Freesurfer October 2014

freesurfer@nmr.mgh.harvard.edu

129 participants
187 discussions

FLASH protocol
by Le Wang 29 Oct '14

29 Oct '14

Hi, I want to do source localization on 128-channel EEG. For that, I need to create 3-layer head models for our subjects. However, our current MRI protocol only includes MPRAGE. I've talked with the (f)MRI team on our project about adding a single FLASH scan in their protocol. They are mainly concerned about the time requirement. So my questions are: 1) Is it possible to get a decent 3-layer head model just from MPRAGE using FreeSurfer or other tools like SPM? 2) If we have to use FLASH, which protocol we should use? I found one at https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&… I don't know if this is the most recent one -- is there a newer FLASH protocol that can produce decent skull boundaries and takes less time to run. 3) Is there a FLASH protocol already imported on Bay 1 (Skyra scanner) at Martinos (where the MPRAGE was run)? If not, is it ok to run FLASH and MPRAGE on different scanners for the same subject? I know this is a lot of questions. I really appreciate any responses. Thanks! Le

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NIH funded postdoctoral position at Harvard Medical School/Brigham and Women's Hospital
by Emily Goard Jacobs 29 Oct '14

29 Oct '14

Professor Jill Goldstein is recruiting a postdoctoral fellow with expertise in affective or cognitive neuroscience to join her lab, the CNL-SD ( http://cnl-sd.bwh.harvard.edu) *Job Description* This position requires the individual to have expertise in functional MRI. Experience with psychiatric disorders is preferable. Knowledge of paradigm development, data analytic software (e.g., SPM, FSL), and statistical underpinnings of fMRI are required. Responsibilities of this position include analyses of fMRI studies of the stress response, mood and anxiety, and hormonal responses; fetal programming of sex differences in mood and psychotic disorders; and implementation and analyses involved in a new neurostimulation study of mood and autonomic nervous system function. Thus, the position includes implementing methods for the analysis of fMRI data; developing project-specific methods when necessary (i.e., ROI analysis); utilization of advanced statistical methods to analyze fMRI, psychophysiological and serology data; preparation of manuscripts for publication; preparation of study findings and presentation at professional meetings; review and summarization of relevant literature for manuscript background and grant preparation; supervision of research assistant working on the study. There are many opportunities for education and growth in multiple domains in which we operate: neuroendocrinology, further neuroimaging training, neuroanatomy, neuro-immune interface. We collaborate with world-class scientists who are part of Brigham and Women’s Hospital, Massachusetts General Hospital, and others outside of the Harvard system. Applicant should have a PhD or ScD in clinical psychology, neuropsychology, and/or neuroscience or have an MD with fMRI expertise. We are committed to diversity, and qualified women and minorities are strongly encouraged to apply. Please email a CV, cover letter of interest, 2-3 written references, and a *brief *writing sample to Ms. Abby Brockman*, (abrockman(a)partners.org <abrockman(a)partners.org>), *Administrative Assistant to Jill Goldstein, PhD, Professor of Psychiatry and Medicine, Harvard Medical School, Director of Research, Connors Center for Women’s Health and Gender Biology, Brigham and Women’s Hospital, Boston, MA 02120.

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Re: [Freesurfer] LGI analysis of single subject
by Maria Holland 29 Oct '14

29 Oct '14

Hi Marie - Thanks for your response. After sending my email I found the hemisphere average values, but the values at each vertex and in each ROI will be very helpful! I tried the command you provided in tkmedit and it looks perfect - thanks! But when I try what I think is the corresponding command in freeview: freeview -v <SUBJ>/mri/brainmask.mgz <SUBJ>/mri/T1.mgz -f <SUBJ>/surf/lh.pial-outer-smoothed the images don't align (see attached). Am I doing something wrong? ~ Maria

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Pial surface with point-to-point correspondance between subjects
by Alexandre Routier 29 Oct '14

29 Oct '14

Dear all, I would like to work with the pial surfaces of my database and more particularly with a point-to-point correspondance between each subject. But I didn't find how to do that, only for longitudinal analysis of a single subject which I am not interested. Thanks in advance for you help, Alexandre

