Freesurfer April 2011

freesurfer@nmr.mgh.harvard.edu

121 participants
166 discussions

Workshop on Diffusion Tensor Imaging in San Francisco on June 7, 2011 (fwd)
by Bruce Fischl 08 Apr '11

08 Apr '11

FYI ---------- Forwarded message ---------- Date: Fri, 8 Apr 2011 15:08:27 -0700 From: Lauren Mullin <lauren.mullin(a)ucsf.edu> To: fischl(a)nmr.mgh.harvard.edu Subject: Workshop on Diffusion Tensor Imaging in San Francisco on June 7, 2011 Dear Dr. Fischl, Dr. Weiner suggested I contact you to see whether you would be interested in advertising this DTI workshop (flyer with information and registration form attached) on the Freesurfer website. Please let me know, thank you & kind regards, Lauren Mullin Administrative Assistant III Center for Imaging of Neurodegenerative Diseases San Francisco Veterans Affairs Medical Center 4150 Clement Street (114M) San Francisco, CA 94121 Tel: 415-221-4810 Ext 6467 Fax: 415-668-2864 Email: lauren.mullin(a)ucsf.edu

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ICV error and talairach registration bad outputs...
by Gonzalo Rojas 08 Apr '11

08 Apr '11

Hi: I forgot the image... Sincerely, Gonzalo Rojas Costa

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ICV error and talairach registration bad outputs...
by Gonzalo Rojas 08 Apr '11

08 Apr '11

Hi: In the image that I am sending attach, there exist a not exact talairach registration in the superior part of the brain... That difference produce an important error in the ICV, or not ?... Sincerely, Gonzalo Rojas Costa

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erroneous ICV volume ?...
by Gonzalo Rojas Costa 08 Apr '11

08 Apr '11

Hi: I have an MRI of a 34 years old patient that have a brain atrophy, but with freesurefer I got an ICV of 1120 cc that is near the normal size for her age... I review the talairach transform, but I think it is ok... What could be the problem ?... Could I upload the MRI volume ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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erroneous ICV volume ?...
by Gonzalo Rojas Costa 08 Apr '11

08 Apr '11

Hi: I have an MRI of a 34 years old patient that have a brain atrophy, but with freesurefer I got an ICV of 1120 cc that is near the normal size for her age... I review the talairach transform, but I think it is ok... Could you please send us the study to process it and send me some tips ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Job Opening: Research Technician in Brain Imaging
by Schiel, Matthew 08 Apr '11

08 Apr '11

The Solodkin/Small Brain Circuits Laboratory at the University of California, Irvine, will soon have an opening for a research technician in image processing. This job would be ideal for someone interested in applying basic skills in signal processing or applied mathematics to a variety of functional and structural neuroimaging studies related to human language processing and motor control, including healthy adults and children, and adults and children with neurological injuries or disease. Job tasks include: analyzing functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) data, performing statistical analyses of processed human data, working with cortical surface maps, managing and updating our imaging database, and helping to improve our processing procedures, including our use of high-performance cluster and grid computers. The ideal candidate will have a B.A. or B.S. degree in engineering, physics, mathematics, or computer science; knowledge of the UNIX operating system; programming experience; interest in biomedical applications; coursework in signal analysis and/or statistics. Variations from these ideals will certainly be entertained in an otherwise highly qualified candidate. Although this position is not yet formally posted, we are interested in hearing from qualified candidates now. If interested, please forward your CV/resume to mschiel(a)uci.edu. This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

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funcroi-config -frame question
by Eiran Vadim Harel 08 Apr '11

08 Apr '11

Hello, I did an FIR analysis and want to get the activation measure for specific ROI at consequent time frames. mkanalysis-sess -analysis context_FIR.rh -surface fsaverage rh -fwhm 5 -paradigm sca_wca.par -event-related -fir 4.4 17.6 -refeventdur 2.2 -mcextreg -TR 2.2 -nconditions 2 -force mkcontrast-sess -analysis context_FIR.rh -contrast strongweak-vs-fix -a 1 -a 2 -c 0 selxavg3-sess -s 0121_MC -analysis context_FIR.rh -force I then gave separate funcroi-config commands to each time frame 0-7 funcroi-config -roi v1.rh.frame0 -label rh.V1 -analysis context_FIR.rh -frame 0 -force funcroi-table-sess -o v1.rh.frame0.table.txt -roi v1.rh.frame0 -a context_FIR.rh -s 0121_MC -map cespct it created the text file with: 0121_MC 84.034 when i ran it for the rest of the time frames it gave me the same number: funcroi-config -roi v1.rh.frame7 -label rh.V1 -analysis context_FIR.rh -frame 7 -force funcroi-table-sess -o v1.rh.frame7.table.txt -roi v1.rh.frame7 -a context_FIR.rh -s 0121_MC -map cespct It gave the same output in the text file: 0121_MC 84.034 I am using freesurfer 5 on shimshon: the project directory: /space/shimshon/2/users/eiran/contproc2 SUBJECT_DIR- /space/shimshon/2/users/eiran/subjects I made the frames according to your instructions on a request from dec. 2010 with the same problem: > > Currently, it is not as convenient to do this with version 5. You have > to create a condition-vs-fixation for each condition that you want a > time course for. Then for each condition, you need to run > funcroi-table-sess for each time point (using the -frame option), then > construct the waveforms from these files. It's a bit of a hassle, but > scriptable. Thanks!

