[Freesurfer] T2pial and [LONG]

[Kasper Jessen]

Dear FreeSurfer,

Currently, we have only manual edited the BASE (the CROSS was left
unedited) in an longitudinal data. However, some cortical areas (f.eks.
such as the inferior temporal area) are difficult to edit accurately due to
image quality. I then read through the release notes (stable v5.2.0) and
found that a T2/FLAIR can be used to improve the pial surface.

Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial
on the [LONG] runs to get extra improvement of the final pial surfaces?

Best regards,
Kasper Jessen
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Re: [Freesurfer] T2pial and [LONG]

[Bruce Fischl]

Hi Kasper,

I don't see why not, but we haven't done this yet I don't think, so there 
may be undiscovered bugs.

Bruce
On Fri, 13 May 2016, Kasper Jessen wrote:


Dear FreeSurfer,
Currently, we have only manual edited the BASE (the CROSS was left unedited)
in an longitudinal data. However, some cortical areas (f.eks. such as the
inferior temporal area) are difficult to edit accurately due to image
quality. I then read through the release notes (stable v5.2.0) and found
that a T2/FLAIR can be used to improve the pial surface.

Question: Is it possible to use a T2 and run either -autorecon3 and -T2pial
on the [LONG] runs to get extra improvement of the final pial surfaces?  

Best regards,
Kasper Jessen

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Re: [Freesurfer] Manual correction for brainstem module

[Jacky Lee]

Just a short note for other people who may use the matlab script to get
volumes from the corrected hard segmentations. The volume in cubic mm
should be total voxels divided by 8 instead of multiplying by 8.

Cheers,
Jacky

2016-05-12 17:44 GMT+02:00 Eugenio Iglesias :

> Yes! But take all the medulla volumes from the script. In other words: do
> not use the script to compute the medulla volumes of the cases you edited,
> and take the medulla volumes from the text file for all other cases. If you
> do that, you'd be introducing a fairly ugly bias in the study.
> Cheers,
> /E
>
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> --
> *From: *"Jacky Lee" 
> *To: *"Eugenio Iglesias" 
> *Cc: *"Freesurfer support list" 
> *Sent: *Thursday, May 12, 2016 4:11:20 PM
>
> *Subject: *Re: [Freesurfer] Manual correction for brainstem module
>
> Hi Eugenio,
>
> Thanks, the script worked.
>
> Actually I only edited the medulla segmentation in 3 out of the 49
> subjects that I have. I suppose the original volumetric estimates for
> midbrain and pons are still valid and I can just calculate and compare the
> new medulla volumes for all subjects. Is that correct?
>
> Jacky
>
> 2016-05-12 12:05 GMT+02:00 Eugenio Iglesias :
>
>> My email client is replacing the combination colon + right parenthesis by
>> a smiley! If the same thing happened to you, please replace the smiley by a
>> colon and a right parenthesis...
>> Next time I'll just attach the code.
>> Sorry for the inconvenience
>>
>> Juan Eugenio Iglesias
>> Postdoctoral researcher BCBL
>> www.jeiglesias.com
>> www.bcbl.eu
>>
>> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>>
>> --
>> *From: *"Eugenio Iglesias" 
>> *To: *"Jacky Lee" 
>> *Cc: *"Freesurfer support list" 
>> *Sent: *Thursday, May 12, 2016 5:59:33 AM
>>
>> *Subject: *Re: [Freesurfer] Manual correction for brainstem module
>>
>> Of course! I haven't tested the code below, but I think it should work
>> right away.
>>
>> Let's assume that FreeSurfer is installed in /usr/local/freesurfer/ (if
>> not, replace the location in the code below). Also, you'd need to replace
>> the name of your subject directory.
>> Finally, I have assumed that brainstemSsLabels.v10.mgz was modified and
>> saved as  brainstemSsLabels.v10.edited.mgz  (again, replace as needed).
>>
>>
>> subjectdir='/mysubjectdir/';
>> editedFileName='brainstemSsLabels.v10.edited.mgz';
>>
>> addpath /usr/local/freesurfer/matlab
>>
>> d=dir(subjectdir);
>>
>> for i=1:length(d)
>>
>>   tentativeSegFile=[subjectdir '/' d(i).name '/mri/' editedFileName];
>>
>>   if d(i).isdir && exist(tentativeSegFile,'file')
>>
>> A=MRIread(tentativeSegFile);
>> MidbrainVol=8*sum(A.vol(:)==173);   % the eight is because each voxel
>> of the segmentation has a volume equal to 0.125 cubic mm
>> PonsVol=8*sum(A.vol(:)==174);
>> MedullaVol=8*sum(A.vol(:)==175);
>> SCPvol=8*sum(A.vol(:)==178);
>>
>> disp(['Subject ' d(i).name ', midbrain = ' num2str(MidbrainVol) ',
>> pons = ' num2str(PonsVol) ', medulla = ' num2str(MedullaVol) ', SCP = '
>> num2str(SCPvol)]);
>>
>>   end
>>
>> end
>>
>> One more thing: if you haven't edited anything around the SCP, I would
>> use the original estimate for this structure. The reason is that, because
>> the SCP is very thing, the voxel count is a much poorer approximation for
>> the volume as computed by the code (i.e., using soft segmentations).
>>
>> Cheers,
>>
>> Eugenio
>>
>>
>> Juan Eugenio Iglesias
>> Postdoctoral researcher BCBL
>> www.jeiglesias.com
>> www.bcbl.eu
>>
>> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>>
>> --
>> *From: *"Jacky Lee" 
>> *To: *"Freesurfer support list" 
>> *Cc: *"Eugenio Iglesias" 
>> *Sent: *Thursday, May 12, 2016 10:32:24 AM
>> *Subject: *Re: [Freesurfer] Manual correction for brainstem module
>>
>> Hi Eugenio,
>>
>> Yes please give me some advice on the matlab commands for this since I am 
>> not very familiar with matlab...
>>
>> Cheers,
>>
>> Jacky
>>
>>
>> Hi Jacky,
>> this is a good question, and unfortunately there isn't a great answer to it.
>> The volume is computed upong a probabilitic segmentation of the voxels that 
>> is
>> not written to disk (this is very similar to what happens with aseg.mgz and
>> aseg.stats). In order to properly update the volume estimates, you would have
>> to know the probability that the inpainted voxels belong to the brainstem as
>> estimated by the algorithm, which we don't currently write to disk.
>> Another option would be to toss the volumes given by the algorithm, and 
>> compute
>> new volumes for all cases and brainstem structures using the hard
>> segmentations. You would simply have to count the number of voxels labeled as
>> midbrain, pons, SCP and medulla for each subject. You can easi

