Freesurfer April 2008

freesurfer@nmr.mgh.harvard.edu

67 participants
102 discussions

sphere.reg in newer versions
by Fred Dick 27 Apr '08

27 Apr '08

Dear Bruce et al., I noticed a while back that there was a thread on local distortions (too much stretching + curlicues) popping up after mris_sphere; we've seen similar things, and thus far haven't been able to fix them by tweaking options. Is there any update on this? More generally, are there some example images of sphere.reg's that you all would rate good/acceptable/not so hot/definitely bad for morphological analysis purposes? Apologies in advance if this has been covered previously and I missed it. best, Fred Dick

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co-regtistering a single subject to fsaverage space
by Dick, Rachel 26 Apr '08

26 Apr '08

Dear FreeSurfer Community... what is the best approach to co-register a single subject to fsaverage space and for the results to have identical number of vertices and faces as fsaverage??? will it work by specifying a single subject in the make_average_surface command?? in other words is the sum of two individual averages (i.e., make_average_surface --subjects subjectA and make_average_surface --subjects subjectB) equal to make_average_surface --subjects subjectA subjectB??? Any guidance is greatly appreciated. Rachel

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Freesurfer analysis on synthetic images
by Christine Ecker 26 Apr '08

26 Apr '08

Hi, We use quantitative T1/T2 mapping to generate a variety of synthetic images e.g. synthetic SPGRs/T1-weighted images. I was wondering whether Freesurfer analysis can be applied to such synthetic images and whether there is anything I need to change in the recon-all processing stream in order to make it work. Thanks, Christine ----------------------------------------- Dr. Christine Ecker Section of Brain Maturation (PO50) Department of Psychological Medicine De Crespigny Park, Denmark Hill London SE5 8AF Phone: 0207 848 0947 Email: c.ecker(a)iop.kcl.ac.uk -----------------------------------------

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Paper citing FreeSurfer - Some hints requested.
by Pedro Paulo de Magalhães Oliveira Junior 26 Apr '08

26 Apr '08

Hi, In the section "Please Cite our Software" from the Wiki (http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/cite.php) we can find some guidelines to cite FreeSurfer. In writing material and methods section of the papers we publish I usually try to describe the FreeSurfer reconstruction analisys using a sometimes not so complete form. However I think one pertinent question is if there is a standard way to cite the FreeSurfer Recon-All procedure in Image Analisys that usually should be present in medical papers? It's possible to give me some pointers? Thanks in advance, Pedro Paulo Oliveira Jr

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differences between last and new version of FS
by Irene Mattisi 25 Apr '08

25 Apr '08

Hi all, I'm trying the new version of FS for a study on multiple sclerosis that our group in Padova (Italy) is doing. When I give the command "mris_anatomical_stats -b -a aparc.annot etc..." to obtain the list of cortices, I obtain about 30 cortices, while in the last version of FS I could obtain about 80 cortices. So, can I obtain 80 cortices also with the new version of FS? How can I do it? Thanks Irene Mattisi Centre of Multiple Sclerosis, Hospital of Padova, Italy

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total brain volume correction
by Ryan Muetzel 25 Apr '08

25 Apr '08

Hello, I was curious if anyone had specific recommendations for correcting ROIs for total brain volume/ICV. From what I can tell, some groups correct each ROI by computing a ratio of ROI/total_brain_volume. Other groups, however, enter total brain volume as a covariate in their statistical models. Both methods seem reasonable, but it seems entering total brain size as a covariate may be more robust, controlling for potential interactions with other IVs (e.g. age, gender). Are there other strategies I am missing? Any advice is much appreciated! Thanks! -Ryan

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Linear registration of subject meshes with FLIRT
by Damian Jenkins 25 Apr '08

25 Apr '08

In the FreeSurfer reliability paper, you recommend linearly registering the subject's meshes to each other and point to the Jenkinson paper. How actually is this done with FLIRT? Dr Damian Jenkins Department of Clinical Neurology Oxford University

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Mean FA values using wmparc
by Damian Jenkins 25 Apr '08

25 Apr '08

Once FA results are co-registered is there an easy way to use the wmparc.mgz to collect the mean FA values by region, or do we need to treat it like FMRI and make masks of each parcel and collect each mean separately? Dr Damian Jenkins Department of Clinical Neurology Oxford University

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percent signal change
by Elif SIKOGLU 24 Apr '08

24 Apr '08

Hello, We want to get the percent signal change for the activated regions and for that we want to use the h.nii and h-offset.nii files. We plan to divide the h.nii by h-offset.nii . First of all is this a correct approach? Second, h.nii has 4 frames in it, which one do we really need? Thanks Elif

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Experience with -localGI on Mac
by Martin Kavec 24 Apr '08

24 Apr '08

Hello folks, I am trying -localGI on Mac, with working Matlab2007. 1. I think that the getmatlab script is not designed to work on Mac out of the box, since it is not by default in the $PATH, so it could be caught by "which". So I uncommented the three lines and set it hard. 2. That was easy, but now I am stacked with execution, as it seems that the script stops after few minutes, after completing the first matlab function "make_outer_surface(...)". The outputs are there, in the $SUBJECT/surf/tmp.... directory. Here is the output from recon-all -s $SUBJECT -localGI set MLF = /tmp/mos"_$$_".m set MLF = /tmp/mos_10410_.m set arg1 = ${tmpdir}/${input}.filled.mgz set arg1 = tmp-mris_compute_lgi/lh.pial.filled.mgz set arg2 = ${closespheresize} set arg2 = 15 set arg3 = ${tmpdir}/${input}-outer set arg3 = tmp-mris_compute_lgi/lh.pial-outer rm -f ${arg3} rm -f tmp-mris_compute_lgi/lh.pial-outer echo "make_outer_surface('${arg1}',${arg2},'${arg3}')" > $MLF echo make_outer_surface('tmp-mris_compute_lgi/lh.pial.filled.mgz',15,'tmp-mris_compute_lgi/lh.pial-outer') echo "=================" echo ================= ================= echo "`cat $MLF`" echo `cat /tmp/mos_10410_.m` cat /tmp/mos_10410_.m make_outer_surface('tmp-mris_compute_lgi/lh.pial.filled.mgz',15,'tmp-mris_compute_lgi/lh.pial-outer') echo "=================" echo ================= ================= if ( $RunIt ) then if ( 1 ) then cat $MLF | ${MATLAB} -display iconic -nojvm -nosplash cat /tmp/mos_10410_.m /Applications/Matlab74/bin/matlab -display iconic -nojvm -nosplash Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.4.0.287 (R2007a) January 29, 2007 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> reading filled volume... closing volume... morphological closing done. writing outer surface... >> After this, the processor goes down and stays like that, nothing is happening. Thanks for help, Martin

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Freesurfer April 2008