Re: [Freesurfer] Longitudinal processing

[Martin Reuter]

Hi Linn,

do you mean the brain mask in the cross sectional runs gets worse after you run 
the longitudinal steps (base and long)? That is not really possible, as these 
steps don't touch the cross data (only read from it).

If you mean that the brain mask in the long looks worse than in the cross (of 
same subject time point), then you need to check the brain mask in the base. 
That one is copied to all the longitudinal runs, so it needs to be accurate in 
the base. If it is accurate there, but still not in a specific longitudinal run 
then that indicates a mis-alignment to the base. If that is the case, the first 
thing I'd try is rename base and all longitudinals and re-run those from scatch 
to make sure it's not a hick-up (e.g. io problem).

Best, Martin


On Jun 18, 2013, at 5:16 AM, Linn Mittlestein  wrote:

> Dear Freesurfer group.
> 
> I am having some concerns about Freesurfer and the different steps. I have 
> used version 5.0 for the cross-sectional timepoints, and I am now using 
> version 5.3 for the longitudinal processing. I am doing therefore the several 
> different steps involved in longitudinal processing, for example -base, -long 
> runs and now for the lme analysis with matlab also the smoothing steps etc. I 
> am very concerned however because looking at the brain masks after these 
> steps have been done (ie the cross-sectional runs), they look much worse than 
> they did before the longitudinal editing began; large chunks of surfaces are 
> missing. Has anybody else reported this problem? Could it be because the 
> longitudinal steps are now being done with version 5.3 as opposed to 5? 
> Surely this should not have such a large effect on the brainmasks, as to 
> completely "deform" them?
> 
> Kind Regards,
> 
> Linn
> 
> 
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-
Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu 

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Re: [Freesurfer] error --qdec long

[Martin Reuter]

Hi Catherine,

probably you are not using 5.3. otherwise it should recognize the --qdec-long 
flag. You can open mris_preproc and take a look (it is a text file), there 
should be a "qdec-long" if you search it.

Best, Martin 

On Jun 17, 2013, at 12:04 PM, Catherine Bois  wrote:

> Dear Freesurfer experts,
> 
> I am trying to prepare my data for linear mixed modeling using the matlab add 
> ons, with this command
> 
> mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi lh --meas 
> thickness --out lh.thickness.mgh
> 
> However I keep getting this error message ERROR: flag --qdec-long not 
> recognized
> 
> I am using version 5.3 and read on the release notes that qdec-long only 
> works with unix input text files (\n newline). I thought that was the format 
> of my textfile, and also confused as to why the wrong format of the file 
> would make the flag unrecognized as opposed to the textfile...I was also 
> wondering whether the -long table needs to be "shrunk" to cross-sectional 
> format as it does in the two stage model? I have attached an excerpt of my 
> textfile qdec, would greatly appreciate help in establishing whether it is 
> somehow the format of the textfile that is the problem?
> 
> Thank you very much for your help,
> 
> Best Wishes,
> 
> Cathy
> 
> 
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
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-
Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu 

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Re: [Freesurfer] problem bbregister onto longitudinal pipeline

[Martin Reuter]

Hi Daniel,

bbregister is completely independent of the longitudinal stream, so if it 
fails, it has other reasons (e.g. bad initial alignment). You could try to 
switch the initial alignment to some other methods.

Best, Martin

On Jun 14, 2013, at 3:25 AM, Daniel Garcia  
wrote:

> Dear Freesurfer Users,
> 
> I'm having a problem to register my PET images into the longitudinal
> pipeline of freesurfer (version 5.1).
> 
> I have use bbregister without any problem to put the PET image into the
> crossectional images but it fails to register to the long version of it.
> Someone can tell me if I'm doing something wrong?
> 
> bbregister -s P09_TA --mov pet_09.nii --init-fsl --reg matrix.mat --o
> pet2free.mgz
> 
> This last command works perfectly, but 
> 
> bbregister -s P09_TA.long.P09 --mov pet_09.nii --init-fsl --reg
> matrix.mat --o pet2free.mgz
> 
> Fails completely.
> 
> My objective is to project my pet cortex into the surface in
> longitudinal that is why I'm interested in this processing. Maybe you
> can tell my another way of doing this.
> 
> Thank you very much.
> 
> Daniel
> 
> 
> 
> 
> 
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> 

-
Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu 

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[Freesurfer] mri_convert and flips

[Ray, Siddharth]

Hi all,

I have some of my subjects with their A/P and L/R labels flipped and using 
mri_convert convert command to make them right. I was little concerned that I 
am just providing command with -in_ourientation and -out_orientation info to 
get the right labeled images, is this anyway going to change my actual image 
data/pixel values?

Please let me know.