Re: [Freesurfer] Manual correction for brainstem module

[Eugenio Iglesias]

Thanks, Jacky. Sorry about that mistake. 

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

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


From: "Jacky Lee"  
To: "Eugenio Iglesias"  
Cc: "Freesurfer support list"  
Sent: Friday, May 13, 2016 8:49:29 AM 
Subject: Re: [Freesurfer] Manual correction for brainstem module 

Just a short note for other people who may use the matlab script to get volumes 
from the corrected hard segmentations. The volume in cubic mm should be total 
voxels divided by 8 instead of multiplying by 8. 

Cheers, 
Jacky 

2016-05-12 17:44 GMT+02:00 Eugenio Iglesias < e.igles...@bcbl.eu > : 



Yes! But take all the medulla volumes from the script. In other words: do not 
use the script to compute the medulla volumes of the cases you edited, and take 
the medulla volumes from the text file for all other cases. If you do that, 
you'd be introducing a fairly ugly bias in the study. 
Cheers, 
/E 


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

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


From: "Jacky Lee" < cyle...@gmail.com > 
To: "Eugenio Iglesias" < e.igles...@bcbl.eu > 
Cc: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu > 
Sent: Thursday, May 12, 2016 4:11:20 PM 

Subject: Re: [Freesurfer] Manual correction for brainstem module 

Hi Eugenio, 

Thanks, the script worked. 

Actually I only edited the medulla segmentation in 3 out of the 49 subjects 
that I have. I suppose the original volumetric estimates for midbrain and pons 
are still valid and I can just calculate and compare the new medulla volumes 
for all subjects. Is that correct? 

Jacky 

2016-05-12 12:05 GMT+02:00 Eugenio Iglesias < e.igles...@bcbl.eu > : 

BQ_BEGIN

My email client is replacing the combination colon + right parenthesis by a 
smiley! If the same thing happened to you, please replace the smiley by a colon 
and a right parenthesis... 
Next time I'll just attach the code. 
Sorry for the inconvenience 

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

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


From: "Eugenio Iglesias" < e.igles...@bcbl.eu > 
To: "Jacky Lee" < cyle...@gmail.com > 
Cc: "Freesurfer support list" < Freesurfer@nmr.mgh.harvard.edu > 
Sent: Thursday, May 12, 2016 5:59:33 AM 

Subject: Re: [Freesurfer] Manual correction for brainstem module 

Of course! I haven't tested the code below, but I think it should work right 
away. 

Let's assume that FreeSurfer is installed in /usr/local/freesurfer/ (if not, 
replace the location in the code below). Also, you'd need to replace the name 
of your subject directory. 
Finally, I have assumed that brainstemSsLabels.v10.mgz was modified and saved 
as brainstemSsLabels.v10.edited.mgz (again, replace as needed). 


subjectdir='/mysubjectdir/'; 
editedFileName='brainstemSsLabels.v10.edited.mgz'; 

addpath /usr/local/freesurfer/matlab 

d=dir(subjectdir); 

for i=1:length(d) 

tentativeSegFile=[subjectdir '/' d(i).name '/mri/' editedFileName]; 
if d(i).isdir && exist(tentativeSegFile,'file') 

