Re: [Freesurfer] Multimodality analysis in FreeSurfer

[Silas]

I've mapped cortical thickness and the myelination data onto the fsaverage, and 
also used general linear modelling to investigate the one sample group mean of 
myelination data og cortical thickness (not very useful since the mean 
thickness or myelination should never be 0) data separately. 
I would like to map the correlation between cortical thickness and myelination 
onto the fsaverage. I've investigated this statistical correlation by a vertex 
wise correlation study in matlab, and it should be possible to map this onto 
the fsaverage. Though, I would like to perform this correlation study entirely 
in FreeSurfer - in this way I would easily be able to correlate for multiple 
comparisons using the standardized pipeline for FreeSurfer group analysis.

Best, Silas


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Tuesday, November 17, 2015 7:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Multimodality analysis in FreeSurfer

I'm not sure what you mean. You say that you have mapped the thickness
and myelin data into fsaverage space but then need to map the
correlation into fsaverage. Isn't it already there?

On 11/17/2015 10:33 AM, Silas wrote:
>
> Dear Freesurfer team,
>
>
> I've scanned a group of subjects and gained structural and myelination
> data. Then, I've used mris_preproc to map the data onto the surface of
> fsaverage (and concatenating the data). I would like to investigate
> the correlation between cortical thickness and myelination by mapping
> this correlation onto the fsaverage (an one sample group mean
> analysis) - is this possible? Do you have an existing guide
> approaching this problem?
>
>
> Thank you!
>
>
> Best, Silas
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] freesurfer vs ITK build from sources on ubuntu(LUCID)

[Nedialko I. Krouchev]

I'd be very grateful for any help provided on this matter.

It has been close to three weeks since I started trying to compile
freesurfer
from its sources (CSV stable5) on 32bit ubuntu ver. 10.04.

I followed to the letter the recipe outlined in:
http://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide

To do so I found additional prerequisite sources in:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/src/

mni.srcbuild.June2015.tgz 12.0 MB 6/19/15, 8:51:00 PM
mni.srcbuild.README.txt 6.5 kB 2/25/09, 12:00:00 AM

tcltktixblt-8.4.6.tgz 11.4 MB 7/26/10, 12:00:00 AM
vtk-5.2.1.tar.gz 16.2 MB 2/26/10, 12:00:00 AM
vxl-1.13.0.zip 34.0 MB 2/26/10, 12:00:00 AM

and then (when I'd have almost given up) the "Hacks" in:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-April/029159.html

In addition, overcame the complex VTK structure of includes ...

Finally, to find I am still missing ITK, which is barely mentioned
elesewhere.

Please correct me if I am wrong, but I assume it is all about
the National Library of Medicine's Insight Segmentation and Registration
Toolkit (ITK).

Then which version of ITK goes with the rest of freesurfer (as described
above)?

http://www.itk.org/ITK/resources/legacy_releases.html
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Re: [Freesurfer] Advice for FreeSurfer developers

[Eugenio Iglesias]

This is a good point. We should run the check right away. Right now, the 
subfield module runs at the end, which means that everything else has completed 
just fine, but we should definitely check at the very beginning and say: 
"either download the runtime or remove the subfield flag" 

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

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


From: "Gronenschild Ed (NP)"  
To: "Freesurfer support list"  
Sent: Tuesday, November 17, 2015 7:09:46 PM 
Subject: [Freesurfer] Advice for FreeSurfer developers 

Hi Doug, 
Yes, I know. It’s the hippocampal subfields segmentation that needs matlab 
runtime. 

Cheers, 
Ed 

On 17 Nov 2015, at 18:00, freesurfer-requ...@nmr.mgh.harvard.edu wrote: 



Message: 8 
Date: Mon, 16 Nov 2015 12:52:20 -0500 
From: Douglas N Greve < gr...@nmr.mgh.harvard.edu > 
Subject: Re: [Freesurfer] Advice for FreeSurfer developers 
To: freesurfer@nmr.mgh.harvard.edu 
Message-ID: < 564a17d4.6090...@nmr.mgh.harvard.edu > 
Content-Type: text/plain; charset=windows-1252; format=flowed 

Do you know what command was looking for matlab? 