Thanks,
-Siddharth
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Re: [Freesurfer] mri_convert segmentation fault in bash

[Bruce Fischl]

are you sure they are using the same binary? The bash shell probably pushes 
a new shell, which sources your dot files, etc...


On Wed, 19 Jun 2013, Caspar M. 
Schwiedrzik wrote:

> Hi Freesurfers,
> I am getting a segmentation fault with the 4.5 version of mri_convert
> when trying to convert an AFNI BRIK file into nii.
> This is my command line:
> mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii
> Strangely, I only get the segmentation fault when I run mri_convert in
> a bash script, in which case it is called like this:
> `mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii`
> When I run mri_convert from the command line, no segmentation fault occurs.
> Any advice?
> Thanks, Caspar
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>
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[Freesurfer] mri_convert segmentation fault in bash

[Caspar M. Schwiedrzik]

Hi Freesurfers,
I am getting a segmentation fault with the 4.5 version of mri_convert
when trying to convert an AFNI BRIK file into nii.
This is my command line:
mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii
Strangely, I only get the segmentation fault when I run mri_convert in
a bash script, in which case it is called like this:
`mri_convert -i input+orig.BRIK -o fde.nii --in_like f.nii`
When I run mri_convert from the command line, no segmentation fault occurs.
Any advice?
Thanks, Caspar
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Re: [Freesurfer] check orientation

[Brigitte Dahmen]

Hi Bruce,

thank you very much!

Brigitte


2013/6/19 Bruce Fischl 

> Hi Brigitte,
>
> could you cc the list so that others can answer? I'm not sure what
> qualifies as "turned around" in FSL. They may have some preferred
> oreintation.  In general we don't, and as long as the direction cosines are
> preserved (i.e. avoid analyze format!) you should be fine
>
> Bruce
>
>
> On Wed, 19 Jun 2013, Brigitte Dahmen wrote:
>
>  Dear Bruce,
>> thank you very much!
>> Please excuse a (potentially naive) follow-up question (as we didn't use
>> external markers): So if in FSL some raw T1 data are found to be "turned
>> around", is it something that Freesurfer "takes care of" at a certain
>> point
>> in the analysis or would you suggest to swap/correct the data after
>> checking
>> w/ FSL and then analyze them with Freesurfer?
>>
>> Thanks again and kind regards!
>> Brigitte
>>
>>
>> 2013/6/19 Bruce Fischl 
>>   Hi Brigette,
>>
>>   not sure how you could do this except visually. Bring the images
>>   up and verify that the directions that we specify are correct
>>   (although of course this isn't possible for L/R unless you have
>>   some type of external fiducial marker like a vitamin E tablet)
>>
>>   cheers
>>   Bruce
>>   On Wed, 19 Jun 2013, Brigitte Dahmen wrote:
>>
>> Dear Freesurfer experts,
>>
>> is there a command in Freesurfer to check for
>> correct orientation (LAS vs.
>> PSR) of T1 images (similar to "fslhd" in FSL)?
>>
>> Thank you very much!
>> Brigitte
>>
>>
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/**complianceline.
>>  If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
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>
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> dispose of the e-mail.
>
>


-- 
Brigitte Dahmen - Benedikt-Schmittmann-Str. 22 - 40479 Düsseldorf /
Mariabrunnstr. 42 - 52064 Aachen - 0160-3774566 - mailto: bigg...@gmail.com
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Re: [Freesurfer] check orientation

[Bruce Fischl]

Hi Brigitte,

could you cc the list so that others can answer? I'm not sure what 
qualifies as "turned around" in FSL. They may have some preferred 
oreintation.  In general we don't, and as long as the direction cosines are 
preserved (i.e. avoid analyze format!) you should be fine

Bruce


On Wed, 19 Jun 2013, Brigitte Dahmen wrote:


Dear Bruce,
thank you very much! 
Please excuse a (potentially naive) follow-up question (as we didn't use
external markers): So if in FSL some raw T1 data are found to be "turned
around", is it something that Freesurfer "takes care of" at a certain point
in the analysis or would you suggest to swap/correct the data after checking
w/ FSL and then analyze them with Freesurfer?

Thanks again and kind regards!
Brigitte


2013/6/19 Bruce Fischl 
  Hi Brigette,

  not sure how you could do this except visually. Bring the images
  up and verify that the directions that we specify are correct
  (although of course this isn't possible for L/R unless you have
  some type of external fiducial marker like a vitamin E tablet)

  cheers
  Bruce
  On Wed, 19 Jun 2013, Brigitte Dahmen wrote:

Dear Freesurfer experts,

is there a command in Freesurfer to check for
correct orientation (LAS vs.
PSR) of T1 images (similar to "fslhd" in FSL)? 

