[Freesurfer] Postdoc Position at the Dynamic Memory Lab at UC Davis
Postdoctoral Researcher: The Dynamic Memory Lab (C. Ranganath, PI) at the University of California, Davis, now has an open position for a funded postdoctoral researcher. We currently are running studies that involve multimodal imaging (EEG, fMRI, ECoG, Diffusion Imaging, MR Spectroscopy) as well as concurrent transcranial electrical stimulation (tDCS/tACS). The lab is located at the UC Davis Center for Neuroscience, which houses a 3T Siemens Skyra MRI scanner, an MR-compatible tDCS/tACS system, and EEG systems both at the lab and in-scanner. Start date is flexible and can be delayed to accommodate defense and publication of thesis work. In addition to lab funding, candidates might be eligible for funding from the NIA T32 grant on the Neuroscience of Cognitive Aging (collaboration with Charles DeCarli) or from a joint R01 to examine memory in schizophrenia (collaboration with J. Daniel Ragland and Cam Carter). Qualifications: Candidates must have completed a Ph.D. in Psychology, Neuroscience, or a related field and have first-authored publications that reflect familiarity with neuroscience techniques (e.g., EEG, fMRI, tDCS/tACS, TMS, etc.). For this position, successful candidates will need to have strong analytical skills in multivariate analysis of fMRI, EEG, or other neurophysiological data. Strong preference will be given to candidates with research background in learning and memory and expertise in probabalistic tractography, model-based analysis, representational similarity analysis, or pattern classification of fMRI data, time-frequency analysis, cortical source estimation and/or multivariate analysis of EEG or MEG in humans, or corresponding LFP analyses in animal models. Beyond experience, we are looking for someone who is resourceful, collaborative, resilient, productive, honest, and enthusiastic about mentoring junior lab members. Prof. Charan Ranganath will go through applicant information starting Nov. 1st, 2016, until position is filled. Interested individuals please send your CV and names of 3 references to DML Lab Manager Nichole Bouffard ( nrbouff...@ucdavis.edu) ___ 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.
[Freesurfer] ROI masks created in FreeSurfer used in FSL??
Dear FreeSurfer Users, I ran recon -all on my structural image and created ROI masks (using mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like to use these masks for further analysis with FSL. However, it seems that the ROI masks generated with mri_label2vol have different header information than that of the original structural image. As a result, I was unable to carry out further analysis with FSL (e.g., converting these ROI masks into functional space with hires2example_func.mat). I was wondering if there is a way to solve this issue. Many thanks in advance. Frank ___ 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.
Re: [Freesurfer] ROI masks created in FreeSurfer used in FSL??
Hi Gari, Thanks so much for the tips! @ Doug: I basically followed the instructions on this site<http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/>to obtain my ROIs. Any thoughts? Many thanks! Frank On Thu, Jan 9, 2014 at 1:22 AM, Garikoitz Lerma-Usabiaga < gariko...@gmail.com> wrote: > Hi, > sorry to jump in, but maybe this solves your problem. What I've been doing > is: > > 1.- Convert the .mgz ROI in Freesurfer to .nii format in FSL: mri_convert > --in_type mgz --out_type nii --out_orientation RAS roi.mgz roi.nii > > 2.- Open the new roi.nii in mricron: mricron nu.nii -o roi.nii . Select > it in the menu and just save it as *_mricron.nii again. (I converted > nu.mgz with the same procedure as above to check that the roi was in > place). This was the only way to make it visible in fslview and work with > the roi in fsl afterwards. > > > Hope this workaround works for you! > Gari > > > On Thu, Jan 9, 2014 at 12:53 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> what was your mri_label2vol command and terminal output? >> doug >> >> On 01/06/2014 02:35 AM, Frank Hsieh wrote: >> > Dear FreeSurfer Users, >> > >> > I ran recon -all on my structural image and created ROI masks (using >> > mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like >> > to use these masks for further analysis with FSL. However, it seems >> > that the ROI masks generated with mri_label2vol have different header >> > information than that of the original structural image. As a result, I >> > was unable to carry out further analysis with FSL (e.g., converting >> > these ROI masks into functional space with hires2example_func.mat). I >> > was wondering if there is a way to solve this issue. >> > >> > Many thanks in advance. >> > Frank >> > >> > >> > ___ >> > 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/ >> >> ___ >> 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. >> >> > > ___ > 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. > > -- Frank ___ 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.
