[Freesurfer] DEFECT 57

2013-02-21 Thread Varghese Chikku
Hi all,
One of my  subject exited with error after 5 days of processing.
This  is what it said,
CORRECTING DEFECT 57 (vertices=101022, convex hull=10822)
Excessive topologic defect encountered: could not allocate 536232126
edges for retessellation
Cannot allocate memory
Darwin chikkus-MacBook-Pro.local 12.2.1 Darwin Kernel Version 12.2.1:
Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64
x86_64

recon-all -s onco4 exited with ERRORS at Fri Feb 15 12:17:05 CET 2013

My question is this much edges normal and how  much memory i need
allocate to process this.

Many Thanks
Chikku
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[Freesurfer] Pial boundaries

2013-02-21 Thread melinaki p-t
Hello,

I would like to ask if there are any commands or any manual edits I can use
to fix the pial boundaries even if the white matter boundaries are fine.
The white matter boundaries follow the white matter pretty good but there
is some grey matter missing at some areas. Its not a massive problem
though.
Thank you in advance.
Melina
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[Freesurfer] Generate mask from surface in diffusion space

2013-02-21 Thread Shani Ben Amitay
Dear freesurfers

I'm using bbregister and mri_surf2surf to transform intermediate cortical
surfaces and mid surfaces normals to diffusion space.
Next I'm trying to generate  volumes from these surfaces (in the same
diffusion space), however the generated volumes are much thicker then the
generated surfaces.
for example to generate surface normals I used the following:
mri_surf2surf --s subjectid  --hemi lh --sval-nxyz
white_surface_in_diffusion --tval lhwhitediffusion_n.mgh
mri_surf2vol --surfval lhwhitediffusion_n.mgh --hemi lh --surf white --reg
mri/register.dat --outvol lh_white_n.img  --template lowb.img
Any idea what am I doing wrong?

Thanks!

Shani
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[Freesurfer] nb0 question

2013-02-21 Thread stdp82
Hi list,
I'm running TRACULA. I do not have problem when I have 16 DTI direction and b=0 
is the first volume: I put nb0=1.
For some subjects I have 16 direction but b=0 is the last of volume in 
dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative to 
position of b=0 in the bvals.txt or to total number (quantitative) of b=0 in 
the bvals.txt?
Thanks,

Stefano
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Re: [Freesurfer] Registration segmentation with FSL - obtaining correlation matrix..

2013-02-21 Thread Sudhin A. Shah

On Feb 20, 2013, at 3:02 PM, Sudhin A. Shah wrote:

Hello

I have run free surfer and co-registered with the rsfMRI via FSL (reg-feat2anat 
 aseg2feat)

When I extract the values (as per the matlab code below), I see NaNs in certain 
regions. Of the 19 datasets that I have analyzed I have see NaNs for the 
following labels

10061033200620132033

Is this a known problem? Is there a solution?

Thanks,
S


On Jan 31, 2013, at 3:41 PM, Douglas N Greve wrote:


Sorry, I don't think we have such a program. You could do it in matlab
fairly easily, eg,

f = MRIread('filtered_func_data');
fmat = fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(seglist)
  ind = find(a.vol == seglist(nthseg));
  roimean(:,nthseg) = mean(fmat(:,ind),2);
end

m = roimean'*roimean;

On 01/31/2013 01:29 PM, Sudhin A. Shah wrote:

Hello,

This worked perfectly 2 years ago :), but now I am having some trouble.

I run reg-feat2anat  aseg2feat with no problem.

I now need a correlation matrix of every ROI (created by freesurfer)
against every other ROI. For this I used @ROI_Corr_Mat
(http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html).
Again - this worked fine in the past.

Now I get an error (working with AFNI to see if it can be fixed).

Question: Is there any alternative to getting this correlation matrix?
i.e every ROI against every other ROI?

Thanks,
S


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Re: [Freesurfer] Pial boundaries

2013-02-21 Thread Bruce Fischl
Can you send us an image?