Thank you very much!
Brigitte




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Re: [Freesurfer] error in lme_mass_fit using matlab tools

[jorge luis]

Hi Cathy

You are getting that error likely because your Matlab version is too old 
(before 2011) and it doesn't support 'matlabpool' parallel computing. Also, I 
notice that you are using only a single random effect (the second column of 
your design matrix). In that case I don't expect a significant increase in 
power from the spatiotemporal model. So you can simply use the traditional 
vertex-wise model 

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


You can find as attachment a non-parallel version of those scripts that may 
work on your Matlab version (I have not written the non-parallel version of the 
spatiotemporal model yet). The scripts are name as their parallel versions but 
with the sufix "1".


Best
-Jorge






>
> De: Catherine Bois 
>Para: freesurfer@nmr.mgh.harvard.edu 
>Enviado: Miércoles 19 de junio de 2013 10:39
>Asunto: [Freesurfer] error in lme_mass_fit using matlab tools
> 
>
>Dear Freesurfer experts,
>
>I have a question about fitting linear mixed models to mass-univariate  
>data using the lme tools in matlab.
>
>I am currently trying to compute the initial vertex-wise temporal  
>covariance estimates by [lhTh0lhRe] =  
>lme_mass_fit_EMinit(X,[2],ni,lhcortex,3]
>
>However, I keep getting this error message:
>
>Undefined function 'matlabpool' for input arguments of type 'char'.
>
>Error in lme_mass_fit_init (line 74)
>if (prs==1) || (matlabpool('size') ~= prs)
>
>Error in lme_mass_fit_EMinit (line 69)
>[Theta1,Re1] = lme_mass_fit_init(X,Zcols,Y,ni,[],prs);
>
>I have defined X, Y etc according to the previous steps available on  
>the wiki. Would be very grateful for any clarification on why this  
>error message keeps coming up.
>
>Thank you very much,
>
>Cathy
>
>-- 
>The University of Edinburgh is a charitable body, registered in
>Scotland, with registration number SC005336.
>
>
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>
>
>function fstats = lme_mass_F1(stats,CM)
% fstats = lme_mass_F1(stats,CM) 
% 
% Inference for the fixed-effects in the linear mixed-effects model. Allows 
% to test a different model at each voxel/vertex (Depends on the Statistics
% toolbox).
%
% Input
% stats: Structure array containing statistiscs for every voxel/vertex (see
% lme_FSfit for more details on these statistics).
% CM: Structure array containing a contrast matrix CM.C for each and every 
% voxel/vertex. If length(CM)==1 the same contrast matrix CM.C is tested at
% each and every voxel/vertex.
%
% Output
% fstats.F: F-Statistic.
% fstats.pval: P-value of the F-Statistic.
% fstats.sgn: Sign of the contrast.
% fstats.df: Degrees of freedom of the F-Statistic.
%
% $Revision: 1.1.1.1 $  $Date: 2012/02/02 11:25:52 $
% Original Author: Jorge Luis Bernal Rusiel 
% CVS Revision Info:
%$Author: jbernal$
%$Date: 2012/02/02 11:25:52 $
%$Revision: 1.1 $
% References: Bernal-Rusiel J.L., Greve D.N., Reuter M., Fischl B., Sabuncu
% M.R., 2012. Statistical Analysis of Longitudinal Neuroimage Data with Linear 
% Mixed Effects Models, NeuroImage, doi:10.1016/j.neuroimage.2012.10.065.
%
tic;
if nargin < 2
error('Too few inputs');
end;
nv = length(stats);
nCM = length(CM);
if nCM ~= nv
if nCM == 1
CM(1:nv) = struct('C',CM.C);
else
error(['The number of elements (contrasts) in CM must be equal to the'...
' number of locations (length(stats))']);
end
end;
for i=1:nv
if (stats(i).lreml ~= -10^10)  &&  (size(CM(i).C,2) ~= length(stats(i).Bhat))
error(['The number of colums in the contrast matrix CM('...
num2str(i) ').C is different from the corresponding number'...
' of fixed effects in stats(' num2str(i) ').Bhat']);
end;
end;
F = zeros(1,nv);
pval = ones(1,nv);
sgn = zeros(1,nv);
df = zeros(2,nv);
display(' ');
display('Computing F statistics, degrees of freedom and P-values ...');
for i=1:nv
if stats(i).lreml ~= -10^10
Bhat = stats(i).Bhat;
C = CM(i).C;
Zcols = stats(i).Zcols;
q = length(Zcols);
nth = q*(q+1)/2+1;
invEI = stats(i).invEI;
Pth = stats(i).Pth;
Qthth = stats(i).Qthth;
%Estimation of the bias in the covariance matrix and computation of the
%F-statistic and the degrees of freedom of the test.
Bias = 0;
CBhat = stats(i).CovBhat;
OM = C'*(C*CBhat*C')^-1*C;
A1 = 0; A2 = 0;
Term1 = OM*CBhat;

