Freesurfer March 2011

freesurfer@nmr.mgh.harvard.edu

111 participants
170 discussions

Longitudinal comparison of thickness data
by Jonathan DuBois 31 Mar '11

31 Mar '11

Hi Freesurfer users, I have been working from the list posting below for vertex comparison of longitudinal thickness data, although there are a couple issues I was hoping someone could help with. Using FS v5.0 with the fixed binaries, I have put together the following steps for data comparison following the third step of the longitudinal stream with their associated commands and questions (highlighted in bold). I am sorry if it is a lot of information, although I thought it might be useful for other users working with longitudinal analysis. Thanks Jonathan ------------------------------ Martin Reuter mreuter at nmr.mgh.harvard.edu <freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Longitudinal%20processing&In-Reply-To=%3C1277843000.24825.221.camel%40riemann.nmr.mgh.harvard.edu%3E> Tue Jun 29 16:23:20 EDT 2010 Hi Sandra, (and the list, I think this might be interesting for others) 1. the longitudinal ?h.thickness files are in registration (within subject) so in order to compute the difference or the rate you can simply use: mris_calc -o lh.outdiff sdir2/surf/lh.thickness sdir1/surf/lh.thickness and for the rate, you can divide by time 1 thickness or by the average thickness. If the time points are not equally spaced across subjects, you can also divide by difference in time. It is best to smooth the thickness files before you do all this (i.e. within time point smooth the ?h.thickness files with mri_surf2surf). 2. then map everything to your template (e.g. fsaverage) with mri_surf2surf 3. there you can stack the thick-differences or thick-rates with mri_concat 4. do the glm Best Gruesse, Martin ------------------------------ 1. Smooth surface data: mri_surf2surf --s subj1_tp1.long.template --sval subj1_tp1.long.template/surf/lh.thickness --tval subj1_tp1.long.template/surf/lh.thickness.fwhm10.mgh --fwhm-src 10 --hemi lh mri_surf2surf: could not read surface /space/mdeh2/1/halgdev/emcbkp/1/halgdev/projects/nyuproj/subjects/subj1_tp1.long.template/surf/lh.sphere.reg No such file or directory *--The longitudinal processing does not create a ?h.sphere.reg or a ?h.sphere for running mri_register. While, the registration is specific to the longitudinal analysis, could I simply copy over the ?h.sphere.reg from the original subject, since it is the same brain? If not, how should this be generated?* ** 2. Compare time point differences within subjects using mris_calc and one of the three options: a. divide tp2 by tp1 - [mris_calc -o lh.NC024_thick_diff_fwhm10.mgh subj1_tp2.long.template/surf/lh.thickness.fwhm10.mgh div subj1_tp1.long.template/surf/lh.thickness.fwhm10.mgh] b. divide by average thickness c. divide by between scan time difference *--Option (a) is straight forward, although option (c) would be ideal given that our subjects vary in time between scans. How would option (b) or © be set up with mris_calc? Would mris_calc work for more than two time points?* 3. Register subjects' between scan difference map to fsaverage mri_surf2surf --s lh.NC024_thickness_diff_fwhm10.mgh --trgsubject fsaverage --tval lh.NC024_thickness_diff_fsaverage.fwhm10.mgh --fwhm-src 10 --hemi lh *--I haven't gotten to this step yet, but I'm not sure that it will work given that there is only a .mgh file without an associated subject? Also, similar problem to question one (no sphere.reg).* ** 4. Stack subjects' difference maps using mri_concat 5. Run GLM using mri_glmfit

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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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Freesurfer March 2011