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LGI fails for fsaverage
by Pierre Mégevand 29 Oct '14

29 Oct '14

Dear all, I've looked a little bit further into why LGI fails for fsaverage. I previously tried simply running recon-all -s fsaverage-localGI but the script exited with errors after a good while. More importantly for me, the lh.pial-outer-smoothed surface, which I am after, did not look right. It seems that the first step, mris_fill, produces a volume that does not look very much like a brain anymore (cf. attached screenshot). Any idea why that would happen? Thanks, Pierre -- Pierre Mégevand, MD, PhD PLOS Neuro Community <http://neuro.plos.org> editor - Follow us on Twitter <http://twitter.com/PLOSNeuro> Postdoc @ Feinstein Institute for Medical Research (NY, USA) Follow me on Twitter <http://twitter.com/pierre_vanmedge> - Read my blog here <http://neuroscimed.wordpress.com>

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adding insula voxels
by Adam Mezher 29 Oct '14

29 Oct '14

Hi Bruce and FS group, Thanks again for the speedy replies and help with everything. Quick question about editing voxels (specifically those in the lh/rh insula). Should I simply add specific voxels to the aparc+aseg for this step? It was a little unclear on the wiki. Also, is there a specific command to re-run the stats/etc. after these edits are performed? Thanks a lot, Adam

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Error when completing cortical thickness analysis
by Claire Morley 29 Oct '14

29 Oct '14

I am conducting cortical thickness analyses between hundreds of individuals for a study we are conducting. I was getting this error Unrecognized sub-option flag 'annot_outline'. and so I tried to do the group analysis tutorial and input the command from the end of it (please see command below) but still got the same error. Freeview would open but it would not show any images. Could you help me to resolve this issue please? Also, what does it mean when it spits out invalid drawable? freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d Thank you so much for your help! Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot*

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Corpus Callosum segmentation
by Nathaniel Lucena 28 Oct '14

28 Oct '14

Is the corpus callosum segmentation based on the Hofer and Frahm functional parcellation, a mathematical formula, or, as listed on the website, 5 equal subdivision roughly along the long axis? What is the preferred citation for this? Thanks.

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GI analysis of single subject
by Maria Holland 28 Oct '14

28 Oct '14

Hi all, I'm trying to get gyrification information about a single subject. I've run the -localGI process but I have a few questions about the results: 1. When I try to plot the smoothed out pial surface over the brainmask in freeview, I use the command freeview -v subject/mri/brainmask.mgz -f subject/surf/lh.pial-outer-smoothed but it appears to be an inflated surface of some sort. It doesn't hug the contours of the brain mask as I expected (or as shown in the top image here: https://surfer.nmr.mgh.harvard.edu/fswiki/LGI) How can I see that surface? 2. I see very little variation in the local GI. I'm wondering if the third image in the link above is typical, and also how to get the blue to red color scale as shown? I can only get red to yellow, which doesn't show as much variation. 3. There is information on how to run analysis on a group of subjects, but I'm wondering if it's possible to get numerical data on a single subject. For instance: average GI in a given ROI, global GI, distribution (min, max, std dev, etc.). If nothing else, can I get the numerical values for each vertex? Thanks for your help! ~ Maria Holland Stanford University

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Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis
by Smith, Michael 28 Oct '14

28 Oct '14

I guess I'm not entirely sure how to do that? Are there any tutorials on how to extract an ROI from the aparc.stats file? -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, October 22, 2014 4:21 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis Why not just get it from the ?h.aparc.stats file? On 10/22/2014 03:43 PM, Smith, Michael wrote: > Hello Freesurfer's > > I am trying to look at the cortical thickness for a specific ROI on > the cortical surface (Primary Auditory Cortex: transverse temporal > gyri). I found a specific tutorial > (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) > however the tutorial assumes I already have an ROI mask created. I was > wondering if anyone had any tips on creating an ROI for the cortical > surface from the parcellation/annotation files. I know you can > "hand-draw" ROI's in tkmedit or freeview but I would prefer something > less subjective that doesn't rely on my untrained eye and unsteady > hand! Thanks in advance. > > Best, > > Michael S. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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(a)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.

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Freesurfer October 2014