On Feb 21, 2013, at 7:24 AM, melinaki p-t tritic...@gmail.com wrote:

 Hello,
 
 I would like to ask if there are any commands or any manual edits I can use 
 to fix the pial boundaries even if the white matter boundaries are fine.
 The white matter boundaries follow the white matter pretty good but there is 
 some grey matter missing at some areas. Its not a massive problem though. 
 Thank you in advance.
 Melina
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Re: [Freesurfer] DEFECT 57

2013-02-21 Thread Bruce Fischl
Hi Chikku
That is a giant defect - almost the size of an entire hemi. Something is badly 
wrong. Check the aseg and filled volumes to see what's going on, and the 
?h.orig.nofix
Bruce 



On Feb 21, 2013, at 5:35 AM, Varghese Chikku chik...@tcd.ie wrote:

 Hi all,
 One of my  subject exited with error after 5 days of processing.
 This  is what it said,
 CORRECTING DEFECT 57 (vertices=101022, convex hull=10822)
 Excessive topologic defect encountered: could not allocate 536232126
 edges for retessellation
 Cannot allocate memory
 Darwin chikkus-MacBook-Pro.local 12.2.1 Darwin Kernel Version 12.2.1:
 Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64
 x86_64
 
 recon-all -s onco4 exited with ERRORS at Fri Feb 15 12:17:05 CET 2013
 
 My question is this much edges normal and how  much memory i need
 allocate to process this.
 
 Many Thanks
 Chikku
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 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 

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Re: [Freesurfer] Pial boundaries

2013-02-21 Thread melinaki p-t
I am afraid I can't...
Can you give any advise without pictures?
Thank you in advance.
Melina

2013/2/21 Bruce Fischl fis...@nmr.mgh.harvard.edu

 Can you send us an image?



 On Feb 21, 2013, at 7:24 AM, melinaki p-t tritic...@gmail.com wrote:

  Hello,
 
  I would like to ask if there are any commands or any manual edits I can
 use to fix the pial boundaries even if the white matter boundaries are fine.
  The white matter boundaries follow the white matter pretty good but
 there is some grey matter missing at some areas. Its not a massive problem
 though.
  Thank you in advance.
  Melina
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 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] longitudinal sulci depth change

2013-02-21 Thread O'Shea,Andrew
Hello,
I was wondering if I could get some clarification regarding the longitudinal 
measure of rate of change in sulci depth. In our study we have a patient 
population that participated in an intervention and a similar group of wait 
list controls. We have scans for pre and post intervention timepoints. I have 
ran the longitudinal analysis in QDEC looking at the thickness change measures, 
however I was also interested in the sulc measures. I was able to get the 
analysis to run with the new measures long.sulc-rate etc. However I am having a 
hard time conceptualizing the meaning of the results. Does a negative rate 
change indicate either a deepening or a shallowing of the sulci? Is the 
opposite the case for gyral regions? Any advice would be greatly appreciated.
-Andrew
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Re: [Freesurfer] nb0 question

2013-02-21 Thread Juan Eugenio Iglesias
Isn't nb0 the *number* of b0 images? Therefore it should be 1 no matter
where in the table it is. From the tutorial:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

Step7.3: Specifying Number Of low-b Images The last step to set up if not
using original DICOMs would be to specify the number of low-b images with
the following variable:

set nb0 = *No. of low-b images*

** - To be replaced with the actual number from the acquisition.






On Thu, February 21, 2013 8:45 am, std...@virgilio.it wrote:
 Hi list,
 I'm running TRACULA. I do not have problem when I have 16 DTI direction
 and b=0 is the first volume: I put nb0=1.
 For some subjects I have 16 direction but b=0 is the last of volume in
 dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative to
 position of b=0 in the bvals.txt or to total number (quantitative) of b=0
 in the bvals.txt?
 Thanks,

 Stefano
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-
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http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.
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Re: [Freesurfer] nb0 question

2013-02-21 Thread Shantanu Ghosh
Hi Juan,
The number of b0 images can be more than 1; it is specified when you
acquire the image.
Hth, Shantanu

On Thu, February 21, 2013 12:16 pm, Juan Eugenio Iglesias wrote:
 Isn't nb0 the *number* of b0 images? Therefore it should be 1 no matter
 where in the table it is. From the tutorial:

