Re: [Freesurfer] fsaverage vertex index to talairach

[Douglas Greve]

Hi Cesar, you can run

mris_convert lh.white lh.white.asc

to convert to ascii. Each vertex is in MNI305 space. Is that good 
enough? There is a matlab script by Matthew Brett that attempts to 
convert to Tal coords. You could easily convert to MNI152 as well.

doug




On 6/24/13 4:34 PM, Cesar Echavarria wrote:

Hello,

Anyone know of a fast way to get the talairach coordinates of a vertex 
index in fsaverage. A function or script is best since I want to do 
this for a large number of vertices.

Thank you for any help you guys can provide.

Cesar


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Re: [Freesurfer] Fwd: DTI questions

[Anastasia Yendiki]

Hi Rotem - No problem. Were these scans by any chance acquired with a 
coronal slice prescription? In the axial views that you sent, the artifact 
that you're pointing to looks like misalignment between consecutive 
coronal slices, which could be due to head motion.


a.y

On Tue, 25 Jun 2013, Rotem Saar wrote:


Dear Anastasia,
 
I tried several times to upload these images in a non-compressed way, but
they were too big and my posts were rejected, with no opportunity for any
other upload way.
Is there any other way for me to upload it so that everyone can see it ?
 
Attached are the images in a non-compressed fashion. I will be very happy if
u will have a look, and post your answer to me and the list to save some
time, until I will be able to consider another way to upload them.
 
I know that we should write to all the list, but at the moment if the images
are not visible this won't help - so I will really appreciate if u will have
a look but also tell me what is the best way to upload them so that all list
members will be able to see them.
 
Thank u very much for your help.
 
Rotem

2013/6/25 Anastasia Yendiki 

  Sorry, can't open the image.

  On Sun, 23 Jun 2013, Rotem Saar wrote:

Hi there,

Long time:). Well I wrote to the list several times
regarding high FA values
I got when performing DTI analysis.
Today we know that the problem was an additional
direction (we had 17
directions instead of 16 - we used a Philips
scanner,1.5T). So we deleted
the additional slices and the high values indeed
disappeared, but then
another problem came up (tried several subjects so
the problem is not
specific to a subject) -

I noticed an artifact that I can't explain - please
see the attached
pictures.

This artifact existed even before I deleted the
additional slices, also - I
see the artifact also when loading the masked
volume...It is cyclic - run
over all slices...

any ideas ?
 
I'm using version 5.2 and I know the command lines
are correct (send it to u
in the past).

Thanks for your help

Rotem




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Re: [Freesurfer] Fwd: DTI questions

[Anastasia Yendiki]

Sorry, can't open the image.

On Sun, 23 Jun 2013, Rotem Saar wrote:


Hi there,

Long time:). Well I wrote to the list several times regarding high FA values
I got when performing DTI analysis.
Today we know that the problem was an additional direction (we had 17
directions instead of 16 - we used a Philips scanner,1.5T). So we deleted
the additional slices and the high values indeed disappeared, but then
another problem came up (tried several subjects so the problem is not
specific to a subject) -

I noticed an artifact that I can't explain - please see the attached
pictures.

This artifact existed even before I deleted the additional slices, also - I
see the artifact also when loading the masked volume...It is cyclic - run
over all slices...

any ideas ?
 
I'm using version 5.2 and I know the command lines are correct (send it to u
in the past).

Thanks for your help

Rotem

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Re: [Freesurfer] Multiple inputs into recon-all -i

[ye tian]

Dear Bruce,

Thank you very much!

Sincerely,
Ye


On Mon, Jun 24, 2013 at 7:32 PM, Bruce Fischl wrote:

> Hi Ye,
>
> you would never have two files, as each file represents one image, or
> slice from a sequence. So you might have two  sequences of files, say
> Barba001-1.img, Barba001-2.img... Barba001-256.ima, and Baraba002-1.ima,
> Barba002-2.ima Barba002-256.ima. Then you would use -i twice, once with
> *one* file from each series (it wouldn't matter which one).
>
>
> cheers
> Bruce
>
> On Mon, 24 Jun 2013, ye tian wrote:
>
>  Dear Bruce,
>> Thank you very much for your suggestion, but I am afraid that I still
>> don't
>> quite understand you.
>>
>> In order to make it simple, suppose I have two files, Barba001.IMA and
>> Barba002.IMA, coming directly from the scanner.
>>
>> Now if I enter  recon-all -s Barba -i Barba001.IMA  from the command
>> line, I
>> am only able to find   001.mgz  in the Barba/mri/orig. Aren't I supposed
>> to
>> to find 001.mgz and 002.mgz?
>>
>> Thank you so much!
>>
>> Sincerely,
>> Ye
>>
>>
>> On Mon, Jun 24, 2013 at 5:41 PM, Bruce Fischl > >
>> wrote:
>>   Hi Ye
>>
>>   you only need to give it a single file from each run and it will
>>   find the rest. The only time you use -i more than once is if you
>>   acquired more than 1 T1-weighted volume. Definitely don't give
>>   it all the files that make up the same volume
>>
>>   cheers
>>   Bruce
>>   On Mon, 24 Jun 2013, ye tian wrote:
>>
>> Dear David,
>> I wonder whether there is a short cut for recon-all
>> -s Barbara -i
>> /path_to_data/scan1.dicom -i
>> /path_to_data/scan2.dicom ... -i
>> /path_to_data/scan100.dicom
>>
>> Recon-all -i takes only a single file as an input. A
>> typical user, however,
>> has hundreds of files for a particular subject. For
>> example, the directory
>> Barbara may have 100 scans. Therefore, the above
>> command is necessary to
>> include all the scans.
>>
>> I understand that I can write loops to a text file
>> and then copy and paste
>> to command line. However, I wonder whether there is
>> a simpler way to input
>> several files or even a directory to recon-all.
>>
>> Thank you very much!
>>
>> Sincerely,
>> Ye
>>
>>
>>
>>
>> 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] Multiple inputs into recon-all -i