A=MRIread(tentativeSegFile); 
MidbrainVol=8*sum(A.vol(:)==173); % the eight is because each voxel of the 
segmentation has a volume equal to 0.125 cubic mm 
PonsVol=8*sum(A.vol(:)==174); 
MedullaVol=8*sum(A.vol(:)==175); 
SCPvol=8*sum(A.vol(:)==178); 

disp(['Subject ' d(i).name ', midbrain = ' num2str(MidbrainVol) ', pons = ' 
num2str(PonsVol) ', medulla = ' num2str(MedullaVol) ', SCP = ' 
num2str(SCPvol)]); 

end 

end 

One more thing: if you haven't edited anything around the SCP, I would use the 
original estimate for this structure. The reason is that, because the SCP is 
very thing, the voxel count is a much poorer approximation for the volume as 
computed by the code (i.e., using soft segmentations). 

Cheers, 

Eugenio 

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

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


From: "Jacky Lee" < cyle...@gmail.com > 
To: "Freesurfer support list" < Freesurfer@nmr.mgh.harvard.edu > 
Cc: "Eugenio Iglesias" < e.igles...@bcbl.eu > 
Sent: Thursday, May 12, 2016 10:32:24 AM 
Subject: Re: [Freesurfer] Manual correction for brainstem module 

Hi Eugenio, 

Yes please give me some advice on the matlab commands for this since I am not 
very familiar with matlab... 

Cheers, 

Jacky 

Hi Jacky, 
this is a good question, and unfortunately there isn't a great answer to it. 
The volume is computed upong a probabilitic segmentation of the voxels that is 
not written to disk (this is very similar to what happens with aseg.mgz and 
aseg.stats). In order to properly update the volume estimates, you would have 
to know the probability that the inpainted voxels belong to the brainstem as 
estimated by the algorithm, which we don't currently write to disk. 
Another option would 

[Freesurfer] 2 unrelated questions regarding structural data

[Josh Gray]

Hello,

1) I am working with the recent release of human connectome data and am
trying to run group analysis (
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). I want
to correlate brain volume with an behavioral variable. It is difficult to
tell which files I need in order for the pipeline to run properly. Since I
did not run recon-all locally, their file arrangement is unique, many files
are zipped, etc. Therefore the scripts (e.g., mris_preproc) do not know
where to look, as they do with the typical file structure. Can you tell me
what specific files this pipeline needs to generate the GLM? Alternatively,
if you have performed this process with the human connectome data you can
tell me which directories/files need to be unzipped and placed in
SUBJECTS_DIR. Just need to know what specific files the scripts in the
group analysis pipeline are searching for when I run them.

2) I am interested in applying the Yeo 2015 cognitive atlas to structural
data. Basically, I want to quantify networks C1-12 in my structural data by
exporting the voxel size of each network for each subject into an text file
(so I would have left and right hemisphere voxel totals for networks C1-12
for each subject). It is analogous to what is routinely done with the
desikan and destrieux atlas. I know you can change the threshold of the
networks, but I suspect 1e-5 is fine (i.e., what is depicted on the
website). Is there a quick way to do this?

Thank you for your help!
Josh

-- 
Graduate Student
Psychology Dept. - Clinical Program
Experimental & Clinical Psychopharmacology Laboratory
University of Georgia
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[Freesurfer] Postdoc Position in Computational Neuroscience, Max Planck Institute, Leipzig, Germany

[Katharina von Kriegstein]

Applications are welcomed for a postdoctoral research position at the Max 
Planck Institute for Human Cognitive and Brain Sciences (MPI-CBS) in Leipzig, 
Germany in collaboration with the Technical University Dresden, Germany. The 
objective of the postdoctoral research project is to use computational 
modelling and neuroimaging to work towards a novel model for 
cortico-subcortical interactions for human communication signals. The project 
is funded by the ERC-consolidator grant SENSOCOM 
(http://cordis.europa.eu/project/rcn/199655_en.html).

The position will be jointly supervised by Katharina von Kriegstein at the 
MPI-CBS and Stefan Kiebel at the TU Dresden. The MPI-CBS offers a unique 
research environment with a 7.0 T MRI scanner, several 3.0 T MRI scanners, a 
306 channels MEG system, TMS/tDCS laboratories, several EEG suites, and 
eye-tracking labs. All facilities and data analyses are supported by 
experienced IT specialists and physicists. The TU Dresden is one out of eleven 
German Universities of Excellence. It houses a state-of-the art neuroimaging 
centre with a strong focus on computational modelling and access to the TU 
Dresden high-performance computing clusters. Besides an excellent 
infrastructure, both centres offer an international and friendly environment 
with researchers from diverse backgrounds.

The position is ideal for candidates interested in research at the interface 
between computational modelling and experimental neuroimaging. The candidates 
must have a PhD (or equivalent) in computational neuroscience, experimental 
psychology, or a related field, and should be able to demonstrate a 
consistently outstanding academic record, including publications. The ideal 
candidate will have expertise in computational neuroscience, physics, 
mathematics, or similar with a strong interest in implementing computational 
models (e.g., Bayesian filtering, hierarchical dynamic models, predictive 
coding) and testing these with neuroimaging experiments.

