Freesurfer

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18 participants
30087 discussions

mc-bbr
by SHAHIN NASR 27 Mar '14

27 Mar '14

Hi, For a project in which subjects have repeated head movements, I want to register every TR to anatomical scans separately to reduce the effect of head movement as much as possible. When I checked the old posts, I noticed that there has been a code since 2011 ( https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-December/021691.…) to do this (named mc-bbr). But I am not sure if it is valid any more and not sure how does it works. As far as I see, there is no flag for mc-bbr or something similar to that in preproc-sess. I appreciate if you guide me through it. Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] Problem about the fMRI Analysis?
by Linda Xu 27 Mar '14

27 Mar '14

Dear Douglas, I do not understand what's your meaning? Yes I think the afni results has already alined to T1.mgz, so it is already in talairach space. I do not know what to do next? As I have two groups subjects. I do not know what to analysis the correlation different between two groups by using surface-based analysis of freesurfer. Linda Message: 5 Date: Wed, 26 Mar 2014 14:05:46 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Problem about the fMRI Analysis? To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <533316FA.50903(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Are the AFNI results already in talairach space? If so, then there is no point in going to surface space. doug On 03/26/2014 01:22 PM, Linda Xu wrote: > I get the correlation result between two condition of the functional > data by using AFNI( I do not know how to do correlation by using > freesurfer) > And then I use the bbregister to aline the correlation result (produce > by Afni) to the anatomical result produced by using freesurfer. > Next I using mri_vol2surf to aline the each one's functional result to > the fsaverage offer by freesurfer. > My question is :1 Should I need to do mri_vol2vol next for each subject? > 2 I have two group of subjects. I want to know > if there is some correlation different between them? What should I do > next? > Thanks very much! > Linda >

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space conversion in the mri_surf2vol
by charujing123 27 Mar '14

27 Mar '14

Dear FS experts, I completed mri_surf2vol converting lh.gender_age.thickness.10.mgh into test.nii based on the fsaverage template. I want to know what space for the two files(*.mgh and *.nii) respectively? Thanks. All the best. Rujing Zha 2014-03-27 charujing123

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MNI CONVERSION PROBLEM
by Gabriel Gonzalez Escamilla 27 Mar '14

27 Mar '14

Dear FS experts, I've been dealing with the conversion to MNI152 of some volumetric labels of my subjects extracted with mris_extract_label in FS v.5.1 but, I've been unable to succeed. I've tried bbregister and mni152reg commands, both of them give me an example to check at the registrations using tktegister2, when I use it everything seems to be OK, but when I do apply with mri_vol2vol any of the matrices to the volumetric masks, they appear to be rotated, I don't know how is it possible or how to fix it. Any help will be really appreciated. Many thanks in advanced, Gabriel

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(no subject)
by Qing Yu 27 Mar '14

27 Mar '14

Dear Freesurfer experts, I'm new to freesurfer and I'm now trying to get anatomical labels from the Destrieux Atlas. I know that we can easily extract labels using the tksurfer GUI by a couple of mouse clicks (load atlas -- click on one label -- save selected label), but I'm just wondering if there is any existing freesurfer command line that can save labels from the terminal (assuming that the index and names of the labels are known)? Thanks so much for any help! Best, Qing

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saving labels from the terminal?
by Qing Yu 27 Mar '14

27 Mar '14

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mris_preproc patch download
by _andreia_＠sapo.pt 27 Mar '14

27 Mar '14

Hello list, I'm working with FS 5.0 and I'll be using either qdec or mri_glmfit for whole brain analysis. The link http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi#Installation takes me to ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mris_prepr… where a script appears. I thought that it would take me to a download page of some type of file that I would use to substitute the mrs_preproc I have now. How should I proceed? Copy and the paste the script text in my current mris_preproc (deleting what is now written) and then save and run qcache. Or, since I already have FS 5.3 installed in a different location, can I simply copy and paste the 5.3 mris_preproc file replacing the 5.0 one? I predict that both approaches are equivalent but I want to be completely sure that I'll be doing it in the right way. Thanks, Andreia

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Cohen's D & Multiple Comparisons
by L. Schweren 27 Mar '14

27 Mar '14

Dear FreeSurfer experts, For my group-level analyses, I created Cohen's D effect size maps. Now I looking the different methods to correct for multiple comparisons (FDR and MC-simulations), it seems to me they are based on p-values, not on effect sizes. I tried applying FDR-correction in tksurfer on the effect size maps. This indeed results in a higher threshold for clusters to appear, but I am not sure whether this is a valid tool to use in statistical maps other than .sig ? As a p-value reflects the "chances" of finding this effect by chance and the MC-correction is about reducing the "chance of false positives", and Cohen's D not reflecting such chances, is correction for multiple comparisons even sound when reporting effect sizes? If so, what would be the best approach to determine an MC-corrected threshold for effect sizes? Thanks again for your help, you have been very helpful so far! Best wishes, Lizanne

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Problem about the fMRI Analysis?
by Linda Xu 27 Mar '14

27 Mar '14

I get the correlation result between two condition of the functional data by using AFNI( I do not know how to do correlation by using freesurfer) And then I use the bbregister to aline the correlation result (produce by Afni) to the anatomical result produced by using freesurfer. Next I using mri_vol2surf to aline the each one's functional result to the fsaverage offer by freesurfer. My question is :1 Should I need to do mri_vol2vol next for each subject? 2 I have two group of subjects. I want to know if there is some correlation different between them? What should I do next? Thanks very much! Linda

2 2

mri_glmfit-sim error
by yd li 27 Mar '14

27 Mar '14

Hello list, I'm working with FS 5.0.3. When I used 'mri_glmfit-sim --glmdir /home/a/freesurfer/g2.lh/C1 --sim mc-z 5000 4 mc-z.abs --sim-sign abs --cwpvalthresh 0.05 --overwrite' for multiple comparison correction, i got an error message 'cannot find /.../g2.lh/C1/mri_glmfit.log'. I found a mri_glmfit.log in folder /.../g2.lh, and copied this file to folder /.../g2.lh/C1/.But i still got an error 'fwhm: Undefined variable.' Can anybody help me settle this problem? Thank you! --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: wheezy/sid Kernel info: Linux 3.5.0-23-generic x86_64

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