[Freesurfer] Opportunity for a research associate in MR imaging

2011-12-20 Thread Direktion, Institut f. Schlaganfall- und Demenzforschung
The Hospital of the University of Munich, Germany, is one of the largest and 
most capable university hospitals in Germany and Europe. 45 specialized 
hospitals, departments and institutions harbouring excellent research and 
education provide patient care at the highest medical level with approximately 
10.000 employees.

The Institute for Stroke and Dementia Research (ISD) is a newly founded 
institution financed from foundation funds. The activity ranges from basic 
research to clinical trials (www.isd-muc.de). After completion of the 
construction phase, the Institute for Stroke and Dementia research will employ, 
around 100 staff members, graduate students, scholars and foreign scholars.

The Institute for Stroke and Dementia Research (ISD) is looking at the earliest 
opportunity for a Research Associate in MR imaging


RESPONSIBILITIES:
We are looking for a motivated scientist with methodological expertise in MR 
imaging and good programming skills (e.g. C, C ++, Pearl, Python, Scripting 
Languages, Matlab). Knowledge in the collection, processing and analysis of 
functional and structural MR imaging data and an interest in neuro-scientific 
questions are desired.


REQUIREMENTS:
University degree.


OFFER:
Our Institute offers an excellent multidisciplinary environment (medical 
scientists, neuro-psychologists, biologists, bioinformaticians, 
epidemiologists) with modern IT infrastructure and defined times on human MR 
scanners (1.5T and 3T). A new building with its own small-animal-imaging 
(micro-PET and -MRI) is currently being built (www.isd-muc.de). The tasks 
include the establishment of new analytical methods for MRI-data, participation 
in ongoing research projects and developing of own project ideas.

Salary is according to TV-L. The position is limited for two years, extension 
is desired. Disabled persons will be preferentially considered in case of equal 
qualification. Presentation costs can unfortunately not be refunded. For more 
information, please contact Mr. Frühauf, Tel.: +49 (0)89 7095 7800 (E-Mail: 
i...@med.uni-muenchen.de).


HOW TO APPLY:
Your application - preferably in electronic form - with the usual documents 
indicating the earliest possible starting date should be directed to:

Klinikum der Universität München,
Institute for Stroke and Dementia Research
Markus A. Frühauf, Managing Director ISD
Heiglhofstr. 55
81377 Munich | Germany
E-Mail: i...@med.uni-muenchen.de
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[Freesurfer] Converting V1 labels to nifti

2011-12-20 Thread Anders Hougaard
Dear Freesurfers,


I would like to use V1 labels (created with the Hinds method) for a
ROI-based analysis on data analyzed with FSL FEAT using FSL featquery.
I have not run a full recon-all segmentation, only recon-all -s subjid
-label-v1

I need to convert the labels to nifti volumes while registering to MNI
standard space.
I guess the right command would be something like
mri_label2vol --label lh.v1.predict.label --reg register.dat --hemi lh
--subject subject --o lh.v1.predict.label

Is there a register.dat from the FSL feat directory that I could use for
this?

Anything else I need to add?
Of course, I would like to keep the resulting volume probabilistic.

All the best,

Anders
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[Freesurfer] recon-all results

2011-12-20 Thread LAOUCHEDI MAKHLOUF
hi everyone
  i run recon-all on some datasets using freesurfer version 
5.1. Instead of having  aparc.a2009s+aseg.mgz at the end of recon-all, i had 
aparc.a2005s+aseg.mgz. what to do to have the good dataset (2009 instead of 
2005)

thanks
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[Freesurfer] Downsampling pial surfaces and mapping output to fsaverage6

2011-12-20 Thread Ecker, Christine
Dear FreeSurfer Experts,

I would like to down-sample the pial surface of individual subjects to have the 
same number of vertices as fsaverage6. I have done so using:

mri_surf2surf --hemi lh --srcsubject 'subjectID' --sval-xyz pial --trgsubject 
fsaverage6 --trgicoorder 6 --trgsurfval 'outputfilename'

This worked well and the pial output surface has 40962 vertices. I now have an 
overlay vector, which was computed on the down-sampled pial surface, which I 
would like to map back to fsaverage6 in order to perform a group comparison.

Please could you advise on how to do this as all scripts I am aware of (e.g. 
mris_preproc) use sphere.reg, which has ~15 vertices.