The starting date for the position is flexible. Initially for two years, the 
position offers the possibility of extension for up to four years. Salary 
depends on experience and is based on regulations of the Max Planck Society.

To apply, please include all documents in one PDF-file in the following order: 
CV, contact information of two referees, a brief statement describing your 
personal qualifications and future research interests, copies of up to three of 
your publications. Applications with the subject heading "CM 16 PD" should be 
sent via email to: perso...@cbs.mpg.de. Closing date for applications is the 
12th June 2016.

Informal enquiries regarding the post should be directed to: Prof. Dr. 
Katharina von Kriegstein (kriegst...@cbs.mpg.de).

For more information about the groups see:
Prof. Katharina von Kriegstein: 
http://www.cbs.mpg.de/independent-research-groups/human-communication
Prof. Stefan Kiebel: 
https://tu-dresden.de/die_tu_dresden/fakultaeten/fakultaet_mathematik_und_naturwissenschaften/fachrichtung_psychologie/i1/ni

A link to the position description is available here: 
http://www.cbs.mpg.de/454795/job_full_offer_10498685?c=7390

The MPI-CBS is an equal opportunities employer, committed to the advancement of 
individuals without regard to ethnicity, religion, gender, or disability.

---

Katharina von Kriegstein

Max Planck Research Group Leader
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstr. 1A, 04103 Leipzig, Germany

Professor of Cognitive and Clinical Neuroscience
Humboldt University of Berlin
Rudower Chaussee 18, 12489 Berlin, Germany

Phone +49 (0) 341-9940-2476
Fax +49 (0) 341-9940-2448
http://www.cbs.mpg.de/independent-research-groups/human-communication
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] 2 unrelated questions regarding structural data

[Harms, Michael]

Hi Josh,
The WU-UMN HCP outputs provide the thickness values already aligned to a common mesh in the *thickness.{32,164}k_fs_LR.dscalar.nii files (both 32k and 164k mesh version available).  You  should be able to run a nice, permutation-based group analysis on
 those using the FSL PALM tool.  If you run into problems in that regard, please let us know your experience on the HCP-Users list.


Alternatively, if you want to use FS-specific tools to run the group analysis, the entire FS output, in the standard FS format, is available as part of the “Structural Extended” packages.  If you download those, the only small additional step you would
 need to do would be to create a “SUBJECTS_DIR” like directory which contains sym-links pointing to the location of the FS data in the HCP file structure.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From:  on behalf of Josh Gray 
Reply-To: "freesurfer@nmr.mgh.harvard.edu" 
Date: Friday, May 13, 2016 at 8:25 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] 2 unrelated questions regarding structural data









Hello,


1) I am working with the recent release of human connectome data and am trying to run group analysis (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). I want
 to correlate brain volume with an behavioral variable. It is difficult to tell which files I need in order for the pipeline to run properly. Since I did not run recon-all locally, their file arrangement is unique, many files are zipped, etc. Therefore the
 scripts (e.g., mris_preproc) do not know where to look, as they do with the typical file structure. Can you tell me what specific files this pipeline needs to generate the GLM? Alternatively, if you have performed this process with the human connectome data
 you can tell me which directories/files need to be unzipped and placed in SUBJECTS_DIR. Just need to know what specific files the scripts in the group analysis pipeline are searching for when I run them.


2) I am interested in applying the Yeo 2015 cognitive atlas to structural data. Basically, I want to quantify networks C1-12 in my structural data by exporting the voxel size of each network for each subject into an text file (so I would have left and right
 hemisphere voxel totals for networks C1-12 for each subject). It is analogous to what is routinely done with the desikan and destrieux atlas. I know you can change the threshold of the networks, but I suspect 1e-5 is fine (i.e., what is depicted on the website).
 Is there a quick way to do this?


Thank you for your help!

Josh





-- 




Graduate Student 
Psychology Dept. - Clinical Program
Experimental & Clinical Psychopharmacology Laboratory
University of Georgia
















 



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Re: [Freesurfer] segfault using brainstem module from dev version

[Eugenio Iglesias]

It seems that mri_robust_register crashed. Martin, any ideas? 
The algorithm worked because the rough registration from the previous step was 
apparently enough to yield a decent segmentation. 
Maybe we should consider stopping the whole process if mri_robust_register 
dies... 

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

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


From: "Vincent Beliveau"  
To: "Freesurfer support list"  
Sent: Friday, May 13, 2016 2:40:11 PM 
Subject: [Freesurfer] segfault using brainstem module from dev version 



Hi list (and Eugenio), 

I've ran the brainstem module from the dev version on some data processed with 
FS v5.3. The module created some great segmentations of brainstem but when 
taking a closer look at the log file, there is 2 seg faults which occur when 
calls to mri_robust_register are made, with the following output (full log 
attached, see line 319 and 371): 

/data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register:
 line 3: 36835 Segmentation fault mri_robust_register.bin "$@" 
/data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register
 --mov imageDump.mgz --dst 
/indirect/data1/vbeliveau/atlas/proc/MR/recon_final/f5249_GD/tmp/BS_T1based//BS-DE-binaryMask_autoCropped.mgz
 -lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50: Segmentation 
fault 
mv: cannot stat ?imageDump_coregistered.mgz?: No such file or directory 

I'm curious about how is this affecting the overall process, as otherwise 
everything appears to be working smoothly. 

