[Freesurfer] BRAIN Initiative postdoc position available at LCN (FreeSurfer team)

[Iglesias Gonzalez, Juan E.]

Dear all,

The Laboratory for Computational Neuroimaging (LCN) is seeking to fill a 
postdoctoral position in image analysis as part of an exciting NIH project 
titled: “Open-source software for multi-scale mapping of the human brain”, 
awarded to Drs. J. Eugenio Iglesias and Bruce Fischl as part of the BRAIN 
Initiative. The project aims to create tools for ex vivo brain MRI analysis, 
laminar analysis, MRI-histology integration, and surface-based sampling, using 
machine learning techniques. The ultimate goal is to make these tools available 
to other BRAIN Initiative sites and the research community in general, by 
integrate them tools into FreeSurfer, the open-source suite distributed by the 
LCN, which has nearly 50,000 worldwide licenses.

We are seeking a talented and enthusiastic postdoctoral researcher to develop 
machine learning and image analysis methods for this project. The postholder 
will work with Drs. Iglesias and Fischl to develop the new tools, and also 
closely collaborate with a software engineer to integrate them with FreeSurfer. 
The postholder will also interact with our collaborators at the Allen Institute 
for Brain Science, which will play the role of use case for the tools.

This project provides an exciting opportunity for a postdoctoral researcher at 
the interface between machine learning, medical image analysis and 
neuroscience, with a huge potential impact on the neuroimaging field.


Applicants should have:

- A Ph.D. degree in computer vision, neuroimaging, or biomedical 
engineering/image analysis. Applicants with degrees in related areas (e.g., 
Engineering, Physics, Applied Mathematics) will also be considered. Applicants 
close to submission of their PhD thesis will be considered as well.
- Strong mathematical and problem solving abilities.
- Expertise in programming, at least with high-level languages / packages.
- An established publication track record.
- Ideally, experience with one/some of the following: neuroimaging, deep 
learning, image registration.

The position is available in summer 2020, and applications will be reviewed as 
they arrive. The duration of the contract is two years, with possibility of 
further extension.

For applications, please send the following documents to 
jiglesiasgonza...@mgh.harvard.edu:
- A cover letter (maximum 1 page)
- CV (maximum 4 pages)
- List of publications




Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


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[Freesurfer] dura edits .mgz~ file?

[KennethSPrice]

External Email - Use Caution

Hello Freesurfers,

I edited the brainmask.mgz file after running recon-all but no changes were 
saved. Instead I have a mysterious 'brainmask.mgz~' file that I cannot open 
with freeview.

What is this file and does it contain my edits? If so how do I convert it? 
Already tried mri_convert.

Thanks,
Ken

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[Freesurfer] Permutation simulation cluster include vertices below cluster-forming threshold

[Fengdan Ye]

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Hello Freesurfers,

I am using mri_glmfit-sim to find significant clusters using permutation 
simulation. My command is as follows:

mri_glmfit-sim \
  --glmdir lh.cn_ad.glmdir \
  --perm 1000 3.0 pos \
  --cwp 0.05 \
  --2spaces \
  --bg 1

When I opened the *.sig.masked.mgh, I noticed that some vertices below the 
cluster forming threshold (3.0) were also included (the lowest value I found in 
the cluster was around 2.5). These vertices also seem to be on the edge of the 
cluster. Based on the FsTutorial, the permutation simulation should exclude all 
vertices below the cluster forming threshold. Is there any sort of smoothing 
done on the clusters that could have caused the vertices below CFT to be 
included?

I checked the mail archive and found this thread that have exactly the same 
question, but with no answer: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15375.html 


Thank you,
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[Freesurfer] mri_glmfit masking strategy

[Barletta, Valeria]

Hello Freesurfers,
I need to perform a GLM in 25 patients versus 19 controls but I need the 
comparison to be done only on normal appearing cortex (in patients), thus 
excluding cortical lesions.

  *   Is it possible to concatenate binary masks projected to surface? What 
command shall I use?
  *   If I use the option --mask for mri_glmfit, will I obtain the same type of 
output with the only difference that clusters are looked for in the 
concatenated masks?

Thank you,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823
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Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

[Boris Rauchmann]

External Email - Use Caution

Please find the logfile attached.

Thank you

Am Do., 4. Juni 2020 um 15:18 Uhr schrieb Douglas N. Greve <
dgr...@mgh.harvard.edu>:

> Can you send the log file?
>
> On 6/4/2020 9:12 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
> Dear FS experts,
>
> In my dataset I have 4 subjects where the T1 was acquired, planning the
> FOV very close to the occipital lobe. I guess that triggers the error:
> getSignalBehindHead ERROR (no slices behind head) WARNING: only 0 < 7
> slices behind head! ERROR: xcerebralseg  and results in gtmseg exited with
> errors.
> How can I fix this?
>
> Best regards,
> Boris
>
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Log file for gtmseg
Thu Jun  4 14:40:20 CEST 2020

setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
/usr/local/freesurfer/bin/gtmseg --s 098_S_6655_20190107

freesurfer-linux-centos6_x86_64-dev-20180911-69aa645
$Id: gtmseg,v 1.19 2016/03/24 17:32:23 greve Exp $
Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
xcerebralseg --s 098_S_6655_20190107
Thu Jun  4 14:40:20 CEST 2020

setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
/usr/local/freesurfer/bin/xcerebralseg --s 098_S_6655_20190107

freesurfer-linux-centos6_x86_64-dev-20180911-69aa645
$Id: xcerebralseg,v 1.12 2017/01/18 21:21:00 zkaufman Exp $
Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
mri_ca_label -align -nobigventricles /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/nu.mgz /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/transforms/talairach.m3z /usr/local/freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh
sysname  Linux
hostname linuxrechner2
machine  x86_64

setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
mri_ca_label -align -nobigventricles /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/nu.mgz /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/transforms/talairach.m3z /usr/local/freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh 


