Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

RFX using custom registration to common space?
by Gabriel A. Tobon 31 Mar '11

31 Mar '11

Hello Freesurfers, Is there any way to run random effects analysis using mri_glmfit with registration to MNI152 instead of MNI309? Also, is there a way to use a nonlinear warp instead of an affine transformation (for example by using "applywarp" from FSL) to bring data to a common space for random effects analysis using mri_glmfit? Thank you! Gabriel

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extracting segmented images with exact values for GM-WM-VL-CSF
by Alexander Lebedev 31 Mar '11

31 Mar '11

Dear FSL users and developers, Please, forgive me for such questions - I am asking because I'm really stuck with it... Would you be so kind to explain me how can I extract segmented image with values for GM-WM-VL(ventricular)-CSF of 150-250-50-10? Purpose: preparation for the high-dimensional warping before SVM classification... -- Sincerely Yours Alexander

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isxconcat-sess question..
by Krishna Srihasam 31 Mar '11

31 Mar '11

Hi, Is there a way to use" isxconcat-sess" to average monkey fMRI data? i.e. I have two groups of monkeys (say, test and control groups) and I want to do group analysis on their data.. Regards, krishna

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other interactions
by Gabriel Go.Es. 31 Mar '11

31 Mar '11

Dear Doug, In the case of a 3x2 design the post hoc contrast for evaluating the interaction effect would be as follows: D1Male D1Female D2Male D2Female D3Male D3Female ANOVA to test the effect of diagnosis (D1, D2, D3) only for males [ 1 0 -1 0 0 0]/2 [ 1 0 0 0 -1 0]/2 ANOVA to test the effect of diagnosis (D1, D2, D3) only for females [ 0 1 0 -1 0 0]/2 [ 0 1 0 0 0 -1]/2 Is this correct? Many thanks again. Gabriel

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FW: interacciones
by Gabriel Go.Es. 31 Mar '11

31 Mar '11

Dear Doug, I would like to be sure that I've understood the rules for the following contrast in a 2x2x2 design with diagnosis (D1, D2), gender (Male, Female) and handedness (Left, Right) as discrete factors. D1MaleLeft D1MaleRight D1FemaleLeft D1FemaleRight D2MaleLeft D2MaleRight D2FemaleLeft D2FemaleRight interaction between Diagnosis, Gender, and handedness [ 1 -1 -1 1 -1 1 1 -1] interaction between Gender and handedness for D1 [ 1 -1 -1 1 0 0 0 0]/2 interaction between Gender and handedness for D2 [ 0 0 0 0 -1 1 1 -1]/2 interaction between Diagnosis and handedness for Males [ 1 -1 0 0 -1 1 0 0]/2 interaction between Diagnosis and handedness for Females [ 0 0 1 -1 0 0 -1 1]/2 interaction between Diagnosis and Gender for Left [ 1 0 -1 0 -1 0 1 0]/2 interaction between Diagnosis and Gender for Right [ 0 1 0 -1 0 -1 0 1]/2 Many thanks in advance. Gabriel

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single subject versus a group map in qdec
by Emily Rogalski 31 Mar '11

31 Mar '11

Using q dec we have run a single patient versus a group of healthy control subjects (n=20ish) and found significant differences even after FDR correction. Could you describe the process qdec uses to compute these differences? Is it legitimate to report these single subject maps? Practically this is very useful for case reports but Im concerned about violating statistical rules. Thanks! -- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogalski(a)gmail.com

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Re: [Freesurfer] Baby's cortical ribbon?
by Lilla Zollei 31 Mar '11

31 Mar '11

Hi Adam, No, Freesurfer is not able to extract the neonatal cortical ribbon and I am not aware of other automatic research tools that would be able to do that. Lilla > ---------- Forwarded message ---------- > Date: Wed, 30 Mar 2011 14:38:26 -0500 > From: "Eggebrecht, Adam" <eggebrechta(a)mir.wustl.edu> > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] Baby's cortical ribbon? > > Hello there, > > Is FreeSurfer able to extract the neonatal cortical ribbon? Typically babies > have a much better contrast with their T2 than with their T1. I know FS uses > the T1 so I assume babies are not well handled by the usual processing. If > not FS, are you aware of another suite which can extract the cortical surface > for babies, or using the T2? > > Many thanks! > > Adam > > > Adam T. Eggebrecht, Ph.D. > Dept. of Radiology > Washington University School of Medicine > St. Louis, MO > 314-362-6942 > > The material in this message is private and may contain Protected Healthcare > Information (PHI). If you are not the intended recipient, be advised that > any unauthorized use, disclosure, copying or the taking of any action in > reliance on the contents of this information is strictly prohibited. If you > have received this email in error, please immediately notify the sender via > telephone or return mail. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

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Hippocampal overinclusion
by T.M. Overbeek 31 Mar '11

31 Mar '11

Dear Freesurfer users, Recently I started using freesurfer. My T1-scans are acquired at 1.5T with a resolution of 1x1x1.4 mm (sagittal). Now I have run into some problems with hippocampal segmentations. Freesurfer occasionally includes large parts of mostly inferior regions to the hippocampus segmentation. Is there any way to fix this without having to manually correct these overinclusions? Thanks in advance! Kind regards, Thomas Overbeek

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Re: [Freesurfer] Recon-all and CT/SPECT images‏
by Marie ERESUE 31 Mar '11

31 Mar '11

Hi Bruce, I have anatomical MRI (MRI 3D T1) and I did recon-all on it. But when I want to register my CT (image1_CT.nii) with my MRI (using bbregister), I have an error. When I use my SPECT I have an error too... Do you have an example of line of command in order to see my faults? thanks

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cortical thickness& curvature index
by Liukarl 30 Mar '11

30 Mar '11

Hello, Freesurfer experts: We are extracting the average cortical thickness of each hemisphere for every subject using mris_anatomical_stats. We found that for one subject (attached below), the thickness measures are quite similar but the “intrinsic curvature index” differs drastically between left/right hemispheres. Will this curvature index affect the validity of our thickness measure? ***the left hemisphere mris_anatomical_stats -l lh.cortex.label -f subject1l.txt subject1 lh limiting computations to label lh.cortex.label. reading volume /usr/local/freesurfer/subjects/subject1/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/subject1/surf/lh.white... reading input pial surface /usr/local/freesurfer/subjects/subject1/surf/lh.pial... reading input white surface /usr/local/freesurfer/subjects/subject1/surf/lh.white... structure is "lh.cortex.label" number of vertices = 157421 total surface area = 102165 mm^2 total gray matter volume = 290073 mm^3 average cortical thickness = 2.488 mm +- 0.694 mm average integrated rectified mean curvature = 0.170 average integrated rectified Gaussian curvature = 0.105 folding index = 4980 intrinsic curvature index = 592.3 ***the right hemisphere mris_anatomical_stats -l rh.cortex.label -f subject1r.txt subject1 rh limiting computations to label rh.cortex.label. reading volume /usr/local/freesurfer/subjects/subject1/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/subject1/surf/rh.white... reading input pial surface /usr/local/freesurfer/subjects/subject1/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/subject1/surf/rh.white... structure is "rh.cortex.label" number of vertices = 158401 total surface area = 102285 mm^2 total gray matter volume = 291519 mm^3 average cortical thickness = 2.482 mm +- 0.707 mm average integrated rectified mean curvature = 0.173 average integrated rectified Gaussian curvature = 0.299 folding index = 5756 Thanks in advance Karl

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