Best, 

Vincent. 


-- 
Vincent Beliveau, MSc 
Neurobiology Research Unit 
Juliane Maries Vej 28, 3rd floor 
Rigshospitalet, building 6931 
DK-2100 Copenhagen, Denmark 

phone: +45 3545 6718 
e-mail: vincent.beliv...@nru.dk 

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properly 
dispose of the e-mail. 
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Re: [Freesurfer] segfault using brainstem module from dev version

[Martin Reuter]

Hi Eugenio and Vincent,

I cannot remember when I say robust_register crash the last time. It 
should never happen. So it could also be that the inputs are already 
corrupted. Can you send the inputs to that command so that I can try to 
replicate and see if this is still a bug or what is going on?


Thanks, Martin


On 05/13/2016 09:54 AM, Eugenio Iglesias wrote:

It seems that mri_robust_register crashed. Martin, any ideas?
The algorithm worked because the rough registration from the previous 
step was apparently enough to yield a decent segmentation.
Maybe we should consider stopping the whole process if 
mri_robust_register dies...


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

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


*From: *"Vincent Beliveau" 
*To: *"Freesurfer support list" 
*Sent: *Friday, May 13, 2016 2:40:11 PM
*Subject: *[Freesurfer] segfault using brainstem module from dev version

Hi list (and Eugenio),

I've ran the brainstem module from the dev version on some data 
processed with FS v5.3. The module created some great segmentations of 
brainstem but when taking a closer look at the log file, there is 2 
seg faults which occur when calls to mri_robust_register are made, 
with the following output (full log attached, see line 319 and 371):


/data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register: 
line 3: 36835 Segmentation fault mri_robust_register.bin "$@"
/data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register 
--mov imageDump.mgz --dst 
/indirect/data1/vbeliveau/atlas/proc/MR/recon_final/f5249_GD/tmp/BS_T1based//BS-DE-binaryMask_autoCropped.mgz 
-lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50: 
Segmentation fault

mv: cannot stat ?imageDump_coregistered.mgz?: No such file or directory

I'm curious about how is this affecting the overall process, as 
otherwise everything appears to be working smoothly.


Best,

Vincent.

--
Vincent Beliveau, MSc
Neurobiology Research Unit
Juliane Maries Vej 28, 3rd floor
Rigshospitalet, building 6931
DK-2100 Copenhagen, Denmark

phone:  +45 3545 6718
e-mail: vincent.beliv...@nru.dk 

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Re: [Freesurfer] segfault using brainstem module from dev version

[Vincent Beliveau]

Hi Martin, 

Thanks for the help. From the brainstem-structures.log,
mri_robust_register is called by the brainstem module as follow: 

/data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register
--mov imageDump.mgz  --dst
/indirect/data1/vbeliveau/atlas/proc/MR/recon_final/f5249_GD/tmp/BS_T1based//BS-DE-binaryMask_autoCropped.mgz
-lta trash.lta --mapmovhdr imageDump_coregistered.mgz  --sat 50 

Best, 

Vincent 

On 13.05.2016 16:13, Martin Reuter wrote:

> Hi Eugenio and Vincent,
> 
> I cannot remember when I say robust_register crash the last time. It should 
> never happen. So it could also be that the inputs are already corrupted. Can 
> you send the inputs to that command so that I can try to replicate and see if 
> this is still a bug or what is going on?
> 
> Thanks, Martin
> 
> On 05/13/2016 09:54 AM, Eugenio Iglesias wrote: 
> 
>> It seems that mri_robust_register crashed. Martin, any ideas? 
>> The algorithm worked because the rough registration from the previous step 
>> was apparently enough to yield a decent segmentation. 
>> Maybe we should consider stopping the whole process if mri_robust_register 
>> dies... 
>> 
>> Juan Eugenio Iglesias
>> Postdoctoral researcher BCBL
>> www.jeiglesias.com [1]
>> www.bcbl.eu [2]
>> 
>> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer [3] 
>> 
>> -
>> 
>> FROM: "Vincent Beliveau" 
>> TO: "Freesurfer support list" 
>> SENT: Friday, May 13, 2016 2:40:11 PM
>> SUBJECT: [Freesurfer] segfault using brainstem module from dev version 
>> 
>> Hi list (and Eugenio), 
>> 
>> I've ran the brainstem module from the dev version on some data processed 
>> with FS v5.3. The module created some great segmentations of brainstem but 
>> when taking a closer look at the log file, there is 2 seg faults which occur 
>> when calls to mri_robust_register are made, with the following output (full 
>> log attached, see line 319 and 371): 
>> 
>> /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register:
>>  line 3: 36835 Segmentation fault mri_robust_register.bin "$@"
>> /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register
>>  --mov imageDump.mgz --dst 
>> /indirect/data1/vbeliveau/atlas/proc/MR/recon_final/f5249_GD/tmp/BS_T1based//BS-DE-binaryMask_autoCropped.mgz
>>  -lta trash.lta --mapmovhdr imageDump_coregistered.mgz --sat 50: 
>> Segmentation fault
>> mv: cannot stat ?imageDump_coregistered.mgz?: No such file or directory 
>> 
>> I'm curious about how is this affecting the overall process, as otherwise 
>> everything appears to be working smoothly. 
>> 
>> Best, 
>> 
>> Vincent. 
>> 
>> -- 
>> Vincent Beliveau, MSc
>> Neurobiology Research Unit 
>> Juliane Maries Vej 28, 3rd floor
>> Rigshospitalet, building 6931
>> DK-2100 Copenhagen, Denmark 
>> 
>> phone:  +45 3545 6718
>> e-mail: vincent.beliv...@nru.dk 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 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.
> 
> -- 
> 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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> 
> 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.

