[Freesurfer] Primary slice direction and image origin?

[falk.luesebr...@med.ovgu.de]

External Email - Use Caution

Dear all,

This is not directly related to FreeSurfer, however, can anyone tell me how the 
primary slice direction and image origin is determined from the DICOM header as 
displayed for example using mri_info?

Best,
Falk



...

[klinikum_logo_schmal_e-mail_blau]
Universitätsklinik für Neurologie


Otto-von-Guericke-Universität Magdeburg
Medizinische Fakultät
Leipziger Str. 44
39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de
http://www.kneu.ovgu.de/kneu.html

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[Freesurfer] freeview parcellation error

[Ebru Ayyürek]

External Email - Use Caution

Hi FreeSurfer Developers,


I'm attempting to perform a freeview visualisation and parcellation to my data 
on Linux.
I can open freeview and load surfaces and volumes.But when I want to load a 
label for parcellation
on freeview ,it can not load label.And I've got an error like this on the 
terminal;

freeview: could not scan # of lines from label file
�
LabelRead failedfreeview: could not scan # of lines from label file
freeview: could not parse 1th line '2  G&S_occipital_inf23  60 
1800' in label file
LabelRead failedfreeview: could not parse 1th line '2  G&S_occipital_inf
23  60 1800' in label file
freeview: could not parse 1th line '2  caudalanteriorcingulate 125 100 
1600' in label file
LabelRead failedfreeview: could not parse 1th line '2  caudalanteriorcingulate  
   125 100 1600' in label file



PS:I've update my freeview as described here  
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

I've searched the list and no similar errors have been reported.
Does anyone have any thoughts on how to trouble-shoot this one?

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) 
Ubuntu version:18.10 3) uname -a: Linux sid 4.18.0-17-generic #18-Ubuntu SMP 
Wed Mar 13 14:34:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

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Re: [Freesurfer] freeview parcellation error

[Bruce Fischl]

Hi Ebru

are you sure yo uare loading a label and not a color lut? What is the name 
of the file you  are trying to load?


cheers
Bruce


On Thu, 2 May 2019, Ebru Ayyürek wrote:



External Email - Use Caution

Hi FreeSurfer Developers,

I'm attempting to perform a freeview visualisation and parcellation to my data 
on Linux.
I can open freeview and load surfaces and volumes.But when I want to load a label for parcellation 
on freeview ,it can not load label.And I've got an error like this on the terminal;

freeview: could not scan # of lines from label file
???
LabelRead failedfreeview: could not scan # of lines from label file
freeview: could not parse 1th line '2  G&S_occipital_inf                23  60 
180    0' in label fi
le
LabelRead failedfreeview: could not parse 1th line '2  G&S_occipital_inf        
        23  60 180  
  0' in label file
freeview: could not parse 1th line '2  caudalanteriorcingulate         125 100 
160    0' in label fi
le
LabelRead failedfreeview: could not parse 1th line '2  caudalanteriorcingulate  
       125 100 160  
  0' in label file
PS:I've update my freeview as described here  
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreevi
ew 
I've searched the list and no similar errors have been reported. 
Does anyone have any thoughts on how to trouble-shoot this one?

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0
2) Ubuntu version:18.10
3) uname -a: Linux sid 4.18.0-17-generic #18-Ubuntu SMP Wed Mar 13 14:34:40 UTC 
2019 x86_64 x86_64 x
86_64 GNU/Linux

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[Freesurfer] inaccurate segmentation from recon-all

[Mun, Anna]

Hi Freesurfer team,

I have a question about segmentation. I am working with scans of patients with 
Down syndrome and the segmentation (aseg.presurf.mgz and aseg.mgz) for a few 
subjects is slightly inaccurate. It mostly affects the areas that we are 
specifically interested in - basal ganglia and thalamus.
Is there any alternative way to correct the segmentation other than doing it 
manually?

Thank you!