[Bruce Fischl]

Hi Ye,

you would never have two files, as each file represents one image, or 
slice from a sequence. So you might have two  sequences of files, say 
Barba001-1.img, Barba001-2.img... Barba001-256.ima, and Baraba002-1.ima, 
Barba002-2.ima Barba002-256.ima. Then you would use -i twice, once with 
*one* file from each series (it wouldn't matter which one).


cheers
Bruce

On 
Mon, 24 Jun 2013, ye tian wrote:



Dear Bruce,
Thank you very much for your suggestion, but I am afraid that I still don't
quite understand you.

In order to make it simple, suppose I have two files, Barba001.IMA and
Barba002.IMA, coming directly from the scanner.

Now if I enter  recon-all -s Barba -i Barba001.IMA  from the command line, I
am only able to find   001.mgz  in the Barba/mri/orig. Aren't I supposed to
to find 001.mgz and 002.mgz?

Thank you so much!

Sincerely,
Ye


On Mon, Jun 24, 2013 at 5:41 PM, Bruce Fischl 
wrote:
  Hi Ye

  you only need to give it a single file from each run and it will
  find the rest. The only time you use -i more than once is if you
  acquired more than 1 T1-weighted volume. Definitely don't give
  it all the files that make up the same volume

  cheers
  Bruce
  On Mon, 24 Jun 2013, ye tian wrote:

Dear David,
I wonder whether there is a short cut for recon-all
-s Barbara -i
/path_to_data/scan1.dicom -i
/path_to_data/scan2.dicom ... -i
/path_to_data/scan100.dicom 

Recon-all -i takes only a single file as an input. A
typical user, however,
has hundreds of files for a particular subject. For
example, the directory
Barbara may have 100 scans. Therefore, the above
command is necessary to
include all the scans. 

I understand that I can write loops to a text file
and then copy and paste
to command line. However, I wonder whether there is
a simpler way to input
several files or even a directory to recon-all.

Thank you very much!

Sincerely,
Ye




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
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Re: [Freesurfer] Multiple inputs into recon-all -i

[ye tian]

Dear Bruce,

Thank you very much for your suggestion, but I am afraid that I still don't
quite understand you.

In order to make it simple, suppose I have two files, Barba001.IMA and
Barba002.IMA, coming directly from the scanner.

Now if I enter  *recon-all -s Barba -i Barba001.IMA*  from the command
line, I am only able to find   *001.mgz*  in the Barba/mri/orig. Aren't I
supposed to to find 001.mgz and 002.mgz?

Thank you so much!

Sincerely,
Ye


On Mon, Jun 24, 2013 at 5:41 PM, Bruce Fischl wrote:

> Hi Ye
>
> you only need to give it a single file from each run and it will find the
> rest. The only time you use -i more than once is if you acquired more than
> 1 T1-weighted volume. Definitely don't give it all the files that make up
> the same volume
>
> cheers
> Bruce
>
> On Mon, 24 Jun 2013, ye tian wrote:
>
>  Dear David,
>> I wonder whether there is a short cut for recon-all -s Barbara -i
>> /path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i
>> /path_to_data/scan100.dicom
>>
>> Recon-all -i takes only a single file as an input. A typical user,
>> however,
>> has hundreds of files for a particular subject. For example, the directory
>> Barbara may have 100 scans. Therefore, the above command is necessary to
>> include all the scans.
>>
>> I understand that I can write loops to a text file and then copy and paste
>> to command line. However, I wonder whether there is a simpler way to input
>> several files or even a directory to recon-all.
>>
>> Thank you very much!
>>
>> Sincerely,
>> Ye
>>
>>
>>
>
> 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] Multiple inputs into recon-all -i

[Bruce Fischl]

Hi Ye

you only need to give it a single file from each run and it will find the 
rest. The only time you use -i more than once is if you acquired more 
than 1 T1-weighted volume. Definitely don't give it all the files that 
make up the same volume


cheers
Bruce
On Mon, 24 Jun 2013, ye tian wrote:


Dear David,
I wonder whether there is a short cut for recon-all -s Barbara -i
/path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i
/path_to_data/scan100.dicom 

Recon-all -i takes only a single file as an input. A typical user, however,
has hundreds of files for a particular subject. For example, the directory
Barbara may have 100 scans. Therefore, the above command is necessary to
include all the scans. 

I understand that I can write loops to a text file and then copy and paste
to command line. However, I wonder whether there is a simpler way to input
several files or even a directory to recon-all.

Thank you very much!

Sincerely,
Ye

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[Freesurfer] Multiple inputs into recon-all -i

[ye tian]

Dear David,

I wonder whether there is a short cut for recon-all -s Barbara -i
/path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i
/path_to_data/scan100.dicom

Recon-all -i takes only a single file as an input. A typical user, however,
has hundreds of files for a particular subject. For example, the directory
Barbara may have 100 scans. Therefore, the above command is necessary to
include all the scans.

I understand that I can write loops to a text file and then copy and paste
to command line. However, I wonder whether there is a simpler way to input
several files or even a directory to recon-all.

Thank you very much!

Sincerely,
Ye
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[Freesurfer] HCP Releases Second Quarter of Brain Connectivity Data

[Jennifer Elam]

June 13, 2013 (repost to Freesurfer list June 24, 2013)

The Human Connectome Project (HCP) WU-Minn consortium is pleased to
announce our second quarterly (Q2) release of HCP image and behavioral data.

