Freesurfer

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30132 discussions

parametric modulator with FS-FAST
by Yuko Yotsumoto 24 Mar '11

24 Mar '11

Hi, I am wondering whether it is possible to use "parametric modulator (SPM term)" in FS-FAST. For example, say I have 4 experimental conditions. These conditions are not independent. Conditions 1-4 are determined post-hoc by subjects responses - for example, attractiveness judgements. Condition 1 for least attractive, condition 4 for most attractive.. and so on. Instead of making contrasts for each condition, I'd like to find areas that show linear relationships (= % signal changes) with the regressors (=attractiveness judgements). I heard there is a way to do this with SPM, but I'd like to do this with FS-FAST. I found this post in the archive, but I need some more info. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14181.html Thanks! Yuko Yotsumoto ----------------------------------- Yuko Yotsumoto, Ph. D. Associate Professor The Global Centers of Excellence Program, Keio University TEL:011-81-3-5427-1156 x 23851 e-mail: yukoyy(a)a7.keio.jp HP : http://web.keio.jp/~yukoyy/ ------------------------------------

2 1

isxconcat-sess question
by SK 24 Mar '11

24 Mar '11

Hi, Is there a way to use” isxconcat-sess” to average monkey fMRI data? i.e. I have two groups of monkeys (say, test and control groups) and I want to do group analysis on their data.. Regards, krishna

1 0

ROI-based fixed effect analysis
by ye xiao 24 Mar '11

24 Mar '11

Hi everyone, Is there any way to do ROI-based fixed effect group analysis in Freesurfer? I want to get the average ces and cesvar (fixed effect) in a specific ROI. Can I just average the gamma and gammavar that in the osgm folder after I ran the voxel-based ffx group analysis in that ROI to get those values, if I have a group data defined ROI? And how to average the gammavar in a ROI? Just mean(gammavar), or sqrt(mean(gammavar^2))? Thanks very much for the answers. regards, Qi Zhu Laboratorium voor Neuro- en Psychofysiologie K.U.Leuven Medical School

1 0

data preparation for SVM classification
by Alexander Ivanov 24 Mar '11

24 Mar '11

*Dear Freesurfers,* Could you please suggest me the best way to prepare structural data for SVM classification? I googled, searched the archives - there're no examples of such preparation using freesurfer algorithms (to my knowledge)... Thank you beforehand. --- *Regards,* *A. Hasfatin*

3 3

extracting segmented images with exact values for GM-WM-VL-CSF
by Alexander Lebedev 23 Mar '11

23 Mar '11

Sorry, that's of course directed to FREESURFER users and developers, and maybe there is a possibility to extract such images cerebellum-stripped?

1 0

From scanner to freesurfer
by Knut J Bjuland 23 Mar '11

23 Mar '11

Hi I am now imported my first dicom files into freesurfer. I have followed the protocol as described in the tutorial. I have some questions. Does recon-all -i /path/to/subject's/mprage.dcm -i /second/mprage/if/you/had/one -all -s subj001 import all dicoms if you pint it to hte first in serie if you are using a Simmens MPRAGE/T1 scan? Is there any other way to make sure all dicom in series is imported or if there are several series in subject. How can I import several series for just one subject. Knut J

2 1

Longitudinal FS References
by Martin Reuter 23 Mar '11

23 Mar '11

Hi everyone, we are preparing a list of papers that make use of the unbiased longitudinal stream in FreeSurfer (in version 4.4 and up). This helps us to keep track of impact and application fields (and it helps you to advertise your research on our Wiki :-) Please sent me your references (if possible with doi link). I also have an update. So far people could only cite our inverse consistent registration paper: Highly Accurate Inverse Consistent Registration: A Robust Approach, M. Reuter, H.D. Rosas, B. Fischl. NeuroImage 53 (4), pp. 1181-1196, 2010. http://dx.doi.org/10.1016/j.neuroimage.2010.07.020 http://reuter.mit.edu/papers/reuter-robreg10.pdf Now we published a small (3 page) comment, containing an overview on several of the steps in FS longitudinal processing: Avoiding Asymmetry-Induced Bias in Longitudinal Image Processing, M. Reuter, B. Fischl. NeuroImage, 2011. http://dx.doi.org/10.1016/j.neuroimage.2011.02.076 http://reuter.mit.edu/papers/reuter-bias11.pdf We plan to publish a more detailed description in the near future. Thanks for using the longitudinal stream and let me know if you have any questions. See you at HBM. Best, Martin

2 2

changing tksurfer window font size...
by Gonzalo Rojas Costa 23 Mar '11

23 Mar '11

Hi: How can I change the font size used in the tksurfer dialogs ?... such as "Configure Overlay Display" dialog ?... Because I changed the font size in Ubuntu GNOME, but it didn't changed the font size used in tksurfer... I asking that because in the "Configure Overlay Display" didn't appears the "Apply", "Close", and "Help" buttons, and I think that it could be for the font size in the GUI, or the screen resolution... Sincerely, Gonzalo Rojas Costa

2 1

autorecon1 memory error
by Paige Scalf 23 Mar '11

23 Mar '11

Hello, I'm getting the memory allocation error that is causing autorecon1 to abort. I've also attached the log file. Please help! \n mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz \n mri_gcut(6855) malloc: *** vm_allocate(size=8421376) failed (error code=3) mri_gcut(6855) malloc: *** error: can't allocate region mri_gcut(6855) malloc: *** set a breakpoint in szone_error to debug terminate called after throwing an instance of 'std::bad_alloc' what(): St9bad_alloc reading mask... use voxels with intensity 110 as WM mask threshold set to: 110.000000*0.360000=39.600000 calculating weights... doing mincut... Abort Thanks, Paige

2 1

changing tksurfer window font size...
by Gonzalo Rojas Costa 23 Mar '11

23 Mar '11

1 0

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