On 11/12/2015 02:10 AM, Gronenschild Ed (NP) wrote: 

BQ_BEGIN
Hi Doug, 

I used mostly the default options, nothing special: 

recon-all -autorecon1 -clean-tal -expert my_options.txt -hires 

where the file my_options.txt contains some options for nu_correct. 
Then I entered 

recon-all -autorecon2 -autorecon3 -hippocampal-subfields-T1 -hires 

The error occurred with the last recon-all command. 
BTW, I really don't know if the -clean-tal option is needed with FS v6. 

Cheers 
Ed 


On 11 Nov 2015, at 18:00, < freesurfer-requ...@nmr.mgh.harvard.edu 
< mailto:freesurfer-requ...@nmr.mgh.harvard.edu >> wrote: 


BQ_BEGIN
Message: 9 
Date: Wed, 11 Nov 2015 11:08:46 -0500 
From: Douglas Greve < gr...@nmr.mgh.harvard.edu 
< mailto:gr...@nmr.mgh.harvard.edu >> 
Subject: Re: [Freesurfer] Advice for FreeSurfer developers 
To:freesurfer@ nmr.mgh.harvard.edu < mailto:freesurfer@nmr.mgh.harvard.edu > 
Message-ID: < 5643680e.1030...@nmr.mgh.harvard.edu 
< mailto:5643680e.1030...@nmr.mgh.harvard.edu >> 
Content-Type: text/plain; charset=windows-1252; format=flowed 

Hi Ed, generally recon-all does not need matlab. Are you running the 
gyrification analysis? That should be the only thing that needs matlab. 
doug 

On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote: 

BQ_BEGIN
Dear developers, 

Is it possible to check the presence of Matlab runtime right at the 
start of recon-all 
in FreeSurfer v6 instead of a long way down in the pipeline. After 
36 hours for 
a high-res data processing I got this unexpected error message. 
Thanks in advance. 

Cheers 
Ed 
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BQ_END

BQ_END

BQ_END



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[Freesurfer] travel grants for April workshop

[Jasmin Alves]

Hello,

Are there possibly any travel grants available to attend the Freesurfer
workshop in April? It would greatly benefit my PhD studies to attend this
workshop to learn more about structural techniques, however my PI does not
have sufficient funds to send me.

Thanks,
Jasmin

-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Re: [Freesurfer] geodesic distance calculation

[Martin Reuter]

Hi Desiree,

I don't know how to do that (and hope someone else will help), but about 
your analysis: make sure you also do the inverse (map right to left). 
Then maybe average the distances. Else you could potentially introduce a 
lateral processing bias (by selecting one hemi as the target).

Best, Martin

On 11/17/2015 06:10 AM, Silvia Désirée Thielemann wrote:
> Dear freesurfer experts,
>
> I'm analysing functional data using fsfast running under
> freesurfer-Linux-centos7_x86_64-dev-20150728. After streaming out the
> maximal activated cluster using mri_surfcluster, I want to calculate
> the geodesic distance between these vertices. Can I do this with
> mris_pmake using sphere.reg as surface?
>
> Furthermore, I would like to evaluate symmetry between the
> hemispheres. I would like to mirror the maximal activated vertice of a
> special contrast of the left hemisphere to the right hemisphere and
> calculate the geodesic distance between the mirrored coordinate and
> the maximal activated vertices of the right hemisphere. Is there a way
> to do this?
>
> Best regards,
> Desiree
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] email

[Jasmin Alves]

jal...@usc.edu
-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Re: [Freesurfer] Multimodality analysis in FreeSurfer

[Douglas N Greve]

I'm not sure what you mean. You say that you have mapped the thickness 
and myelin data into fsaverage space but then need to map the 
correlation into fsaverage. Isn't it already there?