Best,
Anna
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[Freesurfer] Postdoc position available

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Dear all,

We are looking for a postdoc in our ERC project, with two main purposes. First, 
to improve the 3D histology reconstruction tools that we have been developing 
to build an ultra-high resolution atlas of the brain using histology. And 
second, to collaborate in the development of segmentation techniques to apply 
the atlas to the automated analysis of in vivo MRI scans, which hope to 
integrate with FreeSurfer. Our research line is moving toward the integration 
of classic model-based algorithms with modern deep learning techniques (see for 
instance https://arxiv.org/abs/1904.11319).

The postdoc will join the Centre for Medical Image Computing (CMIC) at 
University College London (UCL), which will be soon co-located with the new UCL 
 Artificial Intelligence Centre, located on High Holborn in central London. In 
addition, the postdoc will have the opportunity of visiting our lab at the 
Martinos Center in Boston.

More information here:

www.jeiglesias.com

https://tinyurl.com/y4hv275f


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

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Re: [Freesurfer] inaccurate segmentation from recon-all

[Bruce Fischl]

Hi Anna

can you send us some images of upload a subject so we can see what you 
mean?


cheers
Bruce


On Thu, 2 May 2019, Mun, Anna wrote:


Hi Freesurfer team,

I have a question about segmentation. I am working with scans of patients with 
Down syndrome and the
segmentation (aseg.presurf.mgz and aseg.mgz) for a few subjects is slightly 
inaccurate. It mostly
affects the areas that we are specifically interested in - basal ganglia and 
thalamus. 
Is there any alternative way to correct the segmentation other than doing it 
manually?

Thank you!

Best,
Anna

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Re: [Freesurfer] Primary slice direction and image origin?

[Greve, Douglas N.,Ph.D.]

You can use --slicedirection to get the slice direction (it will also 
get printed out by just running mri_info on a file). What do you mean by 
the image origin?

On 5/2/19 7:16 AM, falk.luesebr...@med.ovgu.de wrote:
>
> External Email - Use Caution
>
> Dear all,
>
> This is not directly related to FreeSurfer, however, can anyone tell 
> me how the primary slice direction and image origin is determined from 
> the DICOM header as displayed for example using mri_info?
>
> Best,
>
> Falk
>
> ...
>
> klinikum_logo_schmal_e-mail_blau
>
> *Universitätsklinik für Neurologie*
>
>
> Otto-von-Guericke-Universität Magdeburg
> Medizinische Fakultät
> Leipziger Str. 44
> 39120 Magdeburg
>
> *Telefon: *+49-391-6117-512
>
> *falk.luesebr...@med.ovgu.de *
> *http://www.kneu.ovgu.de/kneu.html*
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] ERROR! FOV=265.909 > 256

[Greve, Douglas N.,Ph.D.]

Can you send your command line (with -cw256) and the recon-all.log file?

On 4/23/19 6:54 AM, Anik Dar wrote:
>
> External Email - Use Caution
>
> Hello All,
>
> I am running recon-all highres on 10 7T MP2RAGE datasets that has been 
> skull striped and in two subjects, I get the following error  -
>
> I tried the suggested workaround ie I included the flag -cw256 but 
> that didnt help and I got the error again.
>
> Can you suggest how to fix this ?
>
> Many thanks
>
> Ani
>
> P.S. The error below
>
> For more details, see the log file 
> /Applications/freesurfer6/subjects/HighResT1/scripts/recon-all.log
> To report a problem, see 
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> \n
> ERROR! FOV=265.909 > 256
> Include the flag -cw256 with recon-all!
> Inspect orig.mgz to ensure the head is fully visible.
> \n
> Darwin Kernel Version 15.6.0: Thu Jun 21 20:07:40 PDT 2018; 
> root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64
>
> recon-all -s HighResT1 exited with ERRORS at Mon Apr 22 20:20:31 EDT 2019
>
> For more details, see the log file 
> /Applications/freesurfer6/subjects/HighResT1/scripts/recon-all.log
> To report a problem, see 
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
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Re: [Freesurfer] inaccurate segmentation from recon-all

[Mun, Anna]

Bruce,

I have uploaded files via FileDrop, I was not able to use 
freesurfer@nmr.mgh.harvard.edu as a recipient and I used your email instead. 
Please let me know if you are able to access the files.

