Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

creating surface intermediate between white and pial: mri_surf2surf and mri_surf2vol
by Jeff Eriksen 13 Jun '12

13 Jun '12

I am hoping to create a new surface that is half-way between the white and pial surfaces, then project it back to the volume. I have seen some examples of creating normals this way, but I am unclear as to how to just create the surface itself. The Wiki page is not too helpful, as it does not list the -sval switch in the following example: mri_surf2surf --s subject --hemi lh --sval-nxyz pial --tval ./pial_nrml_srf_lh.mgz mri_surf2vol --surfvalpial_nrml_lh.mgz --hemi lh --outvol pial_nrml_vol_lh.mgz --identity subject --template T1.mgz --projfac 0.5 Is there another version of the mri_surf2surf documentation that discusses the —sval switch? For mri_surf2vol, I do not understand the –projfac implementation and cannot find a complete description of it. I would like to use it do do a smooth interpolation between the pial and white surfaces (with normals as well), but it is not apparent to me that this is possible. Thanks, -Jeff

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Export Functional Data Overlayed Onto Sphere
by Luis R. Piloto 13 Jun '12

13 Jun '12

Hello, I've specifically adopted Freesurfer for its ability to map a brain into a sphere. I've ran a subject's structural data through the recon-all pipeline using the -all option. With this reconstruction completed, I'd like to overlay functional data on the sphere. More specifically, I'd like the ability to programmatically query a point on the sphere and get the corresponding activation. Is there a reasonable way to do this within the Freesurfer pipeline? I already have the ability to programmatically query my initial functional data, so it would suffice to get a transformation matrix from my structural data to the spherical coordinates. Any thoughts/suggestions would be appreciated. Regards, Luis Piloto

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vertex-by-vertex thickness
by Shantanu Ghosh 13 Jun '12

13 Jun '12

Hi FS experts, Sorry if this is a newbie question. I want to display how an individual patient's crtical thickness varies from the normal group average, vertex-by-vertex. What is the commandline to do that? I want to display the overlay on MNI152 instead of fsaverage. Thanks in advance, Shantanu -- Shantanu Ghosh, Ph.D. Martinos Center for Biomedical Imaging Harvard-MIT Program in Health Sciences & Technology

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(no subject)
by mdkruepke＠uwalumni.com 13 Jun '12

13 Jun '12

Freesurfers A real real general question here: if i am running a glm_fit for cortical thickness with a fsgd with 2 groups (G1, G2) and 3 continues variables and have a matrix of 1 -1 0 0 0, red/yellow areas mean that G1 is thicker in this area than G2, correct? Best- Michael -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

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aseg inaccuracy in cortex
by Nicole Senecal 13 Jun '12

13 Jun '12

Hi all, I'm noticing that when pulling up a brainmask volume with surfs and aseg on, the pial and white surfaces are (thankfully) very often correct, but the aseg in cortex is a bit off - often including parts of the skull/dura as gray matter - even though the pial surface does follow this boundary correctly. As long as the surfaces are correct, and my primary interest will be cortical thickness, do I need to worry about these inaccuracies in the aseg? Is checking the aseg primarily done for ensuring accuracy in subcortical structures rather than in cortex? thanks, Nicole -- Nicole Senecal Neuroscience Graduate Group Kable Lab 3720 Walnut St., Room C37 Philadelphia, PA 19104 Lab phone: 215-746-4371

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Correction for Multiple Comparisons
by mdkruepke＠uwalumni.com 13 Jun '12

13 Jun '12

Freesurfers- When correcting for multiple comparisons using: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg --cwpvalthresh 0.4\ --overwrite What does the sign mean (ie - the neg, pos, abs). Also for the mc-z simulation type do we no longer need to include the smoothness of our data (FWMH)? Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

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cortical thickness with a continuous variable
by mdkruepke＠uwalumni.com 13 Jun '12

13 Jun '12

Freesurfers- I am looking to investigate the whether cortical thickness varies in regards to a continues variable, while controlling for other continues variables. I am having a little trouble wrapping my head around this as i am unsure how to compare thickness in regards to a continues variable, how the contrast would look, ect. Looking at this example FSGD ( http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V) GroupDescriptorFile 1 Title OSGM Class Group1 Class Group2 Variables Age Input subject1 Group1 30 Input subject2 Group2 40 I am thinking i may need to randomly define two groups, and then use a contrast similar to 0 0 0.5 0.5 (contrast 4 on the same page). Which asks: Null Hypothesis: does mean of group age slope differ from 0? Is there an average affect of age regressing out the effect of group? Am i correct in thinking that if i use this contrast i would be able to determine whether there is a difference in cortical thickness based on any continuous variable (like age, IQ)? Michael -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

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Re: [Freesurfer] specifying multiple contrasts
by Douglas N Greve 12 Jun '12

