Freesurfer

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30096 discussions

mri_surfcluster command syntax
by d.g.lawyer＠medisin.uio.no 05 Jul '06

05 Jul '06

Hi, An oddity re: command syntax for mri_surfcluster. The --ocp flag writes the file sig.cluster.mgh. However, when I also include the --cwsig flag the file sig.cluster.mgh is not generated. Currently I run the command twice, once to generate the sig.cluster.mgh, and once to generate the cluster-wise_sig.mgh. I suspect there is a better way. I am using FreeSurfer 3 stable centos4 mri_surf version 1.26, 2006/02/22

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cluster analysis with mri_glmfit
by d.g.lawyer＠medisin.uio.no 05 Jul '06

05 Jul '06

Hi, I have a couple of specific questions regarding cluster analysis with mri_glmfit that weren't answered at the course the other week and on which the documentation is slightly vauge. My data includes continuous variables (age and IQ, matching the documentaion!) so I should use MC simulation instead of permutation. I have 70 subjects in each group (case/control). The course notes say I can use the mc-z if I have O(80) subjects. How can I tell if I have enough subjects; is there a statistical test that would show if the outputs are reasonable? I would think 70 is close enough to 80, but would like to be able to test it as I assume it is going to depend to a certain extent on the data. The notes say I need to supply the fwhm of the residual. This value is easy to find in the y file, but it is not clear how to specify it to mri_glmfit. Do we use the --fwhm flag as in the example on page 104/202 in the coursebook? Note that the example uses mc-full, not mc-z, and that the --fwhm flag an arguement to mri_glmfit, not a part of the --sim flag. Finally, with regard to the clustering. The commmand as given in the course notes (pg 104/202) works, but the example does not match mri_surfcluster --help. Specifically, the --help text does not mention (that I could see) the --src flag or the --ocp flag. We are using the example from the course as our template. What is the output of the --ocp flag? Thanks!

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registration problems
by bdragans＠uke.uni-hamburg.de 04 Jul '06

04 Jul '06

Dear freesurfers, I got some problems running the mri_ca_register bit of recon-all. The script suddenly brakes down while labeling for the right thalamus is running. Occured twice on the same spot... my specifications: freesurfer-Darwin-tiger-stable-pub-v3.0.3 recon.log file is attached any help is greatly appreciated many thanks

3 2

optseq and psychometric function
by Betina 04 Jul '06

04 Jul '06

Dear List: I have a question concerning optimizing the presentation of a psycho- metric SCASE procedure with optseq. Subjects will view two interleaved SCASE in the scanner. SCASE1 and SCASE2 test the whole length of stimuli strengths for two different conditions. To obtain the best sequences in optseq do I register SCASE1 and SCASE2 as two conditions, or should the individual test steps (ie at 10, 20, 30 % ...) be listed individually as conditions ? Does registering only SCASE1 or SCASE2 without breaking down into individual test units provide accurate efficiency and cost functions in optseq ? Finally, is an efficiency of 25 good for such a design ? Thank you very much for your help!

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File Conversion Inquiry
by Gregory Scott 03 Jul '06

03 Jul '06

We have complex-valued volumes (retinotopic mapping data) in structural space (1,1,1mm) We'd like to convert this to a surface overlay (.w) Can mri_vol2surf handle complex data and can Freesurfer display this? (with some sort of color wheel scheme) Also, does freesurfer require both polar and eccentricity mapping data simulateously or can one display (eg. polar mapping) data separately? Thank you very much for your time and any help Sincerely, Gregory Scott

4 3

surface-based analysis in FsFast
by David Ziegler 03 Jul '06

03 Jul '06

Hi all! Will surface-based fMRI analysis in FsFast show activation in subcortical & MTL structures (caudate, putamen, thalamus, hippo/amygdala) or is it limited to the neocortical surface? If not, is there a way to get such statistics without resorting to a volume analysis? Thanks! David

3 2

tksurfer/suse 10.1 troubles
by Sebastian Moeller 02 Jul '06

02 Jul '06

Hi List, running freesurfer (centos 4 x86_64 3.0.2 pub full under SuSE 10.1 (had to upgrade from 9.3 because of stability issues)) I get the following Error while trying to run surf-sess (over ssh tunneled X11): surfer: ### GL window already open: can't open second % freeglut ERROR: Function <glutBitmapCharacter> called without first calling 'glitInit'. Interestingly both SuSE 9.3 and 10.1 use libglut.so.3.8.0 (freeglut). The exact command I ran from the mystudy directory is: surf-sess -sf sf -df df -analysis a3 -contrast c1_2 -hemi lh -surf inflated This exact command worked with SuSE 9.3 (all OSs 64bit linux). I am downloading 3.0.3 ATM to see whether this was fixed. If any of you have any advise I am keen to hear it ;). Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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mri_segstats only generated values for index 0-82
by Nguyen, Thang Q 30 Jun '06

30 Jun '06

Hello all, I was able to generate statistics on functional overlays but for some reason, the statistics do not have values after the structure name "Right-non-WM-hypointensities." Everything after this region listed has values of zero for the Mean, StdDev, Min, Max, and Range. The command I used is listed below: mri_segstats --brain-vol-from-seg --in subbj1.img --seg aseg-in-subj1.img --ctab-default --sum -subj1.output.txt Is this a problem with the registration, the command line, or something else? Thank you for your help, -Thang Nguyen

3 2

Aseg.stats measurements
by Goradia, Dhruman D 30 Jun '06

30 Jun '06

Hi all, Can anyone tell me how freesurfer defines Intracranial volume, Brain segmentation volume and Brain mask volume? What is the difference between the 3 measures? -Dhruman

3 2

help: freesurfer on debian amd64 (problem with libtiff)
by Davide Anchisi 30 Jun '06

30 Jun '06

Hi, I have an amd64 machine with a Debian GNU/Linux (v. testing) system. I'd like to use freeSurfer but I got some problem. I installed freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz When I run tkmedit (or tksurf) I get the following message: tkmedit: error while loading shared libraries: libtiff.so.3: cannot open shared obj ect file: No such file or directory On my system I have libtiff4. Any suggestion? Thanks, Davide

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