Re: [Freesurfer] How to avoid overlaps between volume labels?

Thank you all for your suggestions. I binarized my labels, used mri_concat --max, then re-binarize the volumes. It worked great. Thanks again, Yuko Yotsumoto On Jun 7, 2012, at 6:58 AM, Douglas Greve wrote: It depends on how graceful you want to be with resolving the overlap. One simple way

Re: [Freesurfer] correction for multiple comparisons

Thank you very much for your answer. Are 10 000 iterations also used when I am running a Monte Carlo simulation in qdec? Thanks, Marie 2012/6/9 Douglas N Greve gr...@nmr.mgh.harvard.edu they are two different correction schemes. If they gave the same answer, then it would not make sense to

Re: [Freesurfer] MNI to RAS surface coordinates

Thank you for your answer. Just one more question, is the fsaverage already in MNI305 space? In this case, the RAS coordinates from tksurfer/QDEC are already MNI? Regards, Yolanda 2012/6/7 Douglas N Greve gr...@nmr.mgh.harvard.edu Here are instructions to go from a surface RAS to the mni305

[Freesurfer] spmT.img maps into fsaverage

Dear Freesurfer experts, How could I overlay spmT.img maps from a VBM study on fsaverage? I would like to convert the significant clusters into labels. Thank you in advance, Yolanda ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] repost - large-scale reconstruction errors

Hi Bruce, Both are uploaded. FI137 is the missing brain from surfs and wm.mgz, and OH120 is the cerebellum in -aseg. We're running freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0. thanks, Nicole On Fri, Jun 8, 2012 at 8:22 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Nicole If you

Re: [Freesurfer] correction for multiple comparisons

yes, though I would probably do it outside of qdec as it can take a while (hours or days) On 06/12/2012 08:03 AM, Marie Schneider wrote: Thank you very much for your answer. Are 10 000 iterations also used when I am running a Monte Carlo simulation in qdec? Thanks, Marie 2012/6/9

Re: [Freesurfer] MNI to RAS surface coordinates

yes On 06/12/2012 08:17 AM, Yolanda Vives wrote: Thank you for your answer. Just one more question, is the fsaverage already in MNI305 space? In this case, the RAS coordinates from tksurfer/QDEC are already MNI? Regards, Yolanda 2012/6/7 Douglas N Greve gr...@nmr.mgh.harvard.edu

Re: [Freesurfer] spmT.img maps into fsaverage

This is not an easy thing to do because there is a non-linear transform between them. One thing you can do is to run recon-all on the VBM registration target. Or, you can average the transformed T1s together and run recon-all on that. doug On 06/12/2012 09:22 AM, Yolanda Vives wrote: Dear

Re: [Freesurfer] [martinos-tech] isxconcat-sess problem

Not sure. In principle no, but it might cause the brain to be non-centered or out of the field of view. I would just run tkregister2 --fstal --s subject and get it more-or-less right (or at least check that it is not out of the field of view). doug On 06/12/2012 09:32 AM, Yue, Xiaomin wrote:

Re: [Freesurfer] Freesurfer - problem with automatic labeling of V1 using the Hinds method in 5.1.0

Dear Dr. Bock, I get the same error in FS 5.1.0 when running recon-all -s subject -label_v1. Did you find a solution? Best regards, Anders Hougaard, MD Danish Headache Center Dept. of Neurology Glostrup Hospital Copenhagen Denmark 2011/11/11 Andrew Bock ab...@u.washington.edu Hello, I am

Re: [Freesurfer] Freesurfer - problem with automatic labeling of V1 using the Hinds method in 5.1.0

try symlinking the ?h.white surfaces to the ?h.smoothwm and see if that solves your problem cheers Bruce On Tue, 12 Jun 2012, Anders Hougaard wrote: Dear Dr. Bock, I get the same error in FS 5.1.0 when running  recon-all -s subject -label_v1. Did you find a solution? Best regards, Anders

Re: [Freesurfer] Building FreeSurfer with OpenMP enabled

Akio, the results of our dev tree will be different from the stable branch (as we are continually incorporating improvements in the dev tree which eventually make their way into the public stable release). The new OpenMP code will also change the results, but we have found not significant

[Freesurfer] ICV measurement in freesrufer

Dear all, How does the freesurfer calculate the ICV? By adding up all the cortical and sub-cortical volumes including WM and GM and CSF? If so does it also include cerebellum and brain stem? Thanks Ayaz The information contained in this message and any attachments is intended only for the

Re: [Freesurfer] ICV measurement in freesrufer

See http://www.freesurfer.net/fswiki/eTIV On 06/12/2012 01:23 PM, Ayaz, Muhammad wrote: Dear all, How does the freesurfer calculate the ICV? By adding up all the cortical and sub-cortical volumes including WM and GM and CSF? If so does it also include cerebellum and brain stem? Thanks

[Freesurfer] urgent help with cortical areas

Hello experts, I have the aparcstat files for corticla thickness. I would want to know is there any information on how may I group these regions more broadly ex frontal , temporal lobe areas. Thanks Rashmi. This document may contain information covered under

[Freesurfer] Correction for Multiple Comparisons

Hey all- This may be a simple question to answer, but in an analysis looking at say cortical thickness between Group 1 and Group 2 with say 3 continues variables (age, anxiety, IQ) there would be a contrast matrix of 1 -1 0 0 0 . How does free surfer correctly remove the effects of the continues

Re: [Freesurfer] urgent help with cortical areas

you might want to look into this: http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation cheers K From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Rashmi Singh [rsi...@laureateinstitute.org]

Re: [Freesurfer] urgent help with cortical areas

YOu can try grouping them into lobes by creating a new annotation with mri_annotation2label --lobesStrict --subject subject --hemi lh Then run mris_anatomical_stats using this annotation doug On 06/12/2012 02:34 PM, Rashmi Singh wrote: Hello experts, I have the aparcstat files for corticla

Re: [Freesurfer] Correction for Multiple Comparisons

It includes them in the model as regressors, so, for example, the Group 1 mean (beta) is computed simultaneously with the slope. Think of a bunch of dots that form a line. You fit it to y = x*m + y0. y0 is the intercept (ie, expected y at x=0). In your case you have two y0's (one for each

[Freesurfer] (no subject)

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

[Freesurfer] specifying multiple contrasts

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

Re: [Freesurfer] matrix error

When I adjusted for the scale, the matrix is still ill-conditioned. It looks like some of the columns are very similar to each other. doug On 06/12/2012 05:15 PM, mdkrue...@uwalumni.com wrote: Hello- I am trying to analyze the cortical thickness between two groups of subjects Cl1 and CL2.

Re: [Freesurfer] specifying multiple contrasts

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

Re: [Freesurfer] Freesurfer - problem with automatic labeling of V1 using the Hinds method in 5.1.0

Here is the hack I use, taken from Krish's previous post. I hope this helps: cd $SUBJECTS_DIR recon-all -s subject -label_v1 /usr/local/freesurfer4.5/freesurfer/bin/mris_spherical_average -osurf v1.invivo.reg -n -o subject label rh.v1.invivo.label rh v1.invivo.reg V1_average