Re: [Freesurfer] export the ROIs in 'Desikan-Killiany' cortical atlas

[Bruce Fischl]

Hi Daniel,

have you run recon-all on your subjects? If so, you can run 
mri_annotation2label to convert the ?h.aparc.annot file into separate 
labels for each ROI, then go from there. Or if you want to do everything in 
average space you can run it on fsaverage (or load the annotation in 
tksurfer, click on the one you want and save it as a label instead of 
converting every parcel to a label)


cheers
Bruce
On Wed, 19 Jun 2013, Yang, Daniel 
wrote:



Hi FreeSurfer expert,

I am interested in a particular region of the Desikan-Killiany atlas and I'd
like to use it as an ROI image mask in my fMRI analysis.

Could you please suggest how I can do that?

From here (http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation), I
see that the DK atlas files are located here:

$FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs

Question 1: how can I read this GCS file?

Question 2: After I read this GCS file, how can I create an ROI image mask?

I am thinking to use the WFU PickAtlas to create an ROI
(http://fmri.wfubmc.edu/software/PickAtlas). Would it be a good fit?

Thanks!
Daniel

-- 
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

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[Freesurfer] export the ROIs in 'Desikan-Killiany' cortical atlas

[Yang, Daniel]

Hi FreeSurfer expert,

I am interested in a particular region of the Desikan-Killiany atlas and I'd 
like to use it as an ROI image mask in my fMRI analysis.

Could you please suggest how I can do that?

From here (http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation), I see 
that the DK atlas files are located here:

$FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs

Question 1: how can I read this GCS file?

Question 2: After I read this GCS file, how can I create an ROI image mask?

I am thinking to use the WFU PickAtlas to create an ROI 
(http://fmri.wfubmc.edu/software/PickAtlas). Would it be a good fit?

Thanks!
Daniel

--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
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Re: [Freesurfer] check orientation

[Bruce Fischl]

Hi Brigette,

not sure how you could do this except visually. Bring the images up and 
verify that the directions that we specify are correct (although of 
course this isn't possible for L/R unless you have some type of external 
fiducial marker like a vitamin E tablet)


cheers
Bruce
On Wed, 19 Jun 2013, Brigitte 
Dahmen wrote:



Dear Freesurfer experts,

is there a command in Freesurfer to check for correct orientation (LAS vs.
PSR) of T1 images (similar to "fslhd" in FSL)? 

Thank you very much!
Brigitte

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[Freesurfer] check orientation

[Brigitte Dahmen]

Dear Freesurfer experts,

is there a command in Freesurfer to check for correct orientation (LAS vs.
PSR) of T1 images (similar to "fslhd" in FSL)?

Thank you very much!
Brigitte
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Re: [Freesurfer] MRIread.m and hippocampal subfields

[Marcos Martins da Silva]

Hi, Doug
Hi, all

This single BASH script line works like a charm for all posterior.mgz
files in a once and keeps the original names (must be in yoursubject/mri
folder).
for f in $(ls posterior*.mgz); do mri_convert -tr 0 -ti 0 -te 0
-flip_angle 0 -i $f -o $f; done

You can also use in a more complete script like:

#!/bin/bash
#usage myrecon subj (for example, myrecon bert)
mkdir ~/freesurfer/subjects/$1/mri/orig -p
cp  ~/freesurfer/ImgOrig/$1/* ~/freesurfer/subjects/$1/mri/orig/
recon-all -all -s $1 -cw256 -hippo-subfields -qcache
cd ~/freesurfer/subjects/$1/mri
for f in $(ls posterior*.mgz); do mri_convert -tr 0 -ti 0 -te 0
-flip_angle 0 -i $f -o $f; done

This way all files will be fixed just after usual recon-all pipeline.
Notice you may adapt for your environment and recon-all options. Also,
ImgOrig is a custom folder where I have 1 folder for each of my subjects
with their respective images already prepared as 00x.mgz.
I hope you think it is useful. 
BTW, I had to specify -i and -o in the command line. Using just the name
of the files did not work.
Thank you again, Doug.