Thank you!

Best,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Thursday, May 2, 2019 11:26 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] inaccurate segmentation from recon-all

Hi Anna

can you send us some images of upload a subject so we can see what you
mean?

cheers
Bruce


On Thu, 2 May 2019, Mun, Anna wrote:

> Hi Freesurfer team,
>
> I have a question about segmentation. I am working with scans of patients 
> with Down syndrome and the
> segmentation (aseg.presurf.mgz and aseg.mgz) for a few subjects is slightly 
> inaccurate. It mostly
> affects the areas that we are specifically interested in - basal ganglia and 
> thalamus.
> Is there any alternative way to correct the segmentation other than doing it 
> manually?
>
> Thank you!
>
> Best,
> Anna
>
>
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[Freesurfer] Research Assistant for Brain Imaging Studies @ Albert Einstein College of Medicine {Disarmed}

[Emily Schwartz]

External Email - Use Caution

The Position:

The Research Assistant will work in the Division of Cognitive and Motor Aging 
to acquire, manage and process behavioral and brain imaging data in ongoing 
neuroimaging studies of older adults.
Responsibilities
•   Recruit, screen and accompany older adults to brain imaging studies
•   Acquire and enter behavioral data into paper and computerized forms, 
review forms for completeness and accuracy
•   Maintain computer databases of behavioral and brain imaging data
•   Read, process, and quality check brain imaging data
Qualifications
•   Bachelor's Degree required
• Coursework in Neuroscience, Neuroanatomy, Cognitive Science/Psychology, 
or Computer science preferred

Skills and Competencies

•   Outstanding interpersonal and computing skills required
•   Strong database management, and clear understanding of clinical and 
research databases highly preferred
•   Previous experience with neuroimaging processing highly preferred.
•   Proficiency in neuroimaging processing software (FreeSurfer, fsl, SPM) 
preferred
•   Previous experience with Linux operating systems and MATLAB software 
preferred

APPLY HERE:

https://careers-einstein.icims.com/jobs/11910/psychology-assistant/job?mobile=false&width=950&height=500&bga=true&needsRedirect=false&jan1offset=-300&jun1offset=-240

Helena M. Blumen, PhD.
Assistant Professor
Department of Medicine (Geriatrics)
Department of Neurology (Cognitive and Motor Aging)
Albert Einstein College of Medicine
E-mail: helena.blu...@einstein.yu.edu
Office Phone: (718) 430 3810
http://www.einstein.yu.edu/faculty/12983/helena-blumen/

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[Freesurfer] resampling to native space for recons with multiple T1s

[Zimmerman, Jared]

External Email - Use Caution

Hi Freesurfers,

What’s the best way to resample recon data such as aparc+aseg.mgz into scanner 
space for recons with multiple T1s?  Right now I’m using mri_vol2vol with 
–regheader to resample from orig space to rawavg, then using mri_vol2vol again 
with the 001.lta, 002.lta etc. registration matrices to get it back to the 
original scanner space for each T1.  Is there a way to do this without two 
interpolation steps?

Thanks,
jared
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Re: [Freesurfer] resampling to native space for recons with multiple T1s

[Greve, Douglas N.,Ph.D.]

First, create an LTA to go from the orig to rawavg space:
tkregister2 --noedit --mov orig.mgz --targ rawavg.mgz --reg deleteme.dat 
--ltaout reg.orig-to-rawavg.lta --regheader
Then concatenate with the input volume lta, eg,
mri_concatenate_lta  -invert2 reg.orig-to-rawavg.lta 001.lta 
reg.orig-to-001.lta
Check:
tkregister2 --mov orig.mgz --targ 001.mgz --reg reg.orig-to-001.lta
The to volumes should be in registration

Then use mri_vol2vol (intensity image) or mri_label2vol (segmenation) to 
resample

