Freesurfer January 2009

freesurfer@nmr.mgh.harvard.edu

72 participants
137 discussions

Average subject
by Kelly Silva 14 Jan '09

14 Jan '09

Hi, When the average subject is built, is it used for the analyses or only to visualize? I want to understand how freesurfer makes the average subject. Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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mri_label2vol aliasing problem
by Ian Malone 14 Jan '09

14 Jan '09

Hi, I'm trying to use mri_label2voxel to produce an image of a segmented region in the original image voxel space and am seeing black lines through the output region, these are oriented parallel to the voxel axes. In the attached image you can see three of them: two parallel horizontal lines and one vertical one just cutting through the right hand side of the region. This appears to be some kind of aliasing artefact; if I move all the labels by adding 0.2 to each of the location values in the labels file then the lines are shifted to different voxels (not the immediately adjacent ones). Using the 1mm^3 voxel registered volume as the template does not show this problem, neither does viewing the label overlaid on orig.mgz in tkmedit. Is there anything I can adjust to avoid this while still outputting a volume in the original image dimensions? Thanks, Ian Malone

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Doubt pial segmentation
by Kelly Silva 14 Jan '09

14 Jan '09

Hello, Thanks por the answers! Now I´m sending 3 images: 1) no segmentation, 2) segmentation with separation of cortex and cerebellum with radius 1, 3) segmentation with separation of cortex and cerebellum with radius 2. Wich image is the best way and use of radius to separate cerebellum from cortex? Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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Doubt pial segmentation
by Kelly Silva 14 Jan '09

14 Jan '09

Hello, Thanks por the answers! Now I´m sending 3 images: 1) no segmentation, 2) segmentation with separation of cortex and cerebellum with radius 1, 3) segmentation with separation of cortex and cerebellum with radius 2. Wich image is the best way and use of radius to separate cerebellum from cortex? Thanks, Kelly ________________________________ Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - Música - Esportes Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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map label to subjects failed?
by David Qixiang Chen 13 Jan '09

13 Jan '09

Hi, I'm running Qdec to gather cortical thickness in specific regions based on the scalar visuals. when I've drawn ROIs over certain areas, I've found "Mapping labels to subjects" would return an error message for certain subjects. There error is as follows: ERROR: srcvtxno = -1 < 0 trgvtxno = 111070, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table. command failed: mri_label2label --srclabel rh.pos.orbitalfrontal --srcsubject fsaverage --trgsubject DI_April08_filtered --trglabel rh.pos.orbitalfrontal --regmethod surface --hemi rh Why would this error occur if the surface data in Qdec is based on the averaging of all the subjects? And how can I best go about fixing this problem? Thanks! - David Qixiang Chen Neurosurgical Research Assistant Toronto Western Hospital

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RE: [Freesurfer] reg-feat2anat failed
by Wang, Xin 13 Jan '09

13 Jan '09

Sorry for the confusion. Let me rephase my questions. question 1: I want to use the example_func2highres.mat created by fsl/FEAT registration to register example_func and orig.mgz. Can the flag --fslregout or --fsl do it? Question 2: These numbers appear in the terminal whenever I click a point in tkregister2? What do these numbers mean? Screen: 256 257 (113,113,113), inorm = 1, mov_frame = 0 Anat: (128 126 127) ( 0.0 -1.0 2.0) 25.0000 32.7 Func: ( 31 32 21) ( 4.2 3.1 1.4) 756.0000 112.5 question 3: I can only see the middle portion of the brain in tkregister2 when I zoomed in. How can I see other parts of the target and movable pictures? Thank you, Xin Wang ________________________________ From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 1/13/2009 4:19 PM To: Wang, Xin Subject: Re: [Freesurfer] reg-feat2anat failed 1) I don't know what you mean. The fslmatout is for creating an fsl mat file from a freesurfer register.dat 2. I don't know what you mean. 3. What do you mean by "moving the two images together"?

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smoothing size
by Wang, Xin 13 Jan '09

13 Jan '09

Hello, Freesurfer group, Could you tell me the default size of smoothing extents (kernel?) of smooth1 and smooth2 in the auto-recon-all? How can I change the size with mris_smooth in the auto-recon-all flow? And why does the smoothing not affect the thickness measure? Thank you in advance, Xin Wang

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mri_convert
by Jared Price 13 Jan '09

13 Jan '09

Hi everybody, We have a set of patients who were all run using the same freesurfer version, except that some of the patients had their dicom files converted to 001.mgz with a somewhat older version of freesurfer. For example some of them went through that step with version 4.0 or 4.0.2 or 4.0.5 etc. Anyway, I was wondering, is there any reason why those 001.mgz files would not be usable?

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[All] postdoc in Harvard Psych Dept. (fwd)
by Bruce Fischl 13 Jan '09

13 Jan '09

---------- Forwarded message ---------- Date: Tue, 13 Jan 2009 12:49:20 -0500 (EST) From: jgreene(a)nmr.mgh.harvard.edu To: all(a)nmr.mgh.harvard.edu Subject: [All] postdoc in Harvard Psych Dept. Hi, All, I'm looking for a postdoc to start Summer/Fall '09 This is for fMRI and/or TMS studies of moral cognition. No prior experience with moral cognition is necessary. I'm looking for someone with good technical skills and a willingness to learn about the field. See ad: https://mcl.wjh.harvard.edu/postdoc2009.html Please send materials to Shauna Gordon-Mckeon: shaunagm(a)wjh.harvard.edu Best, jdg _______________________________________________ All mailing list All(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/all

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Res: [Freesurfer] Segmentation
by Kelly Silva 13 Jan '09

13 Jan '09

Hi, Bruce I´m sending some pictures of aseg.mgz. Is this well done? Is there any objective and specific criteria to separate the cerebelum from the cortex? Is really necessary to do the manual segmentation on that area? Thanks, Kelly ________________________________ De: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Para: Kelly Silva <kcasilva(a)yahoo.com.br> Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Enviadas: Segunda-feira, 12 de Janeiro de 2009 15:40:34 Assunto: Re: [Freesurfer] Segmentation Hi Kelly, did you check the aseg.mgz? Did it separate them properly? cheers, Bruce On Mon, 12 Jan 2009, Kelly Silva wrote: > Hello, > I´m sending an image and I want to know how is the best way to separate cerebelum from the cortex with the preservation of the both structures. > Thanks! > Best regards, > Kelly > > > Veja quais são os assuntos do momento no Yahoo! +Buscados > http://br.maisbuscados.yahoo.com ________________________________ Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - Música - Esportes Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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Freesurfer January 2009