Marcos

Em Ter, 2013-06-18 às 23:45 -0700, Douglas Greve escreveu:

> Hi Marcos, it is weird that the posterior*.mgz does not have that
> info. Maybe Koen or Eugenio know why. In the mean time, you can use
> mri_convert to change/set the parameters, eg
> 
> mri_convert in.mgz out.mgz -tr 0 -ti 0 -te 0 -flip_angle 0
> 
> doug
> 
> 
> 
> 
> 
> 
> On 6/18/13 2:50 PM, Marcos Martins da Silva wrote:
> 
> > 
> > Hi, Freesurfer experts
> > If you try to read one of the posterior*.mgz files generated by
> > reco-all -hippo-subfield into MatLab/Octave using MRIread.m it fails
> > like this:
> > Ps=MRIread('posterior_left_subiculum.mgz')  
> > WARNING: error reading MR params
> > Attempted to access mr_parms(1); index out of bounds because
> > numel(mr_parms)=0.
> > 
> > Error in MRIread (line 100)
> >tr = mr_parms(1);
> > 
> > That is because the posterior*.mgz files does not have this data. I
> > made a  creating a little customized nMRIread.m with the following
> > changes:
> > 
> > if numel(mr_parms) > 0
> >  tr = mr_parms(1);
> > flip_angle = mr_parms(2);
> >  te = mr_parms(3);
> >  ti = mr_parms(4);
> >else
> > mr_parms(1) = 0;
> >  mr_parms(2) = 0;
> >  mr_parms(3) = 0;
> >  mr_parms(4) = 0;
> >  tr = mr_parms(1);
> >  flip_angle = mr_parms(2);
> > te = mr_parms(3);
> > ti = mr_parms(4);
> >   end
> > 
> > That works but it is only a quick workaround since MRIread,m calls
> > load_mgh.m and it shows a warning message about the mr_parms. This
> > message does not block my work but it is not good to see the warning
> > all the time on my screen. Perhaps the best fix would be just
> > creating the posterior*.mgz files with these data defined as 0. But
> > I would be happy if I could just "edit" these files defining these
> > values. Is there a freesurfer tool to make this simple edition? I
> > noticed, for example, that when you use mri_concat to sum these
> > files the resulting concatenated file is fixed and these parameters
> > are defined.
> > Thanks in advance,
> > Marcos. 
> > 
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> 
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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
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
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> properly
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Re: [Freesurfer] recon-all error MRIthickenThinWMStrands

[Bruce Fischl]

nope, never seen that error. Probably from mri_segment. If you send me the 
input volume I'll take a look (check the recon-all.log and see what command 
was running when that happened). Also, definitely check it before sending 
to make sure it's reasonable

On Wed, 19 Jun 2013, 
Sudhin A. Shah wrote:

> Hi
> 
> ERROR: MRIthickenThinWMStrands: invalid x,y,z!
> 
> Numerical result out of range
> 
> 
> Any tips?
> S
> 
>
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Re: [Freesurfer] Segmentation of MR-PET structurals

[Bruce Fischl]

Hi Gabriel

can you give us details of your acquisition? Why is it so noisy?
Bruce


On Wed, 19 Jun 2013, Gabriel Obregon wrote:

> Hi Douglas,
> 
> The brainmask volumes are extremely grainy (similar to the raw structurals),
> i.e., dark voxels throughout the WM and high-intensity voxels across the
> gray matter. As far as I understood, all WM voxels (unless a lesion is
> present) should have a uniform intensity distribution after the
> normalization stages within the volume processing pipeline. Moreover, this
> makes the WM edits particularly challenging, for it's very difficult to
> trace the boundaries of some of the WM strands.
> 
> I don't know if this represents an issue but it's definitely something I
> hadn't encountered before. Any input would be really appreciated!
> 
> Thanks,
> 
> --G
> 
> On Jun 19, 2013, at 2:23 AM, Douglas Greve 
> wrote:
>
>   Hi Gabriel, I don't have experience with the MR-PET yet. Why do
>   you think there is a problem? Try running wm-anat-snr on this
>   subject. In general, you don't want to be smoothing/denoising
>   the anatomical
>   doug
> 
> 
> 
> 
>
>   On 6/18/13 1:13 PM, obre...@nmr.mgh.harvard.edu wrote:
> 
> Hi,
> 
> I've started segmenting several structural scans from an MR-PET study
> conducted in Bay 7, and was wondering if someone has previous experience
> working with MPRAGE images acquired using the MR-PET coils?
> 
> The scans have a very low SNR and I am trying to figure out if this could
> potentially affect the performance of the automated surface
> reconstructions. I've scrolled through the volumes and even though the
> surfaces seem normal, I am somewhat skeptical about their true quality
> given that intermediate stages, such as the intensity normalization, seem
> to be failing (please find an example from one of the brain masks
> attached).
> 
> Is it essential to filter the raw structurals before segmenting them, and
> if so, are there any readily available denoising tools? Furthermore, are
> there any additional issues I should take into consideration?
> 
> Thanks for your help!
> 
> Gabriel
> 
> 
> ___
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> 
> 
> 
>
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Re: [Freesurfer] Interior white matter surfaces

[Bruce Fischl]