What’s in the HCP Q2 data release? The Q2 data include multimodal MRI and
behavioral data collected from 68 healthy young adults scanned in winter
2012-2013.  The current release expands the total (Q1+Q2) number of
released healthy participant data for imaging and/or behavioral measures to
148, including 40 datasets that include the complete HCP protocol (T1w and
T2w MRI, rfMRI, tfMRI, dMRI, and behavioral measures) and an additional 60
that include all modalities other than dMRI. The Q2 release also includes:

· New preprocessing pipelines - Along with the newly processed Q2
datasets, the Q2 release also includes a complete regeneration of the
minimally preprocessed data from Q1. We strongly encourage all
investigators to update their existing Q1 data to stay current with HCP's
latest and greatest.

· More behavioral data, physiological data - Most of the collected
behavioral/individual difference assessments and physiological data for
functional MRI scans of Q1/Q2 participants is now available for a majority
of subjects.

· Restricted Data - Qualified investigators who are approved for
restricted access  will be given access to restricted data through the
ConnectomeDB interface.

· 40 dMRI datasets - Diffusion MRI data is being released for 40
unrelated Q1/Q2 subjects only because HCP has recently implemented an
improved image reconstruction algorithm for dMRI data.  Unprocessed and
minimally preprocessed datasets based on these improved reconstructions for
all Q1, Q2, and Q3 subjects will be included in the Q3 data release
scheduled for August 2013.

Access Q2 data on the HCP website. Explore, download, or order the entire
HCP Q1+Q2 dataset (~3.5TB of data!) via the ConnectomeDB database (
http://humanconnectome.org/data/). Most HCP image and behavioral data is
openly accessible to investigators worldwide who register and accept a
limited set of Open Access Data Use Terms. Note: Please clear your browser
cache before logging in to ConnectomeDB.

Want more information?  Check out the HCP Q2 Data Release Reference Manual (
http://humanconnectome.org/documentation/Q2/) for a comprehensive guide
that includes details on imaging protocols, behavioral measures, and
information that will help users obtain and analyze the Q2 data.

Detailed descriptions of many HCP methods are available in eight papers now
in press for a special issue of NeuroImage in 2013 (Van Essen et al., 2013,
Ugurbil et al., 2013, Glasser et al., 2013, Smith et al., 2013, Barch et
al., 2013, Sotiropolous et al., 2013, Marcus et al., 2013, and Larson-Prior
et al., 2013).

For those who choose to download the HCP data and begin to analyze it, we
encourage you to join and be active in the hcp-users discussion group (
http://www.humanconnectome.org/contact/#subscribe), so that you can tune in
to technical discussions on issues that may be of interest.

Please send us your questions and comments anytime to
i...@humanconnectome.org.

Best,

The WU-Minn HCP Consortium

Jennifer Elam, Ph.D.
Outreach Coordinator, Human Connectome Project
Washington University School of Medicine
Department of Anatomy and Neurobiology, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@pcg.wustl.edu
www.humanconnectome.org
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Re: [Freesurfer] Using the T2 pial flag for pial refinement

[Bruce Fischl]

Hi Mike

the 3.5-4mm thickness probably makes them not usable since it means 
opposing banks of a sulcus will be in the same voxel pretty frequently


sorry
Bruce
On 
Mon, 24 Jun 2013, Michael Kranz wrote:



Hi all,

I'm having trouble determining whether or not to use our T2 images for the
new pial refinement feature. Most importantly, I'm wondering if our T2 image
parameters are sufficient for the T2 pial refinement. The parameters of our
T2 images are as follows:

T2 TSE overlay with a voxel size of 1.1x1.1x3.5 mm (slice thickness).

A couple other studies in our lab have a voxel size of 0.9x0.9x4.0 mm. 

Note that our MPRAGE voxel size is .9x.9x.9mm.

In your release notes, it states we should uaround a 1x1x1mm (let me know if
you need additional specifications such as geometry bandwidth etc):
"T2/FLAIR used for pial surface refinement: if you have T2 or FLAIR scans
~1mm^3, then they can be used by the recon-all stream to refine the pial
surfaces". 

I have experienced about 1/4 of our subjects with errors using the T2 pial
flag. As a next step, if you think the parameters are acceptable, then I can
send you some screen shots different errors that I have encountered wit
these subjects.

Best,
Mike



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[Freesurfer] Using the T2 pial flag for pial refinement

[Michael Kranz]

Hi all,

I'm having trouble determining whether or not to use our T2 images for the
new pial refinement feature. *Most importantly, I'm wondering if our T2
image parameters are sufficient for the T2 pial refinement. The parameters
of our T2 images are as follows:*

T2 TSE overlay with a voxel size of 1.1x1.1x3.5 mm (slice thickness).

A couple other studies in our lab have a voxel size of 0.9x0.9x4.0 mm.

Note that our MPRAGE voxel size is .9x.9x.9mm.

In your release notes, it states we should uaround a 1x1x1mm (let me know
if you need additional specifications such as geometry bandwidth etc):
"T2/FLAIR
used for pial surface refinement: if you have T2 or FLAIR scans ~1mm^3,
then they can be used by the recon-all stream to refine the pial surfaces".

I have experienced about 1/4 of our subjects with errors using the T2 pial
flag. As a next step, if you think the parameters are acceptable, then I
can send you some screen shots different errors that I have encountered wit
these subjects.

Best,
Mike
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Re: [Freesurfer] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh

[Juan Eugenio Iglesias]

Dear Zoe,
have you checked whether all directories within your subject directory 
correspond to subjects which have been reconed with the -hippo-subfields 
flag?