On 11/17/2015 10:33 AM, Silas wrote:
>
> Dear Freesurfer team,
>
>
> I've scanned a group of subjects and gained structural and myelination 
> data. Then, I've used mris_preproc to map the data onto the surface of 
> fsaverage (and concatenating the data). I would like to investigate 
> the correlation between cortical thickness and myelination by mapping 
> this correlation onto the fsaverage (an one sample group mean 
> analysis) - is this possible? Do you have an existing guide 
> approaching this problem?
>
>
> Thank you!
>
>
> Best, Silas
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] Advice for FreeSurfer developers

[Gronenschild Ed (NP)]

Hi Doug,

Yes, I know. It’s the hippocampal subfields segmentation that needs matlab 
runtime.

Cheers,
Ed

On 17 Nov 2015, at 18:00, 
freesurfer-requ...@nmr.mgh.harvard.edu
 wrote:

Message: 8
Date: Mon, 16 Nov 2015 12:52:20 -0500
From: Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Advice for FreeSurfer developers
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 
<564a17d4.6090...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Do you know what command was looking for matlab?

On 11/12/2015 02:10 AM, Gronenschild Ed (NP) wrote:
Hi Doug,

I used mostly the default options, nothing special:

recon-all -autorecon1 -clean-tal -expert my_options.txt -hires

where the file my_options.txt contains some options for nu_correct.
Then I entered

recon-all -autorecon2 -autorecon3 -hippocampal-subfields-T1 -hires

The error occurred with the last recon-all command.
BTW, I really don't know if the -clean-tal option is needed with FS v6.

Cheers
Ed


On 11 Nov 2015, at 18:00, 
mailto:freesurfer-requ...@nmr.mgh.harvard.edu>
> wrote:

Message: 9
Date: Wed, 11 Nov 2015 11:08:46 -0500
From: Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>
>
Subject: Re: [Freesurfer] Advice for FreeSurfer developers
To:freesurfer@nmr.mgh.harvard.edu 

Message-ID: 
<5643680e.1030...@nmr.mgh.harvard.edu
>
Content-Type: text/plain; charset=windows-1252; format=flowed

Hi Ed, generally recon-all does not need matlab. Are you running the
gyrification analysis? That should be the only thing that needs matlab.
doug

On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote:
Dear developers,

Is it possible to check the presence of Matlab runtime right at the
start of recon-all
in FreeSurfer v6 instead of a long way down in the pipeline. After
36 hours for
a high-res data processing I got this unexpected error message.
Thanks in advance.

Cheers
Ed
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Re: [Freesurfer] recon-all

[John Anderson]

Hi Doug,

Thanks you very much for your great and detailed answered.

 

Kindly one more thing:

when I am tring to run recon-all on "001.mgz" (under the folder mri/orig). If the fov is more than 256 ( e.g 320) recon-all failed. I checked the "recon-all.log" file and I found that it failed because the fov is more than 320 and it says that I need to run recon -all with the flag -cw256.

 

How can the fov affect the segmentation? in other words is it better to run recon-all on a file with fov less than 256 or more than 256 ? what is the difference in the final output?

 

 Bests,

John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Thursday, November 05, 2015 at 9:39 AM
From: "Douglas Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all


 
On 11/5/15 8:37 AM, John Anderson wrote:



Thanks a lot Doug!

Kindly  ...

1. What do you mean by intensity normalized?


Removing non-biological intensity fluctuations such as darkening/brightening from multiple head coils



2. What is the purpose of conforming the inputs to 256^3 1mm3


This is something that was done when FS was first programmed to make it easier to program by assuring that all inputs were the same size.



3. In order to move mask to diffusion space (FA map) or PET space I do the following:

           3.1 I register FA map to T1 ( after converting the DICOMs to T1.nii - the voxel dimentions here are 176X256X256)

           3.2 I create mask of interest using mri_binarize ( from the wmparc.mgz atals the voxel dimentions here 256X256X256 )

           3.3 I register FA map to T1 image using FLIRT

           3.4 I register the mask to T1 using FLIRT

           3.5 I use reversed matrix to move the mask to FA map.


Probably works, but very compilcated. You should use bbregister to register the FA or PET directly to the conformed space, then use mri_label2vol to map the mask into FA/PET space.
 


