[Freesurfer] Plot Histograms

2014-05-01 Thread Dídac Vidal
Hi!

I would like to plot an histogram with values from sig.mgh across all
cortical mantle
(as represented in qdec or in tksurfer-overlay options).
Which function would allow me to obtain/create histograms from *mgh files?

I also would like to obtain a similar histogram, but restricted to a
cortical label.
How I could do that?



Thanks in advance



-- 
Dídac Vidal Piñeiro

Dept. Psychiatry and Clinical Psychobiology
Faculty of Medicine
University of barcelona
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[Freesurfer] installing freesurfer on mac

2014-05-01 Thread Demanuele, Charmaine
Hi,

I am trying to install freesurfer on my mac, and I got a license key, which I 
need to save as .license file.
However, the mac is not allowing me to do so.

I tried saving the file in linux and importing to the mac but this failed too.

I also tried saving it as freesurfer.license instead of just .license but I get 
the error:

[Charmaines-MacBook-Pro:/Applications/freesurfer] Charm% tkmedit bert orig.mgz

Couldn't create output file 
.xdebug_tkmedit--

ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.


Any ideas?


Thanks very much,


Best,


Charmaine



---
Charmaine Demanuele, Ph.D.
Psychiatric Neuroimaging
Athinoula A. Martinos Center for Biomedical Imaging
Harvard Medical School
149 13th Street
Charlestown Navy Yard
Charlestown, MA 02129
phone: +1617-724-3170
email: cha...@nmr.mgh.harvard.edu




tel:617-726-4078
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Re: [Freesurfer] per voxel regressor in LME toolbox?

2014-05-01 Thread jorge luis

 
The lme toolbox
allows you to have different regression models across locations. If
there is a missed data value at some location (vertex/voxel) for a
given time-point for a given subject then you can exclude the
corresponding row of the full design matrix at that location using the
parameter Xrows of :

[stats,st] =
lme_mass_fit_vw(X,Zcols,Y,ni,maskvtx,fname,prs,e,Xrows)

This allows you to
use a different number of rows from your design matrix across
locations. Xrows is just a matrix of zeros and ones. Look at the
header of lme_mass_fit_vw for more info. 

If you also want to
have a different number of columns from your 
maximal model design matrix (this the design mtrix for the model that 
contains the
maximum number of regressors you are going to use at any location)
then you need to work directly with 

[stats,st] =
lme_mass_fit(X,Xcols,Xrows,Zcols,Y,ni)      (this script is call by
lme_mass_fit_vw)

Look at the header
of this script for more info. The parameter Xcols is a matrix of
zeros and ones that allows you to choose a different subset of
columns from your “maximal design matrix” at each location.


Hope this makes
sense.

Best
-Jorge
El Miércoles 30 de abril de 2014 18:47, Marnie Shaw marnie.s...@anu.edu.au 
escribió:
 
 
Dear Freesurfers,
 
Is there a way to include a per voxel regressor in an LME model within the 
matlab LME toolbox? Just like you can do with mri_glmfit?
 
Cheers, 
Marnie
 
 
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Re: [Freesurfer] installing freesurfer on mac

2014-05-01 Thread Louis Nicholas Vinke
Hi Charmaine,
Sounds like you just need to change the folder permissions for,

/Applications/freesurfer/

before attempting to copy the .license file to that location.
-Louis

On Thu, 1 May 2014, Demanuele, Charmaine wrote:

 Hi,
 
 I am trying to install freesurfer on my mac, and I got a license key, which I 
 need to save as .license file.
 However, the mac is not allowing me to do so.
 
 I tried saving the file in linux and importing to the mac but this failed too.
 
 I also tried saving it as freesurfer.license instead of just .license but I 
 get the error:
 
 [Charmaines-MacBook-Pro:/Applications/freesurfer] Charm% tkmedit bert orig.mgz
 
 Couldn't create output file 
 .xdebug_tkmedit--
 
 ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.
 
 
 Any ideas?
 