-- 
Vincent Beliveau, MSc
Neurobiology Research Unit 
Juliane Maries Vej 28, 3rd floor
Rigshospitalet, building 6931
DK-2100 Copenhagen, Denmark 

phone:  +45 3545 6718
e-mail: vincent.beliv...@nru.dk 

Links:
--
[1] http://www.jeiglesias.com
[2] http://www.bcbl.eu
[3] http://www.bcbl.eu/legal-disclaimer
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The informat

[Freesurfer] Connectivity from external seeds

[Sahil Bajaj]

Hello FS experts,

I am sorry for reposting this question in the forum:

I calculated subject-wise resting-state FC maps after defining seeds into
subject-wise anatomical space as mentioned in the manual. Now, location of
seed regions across subjects differ a little.

According to manual, FS maps the time-series on fsaverage lh and rh
hemisphere. That means connectivity maps for each subject are registered to
fsaverage space and it should be fine to calculate 2nd level maps.

If that's correct then my questions are:
(a). How seeds can be overlaid on 2nd level maps or 1st level maps because
seeds are not in fsaverage space but both 1st and 2nd level connectivity
maps are. When I see subject-wise FC maps, those are little far from the
actual seed locations which I defined in subject-wise anatomical space.
(b). How FS deals with seed regions in terms of 2nd level analysis because
it calculates FC from seeds which are in subject-wise anatomical space but
it reports FC in fsaverage space, so 2nd level results are even more far
away from actual seed region locations?

I would really appreciate any thoughts/suggestions on this.

Thanks,
Sahil
-- 
-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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Re: [Freesurfer] Connectivity from external seeds

[Douglas N Greve]

a. You can map your seeds to the cortical surface of your subject 
(mri_vol2surf), then to fsaverage (mris_surf2surf), then view them on 
fsaverage.
b. Not sure what you mean by this. The FC analysis just computes maps 
and those maps are compared at the second level. At that point it does 
not really matter how the maps were generated (ie, they could be FC, 
they could be task, they could be thickness, they could be PET).

On 05/13/2016 11:54 AM, Sahil Bajaj wrote:
> Hello FS experts,
>
> I am sorry for reposting this question in the forum:
>
> I calculated subject-wise resting-state FC maps after defining seeds 
> into subject-wise anatomical space as mentioned in the manual. Now, 
> location of seed regions across subjects differ a little.
>
> According to manual, FS maps the time-series on fsaverage lh and rh 
> hemisphere. That means connectivity maps for each subject are 
> registered to fsaverage space and it should be fine to calculate 2nd 
> level maps.
>
> If that's correct then my questions are:
> (a). How seeds can be overlaid on 2nd level maps or 1st level maps 
> because seeds are not in fsaverage space but both 1st and 2nd level 
> connectivity maps are. When I see subject-wise FC maps, those are 
> little far from the actual seed locations which I defined in 
> subject-wise anatomical space.
> (b). How FS deals with seed regions in terms of 2nd level analysis 
> because it calculates FC from seeds which are in subject-wise 
> anatomical space but it reports FC in fsaverage space, so 2nd level 
> results are even more far away from actual seed region locations?
>
> I would really appreciate any thoughts/suggestions on this.
>
> Thanks,
> Sahil
> -- 
> -- 
> -
> Sahil Bajaj
> Post-doctoral Fellow
> Nantz National Alzheimer's Center, Department of Neurology
> The Houston Methodist Research Institute (THMRI)
> Houston, TX, USA.
> E-mail:sahil.br...@gmail.com 
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] Split a lablemap in the .annot format into parts

[Boris Rauchmann]

Dear FS Community,

is there an easy way to split a lablemap in the .annot format into parts?
In detail I would like to split network 6 (frontoparietal) of the yeo atlas 
(fsaverage/label/rh.Yeo2011_7Networks_N1000.annot) into the frontal, parietal 
and temporal part on each side. 
Is there an easy way to do this in FS? 

