Is there a way to change these probability values that are displaying from
1-255?

many thanks

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 27, 2016 at 10:28 AM, Bruce Fischl 
wrote:
  Hi Trisanna

  we need more information if you want us to help you. What does
  "very odd mean"? If you do it in .mgz do you get a different
  answer than in .mnc? If so, why not just compute them in .mgz
  and convert to .mnc at the end?

  cheers
  Bruce


  On Mon, 27 Jun 2016, Trisanna Sprung-Much wrote:

any ideas?
Thanks!

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 22, 2016 at 10:22 PM, Trisanna
Sprung-Much
 wrote:
      thanks Bruce - I had found that option for my
fsaverage maps and
      it worked.
What about if I am importing probability maps formed
as .mnc and
creating overlays from them? The percentages seem to
be very odd for
min and max threshold.

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl
 wrote:
      Hi Trisanna

      if you are using mri_average you can give it
-p as the
      first argument and it will compute a percent
at the end
      Bruce
      On Wed, 22 Jun 2016, Trisanna Sprung-Much
wrote:

      Hi Bruce

      Is there is a way to set the probability of an
      overlay between 0 and 1?
      Would this have to be done when creating the
overlay
      using mri_vol2surf?

      thanks

      Trisanna

      --
      Ph.D. CandidateMcGill University
      Integrated Program in Neuroscience
      Psychology


      On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl
      
      wrote:
            Hi Trisanna

            the binaries that take mandatory
command-line
      arguments (i.e.
            without a -- or - in front of them)
require
      all options to be
            given before the mandatory arguments

            cheers
            Bruce

            On Mon, 20 Jun 2016, Trisanna
Sprung-Much
      wrote:

                  thanks, Bruce. Yes in the end
through
      trial and
                  error I tried "mri_average
-noconform
      input output"
                  and it worked. I was
                  surprised that I had to put the
      -noconform first as
                  normally one can put the argument
      anywhere in the
                  command.

                  Best

                  Trisanna

                  --
                  Ph.D. CandidateMcGill University
                  Integrated Program in Neuroscience
                  Psychology


                  On Mon, Jun 20, 2016 at 9:27 AM,
Bruce
      Fischl
                  
wrote:
                        yes, your last file on the
command
      line should
                  be the output file (the average)

                        cheers
                        Bruce

                        On Mon, 20 Jun 2016,
Trisanna
      Sprung-Much
                  wrote:

                        As a follow-up, here is the
      mri_info for one
                  of my overlays in the 

Re: [Freesurfer] Order of overlays

[Ruopeng Wang]

Hi Reza,

Right now in freeview aparc annotation is always drawn on top of 
overlays, just like in tkSurfer. I'll add an option draw it underneath 
the overlays.


Best,
Ruopeng

On 06/29/2016 10:09 AM, Bruce Fischl wrote:

Hi Reza

can you use freeview? We don't do any development on tksurfer and 
hardly use it anymore. Not sure if this is possible in freeview, I'll 
leave that for Ruopeng

cheers
Bruce
On Wed, 29 Jun 2016, Reza Rajimehr wrote:


Hi,
In Tksurfer, we want to show functional activity map and borders of 
aparc on
a surface. The borders of aparc are always drawn on top of the 
activity map,

which sometimes hide small activation blobs. Is it possible to draw the
activity map on top of the aparc borders?

Reza





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Re: [Freesurfer] tutorial_data

[Krieger, Donald N.]

I can see the sub directories and the distributions via ftp.

