Freesurfer

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30132 discussions

Interpretation of the curvature analysis
by Alexander Lebedev 09 Nov '11

09 Nov '11

Dear Freesurfer Users! Is it wise to interpret the increased curvature index in neurodegenerative disorders as a more expressed atrophy (which manifests as a flattening)... I am just doubting because I have never worked with curvature analysis previously and its interpretations in different articles look quite controversal... The matter is that in our work the observed increase of the curvature index was found in the majority of the "thinned" areas... Thank you very much beforehand. --- Regards, Alex Lebedev Stavanger University Hospital

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Sub-cortical structure
by Jie Shi 09 Nov '11

09 Nov '11

Hi, experts. We need to use FreeSurfer to process some analyze image data. More specifically, we want to extract the hippocampus surfaces. We know that FreeSurfer has done subcortical segmentation during -autorecon2 stage in recon-all. We have checked the resulting aseg.mgz file and found that it contains all substructures. So we wonder if there is a way to get the separated .mgz files for each substructure or could FreeSurfer generate the subcortical surfaces? Thanks a lot. Best, Jie

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MNI152 template regions
by Paolo 09 Nov '11

09 Nov '11

Hello I am a new user of freesurfer. I was wondering whether the brain regions for the MNI152 dataset are available anywhere (i mean the template brain regions for the default MNI152 template). I have also another question: i have the dti fiber tracts extracted and computed and already in .trk format. I was wondering: to bring them back into the template MNI152 space, is it sufficient to apply the talairach.xfm transformation matrix to the vertex data, or do i also need to use the m3z files (which look like a nonlinear deformation field)? thanks in advance! Paolo

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convert nifti to surface file
by kelsi 09 Nov '11

09 Nov '11

Hi all, I would like to convert a nifti zstat file from post-processing analysis to a surface to plot/view in freeview on the fsaverage or MNI152 brain. I think I would use mri_vol2surf, but I am not sure about the registration file. Would i need to run tkregister first? thank you! kelsi

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problem with skullstrip- shoulders and neck remaining
by Julia Hill 09 Nov '11

09 Nov '11

Hi there, I am having difficulties with one of my images. On first inspection, freesurfer had performed a bad skull strip, leaving the base of the skull plus what looked to be the shoulders and neck. I decreased the watershed to 5, and the shoulders/neck still appeared, so i decreased to 2 and now sections of the brain have disappeared (see attached), do you know how i can fix this? Many thanks , Julia Hill Research Assistant School of Psychiatry University of New South Wales Previously Prince of Wales Medical Research Institute www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268

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Resize window using Tcl command
by Jeff Sadino 09 Nov '11

09 Nov '11

Hello, I was wondering if there is a Tcl command to resize the window. I saw this thread, but it would not work on my computer, and I don't see any documentation in the tkmedit tcl scripting guide. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02600.html Thank you, Jeff Sadino

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Fwhm from mgh file produced by mri_glmfit
by Knut J Bjuland 09 Nov '11

09 Nov '11

Hi Is there any way to get fwhm information from an mgh produced by mri_glmfit? I have only the mgh file produce by mri_glmfit. Knut J

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End-of-line detection in text file
by Ed Gronenschild 09 Nov '11

09 Nov '11

Hi, After editing a text file holding the b vecs to be supplied as input to dt_recon this tool did not interpret the text file correctly. It turned out that dt_recon did not recognise the end-of line character in this file: this was decimal code 13 (called "CR"). It seems that dt_recon only accepts decimal code 10 (called "LF"). Is it possible to change dt_recon? I'm on a Mac, OSX 10.6.8. Cheers, Ed

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Compilation warnings as errors
by Panagiotis Foteinos 08 Nov '11

08 Nov '11

Hello list. I am compiling the source code and I get some warnings as errors. Is there a good reason that the switch -Werror is activated, or I can safely deactivate it? Could I assume that the warnings I get are harmless? Best Regards, Panagiotis Foteinos

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selxavg3 out of memory
by Po-Jang (Brown) Hsieh 08 Nov '11

08 Nov '11

Dear Doug, I saw your reply to this question a while ago. I'm using a mac pro with 16G memory but having the same problem. Do you know if this is a matlab memory issue (matlab R2009a) or an overall memory issue of the machine? I'd appreciate if you can give me some helps. (I have 12 runs, each run has 200 TRs and 20 events, TR=2s) Thanks very much! Brown ps. Here are the commands and error messages: mkanalysis-sess -analysis $ANALYSIS -TR 2 -paradigm $PARAFILE -event-related -funcstem $FUNCSTEM -nconditions 9 -mcextreg -runlistfile $RLF -fsd bold -fir 10 30 -native selxavg3-sess -s $SUBJECTID -df sessdir -analysis $ANALYSIS -no-con-ok >>>> Whitening Computing whitening matrices MATLAB(19078,0xb0987000) malloc: *** mmap(size=1382400000) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug ??? Out of memory. Type HELP MEMORY for your options. Error in ==> fast_selxavg3 at 603 Sinv = zeros(ntptot,ntptot,flac0.acfbins); >> pure virtual method calledOpening log file: /var/root/java.log.19078 Abort ------------------------------------------ ERROR: fast_selxavg3() failed\n >>>> I think you might need a bigger computer. A run of that data set will require almost 1G, and there are places in the code where several data structures of the same size will need to exist simultaneously, so you can easily use 2 or 3 or 4 G to process a single run. In theory you could divide them up into smaller bits as long as you handle the stimulus schedule files properly. doug Schadwinkel, Stefan wrote: >*Hi,*>**>*as I tried to show in the posting, I tried it on 3 Machines:*>**>*1) Linux, 1 GB memory: out of memory during OLS Residual Pass, then Java crashes*>*2) Linux, 2 GB memory: out of memory during Whitening*>*3) Mac (Mac OS X 10.5), 4 GB memory: as well: out of memory during Whitening*>**>*Thanks a lot & best regards,*>**>*Stefan Schadwinkel * -- Po-Jang (Brown) Hsieh Neuroscience and Behavioral Disorders Program Duke-NUS Graduate Medical School 8 College Road, Singapore 169857 -- Lab website: Brain & Consciousness Lab<https://sites.google.com/site/brainconsciousnesslab/> <http://brownhsieh.blogspot.com/>

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