 
 Thanks very much,
 
 
 Best,
 
 
 Charmaine
 
 
 
 
 ---
 Charmaine Demanuele, Ph.D.
 Psychiatric Neuroimaging
 Athinoula A. Martinos Center for Biomedical Imaging
 Harvard Medical School
 149 13th Street
 Charlestown Navy Yard
 Charlestown, MA 02129
 phone: +1617-724-3170
 email: cha...@nmr.mgh.harvard.edu
 
 
 
 
 

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[Freesurfer] NIH Staff Scientist Position available, Bethesda, MD, USA

2014-05-01 Thread Thomas, Adam (NIH/NIMH) [E]

Posted on behalf of the CPB:

Department of Health and Human Services (DHHS)
National Institutes of Health (NIH)
National Institute of Mental Health (NIMH)
Division of Intramural Research Programs (DIRP)
Section on Childhood Neuropsychiatric Disorders (SCND)
Child Psychiatry Branch (CPB)

Staff Scientist

The Child Psychiatry Branch, in Bethesda, Maryland, is recruiting
applicants for a Staff Scientist position.  As a Staff Scientist, the
primary duties will include conducting statistical analyses on clinical,
neurobiological and treatment studies carried out in the Branch. This
includes but is not limited to tasks such as maintaining the appropriate
data sets, clearly conveying statistical results and methods both orally
and in writing, reviewing and writing statistical content for manuscripts
prior to submission, and working closely with and providing statistical
support for all Branch members. The
Staff Scientist position entails 25% time allotted to pursuing individual
research interests.

The Child Psychiatry Branch is a highly productive and collaborative group
with a rich, multimodal dataset that seeks to understand
neurodevelopmental disorders, with a focus on childhood-onset
schizophrenia.  There is a strong scientific and statistical computing
core facility in existence, which can benefit this work.  For more
information about the Child Psychiatry Branch, please utilize the
following link:
http://www.nimh.nih.gov/labs-at-nimh/research-areas/clinics-and-labs/chp/in
dex.shtml

Interested candidates must have five years post-doctoral experience.
Applicants should have a strong background in statistics and
programming/computer science, as well as interests and experience in
neuroimaging and behavioral research. The recruit should be adept at
writing his/her own code to clean, organize, analyze, and visualize data.
Unix and python programming skills are also preferable.  In addition some
highly desirable skills include: experience analyzing structural MRI,
functional MRI and/or MEG data; a solid foundation in multivariate
statistics (e.g., cluster analysis, principal components analysis,
independent components analysis), and a background in longitudinal data
analysis (e.g.,
mixed model regression/hierarchical linear modeling); proficiency in
statistical programs such as R and MATLAB and visualization methods.

SALARY RANGE:  Salary is commensurate with experience and accomplishments.

BENEFITS: The federal government offers a comprehensive benefits package
including vacation, sick leave, holidays, life insurance, health benefits,
and participation in the Federal Employees Retirement
System.  For more information go to new employee benefits at the NIH
(http://hr.od.nih.gov/Benefits/permanentemployee.htm) and other employee
benefits information (http://tiny.cc/saVcr).

Interested applicants should send their CV and cover letter to Dr. Judith
Rapoport, NIMH, 10 Center Drive, Bldg. 10, Rm. 3N202 (MSC-1600), Bethesda,
MD  20892 USA, or by email: rapop...@mail.nih.govmailto:rapop...@mail.nih.gov

SUBMISSION DEADLINE:  June 1, 2014

NIH and DHHS are Equal Opportunity Employers.




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Re: [Freesurfer] cortical thickness limit

2014-05-01 Thread Bruce Fischl

Hi Hayyah

that's to prevent outliers corrupting the thickness data. You can rerun 
mris_thickness with -max N to change 5 to whatever N you want


cheers
Bruce
On Thu, 1 May 
2014, Hayyah Clairman wrote:




Hello,

I have done some comparative cortical thickness analyses in children using
FreeSurfer and noticed that the maximum regional thickness value is 5.0. I
was wondering if there is an explanation for this limit. Perhaps this is
because FreeSurfer was designed for adults?

 

Thank you,

Hayyah




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[Freesurfer] cortical thickness limit

2014-05-01 Thread Hayyah Clairman
Hello,
I have done some comparative cortical thickness analyses in children using 
FreeSurfer and noticed that the maximum regional thickness value is 5.0. I was 
wondering if there is an explanation for this limit. Perhaps this is because 
FreeSurfer was designed for adults?

Thank you,
Hayyah



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[Freesurfer] Constraining fMRI data with a surface label generates a bfloat file?

2014-05-01 Thread jaco...@nmr.mgh.harvard.edu
Hello Freesurfer Experts,

Using func2roi (in stable3), we constrained our functional data with
specific surface labels and t thresholds, and over-threshold masks were
outputted as .bfloat files. Does this mean these masks are in volume
format and that the volumetric functional data was mapped to the surface
but then back to the volume again when the mask was created?

We would now like to project these masks onto the fsaverage brain (for
viewing). Can you please let me know how this may be accomplished? It
seems mri_convert can not transpose .bfloat to .label, but I imagine there
is a way!

Thank you again for the help.

Jacob



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Re: [Freesurfer] Constraining fMRI data with a surface label generates a bfloat file?

