Freesurfer April 2011

freesurfer@nmr.mgh.harvard.edu

121 participants
166 discussions

retinotopy manual?
by Michelle Umali 05 Apr '11

05 Apr '11

Dear All, I was wondering if anyone knows of a step-by-step guide on how to do retinotopic analysis with freesurfer. Thanks. Michelle

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Re: [Freesurfer] Interpreting results from Qdec
by Nick Schmansky 05 Apr '11

05 Apr '11

Courtney, if i understand your question, i think one way to do that is to use qdec to draw a label on the blob of interest, and the run 'map label to subjects', which creates a label file in each subjects label dir, then you can run stats on that with mris_anatomical_stats. (btw, i'm putting this answer on the list, as others may have better ideas.) n. On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) [F] wrote: > Hi Nick > > Thanks for the prompt reply. Sorry if my questions seem a bit naïve--this is my first time using Freesurfer. > > A follow up question to your answer for question 1. I see that the group data will be plotted in Qdec for significant blobs, but say there is a significant interaction between two variables and it's not entirely apparent what is driving this interaction. > Is there a way to extract the mean of this blob for each individual (i.e., treat it as an ROI or something similar) to determine what's driving the significance? > > Thanks in advance! > Courtney > > -----Original Message----- > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: Thursday, December 30, 2010 2:44 PM > To: Gallen, Courtney (NIH/NIDA) [F] > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Interpreting results from Qdec > > ans. 1. - the easiest way is to Ctrl- left mouse click on a blob, and a > plot of the data at that surface vertex will appear. the group will be > apparent from that (say, demented group is thinner than non-demented > group). this data is significance data (log p, so '2' is 0.01), so mean > and stdev wouldnt apply in that case. the file 'y.mgh' is the raw data > of all subjects in the analysis, so you could extract mean and stdev > from that. > > ans. 2. - slide the 'annotation' opacity slider to show the annotation > data (cortical parcellation). the ctrl left click will also put the > region info for that vertex on the lower left of the display. > > see also: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis > > n. > > On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) [F] > wrote: > > Hi, > > > > > > > > I’m currently running analyses in Qdec and have identified areas that > > show significant effects in my contrasts. I have two questions related > > to interpreting these results. > > > > > > > > 1. How can you interpret the effect in each “blob?” (i.e., which > > group has a greater cortical surface area, etc.). Right now, all I > > know is that there is an effect in certain areas. Can you export this > > data to get means and standard errors? > > > > 2. Is there a way to localize where these effects are? E.g., a > > tool that tells you this effect is located in __ area of the brain? > > > > > > > > Thanks in advance > > > > Courtney > > > > > > > > Courtney Gallen > > > > Post-baccalaureate IRTA > > > > Neuroimaging Research Branch > > > > National Institute on Drug Abuse (IRP) > > > > 251 Bayview Blvd > > > > Suite 200 > > > > Baltimore, MD 21224 > > > > Tel: (443) 740-2631 > > > > > > _______________________________________________ > > 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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2-Year fMRI Postdoc, Center for Mind/Brain Sciences, University of Trento, Italy
by angelika lingnau 05 Apr '11

05 Apr '11

*2-Year fMRI Postdoc, Center for Mind/Brain Sciences, University of Trento, Italy* At the Center for Mind/ Brain Sciences (CIMeC, http://www.unitn.it/en/cimec<http://www.unitn.it/en/cimec/11702/angelika-lingnau>), University of Trento, there will soon be an opening for a two-year postdoctoral fellowship to work with Dr. Angelika Lingnau. Our group examines the neural systems involved in action execution and observation. Some recent publications as well as further descriptions of our ongoing research projects can be found under the following link: https://sites.google.com/site/angelikalingnau/. The postdoc will be responsible for the design of several fMRI studies, conducting data analysis and leading the write-up of scientific work. The ideal applicant is highly motivated and creative and is capable of working both independently as well as in a young, dynamic group. The applicant furthermore should have experience with functional magnetic resonance imaging and/ or transcranial magnetic stimulation and a solid background in Cognitive Neuroscience. Programming experience with MATLAB or C is very desirable. The Center offers an international and vibrant research setting with access to state-of-the-art neuroimaging methodologies, including a research-only 4T MRI scanner, MEG, EEG and TMS, as well as behavioral, eye tracking and motion tracking laboratories. The University of Trento is ranked first among research universities in Italy. English is the official language of the CIMeC, where a large proportion of the faculty, post-docs and students come from a wide range of countries outside of Italy. Informal inquiries should be sent to Angelika Lingnau ( angelika.lingnau(a)gmail.com)