Best - Don


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, June 29, 2016 10:57 AM
> To: Freesurfer support list
> Cc: bruno fraccini pastorello
> Subject: Re: [Freesurfer] tutorial_data
> 
> try again - hopefully the stale mounts of been fixed now cheers Bruce
> 
> 
> On Wed, 29 Jun 2016, Bennet Fauber wrote:
> 
> > Looks like all downloads are broken, as the same message appears when
> > trying to download the binary distribution,
> >
> > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-
> > Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
> >
> > There are no files on the server advertised to the public:
> >
> > Name (surfer.nmr.mgh.harvard.edu:bennet): anonymous
> > 331 Please specify the password.
> > Password:
> > 230 Login successful.
> > Remote system type is UNIX.
> > Using binary mode to transfer files.
> > ftp> ls
> > 227 Entering Passive Mode (132,183,202,158,147,246).
> > 150 Here comes the directory listing.
> > -rw-r-1 048286 Jul 03  2013 index.html
> > drwxr-xr-x2 004096 Jul 24  2015 pub
> > drwxr-xr-x2 004096 Nov 20  2012 transfer
> > 226 Directory send OK.
> > ftp> cd pub
> > 250 Directory successfully changed.
> > ftp> ls
> > 227 Entering Passive Mode (132,183,202,158,147,224).
> > 150 Here comes the directory listing.
> > 226 Directory send OK.
> > ftp> cd ../transfer
> > 250 Directory successfully changed.
> > ftp> ls
> > 227 Entering Passive Mode (132,183,202,158,147,237).
> > 150 Here comes the directory listing.
> > 226 Directory send OK.
> >
> >
> >
> >
> > On Tue, Jun 28, 2016 at 1:32 PM, bruno fraccini pastorello
> >  wrote:
> >> Dear freesurfer support,
> >> I'm trying to download the freesurfer data to learn freesurfer, but i
> >> can't it. Do you know why? Could you help me?
> >>
> >> I tried use this link
> >> ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz and I
> >> obtain this error: Safari cant open the page
> >> ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz
> >> because Safari can't load any data from this location.
> >>
> >> Thanks in advance
> >> Bruno Pastorello
> >>
> >> PS: I tried use this link too
> >> :https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data  using
> >> curl command on terminal and it has failed too
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> The information in this e-mail is intended only for the person to
> >> whom it is addressed. If you believe this e-mail was sent to you in
> >> error and the e-mail contains patient information, please contact the
> >> Partners Compliance HelpLine at
> >> http://www.partners.org/complianceline . If the e-mail was sent to
> >> you in error but does not contain patient information, please contact
> >> the sender and properly dispose of the e-mail.
> >>
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> ___
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Re: [Freesurfer] tutorial_data

[Bruce Fischl]

try again - hopefully the stale mounts of been fixed now
cheers
Bruce


On Wed, 29 Jun 2016, Bennet Fauber wrote:

> Looks like all downloads are broken, as the same message appears when
> trying to download the binary distribution,
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
>
> There are no files on the server advertised to the public:
>
> Name (surfer.nmr.mgh.harvard.edu:bennet): anonymous
> 331 Please specify the password.
> Password:
> 230 Login successful.
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> ls
> 227 Entering Passive Mode (132,183,202,158,147,246).
> 150 Here comes the directory listing.
> -rw-r-1 048286 Jul 03  2013 index.html
> drwxr-xr-x2 004096 Jul 24  2015 pub
> drwxr-xr-x2 004096 Nov 20  2012 transfer
> 226 Directory send OK.
> ftp> cd pub
> 250 Directory successfully changed.
> ftp> ls
> 227 Entering Passive Mode (132,183,202,158,147,224).
> 150 Here comes the directory listing.
> 226 Directory send OK.
> ftp> cd ../transfer
> 250 Directory successfully changed.
> ftp> ls
> 227 Entering Passive Mode (132,183,202,158,147,237).
> 150 Here comes the directory listing.
> 226 Directory send OK.
>
>
>
>
> On Tue, Jun 28, 2016 at 1:32 PM, bruno fraccini pastorello
>  wrote:
>> Dear freesurfer support,
>> I'm trying to download the freesurfer data to learn freesurfer, but i can't
>> it. Do you know why? Could you help me?
>>
>> I tried use this link
>> ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz and I obtain
>> this error: Safari cant open the page
>> ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz because
>> Safari can't load any data from this location.
>>
>> Thanks in advance
>> Bruno Pastorello
>>
>> PS: I tried use this link too
>> :https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data  using curl
>> command on terminal and it has failed too
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
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Re: [Freesurfer] tutorial_data

[Krieger, Donald N.]

It looks like things aren't quite linked up.
I can reach the server with ftp and I can see directory pub.
But there's no directory pub/dist  .