2014-05-01 Thread Douglas Greve

On 5/1/14 3:59 PM, jaco...@nmr.mgh.harvard.edu wrote:
 Hello Freesurfer Experts,

 Using func2roi (in stable3), we constrained our functional data with
 specific surface labels and t thresholds, and over-threshold masks were
 outputted as .bfloat files. Does this mean these masks are in volume
 format and that the volumetric functional data was mapped to the surface
 but then back to the volume again when the mask was created?
I have no idea. It has been too long. Try looking at it with tkmedit.

 We would now like to project these masks onto the fsaverage brain (for
 viewing). Can you please let me know how this may be accomplished? It
 seems mri_convert can not transpose .bfloat to .label, but I imagine there
 is a way!
You can use mri_vol2surf then mri_surf2surf
doug

 Thank you again for the help.

 Jacob



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Re: [Freesurfer] Rendering in 3ds Max?

2014-05-01 Thread Sourena Soheili-Nezhad
Hi Dorian,

I have tried exporting in .STL with success. 3d max can import this
format. If I recall corretly the command was
 mris_convert ?h.pial ?h_pial.stl

Cheers,
Sourena

On 4/29/14, Dorian P. alb@gmail.com wrote:
 Hi list,

 Anybody has ever tried to bring Freesurfer pial surfaces for render in 3D
 studio max? I would be curious on the procedure to follow, more
 specifically on which file to export/import/convert.

 Thank you.

 Dorian
 TJU



-- 
Sourena Soheili-Nezhad, M.D.
Tehran University of Medical Sciences
Tehran, Iran
Cell: (+98) 912 594 7873
Email1: sourena.sohe...@gmail.com
Email2: soheil...@student.tums.ac.ir
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Re: [Freesurfer] Rendering in 3ds Max?

2014-05-01 Thread Arman Eshaghi
Hi,

Have a look at Anderson's blog here
http://brainder.org/2014/01/08/splitting-cortical-surface-into-independent-regions/

All the best,
Arman

Sent from a mobile device, please excuse my brevity/misspellings. 

 On May 2, 2014, at 1:04 AM, Sourena Soheili-Nezhad 
 sourena.sohe...@gmail.com wrote:
 
 Hi Dorian,
 
 I have tried exporting in .STL with success. 3d max can import this
 format. If I recall corretly the command was
 mris_convert ?h.pial ?h_pial.stl
 
 Cheers,
 Sourena
 
 On 4/29/14, Dorian P. alb@gmail.com wrote:
 Hi list,
 
 Anybody has ever tried to bring Freesurfer pial surfaces for render in 3D
 studio max? I would be curious on the procedure to follow, more
 specifically on which file to export/import/convert.
 
 Thank you.
 
 Dorian
 TJU
 
 
 -- 
 Sourena Soheili-Nezhad, M.D.
 Tehran University of Medical Sciences
 Tehran, Iran
 Cell: (+98) 912 594 7873
 Email1: sourena.sohe...@gmail.com
 Email2: soheil...@student.tums.ac.ir
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Re: [Freesurfer] Plot Histograms

2014-05-01 Thread Bruce Fischl
you can also histogram surface overlays in tksurfer (and I think in 
freeview too now)


Bruce
On Thu, 1 May 2014, Douglas N Greve wrote:



There is no such function from the command line. You can load the data
in matlab (MRIread.m) and do it there. You can load the cortical label
into matlab as well with read_label.m

On 05/01/2014 10:27 AM, Dídac Vidal wrote:

Hi!

I would like to plot an histogram with values from sig.mgh across all
cortical mantle
(as represented in qdec or in tksurfer-overlay options).
Which function would allow me to obtain/create histograms from *mgh files?

I also would like to obtain a similar histogram, but restricted to a
cortical label.
How I could do that?



Thanks in advance



--
Dídac Vidal Piñeiro

Dept. Psychiatry and Clinical Psychobiology
Faculty of Medicine
University of barcelona



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Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla

2014-05-01 Thread Eugenio Iglesias
Hi Josh,
the method fits a statistical atlas of the hippocampal subfields to the image 
data. It is assumed that all subfields other than the fimbria have the same 
distribution of intensities - because they are all assumed to be gray matter. 
Therefore, most of the internal boundaries of the hippocampus rely on the prior 
given by the deformed atlas, which is mostly determined by the global 
hippocampal shape.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: Joshua Lee jki...@ucdavis.edu
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, May 1, 2014 8:03:04 PM
Subject: Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla



Thanks for the clarification Eugenio. Would saying that it relies on shape 
instead of surface be more accurate? I would like to understand better. 
Also, it is good news that there are plans to model the SLRM. 
Josh 