Many thanks,
Christine
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Re: [Freesurfer] Downsampling pial surfaces and mapping output to fsaverage6

2011-12-20 Thread Rudolph Pienaar

Take a look at mris_decimate:

~$mris_decimate -x
Help

NAME
mris_decimate

SYNOPSIS
mris_decimate [options] input surface output surface

DESCRIPTION
This program reduces the number of triangles in a surface and 
outputs

the new surface to a file using the GNU Triangulated Surface (GTS)
Library.

POSITIONAL ARGUMENTS
input surface file

output surface file

REQUIRED FLAGGED ARGUMENTS
None

OPTIONAL FLAGGED ARGUMENTS
-d decimation level
target decimation level of new surface (value between
0--1.0, default: 0.5). The resulting surface will have
approximately triangles = decimationLevel * origTriangles

-m minimum angle
The minimum angle in degrees allowed between faces during
decimation (default: 1.0).

--help
print out information on how to use this program

--version
print out version and exit

REPORTING
Report bugs to freesurfer@nmr.mgh.harvard.edu


On 12/20/11 10:47, Ecker, Christine wrote:

Dear FreeSurfer Experts,

I would like to down-sample the pial surface of individual subjects to 
have the same number of vertices as fsaverage6. I have done so using:


mri_surf2surf --hemi lh --srcsubject 'subjectID' --sval-xyz pial 
--trgsubject fsaverage6 --trgicoorder 6 --trgsurfval 'outputfilename'


This worked well and the pial output surface has 40962 vertices. I now 
have an overlay vector, which was computed on the down-sampled pial 
surface, which I would like to map back to fsaverage6 in order to 
perform a group comparison.


Please could you advise on how to do this as all scripts I am aware of 
(e.g. mris_preproc) use sphere.reg, which has ~15 vertices.


Many thanks,
Christine


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149 (2301) 13th Street, Charlestown, MA 02129 USA

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Re: [Freesurfer] Downsampling pial surfaces and mapping output to fsaverage6

2011-12-20 Thread Bruce Fischl
Hi Christine

I think you do it the same way, just using -sval instead of -sval-xyz 
(since you are mapping a scalar field instead of the coordinates).

cheeers
Bruce
On Tue, 
20 Dec 2011, Ecker, Christine wrote:

 Dear FreeSurfer Experts,
 
 I would like to down-sample the pial surface of individual subjects to have
 the same number of vertices as fsaverage6. I have done so using:
 
 mri_surf2surf --hemi lh --srcsubject 'subjectID' --sval-xyz pial
 --trgsubject fsaverage6 --trgicoorder 6 --trgsurfval 'outputfilename'
 
 This worked well and the pial output surface has 40962 vertices. I now have
 an overlay vector, which was computed on the down-sampled pial surface,
 which I would like to map back to fsaverage6 in order to perform a group
 comparison.
 
 Please could you advise on how to do this as all scripts I am aware of (e.g.
 mris_preproc) use sphere.reg, which has ~15 vertices.
 
 Many thanks,
 Christine
 

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Re: [Freesurfer] Surface-based cortical volume calculation

2011-12-20 Thread Michael Harms

Hi Andreia,

The XhCortexVol measures in the aseg.stats of FS v5.1 are identical to:
`mris_volume Xh.pial` - `mris_volume Xh.white`

To my knowledge, that measure is therefore simply the difference of the
volume encapsulated by the two surfaces.  My point was that the surface
inaccuracies in the hippocampus and amygdala are tiny compared to the
overall variation in CortexVol across individuals, so if you want a
measure of CortexVol I wouldn't worry about the fact that parts of those
structures are included (and parts are excluded) from XhCortexVol.

cheers,
-MH

On Tue, 2011-12-20 at 15:59 +, _andre...@sapo.pt wrote:
 Hi Michael and Doug,
 
 Michael:
 As you noted, the surfaces bisect the hippocampus and amygdala, so the
 small amount of tissue outside the pial surface is not included in the
 surface based measures of total GM volume.  Compared to the overall
 variation in brain size, this should be inconsequential.
 
 cheers,
 -MH
 
 I got a little confused with your answer. The calculation is  
 everything inside the pial surface - everything inside the wm surface.  
 What is outside is half hippocampus/amygdala and is not included, ok.  
 But the other halves are inside the surfaces, being then included,  
 right?
 