 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

 Step7.3: Specifying Number Of low-b Images The last step to set up if not
 using original DICOMs would be to specify the number of low-b images with
 the following variable:

 set nb0 = *No. of low-b images*

 ** - To be replaced with the actual number from the acquisition.






 On Thu, February 21, 2013 8:45 am, std...@virgilio.it wrote:
 Hi list,
 I'm running TRACULA. I do not have problem when I have 16 DTI direction
 and b=0 is the first volume: I put nb0=1.
 For some subjects I have 16 direction but b=0 is the last of volume in
 dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative
 to
 position of b=0 in the bvals.txt or to total number (quantitative) of
 b=0
 in the bvals.txt?
 Thanks,

 Stefano
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 -
 Juan Eugenio Iglesias, PhD
 http://www.jeiglesias.com
 igles...@nmr.mgh.harvard.edu
 Athinoula A. Martinos Center for Biomedical Imaging
 149 Thirteenth Street, Suite 2301
 Charlestown, Massachusetts 2129
 U.S.A.
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-- 
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Harvard Medical School  Massachusetts General Hospital
Martinos Center for Biomedical Imaging

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Re: [Freesurfer] nb0 question

2013-02-21 Thread Juan Eugenio Iglesias
Of course! But, if I understood correctly, Stefano only has one, either at
the beginning of the end of the gradient table, and in both cases nb0=1
Cheers,
/Eugenio


On Thu, February 21, 2013 12:20 pm, Shantanu Ghosh wrote:
 Hi Juan,
 The number of b0 images can be more than 1; it is specified when you
 acquire the image.
 Hth, Shantanu

 On Thu, February 21, 2013 12:16 pm, Juan Eugenio Iglesias wrote:
 Isn't nb0 the *number* of b0 images? Therefore it should be 1 no matter
 where in the table it is. From the tutorial:

 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

 Step7.3: Specifying Number Of low-b Images The last step to set up if
 not
 using original DICOMs would be to specify the number of low-b images
 with
 the following variable:

 set nb0 = *No. of low-b images*

 ** - To be replaced with the actual number from the acquisition.






 On Thu, February 21, 2013 8:45 am, std...@virgilio.it wrote:
 Hi list,
 I'm running TRACULA. I do not have problem when I have 16 DTI direction
 and b=0 is the first volume: I put nb0=1.
 For some subjects I have 16 direction but b=0 is the last of volume in
 dwi.nii.gz. What is the value of nb0 that I should put? nb0 is relative
 to
 position of b=0 in the bvals.txt or to total number (quantitative) of
 b=0
 in the bvals.txt?
 Thanks,

 Stefano
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 -
 Juan Eugenio Iglesias, PhD
 http://www.jeiglesias.com
 igles...@nmr.mgh.harvard.edu
 Athinoula A. Martinos Center for Biomedical Imaging
 149 Thirteenth Street, Suite 2301
 Charlestown, Massachusetts 2129
 U.S.A.
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 --
 Shantanu Ghosh, Ph.D.
 Harvard Medical School  Massachusetts General Hospital
 Martinos Center for Biomedical Imaging





-
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.
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[Freesurfer] dual installation question

2013-02-21 Thread Joshua Lee
If I want to install the new Freesurfer version but retain the older
Freesurfer install as well, what issues might I face?
Is it simply sourcing the usual setup scripts?

export FREESURFER_HOME=freesurfer_installation_directory/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

-
Josh
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Re: [Freesurfer] dual installation question

2013-02-21 Thread Shantanu Ghosh
Hi Josh,
you can modify the SetUpFreeSurfer.sh to source the correct version.
Hth, Shantanu

On Thu, February 21, 2013 12:55 pm, Joshua Lee wrote:
 If I want to install the new Freesurfer version but retain the older
 Freesurfer install as well, what issues might I face?
 Is it simply sourcing the usual setup scripts?

 export FREESURFER_HOME=freesurfer_installation_directory/freesurfer
 source $FREESURFER_HOME/SetUpFreeSurfer.sh

 -
 Josh
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Harvard Medical School  Massachusetts General Hospital
Martinos Center for Biomedical Imaging

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Re: [Freesurfer] dual installation question

2013-02-21 Thread Shantanu Ghosh
Or you may have multiple freesurfer versions within the freesurfer
director, something like
/freesurfer/5.0, /freesurfer/5.1, /freesurfer/5.2b, /freesurfer/5.2 etc.
and then
export FREESURFER_HOME=freesurfer_installation_directory/freesurfer/5.1 etc
Hth, S.