== Number of threads available to mri_ca_label for OpenMP = 1 == 
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
not handling expanded ventricles...
reading 1 input volumes
reading classifier array from /usr/local/freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca
reading input volume from /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/nu.mgz
average std[0] = 20.4
reading transform from /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 7.01
Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 20.4   using min determinant for regularization = 41.8
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment
renormalizing input #0
gca peak = 0.24861 (36)
mri peak = 0.08632 (27)
Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (14329 voxels, overlap=0.008)
Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (14329 voxels, peak = 25), gca=25.0
gca peak = 0.29857 (37)
mri peak = 0.08013 (27)
Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (12114 voxels, overlap=0.010)
Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (12114 voxels, peak = 24), 

Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

[Douglas N. Greve]

Can you send the log file?

On 6/4/2020 9:12 AM, Boris Rauchmann wrote:


External Email - Use Caution

Dear FS experts,

In my dataset I have 4 subjects where the T1 was acquired, planning 
the FOV very close to the occipital lobe. I guess that triggers the 
error: getSignalBehindHead ERROR (no slices behind head) WARNING: only 
0 < 7 slices behind head! ERROR: xcerebralseg  and results in gtmseg 
exited with errors.

How can I fix this?

Best regards,
Boris

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[Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

[Boris Rauchmann]

External Email - Use Caution

Dear FS experts,

In my dataset I have 4 subjects where the T1 was acquired, planning the FOV
very close to the occipital lobe. I guess that triggers the error:
getSignalBehindHead ERROR (no slices behind head) WARNING: only 0 < 7
slices behind head! ERROR: xcerebralseg  and results in gtmseg exited with
errors.
How can I fix this?

Best regards,
Boris
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Re: [Freesurfer] Thalamic nuclei segmentation

[Quentin Devignes]

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Dear Doctor Greve, 

Thank you for your reply. I am trying to do what you advised me. 

For now, I have segmented thalamic nuclei in the left hemisphere, checked and 
corrected this segmentation and used MRI_binarize as advised. However, I don’t 
know what to write for the « projmap » option of vol2surf… Could you please 
help me?

My command line is: vol2surf --vol2surf ***the thalamic segmentation.mgz*** 
***the surface obtained from MRI_binarize*** 1 (for projtype option) -2 (for 
projdist option) X (nothing for projmap option) ‘lta’ (for reg option) ’novsm’ 
(for vsm option) 0 (for interp option) ***My directory*** (for output option). 

Wish you a nice day, 
Best regards, 

Quentin DEVIGNES
PhD candidate in neurosciences
Neuropsychologist
UMR-S 1172 - Lille Neuroscience and Cognition - FRANCE

> Le 1 juin 2020 à 16:40, Douglas N. Greve  a écrit :
> 
> You can create a surface using mri_binarize listing all the thalamic nuclei 
> with --match and specifying a surface output (you may wan to smooth it a 
> little bit to remove the pixelization). You can then use mri_vol2surf (using 
> the vol2surf in the link below with the --vol2surf option  and using the 
> thalamic segmentation itself as the input volume, abs for the projtype and 
> maybe -2 mm for the projdist and interp 0 for nearest). You can then use 
> mris_seg2annot to create an annotation that you can visualize on the surface.
> 
> 
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_vol2surf 
> 
> 
> On 6/1/2020 5:33 AM, Quentin Devignes wrote:
>> External Email - Use Caution
>> 
>> Dear Doctor Iglesias, 
>> 
>> Thanks for your previous reply. As agreed, I post my question on the 
>> Freesurfer list. 
>> 
>> We are doing shape analyses on thalamus in order to determine whether 
>> distinct cognitive profiles in Parkinson’s disease have different 
>> deformation fiels of the thalamic surface. We used SPHARM-PDM tool (shape 
>> analysis module in Slicer4) to obtain deformation fields and p-values map 
>> (cf. attached file; vectors represent the magnitude of deformation between 
>> two groups).We are not developing a new method, we used an existing one 
>> (SPHARM-PDM). However, to be more accurate, we would like to delineate 
>> thalamic nuclei on the surface of our meshes (because the nuclei have 
>> different functional role). Existing atlases (such as yours) are usable on 
>> volumes but not on surfaces. Do you have any idea how we could project your 
>> atlas onto a surface? We did not find any method in the scientific 
>> literature. 
>> 
>> Hope you could help us, 
>> Best regards, 
>> 
>> Quentin DEVIGNES
>> PhD candidate in neurosciences
>> Neuropsychologist
>> UMR-S 1172 - Lille Neuroscience and Cognition - FRANCE
>> 
>> 
>> 
>> 
>> 
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