Cheers,
/Eugenio

On 06/24/2013 04:00 PM, Yang, Zoe wrote:


Hi all,

I am getting error messages while running 
kvlQuantifyHippocampalSubfieldSegmentations.sh, similar to the error 
mentioned in an earlier 
email (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg24430.html). 
We did use the -hippo-subfields flag for all of our subjects first, 
and the output was 20 left and right subfield mgz files (it completed 
without any errors). The subjects had already undergone the standard 
volumetric FreeSurfer pipeline and therefore we ran the command: 
recon-all -s subjectID -hippo-subfields.


The error message for kvlQuantifyHippocampalSubfieldSegmentation that 
I'm getting is:


resultsDirectory ***/HIPPOCAMPAL_TEST

cd ***/HIPPOCAMPAL_TEST

resultsDirectory ***/HIPPOCAMPAL_TEST

startIndex: 1

endIndex: 2

cd subjectID_recon/

Quantifying subject ID_recon left

Doing left side

cd left

cd segmentationWithoutPartialVolumingLog

kvlQuantifyPosteriorProbabilityImages 
/Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt 
posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz 
posterior_left_CA1.mgz posterior_left_CA2-3.mgz   
  posterior_left_fimbria.mgz posterior_left_subiculum.mgz 
posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz   
  > volumeStats_left.txt


terminate called after throwing an instance of 'itk::ExceptionObject'

  what():  itkMGHImageIO.cxx:216:

itk::ERROR: MGHImageIO(0x46b690): Can't find/open file: 
posterior_Left-Hippocampus.mgz


kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: 50779 Abort 
trap  kvlQuantifyPosteriorProbabilityImages 
/Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt 
posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz 
posterior_left_CA1.mgz posterior_left_CA2-3.mgz 
posterior_left_fimbria.mgz posterior_left_subiculum.mgz 
posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz > 
volumeStats_left.txt


failed to do kvlQuantifyPosteriorProbabilityImages 
/Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt 
posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz 
posterior_left_CA1.mgz posterior_left_CA2-3.mgz   
  posterior_left_fimbria.mgz posterior_left_subiculum.mgz 
posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz   
  > volumeStats_left.txt


Is there anything else that we are missing and should run?

Thanks!



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[Freesurfer] fsaverage vertex index to talairach

[Cesar Echavarria]

Hello,

Anyone know of a fast way to get the talairach coordinates of a vertex
index in fsaverage. A function or script is best since I want to do this
for a large number of vertices.
Thank you for any help you guys can provide.

Cesar
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Re: [Freesurfer] infant .tiff templates

[Mark Plantz]

Hi Bruce,

So technically speaking I guess I have three different brain
atlases for neonates, 1 yr olds, and 2 yr olds. Each atlas contains a set
of 3D images made up of the intensity model, tissue probability maps, and
anatomical parcellation map. I obtained these from a study done by UNC (
http://bric.unc.edu/ideagroup/free-softwares/unc-infant-0-1-2-atlases/

).

  I also have about 40 different infant fMRI's that I would like to
reconstruct and analyze with FreeSurfer. However, I believe that the
default template (average.curvature.filled.buckner40.tif) will not work for
these infant brains. My end goal is to be able to convert the provided
brain atlases (from UNC) into a format that can be used for a template in
FreeSurfer (i.e. TIFF image).

   Is there any clear cut way to do that?

Thanks for the help.

- Mark


On Mon, Jun 24, 2013 at 3:02 PM, Bruce Fischl wrote:

> Hi Mark
>
> can you clarify what you mean? What template are you referring to?
>
> Bruec
>
> On Mon, 24 Jun 2013, Mark Plantz wrote:
>
>  Hello freesurfers,
>>   I am currently attempting to create my own .tiff templates for a
>> series of infant fMRI's (neonates, 1 yr olds, and 2 yr olds). I currently
>> have the templates in .nii.gz, .mgz, and .img/.hdr formats.
>>
>> Is there any easy way to convert from one of these formats to a .tiff
>> image
>> to use as an actual template for reconstruction with FreeSurfer?
>>
>> If so, would the conversion distort/ruin the template?
>>
>> Thank you!
>>
>>
>> - Mark Plantz
>>
>>
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Re: [Freesurfer] infant .tiff templates

[Bruce Fischl]

Hi Mark

can you clarify what you mean? What template are you referring to?

Bruec
On Mon, 
24 Jun 2013, Mark Plantz wrote:



Hello freesurfers,
      I am currently attempting to create my own .tiff templates for a
series of infant fMRI's (neonates, 1 yr olds, and 2 yr olds). I currently
have the templates in .nii.gz, .mgz, and .img/.hdr formats. 

Is there any easy way to convert from one of these formats to a .tiff image
to use as an actual template for reconstruction with FreeSurfer?

If so, would the conversion distort/ruin the template?

Thank you!


- Mark Plantz

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[Freesurfer] Question about running kvlQuantifyHippocampalSubfieldSegmentations.sh

[Yang, Zoe]

