[Freesurfer] two postdoctoral positions at Florida International University, Miami, open immediately

[Anthony Dick]

Dear colleagues--Please share widely, we are looking to hire 
immediately. Thanks!


The S.E.L.F Regulation Laboratory (http://self-regulationlab.fiu.edu/; 
PI Dr. Paulo Graziano, PhD) in collaboration with the Developmental 
Cognitive Neuroscience Laboratory (http://dcn.fiu.edu; PI Dr. Anthony 
Dick, PhD) at Florida International University (Miami, FL) is seeking 
two postdoctoral fellows to participate in an NIMH funded study to 
examine the neurobiology of attention deficit hyperactivity disorder in 
young children with a particular focus on their executive function and 
emotion regulation functioning. Candidates should have a PhD in 
psychology, developmental science, neuroscience, clinical science, or 
related discipline. The project will use neuropsychological tests, 
psychophysiology, diffusion-weighted imaging, and functional magnetic 
resonance imaging on children 5-7-years-old (with and without ADHD), and 
thus experience in neuroimaging data collection and analysis, and 
excellent computational and statistical know-how, is highly desired. 
Experience working with young children with developmental disabilities 
is a plus, as is a clinical science background.


The positions are for one year with the possibility of renewal for 
multiple years. Salary is $50,000 plus benefits. The positions are open 
immediately and we hope to fill them by November 1, 2016.


FIU is a multi-campus public research university located in Miami, a 
vibrant, international city. It has a recently established medical 
school that emphasizes medical research and community based medicine, 
and a new imaging facility with a 3 Tesla Siemens Prisma scanner. FIU 
offers more than 180 baccalaureate, masters, professional and doctoral 
degree programs to over 50,000 students.


Interested candidates should send application materials (curriculum 
vitae, sample publications, three references, and a letter describing 
research interests) directly to Dr. Paulo Graziano (pgraz...@fiu.edu) or 
Dr. Anthony Dick (ad...@fiu.edu). Reviews of applications will begin 
immediately.


--
Anthony Steven Dick, Ph.D.
Associate 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: http://myweb.fiu.edu/adick
Join the Society for the Study of Human Development: http://www.sshdonline.org

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Re: [Freesurfer] convert FSFAST files to gifti format

[Sabin Khadka]

Hi Doug- I did try
mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white
$SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz
fmcpr.lh.gifit-file.gii

I still get freadFloat: frear failed error.

Cheers,
Sabin Khadka

On Tue, Sep 13, 2016 at 2:53 PM, Douglas N Greve 
wrote:

> what is your mris_convert command line? You need to include vertex
> position information (eg, -o lh.white)
>
>
> On 09/12/2016 03:32 PM, Sabin Khadka wrote:
> > Hi all,
> >
> > Is there a way to convert FSFAST files
> > (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti
> > format? I've tried mris_convert but it does not work.
> >
> > Thanks for help.
> >
> > Cheers,
> > Sabin Khadka
> >
> >
> > ___
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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
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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Re: [Freesurfer] Pial surface vs. aparc+aseg

[Douglas N Greve]

No, the surface is not valid in those regions as they are not cortex


On 09/12/2016 07:18 PM, Nosal, Eryka [PSY] wrote:
>
> Hi,
>
> I’m very new to Freesurfer, and I am trying to get subject-specific 
> masks from the output of recon all that I can use on my functional 
> data. I was going to isolate regions from the aparc+aseg files to 
> create the ROIs. In my visual checks, I noticed that the pial surface 
> often leaves off parts of the amygdala and hippocampus even though 
> they are contained within the correct label of the aparc+aseg image. 
> For my purposes, should I be concerned that these regions are not 
> contained within the surface?
>
> Sincerely,
>
> */Eryka Nosal/*
>
> Research Tech
>
> The University of Chicago
>
> Department of Psychiatry & Behavioral Neuroscience
>
> Clinical Neuroscience & Psychopharmacology Research Unit (CNPRU)
>
> *Phone:*(773) 834-4113
>
> *Website: *http://cnpru.bsd.uchicago.edu/research.html
>
> 
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> Thank you
> University of Chicago Medicine and Biological Sciences
> 
>
>
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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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Re: [Freesurfer] convert FSFAST files to gifti format

[Douglas N Greve]

what is your mris_convert command line? You need to include vertex 
position information (eg, -o lh.white)


On 09/12/2016 03:32 PM, Sabin Khadka wrote:
> Hi all,
>
> Is there a way to convert FSFAST files 
> (fmcpr.odd.sm5.fsaverage.?h.nii.gz) files to convert into gifti 
> format? I've tried mris_convert but it does not work.
>
> Thanks for help.
>
> Cheers,
> Sabin Khadka
>
>
> ___
> 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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Re: [Freesurfer] Some volumes not loading (corrupted?)

[Douglas N Greve]

Did you run out of disk space? The recon could have been aborted during 
the middle of the write (but unlikely). If the edits were in the 
brainmask, then there is not much you can do. If the edits were not in 
the brainmask, you can just rerun starting at the brainmask and the 
edits will be preserved.