12 Jun '12

The FSGD file is incorrect. It has multiple subjects listed, and the string after the subject name is not the name of a class (Tract1_FA is not the same as Tract1). I would suggest working through the example on the wiki tutorial and/or looking at the slides on group analysis. doug On 06/12/2012 06:05 PM, Shantanu Ghosh wrote: > Hi Doug > > I set up my .fsgd file as follows (4 tracts of interest, 59 subjects > belonging to 2 different groups, CON and PAT): > > GroupDescriptorFile 1 > Title tract_fa > MeasurementName thickness > Class Tract1 > Class Tract2 > Class Tract3 > Class Tract4 > Input Subject1 Tract1_FA > Input Subject1 Tract2_FA > Input Subject1 Tract3_FA > Input Subject1 Tract4_FA > Input Subject2 Tract1_FA > Input Subject2 Tract2_FA > Input Subject3 Tract3_FA > Input Subject3 Tract4_FA > . > . > Input Subject59 Tract4_FA > > and set up the .mtx file for mri_glmfit as: > > C = [zeros(3) eye(4)] > > Is that correct? How do I define the contrast variables = -1 and 0 for the > test? > > I am a little confused. > > Thanks and regards, > shantanu > > On Tue, June 12, 2012 4:57 pm, Douglas N Greve wrote: >> Did you look at the FSGD examples on our wiki? Do a search for FSGD >> doug >> >> On 06/12/2012 04:46 PM, Shantanu Ghosh wrote: >>> Hello Freesurfer experts, >>> >>> How can I specify multiple contrasts for my thickness study with two >>> groups AA and BB, having different number of subjects in each group? My >>> variables are tract-wise FA values, age and IQ. >>> >>> Thanks in advance, >>> Shantanu >>> >>> >>> >> -- >> 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 >> >> >> > -- 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

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matrix error
by mdkruepke＠uwalumni.com 12 Jun '12

12 Jun '12

Hello- I am trying to analyze the cortical thickness between two groups of subjects Cl1 and CL2. When i run the GLM i receive the error: matrix is ill-conditioned or badly scaled, condno = 1e+08 I am under the impression the error could be due to the non-uniformity in the range/scale of the regressors. here is my information: contrast is 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1) mri_glmfit --y lh.PvNPeverything.10.mgh --fsgd PvNPeverything.fsgd dods --C PvNP_everything.mtx --surf UNM_ALLGOOD lh --cortex --glmdir lh.PvNPeverything.glmdir 2) (sample of my fsgd) - there are no columns with all 0's in them GroupDescriptorFile 1 Title Methedone Comparison Class Cl1 Class Cl2 Variables WAISIQ trait_anxiety alcohol_year heroin_year cocaine_year cannabis_year meth_year amphetamines_year meth_amphet_year hallucinogens_year inhalants_year methodne_year opiates_year pills_year opitates_pills_year other_year total_years Input M87160505 Cl1 86 33 10 3 9 11 0 1 1 1 8 0 0 6 6 0 49 Input M87161888 Cl1 109 59 0 0 7 22 0 0 0 0 0 0 0 0 0 0 32 Input M87107477 Cl1 89 34 12 0 9 13 0 9 9 6 10 0 1 9 10 0 57 Input M87199897 Cl1 117 44 0 23 0 10 0 0 0 0 0 9 15 0 15 3 60 Input M87146570 Cl1 94 42 26 0 3 8 0 0 0 0 0 0 0 0 0 6 37 Input M87189755 Cl1 111 59 11 0.5 2 15 0 3 3 1.5 0 0 0 0 0 0 36 Input M87169696 Cl1 86 22 2 0 11 14 0 0 0 0 0 0 0 0 0 0 25 Input M87187366 Cl1 106 51 28 0 27 0 0 20 20 0 0 0 0 0 0 0 75 Input M87178857 Cl2 117 48 0 4 4 8 0 5 5 7 0 4 0 0.08 0.08 0 42.08 Input M87165923 Cl2 103 40 5 2 0 15 0 0 0 0 0 0 0 1 1 0 23 Input M87110556 Cl2 134 60 4 0 1 15 0 0 0 0 0 0 0 0 0 0 20 Input M87183811 Cl2 97 43 15 0 8 3 0 0 0 0 0 0 0 0 0 0 26 3) design matrix 1 0 86 0 33 0 10 0 3 0 9 0 11 0 0 0 1 0 1 0 1 0 8 0 0 0 0 0 6 0 6 0 0 0 49 0 1 0 109 0 59 0 0 0 0 0 7 0 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 1 0 89 0 34 0 12 0 0 0 9 0 13 0 0 0 9 0 9 0 6 0 10 0 0 0 1 0 9 0 10 0 0 0 57 0 1 0 89 0 40 0 15 0 5 0 2 0 30 0 10 0 0 0 10 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 59 0 1 0 77 0 44 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 1 0 91 0 22 0 6 0 0 0 3 0 0 0 0 0 0 0 0 0 0 0 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0 0 0 0 2 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 1 0 77 0 49 0 0 0 0 0 10 0 12 0 0 0 4 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 42 0 1 0 89 0 42 0 0 0 0 0 4 0 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 1 0 117 0 34 0 25 0 0 0 2 0 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 52 0 1 0 83 0 56 0 12 0 0 0 0 0 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 1 0 91 0 33 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 1 0 106 0 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 120 0 50 0 1 0 0 0 0 0 2 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

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specifying multiple contrasts
by Shantanu Ghosh 12 Jun '12

12 Jun '12

Hello Freesurfer experts, How can I specify multiple contrasts for my thickness study with two groups AA and BB, having different number of subjects in each group? My variables are tract-wise FA values, age and IQ. Thanks in advance, Shantanu -- Shantanu Ghosh, Ph.D. Martinos Center for Biomedical Imaging Harvard-MIT Program in Health Sciences & Technology

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