Thank you,

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Re: [Freesurfer] T2pial and [LONG]

[Martin Reuter]

Hi Kasper,
It should work (I tried it a while ago with the dev version and it did 
not crash :-). Could not really tell if it helped much either.
I don't remember if functionality is available in FS5.3 to include that 
in a long run. In dev, you would include the T2 for both the cross and 
long run. The long run then takes the T2 from the cross. Not sure if it 
works passing it directly into a longitudinal run.


Best, Martin

On 05/13/2016 08:43 AM, Bruce Fischl wrote:

Hi Kasper,

I don't see why not, but we haven't done this yet I don't think, so 
there may be undiscovered bugs.

Bruce
On Fri, 13 May 2016, Kasper Jessen wrote:


Dear FreeSurfer,
Currently, we have only manual edited the BASE (the CROSS was left 
unedited)
in an longitudinal data. However, some cortical areas (f.eks. such as 
the

inferior temporal area) are difficult to edit accurately due to image
quality. I then read through the release notes (stable v5.2.0) and found
that a T2/FLAIR can be used to improve the pial surface.

Question: Is it possible to use a T2 and run either -autorecon3 and 
-T2pial

on the [LONG] runs to get extra improvement of the final pial surfaces?

Best regards,
Kasper Jessen





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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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Re: [Freesurfer] Split a lablemap in the .annot format into parts

[Douglas N Greve]

you can try mris_divide_parcellation

On 05/13/2016 01:56 PM, Boris Rauchmann wrote:
> Dear FS Community,
>
> is there an easy way to split a lablemap in the .annot format into parts?
> In detail I would like to split network 6 (frontoparietal) of the yeo 
> atlas (fsaverage/label/rh.Yeo2011_7Networks_N1000.annot) into the 
> frontal, parietal and temporal part on each side.
> Is there an easy way to do this in FS?
>
> Thank you,
>
> Boris
>
>
> ___
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] mri_surf2vol

[stdp82]

Hi list,
I'm using FS-FAST for seed based functional connectivity.For a subject, I would 
like to report the sig.nii.gz from the inflate to volume space.
I'm using
mri_surf2vol --surfval Control21/rest/fc.ramgseed.surf.rh/R_Amygdala/sig.nii.gz 
--hemi rh --fillribbon --subject Control21 --identity Control21 --template 
Control21/orig.mgz --o ramg2rh_sig_volspace.nii.gz

but this error reported below was obtained.
ERROR: dimension inconsistency in source data
   Number of surface vertices = 123044
  Number of value vertices = 163842

Thanks

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Re: [Freesurfer] mri_surf2vol

[Douglas N Greve]

The overlay Control21/rest/fc.ramgseed.surf.rh/R_Amygdala/sig.nii.gz is 
in fsaverage space, so either change the subject to fsaverage, or use 
mri_surf2surf to map the overlay into Control21's space, then run 
mri_surf2vol


On 05/13/2016 06:03 PM, std...@virgilio.it wrote:
> Hi list,
>
> I'm using FS-FAST for seed based functional connectivity.
> For a subject, I would like to report the sig.nii.gz from the inflate 
> to volume space.
>
> I'm using
>
> mri_surf2vol --surfval 
> Control21/rest/fc.ramgseed.surf.rh/R_Amygdala/sig.nii.gz --hemi rh 
> --fillribbon --subject Control21 --identity Control21 --template 
> Control21/orig.mgz --o ramg2rh_sig_volspace.nii.gz
>
> but this error reported below was obtained.
>
> ERROR: dimension inconsistency in source data
>
>Number of surface vertices = 123044
>
>   Number of value vertices = 163842
>
>
> Thanks
>
>
>
> Stefano
>
>
>
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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
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Re: [Freesurfer] WmParc

[Pradeep]

Hi,

This task will be a bit easy using  fslmaths

- convert mgz file to nii using mri_convert
-then use fslmaths  -thr  -uthr 


example:
fslmaths wmparc.nii -thr 1006 -uthr 1006 lh_entorhinal.nii

On Thu, May 12, 2016 at 9:12 AM Douglas N Greve 
wrote:

> What version of FS are you using? You may need a newer version of
> mri_aparc2aseg. Try this one
>
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_aparc2aseg
>
> On 05/12/2016 06:53 AM, Caroline Beelen wrote:
> >
> > If we changed the command –-ribbon to –- no ribbon, the script ran,
> > but when we looked at the stats-file, only cortical grey matte
> >
>
> --
> 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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>
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Re: [Freesurfer] WmParc

