Freesurfer March 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
247 discussions

(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

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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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adding time points to longitudinal base template
by Govindarajan, Koushik Athreya 27 Mar '14

27 Mar '14

Dear FS experts, I have a serial study in which I have run cross-sectional and longitudinal analysis on 5 time points. Now, I want to add a 6th time point to my dataset. Do I have to rerun my base template creation step from scratch or is there a way to just add further time points to an existing template? Thanks Koushik

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local gyrification index in matlab
by Crofts, Jonathan 27 Mar '14

27 Mar '14

Hi I would like to analyse local gyrification data for a number of brains in Matlab. I have ran the command mris_compute_lgi -i lh.pial which results in a file called lh.pial_lgi. However, I was expecting an output of the form lh.pial_lgi.mat which could be immediately read into Matlab. Do you know how I can convert the file I have into a .mat file? Thanks in advance, Jonathan Dr Jonathan J Crofts School of Science and Technology Nottingham Trent University Clifton Campus Nottingham NG11 8NS Office: ERD 181 Tel: +44 (0)115 84 88419 Office hour: 10am-11am Monday DISCLAIMER: This email is intended solely for the addressee. It may contain private and confidential information. If you are not the intended addressee, please take no action based on it nor show a copy to anyone. In this case, please reply to this email to highlight the error. Opinions and information in this email that do not relate to the official business of Nottingham Trent University shall be understood as neither given nor endorsed by the University. Nottingham Trent University has taken steps to ensure that this email and any attachments are virus-free, but we do advise that the recipient should check that the email and its attachments are actually virus free. This is in keeping with good computing practice.

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mris_anatomical_stats aparc pial and aparcstats2table
by _andreia_＠sapo.pt 27 Mar '14

27 Mar '14

Hello list, I'm trying to get aparc surface area from the pial surface in a table using aparcstats2table but I'm not being able to... I've already created the file aparc_pial.stats inside the stats dir running the following command line from the subjects's label dir: mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a ./rh.aparc.annot -c ./aparc.ctab subjectname rh pial And if I open the aparc_pial.stats file the surfaces are bigger then in aparc (white matter). But when I try to get the table using: aparcstats2table --hemi rh --subjects subjectname --parc aparc_pial --meas area -t rh_aparc_surface_pial.txt I get the message: Number of subjects : 1 Building the table.. ERROR: cannot find /home/user/visao/Freesurfer/subjectname/stats/rh.aparc_pial.stats Use --skip flag if you want to continue in such cases What's wrong? Thank you, Andreia

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Re: [Freesurfer] Tksurfer + Histogram
by Bruce Fischl 27 Mar '14

27 Mar '14

try configure->functional overlay or something like that after loading the thickness into a functional overlay On Tue, 11 Mar 2014, Saurabh Thakur wrote: > I am referring one paper. > It mentioned about the freesurfer and cortical thickness they hv got in > tksurfer. > > I m just want to know how to get that done in tksurfer. > > I hv attached that paper for the reference. > > cheers > Saurabh Thakur, > > > > > > > On Tue, Mar 11, 2014 at 7:14 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > what is it that you want to histogram? If the thickness, > tksurfer will do > this for you if you load it as an overlay. Or you can read it > into matlab > and show it there > > On Tue, 11 Mar 2014, Saurabh Thakur > wrote: > > > Hello Freesurfer Expert, > > > > Can anyone help me with histogram plotting of different > surfaces in > > tksurfer. > > > > I looking to calculate the thickness of cortex. > > > > Thanks in advance, > > > > > > Saurabh Thakur, > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > >

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Freesurfer March 2014