Hi Jason

you could try using mris_expand with a negative # of millimeters. At 4mm 
you will lose a lot of the gyri and the procedure will probably fail, but 
for smaller amounts it should work (and is what we've done in the past). 
You can also use mris_distance_transform to compute the distance transform 
for the wm and use negative distances to find the distance into the 
interior

cheers
Bruce


On Wed, 19 Jun 2013, Jason Reed wrote:

> Dear FreeSurfer Experts,
>
> I am attempting to construct surfaces that are 1, 2, 3, and 4 mm
> interior from the GM/WM boundary (?h.white). So going gradually deeper
> into white matter from the GM/WM boundary.  I have successfully used
> mris_fill to fill the ?h.white surface and mri_morphology to erode the
> resulting volume, but I'm not sure on the correct procedure to create
> the new surfaces.  Any advice or suggestions on tools with options to
> use will be greatly appreciated!
>
> My eventual goal is to project coregistered DTI data onto these more
> interior white matter surfaces.
>
> Thanks!
> -Jason
>
>
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Re: [Freesurfer] IOError: [Errno 13] Permission denied: 'aseg_stats.txt'

[Louis Nicholas Vinke]

Hi Chikku,
I think this is a permissions issue.  Check that you have write 
permissions to where you are trying to write the stats table.

-Louis

On Wed, 19 Jun 2013, Varghese Chikku wrote:


Dear FS team,
I  tried to  run this  command

asegstats2table --subjects bert ernie fred margaret --meas volume --tablefile 
aseg_stats.txt

But got this   error,permission denied,

SUBJECTS_DIR : /usr/local/freesurfer/subjects

Parsing the .stats files
Building the table..
Writing the table to aseg_stats.txt
Traceback (most recent call last):
  File "/usr/local/freesurfer/bin/asegstats2table", line 517, in 

    write_table(options, rows, columns, table)
  File "/usr/local/freesurfer/bin/asegstats2table", line 462, in write_table
    tw.write()
  File "/usr/local/freesurfer/bin/datastruct_utils.py", line 58, in write

    fp = open(self.filename, 'w')
IOError: [Errno 13] Permission denied: 'aseg_stats.txt'
freesurfer@freesurfer-VirtualBox:/usr/lib$ 


Many thanks

Chikku

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[Freesurfer] recon-all error MRIthickenThinWMStrands

[Sudhin A. Shah]

Hi

ERROR: MRIthickenThinWMStrands: invalid x,y,z!

Numerical result out of range


Any tips?
S
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Re: [Freesurfer] Segmentation of MR-PET structurals

[Gabriel Obregon]

Hi Douglas,

The brainmask volumes are extremely grainy (similar to the raw structurals), 
i.e., dark voxels throughout the WM and high-intensity voxels across the gray 
matter. As far as I understood, all WM voxels (unless a lesion is present) 
should have a uniform intensity distribution after the normalization stages 
within the volume processing pipeline. Moreover, this makes the WM edits 
particularly challenging, for it's very difficult to trace the boundaries of 
some of the WM strands.

I don't know if this represents an issue but it's definitely something I hadn't 
encountered before. Any input would be really appreciated!

Thanks,

--G

On Jun 19, 2013, at 2:23 AM, Douglas Greve  wrote:

> Hi Gabriel, I don't have experience with the MR-PET yet. Why do you think 
> there is a problem? Try running wm-anat-snr on this subject. In general, you 
> don't want to be smoothing/denoising the anatomical
> doug
> 
> 
> 
> 
> 
> On 6/18/13 1:13 PM, obre...@nmr.mgh.harvard.edu wrote:
>> Hi,
>> 
>> I've started segmenting several structural scans from an MR-PET study
>> conducted in Bay 7, and was wondering if someone has previous experience
>> working with MPRAGE images acquired using the MR-PET coils?
>> 
>> The scans have a very low SNR and I am trying to figure out if this could
>> potentially affect the performance of the automated surface
>> reconstructions. I've scrolled through the volumes and even though the
>> surfaces seem normal, I am somewhat skeptical about their true quality
>> given that intermediate stages, such as the intensity normalization, seem
>> to be failing (please find an example from one of the brain masks
>> attached).
>> 
>> Is it essential to filter the raw structurals before segmenting them, and
>> if so, are there any readily available denoising tools? Furthermore, are
>> there any additional issues I should take into consideration?
>> 
>> Thanks for your help!
>> 
>> Gabriel
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
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[Freesurfer] Interior white matter surfaces

[Jason Reed]

Dear FreeSurfer Experts,

I am attempting to construct surfaces that are 1, 2, 3, and 4 mm 
interior from the GM/WM boundary (?h.white). So going gradually deeper 
into white matter from the GM/WM boundary.  I have successfully used 
mris_fill to fill the ?h.white surface and mri_morphology to erode the 
resulting volume, but I'm not sure on the correct procedure to create 
the new surfaces.  Any advice or suggestions on tools with options to 
use will be greatly appreciated!