Hi all,
I am getting error messages while running 
kvlQuantifyHippocampalSubfieldSegmentations.sh, similar to the error mentioned 
in an earlier email 
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg24430.html). We 
did use the -hippo-subfields flag for all of our subjects first, and the output 
was 20 left and right subfield mgz files (it completed without any errors). The 
subjects had already undergone the standard volumetric FreeSurfer pipeline and 
therefore we ran the command: recon-all -s subjectID -hippo-subfields.
The error message for kvlQuantifyHippocampalSubfieldSegmentation that I'm 
getting is:

resultsDirectory ***/HIPPOCAMPAL_TEST
cd ***/HIPPOCAMPAL_TEST
resultsDirectory ***/HIPPOCAMPAL_TEST
startIndex: 1
endIndex: 2
cd subjectID_recon/
Quantifying subject ID_recon left
Doing left side
cd left
cd segmentationWithoutPartialVolumingLog
kvlQuantifyPosteriorProbabilityImages 
/Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt 
posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz  
   posterior_left_CA1.mgz posterior_left_CA2-3.mgz 
posterior_left_fimbria.mgz posterior_left_subiculum.mgz 
posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz
 > volumeStats_left.txt
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  itkMGHImageIO.cxx:216:
itk::ERROR: MGHImageIO(0x46b690): Can't find/open file: 
posterior_Left-Hippocampus.mgz
kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: 50779 Abort trap   
   kvlQuantifyPosteriorProbabilityImages 
/Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt 
posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz 
posterior_left_CA1.mgz posterior_left_CA2-3.mgz posterior_left_fimbria.mgz 
posterior_left_subiculum.mgz posterior_left_CA4-DG.mgz 
posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt
failed to do kvlQuantifyPosteriorProbabilityImages 
/Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt 
posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz  
   posterior_left_CA1.mgz posterior_left_CA2-3.mgz 
posterior_left_fimbria.mgz posterior_left_subiculum.mgz 
posterior_left_CA4-DG.mgz posterior_left_hippocampal_fissure.mgz
 > volumeStats_left.txt


Is there anything else that we are missing and should run?

Thanks!

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[Freesurfer] infant .tiff templates

[Mark Plantz]

Hello freesurfers,

  I am currently attempting to create my own .tiff templates for a
series of infant fMRI's (neonates, 1 yr olds, and 2 yr olds). I currently
have the templates in .nii.gz, .mgz, and .img/.hdr formats.

Is there any easy way to convert from one of these formats to a .tiff image
to use as an actual template for reconstruction with FreeSurfer?

If so, would the conversion distort/ruin the template?

Thank you!


- Mark Plantz
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[Freesurfer] [FreeSurfer] Freeview: Invalid drawable

[ye tian]

Dear Koen,

Freeview returns 8 lines of the error message "invalid drawable" whenever
executed. The messages are as follows

2013-06-24 14:24:57.930 Freeview[1937:303] invalid drawable
2013-06-24 14:24:57.931 Freeview[1937:303] invalid drawable
2013-06-24 14:24:57.944 Freeview[1937:303] invalid drawable
2013-06-24 14:24:57.945 Freeview[1937:303] invalid drawable
2013-06-24 14:24:57.957 Freeview[1937:303] invalid drawable
2013-06-24 14:24:57.958 Freeview[1937:303] invalid drawable
2013-06-24 14:24:57.971 Freeview[1937:303] invalid drawable
2013-06-24 14:24:57.972 Freeview[1937:303] invalid drawable

In the $FREESURFER_HOME directory, I tried

sed -i "" 's/CA2_3/CA2\/3/g' FreeSurferColorLUT.txt
sed -i "" 's/CA4_DG/CA4\/DG/g' FreeSurferColorLUT.txt

as you suggested in

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22276.html(content
copied at the end of this email)

I checked in FreeSurferColorLUT.txt and made sure all CA2_3 was changed
into "CA2\3", all "CA4_DG" into "CA4\DG", but the problem still persists.

My computer is Mac OS X version 10.8.2.
I downloaded 
freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg

Would you please give me some guidance on how to fix the problem?

Thank you very much!

Sincerely,
Ye Tian





















Hi Ed,

It seems that the 5.1.0 release for the Mac was composed two days
after the one for Linux, and during exactly those two days one of us
made a change to the file $FREESURFER_HOME/FreeSurferColorLUT.txt.

To correct this issue, please make a back-up copy of your
FreeSurferColorLUT.txt file, and execute the following commands:

cd $FREESURFER_HOME
sed -i "s/CA2_3/CA2\/3/g" FreeSurferColorLUT.txt
sed -i "s/CA4_DG/CA4\/DG/g" FreeSurferColorLUT.txt

Thanks,

Koen




On Wed, Apr 4, 2012 at 9:32 AM, Ed Gronenschild
 wrote:
> I have downloaded the file
> freesurfer-Darwin-leopard-i686-stable-pub-v51.0..dmg,
> date 26/05/2011.
>
> Ed
>
>
> On 4 Apr 2012, at 13:09, Koen Van Leemput wrote:
>
>> OK, I see why this is not working. We've been changing some name
>> conventions in our internal FreeSurfer repository after the public
>> release of version 5.1, and somehow you managed to get an incompletely
>> updated version.
>>
>> It appears from
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0 that some
>> versions for the Mac were updated *after* the release date (24 May
>> 2011), so I'll check with the engineers what exactly happened. Do you
>> remember which file you downloaded?
>>
>> Thanks,
>>
>> Koen
>>
>>
>>
>> On Wed, Apr 4, 2012 at 6:59 AM, Ed Gronenschild
>>  wrote:
>>>
>>> Hi Koen,
>>>
>>> No worries.
>>> The result of grep is:
>>>
>>> 500 right_CA2_3 17 85 136 0
>>> 550 left_CA2_3  17 85 137 0
>>>
>>> Ed
>>>
>>>
>>> On 4 Apr 2012, at 12:41, Koen Van Leemput wrote:
>>>
 Hi Ed,

 Can you please do

 "grep _CA2 $FREESURFER_HOME/FreeSurferColorLUT.txt"

 and let me know what the result is?

 Thanks, and sorry this seems so difficult to sort out.