 

The problem in this approach is the voxel dimentions ( between the mask and the T1). Can I use norm.mgz ( which has the same voxel dimentions of the mask ) istead of T1 to do the previous steps?

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Wednesday, November 04, 2015 at 3:44 PM
From: "Douglas N Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all



On 11/04/2015 10:22 AM, John Anderson wrote:
> Hi freesurfers,
> Following recon-all I have a collection of folders inside the subject
> folder.
> Inside the folder "mri" I have collection of files:
> 1. What is the differnce between the file "orig.mgz" and the file
> "norm.mgz" ?
norm has been skull stripped and intensity normalized
> 2. Why the voxel dimentions are differnt? (i.e In norm.mgz the voxel
> dimentions are equal while in orig.mgz it is not)?
They should be the same. It might be differnt than rawavg.mgz or your
input data because we "conform" all inputs to 256^3 1mm3
> 3. Is it correct if I convert norm.mgz to "nii" file and use it as a
> "T1" for further processing?
I don't know without knowing more about the "further processing". It is
not a T1 image itself (ie, the voxel intensities are not T1 in msec).
> bests,
> John Anderson
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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dispose of the e-mail.
 




 

 
 

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Re: [Freesurfer] Same Error in processing for local gyrification index

[Oana Georgiana Rus]

Dear all,

I solved the problem posted earlier that was similar to a problem before.
It was a matlab version problem.

Conclusion :

if *recon-all -localGI command* is stopping at make_roi_paths and you 
use matlab 2013


1. either switch to a older matlab version
or
2. follow the instructions from webpage
http://freesurfer.net/fswiki/ReleaseNotes?highlight=%28%28LGI%29%29

and change the SearchProjectionOnPial.m file.

Freesurfer webpage information:

 *

   *LGI*: issue when using Matlab 2013. the fix is to edit the file
   $FREESURFER_HOME/matlab/SearchProjectionOnPial.m and make these
   changes:

find this line:

< for t=1:step:size(perim,2)

and change to:


si=max(size(perim));
for t=1:step:si



After this it worked for me also.

Best regards,
Georgiana

Am 13.11.2015 um 15:37 schrieb Oana Georgiana Rus:

Dear all,

when I run the recon-all -localGI command.
I encaunter the same problem as previous described by Meenal (see 
email below).

It seems that the processing stops at the matlab command*make_roi_paths*.

Does anybody encaunter a similar problem and somehow solved it?

Thanks in advance.

Georgiana

Am 04.11.2015 um 17:25 schrieb Dr Meenal Yadav:

Hi List,
I am getting the following error when running recon-all ­lgi for 
local gyrification index.
I have changed the script in matlab as we are using matlab 2013b as 
mentioned in the previous thread.

I am attaching the script.
Please let me know what else to do.
Thanks Regards
Meenal Budhiraja
PhD student
Karolinska Institute
Stockholm,Sweden.



preparing pial mesh structure ...
...searching for mesh edges...done (349.20 sec).
... creating path file for vertex 1 / 66330
area file for outer ROIs saved at 1
Improper assignment with rectangular empty matrix.

Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);

Error in reorganize_verticeslist (line 28)
[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));

Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, 
perim,

verticeslist, step);

>>
ERROR:  make_roi_paths did not complete successfully!


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--
Oana Georgiana Rus
PhD Student
Neuroimaging Center TUM-NIC
Klinikum rechts der Isar
Technische Universität München
Einsteinstr.1
81675 München
Raum 5.8

Tel. 089 4140 7971


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--
Oana Georgiana Rus
PhD Student
Neuroimaging Center TUM-NIC
Klinikum rechts der Isar
Technische Universität München
Einsteinstr.1
81675 München
Raum 5.8

Tel. 089 4140 7971

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[Freesurfer] Multimodality analysis in FreeSurfer

[Silas]

Dear Freesurfer team,


I've scanned a group of subjects and gained structural and myelination data. 
Then, I've used mris_preproc to map the data onto the surface of fsaverage (and 
concatenating the data). I would like to investigate the correlation between 
cortical thickness and myelination by mapping this correlation onto the 
fsaverage (an one sample group mean analysis) - is this possible? Do you have 
an existing guide approaching this problem?