 Doug:
 
 If the thickness was 0 in those areas that would make sense. But do  
 the surfaces have the information that in those regions the  
 structures are hippocampus and amygdala?
 
 I checked if the thickness was 0 and from what I'm understanding it is  
 5mm. What I did was to open tkmedit with aparc+aseg and open tksurfer  
 (for both hemispheres). Then, I used the buttons Save point and Go  
 to saved point to go from tkmedit to tksurfer. What happened was that  
 when the point was located in the hippocampus or amygdala in tkmedit  
 it had a correspondence in tksurfer in regions which have a thickness  
 value.
 
 Please see figures in attachement (green arrows are amygdala poinst  
 and blue arrows are hippocampus points)
 
 Am I missing something?
 
 Thank you,
 Andreia
 
 
 
 
 Citando Douglas N Greve gr...@nmr.mgh.harvard.edu:
 
  Hi Andreia, I don't think this is a problem for the GM volume (ie, parts
  of the amyg or hippo getting counted twice). The thickness should be 0
  in those areas, so they should not contribute to GM volume. The
  computation of the WM volume is done in a different way (still surface
  based) but automatically excludes subcortical structures.
  doug
 
  _andre...@sapo.pt wrote:
  Hello,
 
  Recalling these emails:
 
  The methods are somewhat different. For the value in the aseg.stats
  table, the method is to compute the total volume inside the pial surface
  and subtract the total volume inside the white surface. For
  mris_anatomical_stats, the method is to compute the thickness times area
  of each vertex. This method will probably underestimate the total volume
  because it uses the area of the white surface when it should use the
  area of the surface in the middle between the white and pial surfaces.
  I've added this to the list of known issues on our release page.
 
  doug
 
  Alexopoulos, Dimitrios wrote:
 
  I have generated surfaces using the the centos4 build (version 5.0)
  and want to confirm that my surface-based GM and WM volumes are correct.
  For the surface-based GM calculation I originally used
  'mris_anatomical_stats -l lh.cortex.label subjectID hemi'
  (run from within the 'label' subdirectory) and for WM i used
  'mris_wm_volume subjectID hemi' (run from within
  the 'surf' subdirectory).
  When I add the calculated left/right cortical volumes, I get a total
  that is different from what is output in
  the 'aseg.stats' file, which in version 5.0 is noted to contain
  total surface-based GM volume
  (Cortex, CortexVol: Total cortical gray matter volume (based on
  surface-stream).
   What are the correct GM and WM surface-based volumes?
  Thanks. Jim
 
 
 
  I question came up to me:
 
  The surfaces in the hippocampus/amygdala are inaccurate and should be
  ignored. However, in version 5.0 the cortical volume is surface-based,
  thus it takes into account the surfaces in the hippocampus/amygdala,
  is this correct?
 
  If so, it is expected that an error is introduced in the surface-based
  calculation of cortical volume. Has anyone checked the influence of
  this error? Or FS compensates for the inaccuracy of the surface
  estimation of these regions somehow?
 
  Thanks!
 
  Andreia
 
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  Phone Number: 617-724-2358
  Fax: 617-726-7422
 
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Re: [Freesurfer] Downsampling pial surfaces and mapping output to fsaverage6

2011-12-20 Thread Ecker, Christine
Many thanks for your reply.

Unfortunately the option -sval didn't work and it is still using the old
sphere.reg file.

I was however wondering whether mri_surf2surf already sorts vertices and
hence makes them comparable. For instance, is vertex 1 on the resampled
surface the closest match to vertex 1 on the target surface? In that case,
I would not even have to map data back to fsaverage6.

Best,
Christine




On 20/12/2011 15:53, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Christine

I think you do it the same way, just using -sval instead of -sval-xyz
(since you are mapping a scalar field instead of the coordinates).

cheeers
Bruce
On Tue, 
20 Dec 2011, Ecker, Christine wrote:

 Dear FreeSurfer Experts,
 
 I would like to down-sample the pial surface of individual subjects to
have
 the same number of vertices as fsaverage6. I have done so using:
 
 mri_surf2surf --hemi lh --srcsubject 'subjectID' --sval-xyz pial
 --trgsubject fsaverage6 --trgicoorder 6 --trgsurfval 'outputfilename'
 
 This worked well and the pial output surface has 40962 vertices. I now
have
 an overlay vector, which was computed on the down-sampled pial surface,
 which I would like to map back to fsaverage6 in order to perform a group
 comparison.
 