- 

Joshua Lee 
Doctoral Candidate 

Department of Psychology  
Center for Mind and Brain University of California, Davis 
530.747.3805 


On Mon, Apr 28, 2014 at 12:18 AM, Eugenio Iglesias  e.igles...@bcbl.eu  
wrote: 


Dear all, 
the current module in FreeSurfer works with 1mm T1 data, by relying on strong 
shape priors. So, at this point, feeding the algorithm data from a 3T scanner 
or a 1.5T scanner is pretty much the same. 
Joshua, it is indeed inaccurate to say that the method relies on a generated 
hippocampal surface, but you are definitely right regarding the SLRM: it is not 
modeled at this point (we have a new version that models it coming out 
hopefully soon!). 
Cheers, 
/Eugenio 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 



- Original Message - 
From: Joshua Lee  jki...@ucdavis.edu  
To: Freesurfer support list  freesurfer@nmr.mgh.harvard.edu  
Sent: Friday, April 25, 2014 2:10:29 AM 
Subject: Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla 




Hi Alan, 

Typically subfields segmentation requires hi-resolution data (e.g. 0.4 x 0.4 mm 
in-plane resolution). The thickness of a CA subfield typically range between 
0.5-1.00 mm, but 1.5 T data does not achieve sub-millimeter resolutions. 
Further, subfield segmentation typically requires high-contrast data to discern 
the internal boundaries formed by the stratum radiatum/stratum 
lacunosum-moleculare (SLRM). I doubt that images produced on a 1.5 T magnet can 
achieve the necessary contrast. Last, and please someone correct me if what I 
say is inaccurate, but doesn't the Van Leemput method use statistical priors to 
apply label probabilities in reference to a generated hippocampal surface? This 
would imply that the method assigns label probabilities without reference to a 
subject's SLRM intensity information. For volumetry, I am somewhat skeptical 
that a method that only relies on a generated surface would be sensitive to 
group x subfield interactions; especially double dissociations in ! 


which overall volume/shape of the hippocampus may be similar across groups. 
That the that was generated from potentially low resolution, low contrast data 
cannot help the matter. Some may disagree about this though and I'd be 
interested in hearing what other people think about the matter. In general, I 
am quite optimistic about automated methods to segment the subfields. 




Joshua 







- 

Joshua K. Lee 
Doctoral Candidate 

Department of Psychology  
Center for Mind and Brain University of California, Davis 




On Thu, Apr 24, 2014 at 12:24 PM, Alan Francis  alandarkene...@gmail.com  
wrote: 



Hi Bruce and FreeSurfers: 

I have received a manuscript to review for possible publication. The authors 
have used the subfields algorithm on 1.5T scans and obtained a parcellation 
with values. They have drawn some major conclusions on the basis of the 
findings. My understanding is that this method can only be done on 3T. Is the 
1.5T results valid? 

Please advice. 

thanks, 

Alan Francis 
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Re: [Freesurfer] problems about extracting specific vertex thickness value and getting a average thickness for a specific mask

2014-05-01 Thread charujing123
Hi all,
Looking forward someone can help me.
Thanks.
All the best.
Rujing Zha

2014-05-02 

charujing123 



发件人:charujing123charujing...@163.com
发送时间:2014-05-01 11:38
主题:[Freesurfer] problems about extracting specific vertex thickness value and 
getting a average thickness for a specific mask
收件人:freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu
抄送:

Hi FS experts and users
I have done the each subjects' surface regestration on fsaverage surface, and 
merge all of them into a *.mgh. Group analysis is also completed. 
Now I have two questions:
1,I want to extract the VtxMax vertex number thickness for all subjects. The 
VtxMax vertex number can be got in the *.sig.cluster.summary file. And it 
represents the most significant vertex in that cluster. I search my question in 
google and find these scripts which maybe helpful:
for i in `seq 1 $numsubject`
   do
 mri_convert --frame $i y.mgh $SUBJECTS_DIR/fsaverage/surf/lh.$i.mgh
 mris_convert -c $i.mgh $SUBJECTS_DIR/fsaverage/surf/lh.inflated 
lh.$i.asc
   done
I got the lh.*.asc file and open it. there are five columes in this file: I 
guess that: first colume is vertex number, the 2nd-4th columes represent MNI 
coordinates in surface, and the 5th colume is thickness of this vertex. If I 
want to deal with my 1st question, all I need to get the lh.*.asc file and 
search the specific vertex number in this file. All of above, is there anything 
wrong?
2, I created a surface mask, and want to extract the average thickness value in 
this mask for every subject. How can I complete it?
Any reply will be highly appreaciated.
Thanks
All the best.
Rujing Zha

2014-05-01


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