My eventual goal is to project coregistered DTI data onto these more 
interior white matter surfaces.

Thanks!
-Jason

-- 
Jason Reed
VA San Diego Healthcare System (116A-13)
3350 La Jolla Village Drive
San Diego, CA 92161
Phone: (858) 552-8585 ext. 2946
Fax: (858) 642-3836
jr...@vapop.ucsd.edu


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[Freesurfer] IOError: [Errno 13] Permission denied: 'aseg_stats.txt'

[Varghese Chikku]

Dear FS team,
I  tried to  run this  command

asegstats2table --subjects bert ernie fred margaret --meas volume
--tablefile aseg_stats.txt

But got this   error,permission denied,

SUBJECTS_DIR : /usr/local/freesurfer/subjects
Parsing the .stats files
Building the table..
Writing the table to aseg_stats.txt
Traceback (most recent call last):
  File "/usr/local/freesurfer/bin/asegstats2table", line 517, in 
write_table(options, rows, columns, table)
  File "/usr/local/freesurfer/bin/asegstats2table", line 462, in write_table
tw.write()
  File "/usr/local/freesurfer/bin/datastruct_utils.py", line 58, in write
fp = open(self.filename, 'w')
IOError: [Errno 13] Permission denied: 'aseg_stats.txt'
freesurfer@freesurfer-VirtualBox:/usr/lib$

Many thanks

Chikku
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[Freesurfer] error in lme_mass_fit using matlab tools

[Catherine Bois]

Dear Freesurfer experts,

I have a question about fitting linear mixed models to mass-univariate  
data using the lme tools in matlab.

I am currently trying to compute the initial vertex-wise temporal  
covariance estimates by [lhTh0lhRe] =  
lme_mass_fit_EMinit(X,[2],ni,lhcortex,3]

However, I keep getting this error message:

Undefined function 'matlabpool' for input arguments of type 'char'.

Error in lme_mass_fit_init (line 74)
if (prs==1) || (matlabpool('size') ~= prs)

Error in lme_mass_fit_EMinit (line 69)
[Theta1,Re1] = lme_mass_fit_init(X,Zcols,Y,ni,[],prs);

I have defined X, Y etc according to the previous steps available on  
the wiki. Would be very grateful for any clarification on why this  
error message keeps coming up.

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] MRIread.m and hippocampal subfields

[Marcos Martins da Silva]

I knew you would have a clean solution. :-)
Thank you, Doug.
Em Ter, 2013-06-18 às 23:45 -0700, Douglas Greve escreveu:

> Hi Marcos, it is weird that the posterior*.mgz does not have that
> info. Maybe Koen or Eugenio know why. In the mean time, you can use
> mri_convert to change/set the parameters, eg
> 
> mri_convert in.mgz out.mgz -tr 0 -ti 0 -te 0 -flip_angle 0
> 
> doug
> 
> 
> 
> 
> 
> 
> On 6/18/13 2:50 PM, Marcos Martins da Silva wrote:
> 
> > 
> > Hi, Freesurfer experts
> > If you try to read one of the posterior*.mgz files generated by
> > reco-all -hippo-subfield into MatLab/Octave using MRIread.m it fails
> > like this:
> > Ps=MRIread('posterior_left_subiculum.mgz')  
> > WARNING: error reading MR params
> > Attempted to access mr_parms(1); index out of bounds because
> > numel(mr_parms)=0.
> > 
> > Error in MRIread (line 100)
> >tr = mr_parms(1);
> > 
> > That is because the posterior*.mgz files does not have this data. I
> > made a  creating a little customized nMRIread.m with the following
> > changes:
> > 
> > if numel(mr_parms) > 0
> >  tr = mr_parms(1);
> > flip_angle = mr_parms(2);
> >  te = mr_parms(3);
> >  ti = mr_parms(4);
> >else
> > mr_parms(1) = 0;
> >  mr_parms(2) = 0;
> >  mr_parms(3) = 0;
> >  mr_parms(4) = 0;
> >  tr = mr_parms(1);
> >  flip_angle = mr_parms(2);
> > te = mr_parms(3);
> > ti = mr_parms(4);
> >   end
> > 
> > That works but it is only a quick workaround since MRIread,m calls
> > load_mgh.m and it shows a warning message about the mr_parms. This
> > message does not block my work but it is not good to see the warning
> > all the time on my screen. Perhaps the best fix would be just
> > creating the posterior*.mgz files with these data defined as 0. But
> > I would be happy if I could just "edit" these files defining these
> > values. Is there a freesurfer tool to make this simple edition? I
> > noticed, for example, that when you use mri_concat to sum these
> > files the resulting concatenated file is fixed and these parameters
> > are defined.
> > Thanks in advance,
> > Marcos. 
> > 
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> 
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> 
> 
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> contains patient information, please contact the Partners Compliance HelpLine 
> at
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Re: [Freesurfer] Reviewer not satisfied

[Bruce Fischl]

read_curv.m should do the trick
On Wed, 19 Jun 2013, Jürgen Hänggi wrote:


Dear Bruce

Yes, the .max and the .min files were produced, but how to access the values
in it. Is there a possibility to import these files into MATLAB?