 Koen


 On Wed, Apr 4, 2012 at 6:14 AM, Ed Gronenschild
  wrote:
>
>
> Hi Koen,
>
> As already mentioned, I'm using v5.1.0, Mac Intel
> Leopard version.
> The voxel values of posterior_left_CA2-3.mgz and
> posterior_right_CA2-3.mgz are between 0 and 255,
> if that is what you mean by "results".
> By the way: I always get the 8 lines with "invalid
> drawable" messages from freeview.
>
> Ed
>
>
> On 3 Apr 2012, at 21:29, Koen Van Leemput wrote:
>
>> Hi Ed,
>>
>> What version of the FreeSurfer build are you using?
>>
>> Also, could you please let me know what the result is of "ls
>> posterior_left_CA2*"?
>>
>> Thanks,
>>
>> Koen
>>
>>
>>
>> On Tue, Mar 27, 2012 at 8:29 AM, Ed Gronenschild
>>  wrote:
>>>
>>>
>>>
>>> Hi,
>>>
>>> I followed the instructions to visualize the hippocampal subfield
>>> segmentation
>>> by entering the command (in the subject's mri directory)
>>>
>>> freeview nu.mgz \



  -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \
  -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \
  -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
>>>
>>>
>>>
>>>
>>> and got the following messages:
>>>
>>> 2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable
>>> 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable
>>> 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable
>>> 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable
>>> 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable
>>> 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable
>>>

[Freesurfer] retinotopy betas

[dgw]

Hi,

I am examining the affect a metal artifact has on fMRI data, and I am
using Eccentricity mapping with the retinotopy analysis in FSFast. I
was recently asked to switch from examining the difference in the fsig
to examining the difference in the betas. I opened up beta.nii.gz and
I can see that it has a size of:

1 #of vertices 1 39

Can you explain to me, how I figure out where each of the 39 come from
(and possibly point me to which of these might be appropriate to
use?)?

Thank You,
Dan
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[Freesurfer] Is there any way of finding out RESEL number in the GLM output?

[Glen Lee]

Hello Freesurfer users,
I'd hope to know the RESEL number in my group GLM analysis data.
I can calculate the number of vertices and also see the fwhm.dat in the
ouput GLM folder, but I wonder if there is anyway of finding out RESEL size
if freesurfer also provides that info like SPM does.
-Glen
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Re: [Freesurfer] Help with QDEC error

[Manish Dalwani]

Hi Nick and Doug, 

Can you suggest an alternative way if QDEC is unable to handle a single group?  
I would like to run these analyses to address reviewers comments. 

 Best,
Manish



 From: Douglas Greve 
To: Manish Dalwani  
Cc: "freesurfer@nmr.mgh.harvard.edu"  
Sent: Thursday, June 20, 2013 11:16 PM
Subject: Re: [Freesurfer] Help with QDEC error
 



I thought it would have worked with a single group. Maybe Nick knows
of the top of his head.
doug




On 6/20/13 12:36 PM, Manish Dalwani wrote:

Hi Doug and Freesurfers, 
>
>
>I realized that I hadn't updated my group levels to one group. However, when I 
>do that..the qdec complains about group.level having at minimum two levels. 
>How can I run (using QDEC) single group regression? 
>
>
>Thanks,
>Manish
>
>
>
>
> From: Manish Dalwani 
>To: Douglas Greve ; 
>"freesurfer@nmr.mgh.harvard.edu"  
>Sent: Thursday, June 20, 2013 1:26 PM
>Subject: Re: [Freesurfer] Help with QDEC error
> 
>
>
>Hi Doug, 
>
>
>I was out of town for a conference. Please see my attachments. I have the log 
>file and screenshots of ill-matrix conditioning.
>Thanks for your help!
>Manish
>
>
>
>
> From: Douglas Greve 
>To: freesurfer@nmr.mgh.harvard.edu 
>Sent: Saturday, June 15, 2013 11:09 AM
>Subject: Re: [Freesurfer] Help with QDEC error
> 
>
>
>
>Can you send the mri_glmfit.log file from 
>/Applications/freesurfer/subjects/qdec/Untitled ?
>doug
>
>
>
>On 6/14/13 4:57 PM, Manish Dalwani wrote:
>
>Hello Freesurfers, 
>>
>>
>>I am trying to run regression analyses within patients and one variable of 
>>interest which adjusting for the nuisance variables age, IQ, thickness. When 
>>i select the group and the CD (variable of interest) and run analyses (DODS), 
>>I get the following error: 
>>
>>
>>Qdec 1.4 (Qdec1.4)
>>
>>
>>Type: Error
>>Time: Fri Jun 14 14:49:37 2013
>>Description: Error in Analyze: command failed: mri_glmfit --y 
>>/Applications/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd 
>>/Applications/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir 
>>/Applications/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --C 
>>/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
>> --C 
>>/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-CD-Cor.mat
>> --C 
>>/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Intercept-thickness.mat
>> --C
/Applications/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-CONTROLS-PATIENTS-Cor-thickness-CD.mat
>>
>>
>>Please advice!
>>
>>
>>Regards,
>>Manish Dalwani
>>Instructor
>>Dept. of Psychiatry
>>University of Colorado
>>
>>
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  only for the person to whom it is
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  to you in error and the e-mail
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[Freesurfer] mri_glimfit paired analysis

[Gayane Aghakhanyan]

Dear FreeSurfers

I'm using Freesurfer 5.1 on Ubuntu 12.04 LTS.
Currently running paired analysis as described here
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis

After

mri_glmfit \
 --glmdir lh.paired-diff \
 --y lh.paired-diff.thickness.sm05.mgh \
 --fsgd paired-diff.fsgd \
 --C mean.mtx \
 --C age.mtx

I've got an error "ERROR: you must use '--surface subject hemi' with
surface data".
Any idea how to fix it?