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Mapping segmentations to SPM Functional Space
by Palzes, Vanessa 05 Apr '11

05 Apr '11

I am wondering if there is a similar function as aseg2feat (which maps the automatic segmentations from Freesurfer to FSL FEAT functional space) for the use in SPM functional analysis. This tool poses to be very useful in creating ROI masks, however, we are using SPM for functional analysis rather than FSL FEAT. Thanks, Vanessa Palzes Research Assistant Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155

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Convert annotations longitudinally
by Andrew Dumas 05 Apr '11

05 Apr '11

Hi FreeSurfer experts, Is there a way to move annotations from the same subject at one timepoint to another? I've tried doing this using a discrete-valued surface and using seg2annot, but, when I convert surfaces there are vertices between regions whose values are averages of bordering vertices. This ruins the continuity of each individual label with little islands of various values. Is there a mri_annot2annot or equivalent? Thanks! Andrew Dumas

3 3

different vertexes and faces on pial and inflated surface of the same hemisphere
by Forrest Sheng Bao 05 Apr '11

05 Apr '11

hi all, I encountered a strange problem today. I used recon-all -all to get surfaces of a subject. I have no problem with his/her left hemisphere. But for the right hemisphere, the numbers of vertexes and faces of pial surface are different from those of the inflated surface. I checked the headers of curavture and convexity maps also. They all tell the same information as the pial surface's header. But not the same as the header of inflated surface. I also checked the file content. The file did not seem like corrupted. I have never had the problem with other data i have. Only on this hemisphere of the subject. Has anyone out there experienced the same problem before? Cheers, Forrest

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edit volume remotely
by Sara Lozano-Zahonero 05 Apr '11

05 Apr '11

Dear all, We are trying to edit a new wm volume remotely. We want to substitute the mouse click with an external command. Since we are not familiar with tcl/tk we don't know where this action (mouse click to edit volume) happens within the script tkmedit.tcl. Could you please help us: How could we edit (or delete) voxel programmatically? The resulted wm volume should be saved for regenerating the surfaces with ?recon-all?. Thanks in advance for your help Sara

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N3 for improving cerebellum segmentation
by Tetiana Dadakova 05 Apr '11

05 Apr '11

Dear list, I have a question regarding intensity non-uniformity correction using N3 (as in Boyes et al, 2008). Does anyone have experience of using it for improving cerebellum segmentation, specifically distinguishing between white and grey matter in cerebellum? If yes, what are the best values for the options: -distance and -iterations? Cerebellum is very important for our study, therefore I am looking for ways of how to make the segmentation as good as possible. Thank you for your time and help, Tanja.

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help with CT scaling
by Andrew R. Dykstra 04 Apr '11

04 Apr '11

Hi all, I'm having problems either or converting a series of dicoms from a CT scan obtained at MGH main. When viewing them in the standard hospital viewer, they appear normal, but when viewing them in TKMEDIT (either the original dicom series or converted mgz file), the scaling changes. Are there any options in mri_convert I can use to overcome this problem? See attached view of the mgz file. Cheers, Andy

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resampling vol to surface
by GREGORY R KIRK 04 Apr '11

04 Apr '11

Hi guys, i am using the freesurfer-fsl integration to use labels from the freesurfer cortical surface as seeds for probtrackx probabilistic diffusion tractography. when the output of probtrackx is generated it is already in the freesurfer conformed space. I want to resample the output of probtrackx onto the cortical surface. I have the transformations from the diffusion data to freesurfer conformed space generated using bbregister to do the tractography but to use mri_vol2surf i need to first tranfrorm the output of probtrackx back into the epi space with the inverse of the bbregister tranform ( output in the fsl format) and resample it to the lower resolution epi resolution. i.e. there is not an option for mri_vol2surf to assume the data to be resampled onto the cortical surface is already in freesurfer conformed space. i suppose i could compute transformations from freesurfer conformed space to say brain.mgz, which would essentially be the identity transformation. mriconvert -it mgz -ot nii brain.mgz brain.nii i.e. bbregister --mov brain.nii --t1 -s subject -init-fsl --reg register.dat or i could make a fake identity transform like 1.0 1.0 ? don't know what this number is 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 round ? what should i use here. whats the best way to go here thanks greg

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Freesurfer April 2011