Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

[Fressurfer] fMRI and anatomical T1
by leonardo kay 23 Mar '11

23 Mar '11

Hi all Can anyone help me overlaying fMRI activations from fsl on a anatomical T1 volume in freesurfer. Is there any previous format conversion to do before? Thanks in advance best regards, -- Leo Kay.

2 1

recon-all errors
by Alfredo Damasceno 23 Mar '11

23 Mar '11

Hello, I had some problems with 3 images of different patients running the recon-all comand. With one of them, I received the following message: ERROR: vbmAMIPP.nii exists but is not readable With the others two there were no error messages, but both stopped at the same point: gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.10 x + 0 estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.85 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux tupa.neuroimg.hc.unicamp.br 2.6.18-194.26.1.el5 #1 SMP Tue Nov 9 12:54:20 EST 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Mar 18 17:24:55 BRT 2011 Could anyone help in solving these problems? Thanks in advance Alfredo

1 1

Calculating BPF
by Andrew Dumas 22 Mar '11

22 Mar '11

Hi, I've been looking through the mailing list archives for anything on calculating BPF (Brain Parenchymal Fraction) and have only found some fuzzy descriptions of how to calculate this using FreeSurfer. I know I can get ICV from the aseg.stats, but how can I obtain the volumes of total white and gray matter (i.e. total brain parenchyma volume)? One possible method I saw suggested mris_anatomical_stats-- but that looks like it only calculates gray matter volumes. Any ideas? Thanks in advance for your help! Andrew

2 1

average_thickness&mris_anatomical_stats
by Liukarl 22 Mar '11

22 Mar '11

Hello, Freesurfer experts: I am using the mris_anatomical_stats to extract the average cortical thickness: mris_anatomical_stats -l lh.cortex.label -f subject1.txt subject1 lh the output is number of vertices = 127190 total surface area = 84246 mm^2 total gray matter volume = 257279 mm^3 average cortical thickness = 2.628 mm +- 0.698 mm average integrated rectified mean curvature = 0.158 average integrated rectified Gaussian curvature = 0.146 folding index = 6266 intrinsic curvature index = 403.9 My question is whether the average cortical thickness here is from white matter surface or pial surface? How can I get the pial surface average thickness? Our goal is to use average cortical thickness as a covariate to examine the possible local thickness difference, like in the prefrontal lobe. Which average cortical thickness, pial or white, is a better fit in our case? Thanks in advance Karl

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Re: [Freesurfer] 2x2x2 design
by Gabriel Go.Es. 22 Mar '11

22 Mar '11

Just ideas I had about how to set the contrast for ANOVA, but not sure if any of them is valid. Gabriel > Date: Fri, 18 Mar 2011 13:57:31 -0400 > From: greve(a)nmr.mgh.harvard.edu > To: gabriellbk(a)hotmail.com > CC: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] 2x2x2 design > > Gabriel, what are options 1 and 2 supposed to represent? > doug > > Gabriel Go.Es. wrote: > > > > Dear Freesurfer experts, > > I'm wondering how to set a 2x2x2 anova > > > > (diagnosis)x(gender)x(apoe) > > > > g1MaleE4 > > g1MalenoE4 > > g1FemaleE4 > > g1FemalenoE4 > > g2MaleE4 > > g2MalenoE4 > > g2FemaleE4 > > g2FemalenoE4 > > > > option 1 > > [1 1 -1 -1 0 0 0 0] > > [1 1 0 0 -1 -1 0 0] > > [1 1 0 0 0 0 -1 -1] /2 > > > > option 2 > > [1 1 1 1 -1 -1 -1 -1] > > [1 1 -1 -1 1 1 -1 -1] > > [1 -1 1 -1 1 -1 1 > > -1] /4 > > > > > > And really have no idea about the interections between factors. Could > > you tell me for example how to evaluate the diagnosis x gender > > interaction effect and the interaction among the three factors > > (diagnosis x gender x apoe). > > > > Bests regards, > > Gabriel > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. >

2 1

tkmedit undo volume?
by Nugent, Allison C. (NIH/NIMH) [E] 22 Mar '11

22 Mar '11

Hi - I'm doing manual edits in tkmedit. In the tkmedit "working with data" page on the wiki, it states that there are three ways to "undo", one taking advantage of the "undo volume." The instructions say to select View->Undoable voxels, then use the shift key and mouse button 2 with the edit voxel tool active, the voxels will be returned to their original values. I have the latest version of freesurfer, and there is no "undoable voxels" in the view menu. I can view edited voxels. However, nothing is undone when I hold the shift key. Under edit, however, there is an option to "clear undo volume" which makes me think that the undo volume still exists. Is this still an option for editing? Thanks, Allison Allison Nugent, PhD MRI Physicist Section on Neuroimaging in Mood Disorders Experimental Therapeutics and Pathophysiology Branch NIMH/NIH/DHHS Ph. 301-451-8863 nugenta(a)mail.nih.gov

2 2

[New release] - iSurf Brainview 2.1.0
by Pedro Paulo de Magalhães Oliveira Junior 22 Mar '11

22 Mar '11

Today it was released a new major upgrade of iSurf Brainview. (2.1.0) New features: - New Atlas: Chistophe Destrieux 2009 Atlas - Improved Interface - Retina Display - iOS 4.3 As usual suggestions are welcome. Upcoming features will include 3D visualization. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423… Cheers Pedro Paulo Jr.

4 3

Content of .tif files
by Anderson Winkler 21 Mar '11

21 Mar '11

Hi all, The .tif files (templates) contain 9 pages each, which seem to be organized as 3+3+3. I think I understand that they are equirectangular projections of the latitude/longitude of curvature and sulcal depth, is this correct? But what exactly each of these 9 frames contain? Thanks! Anderson

4 10

using multiple processors with freesurfer?
by jim kroger 20 Mar '11

20 Mar '11

Hello, I just downloaded freesurfer and am processing some of my data. I am using an 8 core machine, but I'm guessing freesurfer is using only one processor. Can you point me to information about taking advantage of multi cores when using freesurfer, if that is possible? Many thanks, Jim Kroger NMSU Psychology Los Alamos National Labs -- Cell: 575-571-8274 Email: jkk251(a)gmail.com Email to my other, work address will still reach me.

3 2

recon-all parallel execution of hemi stages
by Satrajit Ghosh 20 Mar '11

20 Mar '11

it seems we could run lh/rh processing stages of recon-all in parallel. however, i think they will write to the same log files. is there a way to specify a different log-file prefix? are there any other common files that these hemisphere based operations write to? concurrent reading i'm assuming is ok. cheers, satra

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