Thank you!


Best, Silas
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Re: [Freesurfer] grossly abormal brain

[Krieger, Donald N.]

Thanks very much, Bruce.
I have 6Beta running now with -bigventricles and -fingerscrossed.

Thanks very much, Anthony, for the reference.
I'll fetch it and see what I can do as that approach is interesting from 
several angles for our work.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anthony Dick
Sent: Tuesday, November 17, 2015 9:12 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] grossly abormal brain

Don, if that doesn't work, try the procedure outlined in this paper, although 
it is rather involved: 
http://www.architalbiol.org/index.php/aib/article/viewArticle/1221

Anthony

On 11/17/15 8:27 AM, Bruce Fischl wrote:
Hi Don

it's impossible to say. Certainly 6.0 will be your best bet as it handles 
enlarged ventricles much better. Try 6.0 beta with the -bigventricles flag and 
see how it goes

cheers
Bruce
On Tue, 17 Nov 2015, Krieger, Donald N. wrote:



A few cuts from a grossly abnormal scan are attached.

Do you think freesurfer can effectively segment this one?

If so, please point us in the right direction to get started with it.

Thanks. - Don








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--

Anthony Steven Dick, Ph.D.

Assistant Professor

Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience

Department of Psychology

Florida International University Modesto A. Maidique Campus AHC4 454

11200 S.W. 8th Street

Miami, FL 33199

Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879

Email: ad...@fiu.edu

Webpage: faculty.fiu.edu/~adick; Lab Webpage: http://dcn.fiu.edu

Join the Society for the Study of Human Development: http://www.sshdonline.org


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Re: [Freesurfer] grossly abormal brain

[Anthony Dick]

Don, if that doesn't work, try the procedure outlined in this paper, 
although it is rather involved: 
http://www.architalbiol.org/index.php/aib/article/viewArticle/1221


Anthony

On 11/17/15 8:27 AM, Bruce Fischl wrote:

Hi Don

it's impossible to say. Certainly 6.0 will be your best bet as it 
handles enlarged ventricles much better. Try 6.0 beta with the 
-bigventricles flag and see how it goes


cheers
Bruce
On Tue, 17 Nov 2015, Krieger, Donald N. wrote:



A few cuts from a grossly abnormal scan are attached.

Do you think freesurfer can effectively segment this one?

If so, please point us in the right direction to get started with it.

Thanks. - Don








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--
Anthony Steven Dick, Ph.D.
Assistant Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: ad...@fiu.edu
Webpage: faculty.fiu.edu/~adick; Lab Webpage: http://dcn.fiu.edu
Join the Society for the Study of Human Development: http://www.sshdonline.org

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Re: [Freesurfer] grossly abormal brain

[Bruce Fischl]

Hi Don

it's impossible to say. Certainly 6.0 will be your best bet as it handles 
enlarged ventricles much better. Try 6.0 beta with the -bigventricles 
flag and see how it goes


cheers
Bruce
On Tue, 17 Nov 2015, Krieger, Donald N. wrote:



A few cuts from a grossly abnormal scan are attached.

Do you think freesurfer can effectively segment this one?

If so, please point us in the right direction to get started with it.

Thanks. - Don

 


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[Freesurfer] SNR Tracula

[Scott Quadrelli]

Thanks Barbara, that is what I was after.

Cheers,

Scott


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[Freesurfer] grossly abormal brain

[Krieger, Donald N.]