On Thu, February 21, 2013 12:59 pm, Shantanu Ghosh wrote:
 Hi Josh,
 you can modify the SetUpFreeSurfer.sh to source the correct version.
 Hth, Shantanu

 On Thu, February 21, 2013 12:55 pm, Joshua Lee wrote:
 If I want to install the new Freesurfer version but retain the older
 Freesurfer install as well, what issues might I face?
 Is it simply sourcing the usual setup scripts?

 export FREESURFER_HOME=freesurfer_installation_directory/freesurfer
 source $FREESURFER_HOME/SetUpFreeSurfer.sh

 -
 Josh
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 --
 Shantanu Ghosh, Ph.D.
 Harvard Medical School  Massachusetts General Hospital
 Martinos Center for Biomedical Imaging

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-- 
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Harvard Medical School  Massachusetts General Hospital
Martinos Center for Biomedical Imaging

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[Freesurfer] Tkregister2 / Tksurfer / Tkmedit Won't Open

2013-02-21 Thread Daniel Cole
Hello freesurfers,
I just ran registration of my functional images and am trying to visualize
the registration for assessment.  However, when I use the commands
tkregister-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -fsd bold -funcstem f
or

tkregister2 --targ T1.mgz --fstarg --s $SUBJECTID --surf --mov
$FUNCTIONAL_MRI --reg $REG_DAT --plane sag --movbright $MYBRIGHTNESS

the command gets stuck on Opening window SUBJECT01.


I've also tried just opening tksurfer and tkmedit but the terminal produces
no output/windows opening and simply freezes.

Any ideas to why this could be occurring?  I've let it sit at this stage
for multiple hours without anything popping up and without any errors.


Thanks!

Daniel


-- 
Daniel Cole
University of Rochester
Brain and Cognitive Sciences
dcol...@u.rochester.edu
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[Freesurfer] tkregister2 window error: Remote login

2013-02-21 Thread Sudhin A. Shah
Hello,

I am remotely logged in to my Ubuntu system(from Mac). I have previously run 
tkregister2 but am now having trouble;

Opening window subj
Window type not found
register: tkoinitwindow(name) failed.

Is there a solution to this?

Thanks,

S
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Re: [Freesurfer] dual installation question

2013-02-21 Thread Joshua Lee
Thanks.
Best,
-
Josh


On Thu, Feb 21, 2013 at 10:05 AM, Shantanu Ghosh 
shant...@nmr.mgh.harvard.edu wrote:

 Or you may have multiple freesurfer versions within the freesurfer
 director, something like
 /freesurfer/5.0, /freesurfer/5.1, /freesurfer/5.2b, /freesurfer/5.2 etc.
 and then
 export FREESURFER_HOME=freesurfer_installation_directory/freesurfer/5.1
 etc
 Hth, S.


 On Thu, February 21, 2013 12:59 pm, Shantanu Ghosh wrote:
  Hi Josh,
  you can modify the SetUpFreeSurfer.sh to source the correct version.
  Hth, Shantanu
 
  On Thu, February 21, 2013 12:55 pm, Joshua Lee wrote:
  If I want to install the new Freesurfer version but retain the older
  Freesurfer install as well, what issues might I face?
  Is it simply sourcing the usual setup scripts?
 
  export FREESURFER_HOME=freesurfer_installation_directory/freesurfer
  source $FREESURFER_HOME/SetUpFreeSurfer.sh
 
  -
  Josh
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  --
  Shantanu Ghosh, Ph.D.
  Harvard Medical School  Massachusetts General Hospital
  Martinos Center for Biomedical Imaging
 
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 --
 Shantanu Ghosh, Ph.D.
 Harvard Medical School  Massachusetts General Hospital
 Martinos Center for Biomedical Imaging



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 is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
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 HelpLine at
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 error
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 properly
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