On 5/2/19 4:15 PM, Zimmerman, Jared wrote:
>
> External Email - Use Caution
>
> Hi Freesurfers,
>
> What’s the best way to resample recon data such as aparc+aseg.mgz into 
> scanner space for recons with multiple T1s?  Right now I’m using 
> mri_vol2vol with –regheader to resample from orig space to rawavg, 
> then using mri_vol2vol again with the 001.lta, 002.lta etc. 
> registration matrices to get it back to the original scanner space for 
> each T1.  Is there a way to do this without two interpolation steps?
>
> Thanks,
>
> jared
>
>
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Re: [Freesurfer] Failure to import cortical surface extracted with Freesurfer into Matlab using ft_read_headshape

[Bruce Fischl]

Hi Darinka

what is fieldtrip? I don't think it is anything of ours.  What happens if 
you call read_surf directly?


cheers
Bruce
On Wed, 1 May 2019, Darinka Trübutschek wrote:



External Email - Use Caution

Dear freesurfer community,

I am currently trying to import cortical surfaces extracted with freesurfer 
(version:
freesurfer-linux-centos7_x86_64-dev-20190403-dacefd1) into Matlab (version: 
R2018b) using the
fieldtrip function ft_read_headshape (version: 20190329). All of this is run in 
an Ubuntu 18.04.2
LTS environment. While all of the extracted surfaces seem fine upon visual 
inspection in freeview,
the import into Matlab fails, throwing the following error message:

pial = ft_read_headshape('freesurfer/surf/lh.pial');
Error using fread
Invalid size.

Error in read_surf (line 72)
  vertex_coords = fread(fid, vnum*3, 'float32') ;

Error in ft_read_headshape (line 909)
    [pos, tri] = read_surf(filename);

It is most certainly related to the fact that, both for the number of vertices 
(vnum) and the number
of faces (fnum), the function read_surf returns non-sensible (?) values (i.e., 
vnum = -1.0263e+09
and fnum  =  -1.0529e+09). The same code produces no error when run on the same 
pial surface
extracted with a different version of freesurfer
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) in a different 
Ubuntu environment
(Ubuntu 16.04 LTS). 

As visual inspection in Freeview of the 2 surfaces from the two different 
Freesurfer versions
reveals no obvious differences, I am therefore at a loss as where exactly to 
start to fix this
problem and would be grateful for any help.

Many thanks!
Darinka

--
Darinka Trübutschek, PhD

Department of Experimental Psychology
Anna Watts Building
Radcliffe Observatory Quarter
Woodstock Road
Oxford, OX2 6GG
UK

website: https://sites.google.com/site/dtruebutschek/

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Re: [Freesurfer] [External] Re: resampling to native space for recons with multiple T1s

[Zimmerman, Jared]

External Email - Use Caution

Thanks, I'll give this a shot.


On 5/2/19, 4:39 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Greve, Douglas N.,Ph.D."  wrote:

First, create an LTA to go from the orig to rawavg space:
tkregister2 --noedit --mov orig.mgz --targ rawavg.mgz --reg deleteme.dat 
--ltaout reg.orig-to-rawavg.lta --regheader
Then concatenate with the input volume lta, eg,
mri_concatenate_lta  -invert2 reg.orig-to-rawavg.lta 001.lta 
reg.orig-to-001.lta
Check:
tkregister2 --mov orig.mgz --targ 001.mgz --reg reg.orig-to-001.lta
The to volumes should be in registration

Then use mri_vol2vol (intensity image) or mri_label2vol (segmenation) to 
resample

On 5/2/19 4:15 PM, Zimmerman, Jared wrote:
>
> External Email - Use Caution
>
> Hi Freesurfers,
>
> What’s the best way to resample recon data such as aparc+aseg.mgz into 
> scanner space for recons with multiple T1s?  Right now I’m using 
> mri_vol2vol with –regheader to resample from orig space to rawavg, 
> then using mri_vol2vol again with the 001.lta, 002.lta etc. 
> registration matrices to get it back to the original scanner space for 
> each T1.  Is there a way to do this without two interpolation steps?
>
> Thanks,
>
> jared
>
>
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