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functional ROI analysis problem
by Katie Bettencourt 08 Apr '11

08 Apr '11

Hi all, I'm doing ROI analysis on functional data with an anatomical label, and while the activity looks strong and robust in tksurfer, the % signal changes I am getting are very low (and much lower than we've previously found), and I'm not sure what's going on. I'm running Freesurfer 4.5 on red hat linux. The design is a blocked design with 4 non-null conditions, baseline is fixation. Attached is a picture of the activity I get for 2 subjects for on of the conditions vs fixation (baseline) at a p<0.05 threshold with the ROI outlined in black as well as the output from roisummary-sess for these two subjects in that roi. I calculate % signal change based of the output from roisummary-sess, dividing each condition by the baseline in that file and then multiplying by 100. % signal changes are listed below, along with all commands run. % signal change: 110222SKJ_connected 110222SP_connected 0.000988998467052 0.000533852720367 0.00105349836708 0.000556814127695 0.000408499366826 0.000327200054419 0.000440749316839 0.000436266739225 commands: mkanalysis-sess -analysis connect -TR 2 -paradigm connect.dat -designtype blocked -funcstem fmc -motioncor -runlistfile connect_runs.txt -inorm -tpexclude tpexclude.dat -nconditions 4 -timewindow 20 -gammafit 2.25 1.25 -noautostimdur mkcontrast-sess -analysis connect -contrast connected_vs_unconnected -a 1 -c 2 mkcontrast-sess -analysis connect -contrast connected_vs_noise -a 1 -c 3 mkcontrast-sess -analysis connect -contrast connected_vs_phase -a 1 -c 4 mkcontrast-sess -analysis connect -contrast connected_vs_fix -a 1 -c 0 mkcontrast-sess -analysis connect -contrast unconnected_vs_noise -a 2 -c 3 mkcontrast-sess -analysis connect -contrast unconnected_vs_phase -a 2 -c 4 mkcontrast-sess -analysis connect -contrast unconnected_vs_fix -a 2 -c 0 mkcontrast-sess -analysis connect -contrast noise_vs_phase -a 3 -c 4 mkcontrast-sess -analysis connect -contrast noise_vs_fix -a 3 -c 0 mkcontrast-sess -analysis connect -contrast shape_vs_noise -a 1 -a 2 -c 3 mkcontrast-sess -analysis connect -contrast shape_vs_phase -a 2 -a 1 -c 4 mkcontrast-sess -analysis connect -contrast shape_vs_noisephase -a 2 -a 1 -c 3 -c 4 mkcontrast-sess -analysis connect -contrast act_vs_fix -a 2 -a 1 -a 3 -a 4 -c 0 selxavg3-sess -sf connect-sess -df connect.dir -analysis connect #run ROIs setenv anal connect foreach roi ( infIPS supIPS loc ) foreach h (lh rh) func2roi-sess -roidef ${roi}-${anal}-${h} -analysis $anal -anatlabel ips_loc/${roi}-${h} -sf connect-sess -df connect.dir roisummary-sess -sumfile ips-rois/${anal}_${roi}-${h}.dat -roidef ${roi}-${anal}-${h} -analysis ${anal} -sf connect-sess -df connect.dir python roi_reader.py -r ${roi} -a ${anal} -z ${h} -f ips-rois -c 4 end end Thanks, Katie

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How to overlay anatomical surfaces with externally calculated quantities?
by Rummel, Christian 08 Apr '11

08 Apr '11

Dear FreeSurfer team, I want to analyze regional cortical thickness using higher-order statistics implemented in an external C routine. This is currently done exporting thickness information in spherical coordinates for all subjects to ascii files for subsequent analysis (mris_convert -c lh.thickness lh.sphere lh.thickness-sphere.asc) After analysis I end up with one file for each subject having the same format as lh.thickness-sphere.asc but with thickness replaced by some higher-order statistics. Is there an easy way of bringing back this information into FreeSurfer format for display with tksurfer? If not, what else would one do to display information on anatomical surfaces, given FreeSurfer's vertex identification number and a scalar quantity? Thanks, Christian ______________________________________________________________ Christian Rummel (PhD) Support Center for Advanced Neuroimaging (SCAN) Institute for Diagnostic and Interventional Neuroradiology Inselspital, 3010 Bern, Switzerland

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effect size for cortical thickness changes
by Ritobrato Datta 07 Apr '11

07 Apr '11

Hello All, Are there reports of studies of cortical thickness changes using freesurfer which report effect sizes for the ROIs of interest ie how much of a change in millimeters was observed as opposed to p-values reported. Please let me know. Thanks a lot Ri

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Freesurfer April 2011