Freesurfer July 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
135 discussions

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read in .vtk files ?
by Ritobrato Datta 17 Jul '09

17 Jul '09

Hello All, Can freesurfer read in .vtk surface files ? Please let me know. Thanks Ri

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follow-up to Hausdorff distance question
by Jared Price 16 Jul '09

16 Jul '09

Hi all, I asked an earlier question about Hausdorff distance and was told there was a binary "mri_hausdorff_dist" that could calculate it, but I don't see it in the /Applications/freesurfer/bin directory. Is it elsewhere? Is it included with 4.4.0?

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mean symmetric surface distance, Hausdorff distance etc..
by Jared Price 16 Jul '09

16 Jul '09

Hi freesurfer masters, I was wondering if freesurfer had a way of comparing two segmentations for surface differences, something along the lines of a Hausdorff distance or the symmetric mean absolute surface distance Cheers, Jared

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running freesurfer after talairach touch-ups...
by Ritobrato Datta 16 Jul '09

16 Jul '09

Hello all, I ran recon-all -autorecon-all -s <subjid> After it ran all the way through, I ran tkregister2 --mgz --s <subjid> --fstal --surf orig and saved everything with the SAVE REG button in the tkregister2 toolbar. Since I initially ran all the steps before the talairach touch-ups, what do I run to re-process the data and re-write with the new talairach modifications ? Do I have to use ' -force ' with the command ? I have a same question for the step, Using Control Points to Fix Intensity Normalization. What command do I run after I am done adding control points ? Thanks Ri

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ideal freesurfer input?
by Stephen Towler 16 Jul '09

16 Jul '09

Hi freesurfers, Are many groups getting good results from single 1mm isovoxel T1 inputs? Anyone experimented with multispectral input? We're acquiring a number of participants on a Philips Achieva 2.5 system with 8-ch SENSE coil. Good scans, very little movement. I realize that the selection of freesurfer inputs and averaging is empirically driven and idiosyncratic to each scanner/sequence/coil combination, but I just want to solicit any thoughts about possible benefit from non-standard sequences. Due to other priorities we are unable to collect two identical T1s in each study, but this is what we do get that might aid automated structural segmentation: - 3D T1 TFE (1 mm3, good contrast among gray, white, and CSF) - 3D T2 FLAIR (1 mm3, high gm/csf contrast but no gm/wm contrast, except for wm hyperintensities) - 3D T1 "FGATIR" (.75 mm3, very high gm/wm contrast but very low gm/ csf contrast) This last sequence is the one I'm most curious about: might the very high gm/wm contrast be used to help freesurfer's segmentation? Image attached, showing a participant's standard 3D T1 TFE on the right and the high g/w contrast T1 on the left. This paper describes the FGATIR sequence: Sudhyadhom, A., Haq, I. U., Foote, K. D., Okun, M. S., & Bova, F. J. (2009). A high resolution and high contrast MRI for differentiation of subcortical structures for DBS targeting: The Fast Gray Matter Acquisition T1 Inversion Recovery (FGATIR). NeuroImage. doi: 10.1016/ j.neuroimage.2009.04.018. Thanks! Stephen -- Stephen Towler Graduate Student, Neuropsychology Dept. Clinical and Health Psychology

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changing image orientation
by Jose Luis Cantero Lorente 16 Jul '09

16 Jul '09

Hi there, I got some mgz files badly reoriented (saggital right - nose bottom, and needed them in saggital left - nose up). Would it be feasible to change the reorientation and save them to mgz from the Freesurfer command line? Thanks in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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Freeview for Mac
by jentis＠nmr.mgh.harvard.edu 16 Jul '09

16 Jul '09

Hi, I have a quick question: has freeview been compiled for an intel macbook pro? Thanks, Jon

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window refresh problem with freesurfer v4.4.0
by yzhangd＠artsci.wustl.edu 15 Jul '09

15 Jul '09

Whenever i try to open two windows(ie.' tkmedit bert orig.mgz 'and' tksurfer bert rh pial') the original one will not respond or refresh unless i close the second one,even i turn on the redraw button in the tksurfer. Also,i put the two windows side by side and did not overlay them. i've tried a few combinations, ie. two tkmedit windows, one tkmedit one tksurfer, etc. all of them have the same problem. any idea what's going on? thanks a lot Yuning Zhang 4525 scott ave, medical school,Washington University in St.Louis,63110 Phone:314-362-1219

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averaging mgz files
by Jose Luis Cantero Lorente 15 Jul '09

15 Jul '09

Hi there, is there any FS command to average two .mgz files from the same subject withouth going through the recons steps. I just need to obtain a new mgz file resulting from the average of several mprage of the same patient. Thanks in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

4 3

Paper for Subcortical Parc
by Vina Goghari 15 Jul '09

15 Jul '09

Hi group, Is there a paper to cite for the subcortical parcellation done by FreeSurfer? Thanks, Vina

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Freesurfer July 2009