Re: [Freesurfer] ROI masks created in FreeSurfer used in FSL??
Hi Doug, many thanks for your help!
This is the command i used:
mri_label2vol --label lh.parstriangularis.label --temp $DIR/mri/orig.mgz
--subject sub${isub} --hemi lh --o
$OUTDIR/labels/sub${isub}_parstriangularis.nii.gz --proj frac 0 1 .1
--fillthresh .3 --reg $OUTDIR/labels/sub${isub}_register.dat
Here are the terminal outputs:
**
PVF (null)
Thesholding hit volume.
mri_label2vol done
Number of labels: 1
/Users/EXPTS/sub01/labels/rh.rostralmiddlefrontal.label
Annot File: (null)
Template Volume: /Applications/freesurfer/subjects/sub01/mri/orig.mgz
Outut Volume: /Users/EXPTS/sub01/labels/sub01_rh_DLPFC.nii.gz
Registration File: /Users/EXPTS/sub01/labels/sub01_register.dat
Fill Threshold: 0.3
Label Vox Vol: 1
ProjType: frac
ProjTypeId: 2
ProjStart: 0
ProjStop: 1
ProjDelta: 0.1
Subject: sub01
Hemi: lh
UseNewASeg2Vol: 1
DoLabelStatVol 0
LabelCodeOffset 0
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox:
-1.000 0.000 0.000 128.000;
-0.000 -0.000 -1.000 128.000;
-0.000 1.000 -0.000 128.000;
0.000 0.000 0.000 1.000;
Template Voxel Volume: 1
nHits Thresh: 0.3
Loading registration from /Users/EXPTSsub01/labels/sub01_register.dat
RegMat:
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
Label RAS-to-Vox:
-1.000 0.000 0.000 128.000;
0.000 0.000 -1.000 128.000;
0.000 1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading surface /Applications/freesurfer/subjects/sub01/surf/lh.white
nvertices = 145372
Reading thickness /Applications/freesurfer/subjects/sub01/surf/lh.thickness
nlabels = 1
Allocating Hit Volume (16777216) voxels
Loading /Users/EXPTS/sub01/labels/rh.rostralmiddlefrontal.label
On Jan 9, 2014, at 9:24 AM, Douglas N Greve wrote:
> Frank, can you send the commands you used and the terminal output?
> doug
>
> On 01/09/2014 04:35 AM, Frank Hsieh wrote:
>> Hi Gari, Thanks so much for the tips!
>> @ Doug: I basically followed the instructions on this site
>> <http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/>
>> to obtain my ROIs. Any thoughts?
>>
>> Many thanks!
>> Frank
>>
>>
>> On Thu, Jan 9, 2014 at 1:22 AM, Garikoitz Lerma-Usabiaga
>> mailto:gariko...@gmail.com>> wrote:
>>
>>Hi,
>>sorry to jump in, but maybe this solves your problem. What I've
>>been doing is:
>>
>>1.- Convert the .mgz ROI in Freesurfer to .nii format in FSL:
>>mri_convert --in_type mgz --out_type nii --out_orientation RAS
>>roi.mgz roi.nii
>>
>>2.- Open the new roi.nii in mricron: mricron nu.nii -o roi.nii.
>>Select it in the menu and just save it as *_mricron.nii again. (I
>>converted nu.mgz with the same procedure as above to check that
>>the roi was in place). This was the only way to make it visible in
>>fslview and work with the roi in fsl afterwards.
>>
>>
>>Hope this workaround works for you!
>>Gari
>>
>>
>>On Thu, Jan 9, 2014 at 12:53 AM, Douglas N Greve
>>mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>>what was your mri_label2vol command and terminal output?
>>doug
>>
>>On 01/06/2014 02:35 AM, Frank Hsieh wrote:
>>> Dear FreeSurfer Users,
>>>
>>> I ran recon -all on my structural image and created ROI
>>masks (using
>>> mri_label2vol) based on FreeSurfer's cortical parcellation.
>>I'd like
>>> to use these masks for further analysis with FSL. However,
>>it seems
>>> that the ROI masks generated with mri_label2vol have
>>different header
>>> information than that of the original structural image. As a
>>result, I
>>> was unable to carry out further analysis with FSL (e.g.,
>>converting
>>> these ROI masks into functional space with
>>hires2example_func.mat). I
>>> was wondering if there is a way to solve this issue.
>>>
>>> Many thanks in advance.
>>> Frank
>>>
>>>
>>> ___
>