A few cuts from a grossly abnormal scan are attached.
Do you think freesurfer can effectively segment this one?
If so, please point us in the right direction to get started with it.
Thanks. - Don

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[Freesurfer] geodesic distance calculation

[Silvia Désirée Thielemann]

Dear freesurfer experts,

I'm analysing functional data using fsfast running under  
freesurfer-Linux-centos7_x86_64-dev-20150728. After streaming out the  
maximal activated cluster using mri_surfcluster, I want to calculate  
the geodesic distance between these vertices. Can I do this with  
mris_pmake using sphere.reg as surface?

Furthermore, I would like to evaluate symmetry between the  
hemispheres. I would like to mirror the maximal activated vertice of a  
special contrast of the left hemisphere to the right hemisphere and  
calculate the geodesic distance between the mirrored coordinate and  
the maximal activated vertices of the right hemisphere. Is there a way  
to do this?

Best regards,
Desiree

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[Freesurfer] Problem with hippocampal subfields segmentation FS v6 - Solved

[Gronenschild Ed (NP)]

Hi,

It seemed to be a problem with Java Runtime which I installed because
it is required to do the hippocampal subfields segmentation. After
starting the Matlab R2012a application itself the problem was gone.

Cheers,
Ed

Begin forwarded message:

From: "Gronenschild Ed (NP)" 
mailto:ed.gronensch...@maastrichtuniversity.nl>>
Date: 13 November 2015 08:59:59 CET
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Problem with hippocampal subfields segmentation FS v6

Hi,

At the very beginning of the hippocampal subfields segmentation
the following message window popped up:

segmentSubjectT1_autoEstimateAlveusML cannot be opened
because of a problem.
Check with the developer to make sure
segmentSubjectT1_autoEstimateAlveusML works with this version
of Mac OS X.  etc.

I have installed Matlab runtime and also Java Runtime

Environment:
Mac OSX10.7.5
the command "uname -m" outputs x86_64
FreeSurfer V6 beta release 15 Oct 2015

Cheers,
Ed

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[Freesurfer] R: R: Re: R: Re: R: Re: R: Re: average z-score of each subject from a common cluster

[stdp82]

I have run 
cat ... /my-glm.wls/group.diff/cache.th13.neg.sig.cluster.summary

and I have obtained 

ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWP
CWPLowCWPHi   NVtxs   Annot
1   -3.595  110577865.93 11.8   39.4   -0.1  0.00620  
0.00520  0.00720  1672  rostralanteriorcingulate

after 
mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg.sig.
cluster.nii.gz --i Control21/rest/fc.seed.surf.rh/R_Seed/z.nii.gz --
sum 
summaryfile_Control

and summary file is:

# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev 
Min Max Range  
1  -2  1672 1672.0  Seg-002-2.2757 2.2172   
-6.4504 2.5762 9.0266  
2   0162170   162170.0  Seg 1.3956 1.6398
-7.047114.145221.1923 

I have two raw. Which is the raw which contains the average z-score 
in 
the cluster? What's meaning, in term of location, Seg-002/0? In 
cluster. cache.th13.neg.sig.cluster.summary contains only 
rostralanteriorcingulate.

Thanks,


Stefano

>
>
>
>>>Messaggio originale
>>>Da: gr...@nmr.mgh.harvard.edu
>>>Data: 9-nov-2015 23.59
>>>A: 
>>>Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: average z-score of each 
>>subject from a common cluster
>>>
>>>
>>>
>>>On 11/07/2015 07:29 PM, std...@virgilio.it wrote:
 Thanks. But what's meaning "colheader"?
>>>Column header. The title of the column
 In my cache.th13.neg.sig.masked.nii.gz I have only a significant 
>>ROI.
 In the summary file there are five column and 5 different value 
of
 "mean".
 Which is the correct, expressing the mean z-score of the cluster?
>>>The column labeled "Mean", probably the 6th column

