Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

Re: [Freesurfer] read in .vtk files ? (fwd)
by Ruopeng Wang 17 Jul '09

17 Jul '09

I'm not quite sure but I think freesurfer surface has some strict format that may be difficult to covert to from an external mesh. (Someone correct me if I'm wrong). As to freeview, the stable release is not the latest version. Ruopeng Ritobrato Datta wrote: > Hello Dr. Wang, > > Thanks for your kind reply. Can freesurfer convert .vtk files to freesurfer format ? I need to take a .vtk mesh and work it backward to volumetric data using freesurfer. Do you think thats possible ? > > Please let me know. > > Is freeviewer in the latest version of freesurfer ?? > > Thanks a lot for the help > > Sincerely > > Ri > > Ritobrato Datta, Ph.D. > Post Doctoral Fellow > Department of Neurology > University of Pennsylvania School of Medicine > 3rd Floor Gates Building > 3400 Spruce St. > Philadelphia > Pa 19104 > > > > ----- Original Message ----- > From: "Ruopeng Wang" <rpwang(a)nmr.mgh.harvard.edu> > To: "Ritobrato Datta" <ridatta(a)mail.med.upenn.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Friday, July 17, 2009 12:20:30 PM GMT -05:00 US/Canada Eastern > Subject: Re: [Freesurfer] read in .vtk files ? (fwd) > > Hi, > > What program in freesurfer do you want to load .vtk surface with? I can > potentially add .vtk file support for freeview. It will only be pure > visualization, though. Do you need to do anything with the surface? > > Ruopeng > > >> ---------- Forwarded message ---------- >> Date: Fri, 17 Jul 2009 00:10:19 -0400 (EDT) >> From: Ritobrato Datta <ridatta(a)mail.med.upenn.edu> >> To: freesurfer(a)nmr.mgh.harvard.edu >> Subject: [Freesurfer] read in .vtk files ? >> >> Hello All, >> >> Can freesurfer read in .vtk surface files ? >> >> Please let me know. >> >> Thanks >> >> Ri >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > >

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Confusion about mri_label2label
by Stephen Tyree 17 Jul '09

17 Jul '09

Hello, I'm attempting to convert labels from one subject's cortical surface to locations or nodes on another's cortical surface via spherical registration. My thought was to use mri_label2label, e.g. mri_label2label --srcsubject Bob --srclabel Bob/label/lh.cortex.label --trgsubject bert --trglabel Bob/label/bobToBert.lh.cortex.label --regmethod surface --hemi lh My understanding is that this should translate the labels for the nodes on Bob's lh surface to labels/nodes/locations (I'm not really sure which) on bert's lh surface. However, each label file seems to end up with a different number of labels. Bob/label/lh.cortex.label: 146415 Bob/label/bobToBert.lh.cortex.label: 122917 bert/label/lh.cortex.label: 122108 bert/label/bertToBob.lh.cortex.label: 145629 Can someone explain more precisely what mri_label2label does and what output it produces? Thanks. -- Stephen Tyree Neuroimaging Computer Scientist Laureate Institute for Brain Research Tulsa, OK, USA

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Hausdorff distance
by Jared Price 17 Jul '09

17 Jul '09

Hi gurus, I am evaluating two segmentation routines relative to a gold standard and would like to calculate the Hausdorff distance for each routine relative to the gold standard in the left and right Amygdala, Caudate, Putamen, and Hippocampus. I know that there are 3 main options to the mri_hausdorff_dist binary, namely -b <thresh> (binarize input volumes with threshold <thresh>), -g <sigma> (blur the input image with Gaussian <sigma>) and -max (compute the max of the min distances instead of the mean) but I am not quite sure how to use them to get the desired result. Does anyone know how best to use this tool to get structure-specific Hausdorff distances from 2 aseg.mgz volumes?

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from dicom to mgz
by Jose Luis Cantero Lorente 17 Jul '09

17 Jul '09

Hi, I am trying to convert from dicom to mgz (or nii) in Freesurfer by using dicom files as the one attached to this message. However, Freesurfer reports that this file is not a dicom. It seems weird to me since it can be opened with MRIcro, SPM as dicom, but not with Freesurfer. Could anyone tell me if there is another Freesurfer command to covert these dicoms to mgz from the 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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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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