On 09/13/2016 01:31 PM, Rachel Romeo wrote:
> Hi all,
>
> After doing some manual edits to the wm and pial masks, I recently had 
> a recon fail with the following error:
>
>
> mghRead(/subject_177/mri/brainmask.mgz, -1): read error
>
> Invalid argument
>
> mri_em_register: could not open mask volume brainmask.mgz.
>
>
> When trying to load either the brainmask.mgz or wm.mgz into freeview, 
> these also fail, e.g.:
>
> mghRead(/subject_177/mri/brainmask.mgz, -1): read error
>
> MRIread failed: Unable to read from /subject_177/mri/brainmask.mgz
>
>
> All other volumes load fine.
>
> Can you think of what I might have done to corrupt these volumes? And 
> is there a way to revert to the most recent version, so that I don't 
> lose previous edits?
>
> Thanks so much,
> Rachel
>
>
>
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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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Re: [Freesurfer] cannot read white surface

[Douglas N Greve]

Can you send the full terminal output?


On 09/13/2016 01:26 PM, Claudia Dacquino wrote:
> Hi freesurfers,
> I'm trying to create an average subject for GLM analysis from my 
> group, using
>
> make_average_subject --out newtemplate
>
> and I got this error:
>
> Reading surface
>  /media/TREKSTOR/SUBJ/newtemplate/surf/lh.white
> No such file or directory
> ERROR: could not read /media/TREKSTOR/SUBJ/newtemplate/surf/lh.white
> ERROR: make_average_surface
>
> Any ideas on what the problem is? Why cannot find white surface?
> I'm using 5.1 version, but I got the same problem with version 5.3.
>
> Thanks to all.
> Claudia
>
>
> -- 
>
> Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia
>
> Laboratorio di Neuropsichiatria
>
> Dipartimento di Neurologia Clinica e Comportamentale
>
> IRCCS Fondazione Santa Lucia
>
> via Ardeatina 306 - 00179 Roma
>
> Tel. +39 (0)6 51501358
>
> Fax +39 (0)6 51501575
>
> web: http://www.neuropsichiatrialab.com 
> 
>
>
>
>
>
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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
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] QA tools

[John Anderson]

Hello, FS experts,

I am trying to use QA tool: 

I ran the following command 

recon_checker -snaps-only -s-file subjects.txt

 

The script output the following:


X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0

     Taking snapshots for subject ALS-0038
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0
X11 connection rejected because of wrong authentication.
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:12.0

 

 

At the end it said that he process finshed. I checked the AQ folder and the snaps where not there 

 

Any suggestions!


 

Bests,
John 
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[Freesurfer] Some volumes not loading (corrupted?)

[Rachel Romeo]

Hi all,

After doing some manual edits to the wm and pial masks, I recently had a
recon fail with the following error:


mghRead(/subject_177/mri/brainmask.mgz, -1): read error

Invalid argument

mri_em_register: could not open mask volume brainmask.mgz.


When trying to load either the brainmask.mgz or wm.mgz into freeview, these
also fail, e.g.:

mghRead(/subject_177/mri/brainmask.mgz, -1): read error

MRIread failed: Unable to read from /subject_177/mri/brainmask.mgz

All other volumes load fine.

Can you think of what I might have done to corrupt these volumes? And is
there a way to revert to the most recent version, so that I don't lose
previous edits?

Thanks so much,
Rachel
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[Freesurfer] cannot read white surface

[Claudia Dacquino]

Hi freesurfers,
I'm trying to create an average subject for GLM analysis from my group,
using

make_average_subject --out newtemplate

and I got this error:

Reading surface
 /media/TREKSTOR/SUBJ/newtemplate/surf/lh.white
No such file or directory
ERROR: could not read /media/TREKSTOR/SUBJ/newtemplate/surf/lh.white
ERROR: make_average_surface

Any ideas on what the problem is? Why cannot find white surface?
I'm using 5.1 version, but I got the same problem with version 5.3.

Thanks to all.
Claudia


-- 

Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia

Laboratorio di Neuropsichiatria

Dipartimento di Neurologia Clinica e Comportamentale

IRCCS Fondazione Santa Lucia

via Ardeatina 306 - 00179 Roma

Tel. +39 (0)6 51501358

Fax +39 (0)6 51501575

web: http://www.neuropsichiatrialab.com

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[Freesurfer] cannot read white surface

[Claudia Dacquino]

Hi freesurfers,
I'm trying to create an average subject for GLM analysis from my group,
using

make_average_subject --out newtemplate

and I got this error:

Reading surface
 /media/TREKSTOR/SUBJ/newtemplate/surf/lh.white
No such file or directory
ERROR: could not read /media/TREKSTOR/SUBJ/newtemplate/surf/lh.white
ERROR: make_average_surface

Any ideas on what the problem is? Why cannot find white surface?
I'm using 5.1 version, but I got the same problem with version 5.3.

Thanks to all.
Claudia

-- 

Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia

Laboratorio di Neuropsichiatria

Dipartimento di Neurologia Clinica e Comportamentale

IRCCS Fondazione Santa Lucia

via Ardeatina 306 - 00179 Roma

Tel. +39 (0)6 51501358

Fax +39 (0)6 51501575

web: http://www.neuropsichiatrialab.com

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