 Stefano

> Messaggio originale
> Da: gr...@nmr.mgh.harvard.edu
> Data: 6-nov-2015 23.07
> A: 
> Ogg: Re: [Freesurfer] R: Re: R: Re: average z-score of each 
>>subject
 from a common cluster
> under the "Mean" column
>
> On 11/06/2015 07:46 AM, std...@virgilio.it wrote:
>> I have run
>> mri_segstats --seg .../my-glm.wls/group.diff/cache.th13.neg.
sig.
 masked.
>> nii.gz rh parc --i subj/fc.seed.surf.rh/R_seed/z.nii.gz --sum
>> summaryfile
>>
>> and I have obtained 9 columns and 5 rows.
>> I'm confused on results. Where is the mean z-score for cache.
>>th13.
 neg.
>> sig.masked.nii.gz?
>>
>> # ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean 
>>StdDev
>> Min Max Range
>> 1  -4 77.0  Seg-004-2.4544 0.5023
>> -3.2164-1.7619 1.4545
>> 2  -3   153  153.0  Seg-003-2.6662 1.4724
>> -6.2120 1.7587 7.9707
>> 3  -2   848  848.0  Seg-002-2.4930 2.0088
>> -6.4504 2.3528 8.8032
>> 4  -1  1518 1518.0  Seg-001-2.1416 1.6727
>> -6.4227 2.5420 8.9648
>> 5   0161316   161316.0  Seg 1.4152 1.6218
>> -7.047114.145221.1923
>>
>> Because my data are on surface mri_surfcluster should be 
>helpful?
>>
>> Thanks.
>>
>>
>> Stefano
>>
>>
>>> Messaggio originale
>>> Da: gr...@nmr.mgh.harvard.edu
>>> Data: 3-nov-2015 19.55
>>> A: 
>>> Ogg: Re: [Freesurfer] R: Re: average z-score of each subject 
>>from
 a
>> common cluster
>>> look in the summaryfile. Also, don't use --seg z.nii.gz. In 
the
>> command
>>> below, it works because you have --annot afterwards, but in
 general
>> it
>>> is not correct
>>>
>>> On 10/30/2015 04:22 PM, std...@virgilio.it wrote:
 Thanks.
 I have obtained:

 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp 
$

 cwd

 cmdline mri_segstats --seg z.nii.gz --annot Control21_FS rh 
>>aparc
 --
>> i
 z.nii.gz --sum summaryfile

 sysname  Darwin

 hostname iMac-di-Stefano.local

 machine  x86_64

 user Stefano

 UseRobust  0

 Loading z.nii.gz

 Loading z.nii.gz

 Voxel Volume is 1 mm^3

 Generating list of segmentation ids

 Found  22 segmentations

 Computing statistics for each segmentation

 0-7   2   2.000

 1-6 110 110.000

 2-5 255 255.000

 3-4 518 518.000

 4-3   11901190.000

 5-2   16921692.000

 6-1   41044104.000

 7 0   61577   61577.000

 8 1   42598   42598.000

 9 2   28146   28146.000

10 3   14859   14859.000

11 4   58

[Freesurfer] R: R: Re: R: Re: R: Re: R: Re: error MRS voxel as seed in FS-FAST

[stdp82]

Thanks.
But the MRS_mask should be in Tal, MNI or native?
Now I'm using a masks that overlaps orig.nii.gz.
Second, if I would like to create a sphere and use it as seed, there 
is a specific command line?