Thanks in advance
Cheers
Jürgen


On [DATE], "Bruce Fischl" <[ADDRESS]> wrote:


.H is mean and .K is Gaussian curvature. It should also write a .max and
.min, doesn't it? Those are the principal curvatures that you want.

Bruce

On Tue, 18 Jun 2013, Jürgen Hänggi
wrote:


Dear Bruce

Thanks a lot for the info. It worked fine, but how can I open the resulting
.H and .K files?

Cheers
Jürgen


On [DATE], "Bruce Fischl" <[ADDRESS]> wrote:


Hi Jürgen

you could quantify this if you want. Use mris_curvature to compute the
mean curvature maps independently (the first and second principal
curvatures). These have the units of 1/mm and are exactly the radius of
curvature. You could histogram them and look at the distribution.

cheers
Bruce

p.s. I think you want -w -max and -w -min flags for it

On Fri, 14 Jun 2013, Jürgen Hänggi
wrote:


Dear FS experts

In one of our paper, I tried to explain how FS is able to produce cortical
thickness maps in a spatial resolution that go beyond the resolution of the
original MRI acquisition.

We wrote the following:

The thickness maps produced are not limited to the voxel resolution of the
image and thus sensitive for sub-millimeter differences between groups
(Fischl, Dale 2000). The way in which the resolution of the cortical
thickness maps goes beyond the resolution of the original acquisition can
be
imagined as a (conventional) partial volume correction procedure. The
cortex
is smooth at the spatial scale of a couple of millimeters, which is imposed
as constraint by FreeSurfer to estimate the location of the surface with
subvoxel accuracy. For instance, if a given voxel is darker than its
neighbouring grey matter it probably contains more CSF and so the surface
model is at a slightly different position than if the neighbouring voxels
were brighter and therefore contain probably more white matter.

Now, the reviewer says that we are to vague in our description. He would
like to know what is exactly meant by a "couple of millimeters".

Is this 1-3 mm or rather 3-5 mm or any other value?

Thanks in advance for any suggestion
Regards
Jürgen Hänggi



---
-

Jürgen Hänggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

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Jürgen Hänggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

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[Freesurfer] TRACULA - tract volume and length

[Fred Sanders]

Dear DTI experts,

I am trying to understand how to interpret tract length & volume
measurements that TRACULA provides.  For example, let’s say a clinical
population differs from a control group in mean FA of a particular
tract, and tract length & volume are comparable across the 2 groups.
I think this would support the notion that the tract’s diffusion
properties are indeed different across the two groups and that the FA
finding are unlikely to be an artifact of probabilistic tractography.
Is this a correct interpretation?  Conversely, if group differences in
tract volumes were detected, would you recommend comparing mean FA
across the two group while covarying for tract volume?

Thanks!

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Re: [Freesurfer] problem downloading Xhemi files

[amirhossein manzouri]

I use curl to download in MAC with the links you mentioned and it is not
there!
amir% curl -O
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg
  % Total% Received % Xferd  Average Speed   TimeTime Time
 Current
 Dload  Upload   Total   SpentLeft
 Speed
  0 00 00 0  0  0 --:--:--  0:00:01 --:--:--
  0
curl: (78) RETR response: 550



On Wed, Jun 19, 2013 at 8:42 AM, Douglas Greve wrote:

>  try now
>
>
> On 6/18/13 9:37 PM, amirhossein manzouri wrote:
>
>  I have version 5.1 so please recreate the links!
>  BR
>
>
> On Tue, Jun 18, 2013 at 8:43 AM, Douglas Greve 
> wrote:
>
>>
>> Hi Amir, if you are using 5.2 or 5.3, then you should already have it. If
>> not, I'll have to recreate the links. let me know
>> doug
>>
>>
>> On 6/17/13 6:52 AM, amirhossein manzouri wrote:
>>
>>   Dear Doug,
>> I can not download the files needed for Xhemi in mentioned link. Would
>> you please advise how to download them?
>>
>>  --
>> Best regards,
>> Amir
>>
>>
>>
>>
>>
>>
>>  ___
>> Freesurfer mailing 
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>>
>>
>>
>> ___
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>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
>  --
> Best regards,
> Amirhossein Manzouri
>
>
>
>
>


-- 
Best regards,
Amirhossein Manzouri
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