Below is the full output:

utente@RM-user:~/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis$
mri_glmfit --glmdir lh.paired-diff --y
lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx
--C age.mtx

gdfReadHeader: reading paired-diff.fsgd
INFO: ignoring tag ,9
INFO: ignoring tag ,9
INFO: ignoring tag ,3
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)

0 Age 57 11.0454
Class Means of each Continuous Variable
1 Main  57.
INFO: gd2mtx_method is dods

$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd 
/home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis

cmdline mri_glmfit --glmdir lh.paired-diff --y
lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx
--C age.mtx
sysname  Linux
hostname RM-user
machine  x86_64
user utente
FixVertexAreaFlag = 1

UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis/lh.paired-diff.thickness.sm05.mgh
logyflag 0
usedti  0
FSGD paired-diff.fsgd

glmdir lh.paired-diff
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.paired-diff
Loading y from 
/home/utente/Documenti/Gayane/POCD_quantitative/freesurfer_pocd/longitudinal_2013/pairedAnalysis/lh.paired-diff.thickness.sm05.mgh

ERROR: you must use '--surface subject hemi' with surface data

Thanks for yuo help

Gayane
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Re: [Freesurfer] lme issues + failure to converge

[jorge luis]

 
Hi Cathy

If you only have three groups  in your
data (Control subjects, High risk patients, Ill patients) then you should drop 
the
“Controls versus all others and controls*time interaction”  terms
from your design matrix. Otherwise it is ill-conditioned. One way to
check your design matrix is by performing a simple univariate
analysis using data from a single vertex, eg. at vertex 1000:

lhstats = lme_fit_FS(X,[1
2],Y(:,lhcortex(1000)),ni);

and
check the behavior of the optimization procedure. Make
sure that both your design matrix X and the cortical thickness data Y are 
ordered in a
way that they contain all the repeated measures for the first
subject (ordered by time), then all the repeated measures for the second 
subject and
so on. The first element of the vector ni must indicate the number of
repeated measures in the design matrix X for the first subject, the
second element of that vector must indicate the number of repeated
measures in the design matrix for the second subject and so on.
Finally you should include the data Y as an argument of the fitting
function:

lhstats = lme_mass_fit_vw(X,[1
2],Y,ni,lhcortex);

This will fit a linear mixed effects model with two random effects (intercept 
and time).


Best

-Jorge




>
> De: Catherine Bois 
>Para: Jorge  
>CC: freesurfer@nmr.mgh.harvard.edu 
>Enviado: Lunes 24 de junio de 2013 5:14
>Asunto: Re: [Freesurfer] lme issues + failure to converge
> 
>
>Hi,
>
>So, the model we fitted was one with only 1 random effect apparently  
>(the intercept term), so we used the script you sent for older  
>versions of matlab;
>
>lhstats = lme_mass_fit_vw1(X,[1],ni,lhcortex)
>
>The model took 861 minutes to run, and at the end it now said that the  
>model failed to converge at ca 85% of locations...
>
>The matrices columns are as follows; the intercept term, time (I guess  
>due to only using one random effect in our model it will be treated as  
>a fixed effect by Matlab?), High risk versus all other patients, high  
>risk versus time interaction, Controls versus all others,  
>controls*time interaction, ill*all others, ill*time interaction,  
>Gender, Age. There are ca 170 subjects, with varying and unbalanced  
>repeated measures (ranging up to 5/subject).
>
>Since we would like to fit a model with both intercept and time (and  
>in the long run) also family as random effects, perhaps we need to use  
>the spatiotemporal models instead to make our model converge? If so,  
>will the scripts for fitting these in older versions of Matlab be  
>available soon?
>
>Have we missed an obvious step which is making our model not converge  
>at 85% of the positions?
>
>Thank you for your help,
>
>Best Wishes,
>
>Cathy
>
>
>X = [ones(length(M),1) M(:,1) Mat(:,1) Mat(:,1).*M(:,1) Mat(:,2)
>>> Mat(:,2).*M(:,1) Mat(:,3) Mat(:,3).*M(:,1) M(:,3)-1 M(:,4)];
>
>
>Quoting Jorge  on Fri, 21 Jun 2013 10:42:11 -0700:
>
>> Hi Cathy
>>
>> You should put a comma between X and [1 2]
>>
>>> lhstats = lme_mass_fit_vw(X, [1 2],ni,lhcortex);
>>
>> The model with a single random effect for the intercept term must  
>> always converge:
>>
>>> lhstats = lme_mass_fit_vw(X, [1],ni,lhcortex);
>>
>>
>> Can you tell me with words what the columns of your design matrix  
>> are?  How many subjects and how many repeated measures for each  
>> subject do you have?
>>
>> Best
>> -Jorge
>>
>>
>>
>> Sent from my iPad
>>
>> On Jun 21, 2013, at 4:53, Catherine Bois  wrote:
>>
>>> Dear Jorge/freesurfer group,
>>>
>>> I am using the scripts you sent me that do not require the newer
>>> version of matlab, and now using a computer that has the Statistics
>>> toolbox. I can get the scripts (with the suffix 1) to run with;
>>> lhstats = lme_mass_fit_vw(X[1 2],ni,lhcortex);) however it "fails to
>>> reach convergence" at most vertices. We have tried simplifying the
>>> model to include only one random effect at a time, however the problem
>>> persists. Our design matrix is as follows;
>>>
>>>  X = [ones(length(M),1) M(:,1) Mat(:,1) Mat(:,1).*M(:,1) Mat(:,2)
>>> Mat(:,2).*M(:,1) Mat(:,3) Mat(:,3).*M(:,1) M(:,3)-1 M(:,4)];
>>>
>>> I have read on the mailing list that non-convergence at some vertices
>>> is normal, however what we are getting far exceeds 10%. Any help on
>>> this matter would be greatly appreciated!
>>>
>>> Best Wishes,
>>>
>>> Cathy
>>>
>>> --
>>> The University of Edinburgh is a charitable body, registered in
>>> Scotland, with registration number SC005336.
>>>
>>>
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>>> the e-mail
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>>> Compliance HelpLine at
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[Freesurfer] problem with surface area regression