Stefano


>>Messaggio originale
>>Da: gr...@nmr.mgh.harvard.edu
>>Data: 9-nov-2015 23.24
>>A: 
>>Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: error MRS voxel as seed 
in 
>FS-FAST
>>
>>So that mask has 22926 non-zero voxels? The only other thing I can 
>think 
>>of is that the registration is off. Have you checked that?
>>
>>On 11/06/2015 07:16 AM, std...@virgilio.it wrote:
>>> I hope that this information are fine
>>>
>>> fslinfo $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz
>>> data_type  FLOAT32
>>> dim1   256
>>> dim2   256
>>> dim3   256
>>> dim4   1
>>> datatype   16
>>> pixdim11.00
>>> pixdim21.00
>>> pixdim31.00
>>> pixdim40.00
>>> cal_max0.
>>> cal_min0.
>>> file_type  NIFTI-1+
>>>
>>>
>>> fslstats $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz -V
>>> 22926 22926.00
>>>
>>> Thanks,
>>>
>>>
>>> Stefano
>>>
>>>
 Messaggio originale
 Da: gr...@nmr.mgh.harvard.edu
 Data: 5-nov-2015 23.43
 A: 
 Ogg: Re: [Freesurfer] R: Re: R: Re: error MRS voxel as seed in 
FS-
>>> FAST
 How many non-zero voxels are in MRS_MASK.mgz? Is MRS_MASK.mgz 
>256^3,
>>> 1mm3 ?
 On 11/05/2015 04:47 PM, std...@virgilio.it wrote:
> Please see the file attached.
> Thanks
>
> Stefanofile
>
>  Messaggio originale
>  Da: gr...@nmr.mgh.harvard.edu
>  Data: 5-nov-2015 15.43
>  A: 
>  Ogg: Re: [Freesurfer] R: Re: error MRS voxel as seed in FS-
>FAST
>
>  sorry, should have been
>
>  fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config |& 
>tee
>>> doug.log
>
>
>  On 11/4/15 6:05 PM, std...@virgilio.it wrote:
>>  Hi Dough,
>>  in summary:
>>  I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri
>>  thus, I have copy this file in fMRI directory
>>> (fMRI/Control22_FS) the
>>  MRS_MASK.mgz
>>  and run:
>>  fcseed-config -segid 1 -seg Control22_FS/MRS_MASK.mgz -fsd
>>> rest -mean -
>>  cfg MRS_MASK.config
>>  fcseed-sess -s Control22_FS -cfg MRS_MASK.config
>>
>>  ...Writing to
>>  
>>> /Applications/freesurfer/subjects/fMRI/Control22_FS/rest/001/tmp.
>>> fcseed-
>>  sess.12305/avgwf.mgh
>>  Segmentation fault
>>
>>  Therefore, according with your suggestion, I have now run:
>>  fcseed-sess -debug -s -cfg MRS_MASK.config | & tee doug.
log
>>  ERROR: cound not find session -cfg
>>
>>  The doug.log is attached.
>>
>>  Thanks,
>>
>>
>>  Stefano
>>
>>
>>
>>
>>>  Messaggio originale
>>>  Da:gr...@nmr.mgh.harvard.edu
>>>  Data: 4-nov-2015 16.58
>>>  A:
>>>  Ogg: Re: [Freesurfer] error MRS voxel as seed in FS-FAST
>>>
>>>  First, when running fcseed-config, don't give it the full
>>> path, just
>>  the
>>>  path relative to subject/mri (in this case only MRS_MASK.
>mgz)
>>>
>>>  However, I don't think that is the  problem. Please run
>>>
>>>  fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug.
log
>>>
>>>  and send  me doug.log
>>>
>>>
>>>
>>>
>>>
>>>  On 11/04/2015 04:14 AM,std...@virgilio.it  wrote:
  Hi list, this error is still occurring:

  mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz
  $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz
  fcseed-config -segid 1 -seg 
>$SUBJECTS_DIR//subj/mri/MRS_MASK.
>>> mgz -
>>  fsd
  rest -mean -cfg MRS_MASK.config
  fcseed-sess -s -cfg MRS_MASK.config

  During

  fcseed-sess -s subj -cfg MRS_MASK.config

  Voxel Volume is 64.5752 mm^3
  Generating list of segmentation ids
  Found   1 segmentations
  Computing statistics for each segmentation
  0 1  0
>>> 0.000
  MRIalloc(0, 1, 1): bad parm
  Reporting on   0 segmentations
  Computing spatial average of each frame

  Writing to
>>> /Applications/freesurfer/subjects/fMRI/sub/rest/001/tmp.
  fcseed-sess.97908/avgwf.mgh
  Segmentation fault

  I have read your previous message and you can check the 
>MRS
>>> voxel
  features.
  MRS voxel mask is in subj directory where I have run 
>recon
>>> all -
>>  all.
  data_type  FLOAT32
  dim1   256
  dim2