[Douglas N Greve]

you can also use
mri_binarize --i wmparc.nii --match 1006 --o lh_entorhinal.nii

On 05/13/2016 06:12 PM, Pradeep wrote:
> Hi,
>
> This task will be a bit easy using  fslmaths
>
> - convert mgz file to nii using mri_convert
> -then use fslmaths  -thr  -uthr  
> 
>
> example:
> fslmaths wmparc.nii -thr 1006 -uthr 1006 lh_entorhinal.nii
>
> On Thu, May 12, 2016 at 9:12 AM Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> What version of FS are you using? You may need a newer version of
> mri_aparc2aseg. Try this one
>
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_aparc2aseg
>
> On 05/12/2016 06:53 AM, Caroline Beelen wrote:
> >
> > If we changed the command –-ribbon to –- no ribbon, the script ran,
> > but when we looked at the stats-file, only cortical grey matte
> >
>
> --
> 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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>
>
> 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
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> contains patient information, please contact the Partners
> Compliance HelpLine at
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-- 
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
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[Freesurfer] V1 Atlas ( brodman maps)

[John Anderson]

Dear Experts,






I want to calculate PET signal within each Brodman map! I will give an example: If I want to caclulate PET singal for every parcellate and segment in the brain I do the following:

 

bbregister  --t1 --mov T1_MPRAGE.nii.gz --init-fsl --reg t1.reg.dat --s SUBJID 

 

mri_vol2vol --mov PET_MAP.nii --reg t1.reg.dat --fstarg --interp nearest --o PET_MAP.anat.nii 
mri_segstats --seg $SUBJECTS_DIR/SUBJID/mri/wmparc.mgz  --ctab-default --i PET_MAP.anat.nii --mask PET_MAP.anat.nii --sum PET_MAP.summary.dat 

 

How can I do the same previous steps ( or something similar) on the atlas V1. I.e how can I replace the atalas "wmparc" in the command "mri_segstat" with the atals V1 to get PET signal for every brodman?. I can't locate the atals V1 as a file like wmparc.mgz or aseg.mgz is there any method to creat this atlas?

 

 

 

Many thanks for any advice!

 

John 


 

 








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addressed. If you believe this e-mail was sent to you in error and the e-mail
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[Freesurfer] R: Re: mri_surf2vol

[stdp82]

Thanks.
I'm reading the surf2surf help but I do not understand the --trgsurfreg 
options.
I'using 
mri_surf2surf --hemi rh --srcsubject fsaverage --srcsurfval thickness --
src_type curv --trgsubject Control21 --trgsurfval file??
Which is the file?

Thanks

Stefano


>Messaggio originale
>Da: Douglas N Greve 
>Data: 14-mag-2016 0.06
>A: 
>Ogg: Re: [Freesurfer] mri_surf2vol
>
>The overlay Control21/rest/fc.ramgseed.surf.rh/R_Amygdala/sig.nii.gz is 
>in fsaverage space, so either change the subject to fsaverage, or use 
>mri_surf2surf to map the overlay into Control21's space, then run 
>mri_surf2vol
>
>
>On 05/13/2016 06:03 PM, std...@virgilio.it wrote:
>> Hi list,
>>
>> I'm using FS-FAST for seed based functional connectivity.
>> For a subject, I would like to report the sig.nii.gz from the inflate 
>> to volume space.
>>
>> I'm using
>>
>> mri_surf2vol --surfval 
>> Control21/rest/fc.ramgseed.surf.rh/R_Amygdala/sig.nii.gz --hemi rh 
>> --fillribbon --subject Control21 --identity Control21 --template 
>> Control21/orig.mgz --o ramg2rh_sig_volspace.nii.gz
>>
>> but this error reported below was obtained.
>>
>> ERROR: dimension inconsistency in source data
>>
>>Number of surface vertices = 123044
>>
>>   Number of value vertices = 163842
>>
>>
>> Thanks
>>
>>
>>
>> Stefano
>>
>>
>>
>> ___
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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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>contains patient information, please contact the Partners Compliance HelpLine 
at
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[Freesurfer] postdoc at UCSF

[Bruce Fischl]

The Neuroradiology Section and Memory and Aging Center (MAC) at the
University of California, San Francisco (UCSF) are seeking an exceptional
postdoctoral candidate in imaging genetics of neurodegenerative disorders.
Using a variety of techniques, ranging from human structural and functional
MRI to whole genome sequencing, our research involves elucidating the
genetic, neuroanatomic, and molecular characteristics of Alzheimer's disease,
frontotemporal lobar degeneration, Parkinson's disease and neuroinflammation.

We seek a postdoctoral candidate with a strong background in genetics (and
preferably, human imaging) and a desire to use a multi-disciplinary approach
to pursue neurodegenerative research. The candidate should have considerable
experience with Matlab, R, PLINK and potentially, MRI image analysis tools
such as Freesurfer, FSL and SPM. Applicants should have a Ph.D. or M.D.
degree with less than five years of postdoctoral experience. Highly motivated
individuals with a record of productive research are encouraged to apply. The
position is available starting July 1, 2016.

Salary is commensurate with qualifications and experience. Interested
applicants should send curriculum vitae/NIH biosketch, and three references
to: Drs. Rahul Desikan (rahuldesi...@gmail.com) and Jennifer Yokoyama
(jennifer.yokoy...@ucsf.edu).
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