Best - Don

> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, June 29, 2016 10:13 AM
> To: Freesurfer support list
> Cc: bruno fraccini pastorello
> Subject: Re: [Freesurfer] tutorial_data
> 
> it should all be working now, no?
> On Wed, 29 Jun 2016, Bennet Fauber wrote:
> 
> > Looks like all downloads are broken, as the same message appears when
> > trying to download the binary distribution,
> >
> > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-
> > Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
> >
> > There are no files on the server advertised to the public:
> >
> > Name (surfer.nmr.mgh.harvard.edu:bennet): anonymous
> > 331 Please specify the password.
> > Password:
> > 230 Login successful.
> > Remote system type is UNIX.
> > Using binary mode to transfer files.
> > ftp> ls
> > 227 Entering Passive Mode (132,183,202,158,147,246).
> > 150 Here comes the directory listing.
> > -rw-r-1 048286 Jul 03  2013 index.html
> > drwxr-xr-x2 004096 Jul 24  2015 pub
> > drwxr-xr-x2 004096 Nov 20  2012 transfer
> > 226 Directory send OK.
> > ftp> cd pub
> > 250 Directory successfully changed.
> > ftp> ls
> > 227 Entering Passive Mode (132,183,202,158,147,224).
> > 150 Here comes the directory listing.
> > 226 Directory send OK.
> > ftp> cd ../transfer
> > 250 Directory successfully changed.
> > ftp> ls
> > 227 Entering Passive Mode (132,183,202,158,147,237).
> > 150 Here comes the directory listing.
> > 226 Directory send OK.
> >
> >
> >
> >
> > On Tue, Jun 28, 2016 at 1:32 PM, bruno fraccini pastorello
> >  wrote:
> >> Dear freesurfer support,
> >> I'm trying to download the freesurfer data to learn freesurfer, but i
> >> can't it. Do you know why? Could you help me?
> >>
> >> I tried use this link
> >> ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz and I
> >> obtain this error: Safari cant open the page
> >> ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz
> >> because Safari can't load any data from this location.
> >>
> >> Thanks in advance
> >> Bruno Pastorello
> >>
> >> PS: I tried use this link too
> >> :https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data  using
> >> curl command on terminal and it has failed too
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> The information in this e-mail is intended only for the person to
> >> whom it is addressed. If you believe this e-mail was sent to you in
> >> error and the e-mail contains patient information, please contact the
> >> Partners Compliance HelpLine at
> >> http://www.partners.org/complianceline . If the e-mail was sent to
> >> you in error but does not contain patient information, please contact
> >> the sender and properly dispose of the e-mail.
> >>
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
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Re: [Freesurfer] tutorial_data

[Bruce Fischl]

it should all be working now, no?
On Wed, 29 Jun 2016, Bennet Fauber wrote:

> Looks like all downloads are broken, as the same message appears when
> trying to download the binary distribution,
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
>
> There are no files on the server advertised to the public:
>
> Name (surfer.nmr.mgh.harvard.edu:bennet): anonymous
> 331 Please specify the password.
> Password:
> 230 Login successful.
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> ls
> 227 Entering Passive Mode (132,183,202,158,147,246).
> 150 Here comes the directory listing.
> -rw-r-1 048286 Jul 03  2013 index.html
> drwxr-xr-x2 004096 Jul 24  2015 pub
> drwxr-xr-x2 004096 Nov 20  2012 transfer
> 226 Directory send OK.
> ftp> cd pub
> 250 Directory successfully changed.
> ftp> ls
> 227 Entering Passive Mode (132,183,202,158,147,224).
> 150 Here comes the directory listing.
> 226 Directory send OK.
> ftp> cd ../transfer
> 250 Directory successfully changed.
> ftp> ls
> 227 Entering Passive Mode (132,183,202,158,147,237).
> 150 Here comes the directory listing.
> 226 Directory send OK.
>
>
>
>
> On Tue, Jun 28, 2016 at 1:32 PM, bruno fraccini pastorello
>  wrote:
>> Dear freesurfer support,
>> I'm trying to download the freesurfer data to learn freesurfer, but i can't
>> it. Do you know why? Could you help me?
>>
>> I tried use this link
>> ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz and I obtain
>> this error: Safari cant open the page
>> ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz because
>> Safari can't load any data from this location.
>>
>> Thanks in advance
>> Bruno Pastorello
>>
>> PS: I tried use this link too
>> :https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data  using curl
>> command on terminal and it has failed too
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
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>
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Re: [Freesurfer] checking freesurfer output

[Bruce Fischl]

Hi Gabor

the only way is to look at the parcellation over the white surface I guess. 
There are some not-very-well documented interventions, but maybe your best 
bet would be just to exclude subjects (since it almost never fails)

cheers
Bruce


  On Wed, 29 Jun 2016, Gabor Perlaki 
wrote:

> Dear Bruce,
> 
> Thank you for your answer. We will check the pial and white surfaces, but
> how to check the accuracy of the cortical parcellation beyond that? We don't
> find any suggestion on Freesurfer's troubleshooting page how to realize or
> correct such an error, where the pial and white surfaces are good but the
> cortical parcellation is not accurate. Manual intervention is only suggested
> for the aseg segmentations. Could you please suggest some more details about
> how to check/correct the possible errors in cases where both pial and white
> surfaces are accurate?
> 
> Best Regards,
> Gabor
> 
>
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[Freesurfer] Qdec-correction for multiple comparison

[John Anderson]

Dear FS experts,

I will re post this thread again looking for your help and support:

 

I ran cortical thickness analysis between two groups using Qdec and I want to correct the results for multiple comparison.