 Please could you advise on how to do this as all scripts I am aware of
(e.g.
 mris_preproc) use sphere.reg, which has ~15 vertices.
 
 Many thanks,
 Christine
 



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Re: [Freesurfer] Reliability and accuracy of Freesurfer

2011-12-20 Thread Martin Reuter
Hi Donald,

I have a paper almost published on the longitudinal stream including
several repeatability measures (although not everything that you ask
for). Let me know if you want to take a peek at it before it goes out. I
might be able to send a pre-print version.

Best, Martin


On Tue, 2011-12-20 at 11:37 +0800, Thomas Yeo wrote:
 Hi Donald,
 
 With regards to longitudinal analysis, I am not as familiar with the
 issue you are mentioning. Perhaps some other person on the list can
 comment.
 
 With regards to your other comments, I think your reading is correct.
 However, I should mention that the reported accuracies *really*
 depends on what structures (cytoarchitectural areas versus functional
 areas versus macro-anatomical areas) and what accuracy measures (e.g.,
 volume of structures versus overlap of structures, etc.) you are
 looking at. You probably already know this, but I will elaborate
 anyhow:
 
 The references by Fischl, Hinds, Yeo (from the previous email) are
 talking about the accuracy of localizing cortical cytoarchitectural
 and functional areas. Since freesurfer (and most other software
 packages) uses macro-anatomy (e.g., sulci, gyri, MR intensity) for
 processing (e.g, alignment of subjects, segmentation) and
 macro-anatomy does not predict function/cytoarchitecture completely,
 we expect the accuracy for cytoarchitectural and functional areas to
 be bounded by the predictive relationship between macro-anatomy and
 function/cytoarchitecture. In particular, V1 turns out to be very
 well-predicted by the cortical folds (calcarine), and so when we align
 sulci/gyri across subjects, there's very small errors in localizing
 the boundaries of V1. On the other hand, MT turns out to be not as
 well predicted by the cortical folds, thus the accuracy of MT
 alignment after freesurfer processing is lower.
 
 Conversely, for macroanatomical structures (stuff that is visibly seen
 in MR) like superior temporal sulcus and the thalamus (in aparc+aseg),
 we expect the accuracy to be much higher. Even then the accuracy for
 individual structures may vary. For example, thalamus is more
 accurately segmented than the amygdala. For individual thalamic
 nuclei, which are less visible (if not invisible!) in 3T MR, the
 accuracy is probably much less.
 
 You also mentioned that some areas would be larger than the true
 underlying labels for certain individuals, and some would be smaller.
 That is certainly the case, but I don't think it is explicitly shown
 in the papers by Fischl, Hinds, Yeo (although you can probably infer
 that from other papers listed in the links I sent you). As an extreme
 example, in one of the experiments in Yeo et al. 2010, ground truth
 functional MT+ for each subject was defined by thresholding the fMRI
 activation map using a size threshold. Therefore, the way the ground
 truth was set up in that particular experiment, any errors in
 predicted MT+ is due to errors in predicting MT+ location, rather than
 size difference. On the other hand, if you look at Figure 3 in Fischl
 et al, 2002 (Whole Brain Segmentation: Automated Labeling of
 Neuroanatomical Structures in the Human Brain), there is no obvious
 systemic differences between volumetric measurement of structures
 obtained by manual labeling versus automated segmentation in
 FreeSurfer (circa 2002).
 
 --Thomas
 
 
 On Tue, Dec 20, 2011 at 2:05 AM, MCLAREN, Donald
 mclaren.don...@gmail.com wrote:
  Excellent references. From my reading of these papers, the boundaries of an
  individuals subject can shift by up to ~7mm. Meaning that some areas would
  be largers than the standard labels and others would be smaller.
 
  Is my reading of this correct?
 
  In longitudinal analysis of regional volume measures, do you know of anyway
  to correct for the potential correlation induced by the mislabelling of
  nodes that go into each regional volume?
 