[wen.zhang55]

Dear Freesurfer,   
   
I have checked the mail list, none could answer my problem.   
I added up the value of all vertxes in the .area or .area.pial files, find that 
brain size did not contribute much to that vertex-sum. However, some experiment 
used total brain volume as a regreesion coefficient to remove brain size 
effect. In these case, with the comparison of surface area in vertex-to-vertex, 
is it proper to use the above vertex-sum as the regression coefficient to 
remove different brain size?
Thank you very much!   
   
Cowen   
   
2013-06-24   
   
   
   
wen.zhang55   

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[Freesurfer] Error for mri_glmfit contrast

[Catherine Bois]

Dear Freesurfer experts, I am currently trying to do a cortical  
thickness group analysis with one factor, three levels . I have run  
mri_preproc and mri_surf2surf, and am now trying to run

mri_glmfit --y lh.group.thickness.10B.mgh --fsgd easy2.file --C  
contrast1.mtx --surf fsaverage lh --cortex --glmdir lh.group

However, I keep getting this error;

INFO: gd2mtx_method is doss
Saving design matrix to lh.group/Xg.dat
Normalized matrix condition is 1
Matrix condition is 7
Found 149955 points in label.
Pruning voxels by thr: 0.00
Found 149953 voxels in mask
Saving mask to lh.group/mask.mgh
Reshaping mriglm->mask...
search space = 74612.446501
MatrixReadTxT: could not scan value [2][1]


The format of both the fsgd file and the contrast file is ASCII text

My fsgd file is formatted as follows:

GroupDescriptorFile 1
Title Group analysis
Class HR
Class Con
Class ILL
Input EHRS__2 HR
Input EHRS__2 HR
Input EHRS__2 HR
Input EHRS__2 Con
Input EHRS__2 Con
Input EHRS__2 ILL

and my contrast file is;

1 -1 0

I do not understand why I keep getting this error. When I include the  
flag -no-contrasts-is-ok, the mri_glmfit does work. There are no  
commas in either file.
  This leads me to believe something is wrong with my contrast file?  
However I am not certain what this could be. Help would be greatly  
appreciated.

Thank you very much,

Cathy

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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Re: [Freesurfer] retinotopic mapping selxavg3-sess error

[Bianca van Kemenade]

Sorry for the delay. I'm new to FSL, Freesurfer, and VB, so maybe I'm doing
it wrong, but I have the impression I cannot run FSL from the VB:
- Typing 'fsl' yields 'fsl: Command not found'.
- Checking the environment with 'echo $FSLDIR' yields 'FSLDIR: undefined
variable'
- Checking the path with 'flirt -version' yields 'flirt: Command not found'

However, typing 'fsl' + tab shows the following available commands:
- fsl2par
- fsl_label2voxel
- fslmaths.fsl
- fslorient.fsl
- fslregister
- fslregister -sess
- fsl_rigid_register
- fslsfonts
- fsl_sub_seychelles
- fslswapdim.fsl

So it seems there are some FSL-related files installed, but apparently not
all. I did download the virtual disk image for Freesurfer, so I assumed a
complete FSL version would be included? I'm sorry if there's an obvious
solution, but I can't seem to find it...

Thanks again,
Bianca


On Fri, Jun 21, 2013 at 6:16 PM, Douglas Greve wrote:

>
> Can you run FSL at all in your VB?
>
>
>
>
> On 6/21/13 7:49 AM, Bianca van Kemenade wrote:
>
>  Dear Freesurfers,
>
> I'm setting up freesurfer to do retinotopic mapping. I use a PC with
> Windows XP, so I installed Freesurfer using the VirtualBox (with Xubuntu).
> I managed to get through the initial steps for retinotopic mapping, but I
> get stuck at the actual analysis.
>
> The point where I get stuck is:
>
> selxavg3-sess -a rtopy.self.lh -s P2_BK
>
>  It starts the analysis, but runs into problems at the stage "Using FSL's
> BET to extract brain" and gives the following error output:
>
>  # -- Using FSL's BET to Extract Brain-- #
> /home/virtualuser/freesurfer/
> shared/P2_BK/bold
> bet.fsl /tmp/mkbrainmask_4425/in.nii /tmp/mkbrainmask_4425/brain -m -f 0.1
> /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found
> /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found
> /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found
> [: 158: =: unexpected operator
> /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found
> /bin/rm: cannot remove `_tmp*': Protocol error
> ERROR: bet failed
>
>  I tried updating FSL in case that is the problem, but it is only
> available for Ubuntu 10.04 and up, whereas the Ubuntu system that is
> provided to install the Freesurfer virtual disk image is 9.04. If anyone
> has an idea how to proceed let me know, any help is much appreciated.
>
> Thanks,
> Bianca
>
>
>
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>
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> 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
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Bianca van Kemenade, MSc
Doctoral Candidate, Berlin School of Mind and Brain

Klinik für Psychiatrie und Psychotherapie
Campus Charité Mitte
Charitéplatz 1
10117 Berlin
http://www.mind-and-brain.de/



-- 
Bianca van Kemenade, MSc
Doctoral Candidate, Berlin School of Mind and Brain

Klinik für Psychiatrie und Psychotherapie
Campus Charité Mitte
Charitéplatz 1
10117 Berlin
http://www.mind-and-brain.de/
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