In Qdec there are two choices to correct the data for multiple comparison (FDR and montecarlo) . Which method do you recommend to correct the results of cortical thickness analysis? Are there any rules that I need to follow when I choose my method to correct the results for multiple comparison ( i.e FDR or montecarlo)

 

Thank you very much for any comment!
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419


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Re: [Freesurfer] Failed to download Freesurfer from ftp, server seems empty

[Bernardo Oliveira Pinto]

Hi!

I found a non official github repository here:
https://github.com/neurodebian/freesurfer you can try to compile that
source code in the meantime.

On Wednesday, 29 June 2016, Bruce Fischl  wrote:

> Hi Minos
>
> we are having major hardware issues that we hope to have resolved
> tonight. Try again tomorrow
>
> cheers
> Bruce
> On Wed, 29 Jun 2016, C. Minos Niu wrote:
>
> > Hello,
> >
> > I tried to have my new students download and install Freesurfer from
> > https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall, but all
> > download links gave "550 Failed to change directory" error. I logged into
> > the FTP anonymously only to find it empty under "pub/".
> >
> > Any idea how to proceed with the downloading? Thanks!
> >
> > -Minos
> >
> >
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>

-- 
Bernardo Oliveira Pinto
http://about.me/b.oliveirapinto
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[Freesurfer] Diffusion MRI Workshop, 12-16 September, 2016

[Tim Dyrby]

Dear Freesurfer users,


Registration is officially open for the 4th ISMRM Diffusion MRI Workshop 
"Breaking Barriers in Diffusion MRI" to be held September 12-16 in 
Lisbon, Portugal!


Dates: September 12-16, 2016
Venue: Sheraton Lisboa, Lisbon, Portugal
Deadline for abstracts: July 21, 2016
Facebook: https://www.facebook.com/DSGworkshop2016/

As with the first three workshops held in 2002, 2005 and 2013, the 
workshop has been designed as the primary scientific venue for basic 
scientists and clinical researchers in the diffusion MR community to 
learn, meet the experts, discuss the latest advances in the field, and 
network. There is an optional bootcamp for trainees and those new to the 
field of diffusion MR on September 12. The formal scientific program 
from September 13-16 will cover the full scope of diffusion MR topics 
from acquisition to microstructure and modeling, anatomy, tractography, 
connectomics, validation, clinical application, and future strategies 
for innovation.


Whether you are new to the field, a PhD student, postdoc, senior 
researcher or physician, we hope that you will be able to participate in 
the workshop and interact with the leaders in the field. *Please note 
that the deadline for scientific abstract submission is July 21, 2016.*


For physicians in practice, the ISMRM is accredited by the ACGME to 
provide up to 25.75 AMA PRA Category 1 credits for participation in the 
workshop.


For additional details, please visit the workshop website: 
http://www.ismrm.org/workshops/Diffusion16 or contact any of the 
organizing committee:


/
Mara Cercignani, Brighton & Sussex Medical School, Brighton, England, UK
Maxime Descoteaux, Sherbrooke University, Sherbrooke, QC, Canada
Tim B. Dyrby, Danish Research Centre for Magnetic Resonance, Hvidovre, 
Denmark

Christopher Hess, University of California, San Francisco, CA, USA
Alexander Leemans, University Medical Center Utrecht, Utrecht, The 
Netherlands

/


--
Tim B. Dyrby
Associate Professor
Danish Research Centre for Magnetic Resonance (DRCMR), section 714
Center for Functional and Diagnostic Imaging and Research
Copenhagen University Hospital Hvidovre
Kettegård Allé 30
2650 Hvidovre
Denmark
Office phone: +45 38626542  Mobile:+45 40790282
web: http://dig.drcmr.dk and www.drcmr.dk
&
Image Analysis and Computer Graphics section
Department of Applied Mathematics and Computer Science
Technical University of Denmark
Richard Petersens Plads, Building 324
2800 Kongens Lyngby
Denmark
Office Phone: +45 45253424

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