 
  Best Regards, Donald McLaren
  =
  D.G. McLaren, Ph.D.
  Postdoctoral Research Fellow, GRECC, Bedford VA
  Research Fellow, Department of Neurology, Massachusetts General Hospital and
  Harvard Medical School
  Office: (773) 406-2464
  =
  This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
  HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
  intended only for the use of the individual or entity named above. If the
  reader of the e-mail is not the intended recipient or the employee or agent
  responsible for delivering it to the intended recipient, you are hereby
  notified that you are in possession of confidential and privileged
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  action in reliance on the contents of this information is strictly
  prohibited and may be unlawful. If you have received this e-mail
  unintentionally, please immediately notify the sender via telephone at (773)
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  On Sat, Dec 17, 2011 at 9:28 PM, Thomas Yeo 

[Freesurfer] mri_matrix_multiply to move functional images to common space

2011-12-20 Thread Andrew Dumas
Hi,

I'm trying to move a bunch of partial FOV functional images (occipital
cortex only with oblique coronal slices) into common space. For each
subject, I have a registration file (register.dat) to register
functional images to anatomicals, and I'd like to incorporate the
talairach.xfm registration so that I have a matrix that registers the
functional images to the mni305 volume. I've been using the following,
but registrations aren't coming out properly:

mri_matrix_multiply -im register.dat -iim
subject/mri/transforms/talairach.xfm -om reg_to_common.dat

I'm checking them using tkregister2, but the results don't look great.
Is there a better/easier way to do this? Thanks!

Andrew

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Re: [Freesurfer] Selxavg3 sets high activation to zero

2011-12-20 Thread Douglas N Greve
I think this is due to the high DOF and probably high t-value causing 
the significance in matlab to be computed as 0. This gets converted to 
Inf (infinity) when the -log10(p) calculation is made, then the Inf gets 
set to 0 when the volume is saved. The quick fix for you is to change 
fast_selxavg3.m (in $FREESURFER_HOME/fsfast/toolbox). There is a single 
line that reads:

fsigmat = -log10(pmat)

change this to

fsigmat = -log10(pmat + eps(0));

Let me know if this works and I'll update our source code.

doug





Qi Zhu wrote:
 Dear Doug,

 I used selxavg3-sess in freesurfer 5.0 to run a big GLM analysis on a
 monkey data set containing 147 runs. But When I check the results, I
 found that in the voxels where the t-values should be very high were
 turned out to have a value of zero. I checked the brainmask, the ces
 and the cesvar values, they all look fine. It seems that only the ces
 values in these voxels are a bit high compared to the nearby normal
 voxels (e.g. 1.17 (ces)/0.00048(cesvar) compared to 0.74/0.00040 in a
 nearby normal voxel). And it seems that not only me have this problem
 (similar problem posted in the mailinglist before.
 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13789.html).
 Do you know what the problem would be and how to solve it? Thanks very
 much for your help.

 Attached please find an image of the problem.

 Best,

 Qi Zhu, PostDoc
 Laboratorium voor Neuro- en Psychofysiologie
 K.U.Leuven Medical School
 Herestraat 49, B-3000 Leuven (Belgium)
   

 


-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] mri_matrix_multiply to move functional images to common space

2011-12-20 Thread Douglas N Greve
Hi Andrew, use mri_vol2vol with the --tal --talres 2 or 2mm option (or 
--talres 1 for 1mm isotropic) option. This will put it into an MNI305 
space. So something like

mri_vol2vol --reg register.dat --mov yourvolume.nii --tal --talres 2 --o 
yourvolume.mni305.nii

If you did not create the register.dat with bbregister, I would strongly 
suggest it. It works really well on the partial volume files. If you do, 
you should specify your current register.dat as the init registration.

doug

Andrew Dumas wrote:
 Hi,

 I'm trying to move a bunch of partial FOV functional images (occipital
 cortex only with oblique coronal slices) into common space. For each
 subject, I have a registration file (register.dat) to register
 functional images to anatomicals, and I'd like to incorporate the
 talairach.xfm registration so that I have a matrix that registers the
 functional images to the mni305 volume. I've been using the following,
 but registrations aren't coming out properly:

 mri_matrix_multiply -im register.dat -iim
 subject/mri/transforms/talairach.xfm -om reg_to_common.dat

 I'm checking them using tkregister2, but the results don't look great.
 Is there a better/easier way to do this? Thanks!

 Andrew

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