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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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Re: [Freesurfer] recon-all on version 4.5
by Saad Ramadan 07 Apr '11

07 Apr '11

Hi Bruce, I found on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Fixing Bad Output From the Talairach Registration FreeSurfer computes a linear Talairach transform contained in a 3x4 matrix in a file called talairach.xfm and is located in the <subject name>/mri/transforms directory. Under some circumstances, the alignment can *fail the automatic failure detection scheme* (-tal-check flag, which can be disabled via -notal-check). Indeed, when I run recon-all with -notal-check, I donot see: *#@# Talairach Failure Detection Wed Apr 6 12:36:53 EDT 2011 in recon-all-staus.log file any more. Does this mean I have to do the manual talairach registration every time I run my recon-all, as it is a time consuming process? Is there any thing (from an acquisition perspective or otherwise) to eliminate this problem? Thanks in advance. On Thu, Apr 7, 2011 at 12:27 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > but you don't know what else was running on the same node at the time, do > you? Can you lock the amount of memory you will need? I think to be safe you > want 3G, but maybe Nick can chime in > > > On Thu, 7 Apr 2011, Saad Ramadan wrote: > > Hi Bruce, >> >> it is a cluster here a Brigham and wouldnot expect it to be low on memory. >> When I run a shell: >> free -mt >> >> I get: >> >> >> total used free shared buffers >> cached >> Mem: 3950 2918 1031 0 163 1596 >> -/+ buffers/cache: 1158 2791 >> Swap: 3820 125 3694 >> Total: 7770 3044 4725 >> >> >> On Thu, Apr 7, 2011 at 10:52 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> >wrote: >> >> how much memory do you have in that machine? >>> >>> Bruce >>> >>> On Thu, 7 Apr 2011, Saad Ramadan wrote: >>> >>> Dear all, >>> >>>> >>>> >>>> I ran (on an isotropic MPRAGE ): >>>> >>>> recon-all -subject mysubject -i >>>> ./DICOM/test.25.1.2010.04.27.21.51.18.31250.14004670.IMA -autorecon-all >>>> >>>> which ran for few hours and then exited without a successful end as can >>>> be >>>> seen on log file below. >>>> >>>> >>>> Contents of *recon-all-status.log* are: >>>> >>>> Wed Apr 6 12:31:55 EDT 2011 >>>> #@# MotionCor Wed Apr 6 12:33:10 EDT 2011 >>>> #@# Nu Intensity Correction Wed Apr 6 12:33:40 EDT 2011 >>>> #@# Talairach Wed Apr 6 12:35:22 EDT 2011 >>>> *#@# Talairach Failure Detection Wed Apr 6 12:36:53 EDT 2011 >>>> *#@# Intensity Normalization Wed Apr 6 12:36:53 EDT 2011 >>>> #@# Skull Stripping Wed Apr 6 12:41:44 EDT 2011 >>>> #@# EM Registration Wed Apr 6 14:16:04 EDT 2011 >>>> #@# CA Normalize Wed Apr 6 15:18:54 EDT 2011 >>>> #@# CA Reg Wed Apr 6 15:22:59 EDT 2011 >>>> >>>> The last few lines of *recon-all.log* produces: >>>> >>>> 0091: dt=0.112000, rms=0.700 (-0.001%), neg=0, invalid=766 >>>> resetting metric properties... >>>> setting smoothness coefficient to 10.00 >>>> blurring input image with Gaussian with sigma=2.000... >>>> 0000: dt=0.000, rms=0.638, neg=0, invalid=766 >>>> 0092: dt=0.772947, rms=0.623 (2.335%), neg=0, invalid=766 >>>> 0093: dt=0.028000, rms=0.622 (0.145%), neg=0, invalid=766 >>>> 0094: dt=0.028000, rms=0.622 (-0.063%), neg=0, invalid=766 >>>> blurring input image with Gaussian with sigma=0.500... >>>> 0000: dt=0.000, rms=0.622, neg=0, invalid=766 >>>> >>>> >>>> Do you have any idea what is going wrong here? >>>> >>>> Thanks >>>> >>>> >>>> >>> The information in this e-mail is intended only for the person to whom >>> it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >>> >>

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gcut
by Dougherty, Michael 07 Apr '11

07 Apr '11

Hello all, I would like to take advantage of the gcut feature to remove dura that gets included in many subjects in my dataset. I am using v5.0.0, but when i enter the command from the wiki: recon-all -skullstrip -clean-bm -gcut -subjid <subjid> , i get an exit recon-all with errors, saying "ERROR: Flag -gcut unrecognized." Any suggestions, so that I can avoid doing all of these edits manually? Michael

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Slice Order
by Rita Loiotile 07 Apr '11

07 Apr '11

If my BOLD scan has 30 slices in "interleaved" series, can I assume the slice order is 1,3,5,7,9...29,2,4,6,8..30? In other words, 1:2:30,2:2:30?

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Clusterwise correction
by Irene Altarelli 07 Apr '11

07 Apr '11

Dear Freesurfers, I am doing a vertex-by-vertex analysis on a label, using mri_glmfit. As a result, I got a very small cluster (62 vertices) at p<0.01. Then I tried running clusterwise correction using the following command: mri_glmfit-sim \ --glmdir fMRIfaces20.glmdir \ --sim mc-z 5000 2 mc-z.pos \ --sim-sign pos \ --overwrite I am a bit surprised by the result: one cluster is reported in mc-z.pos.sig.cluster.summary, and it is bigger than the one previously identified. Could this be correct? if not, what could I be doing wrong? Please find attached mc-z.pos.sig.cluster.summary and mc-z.pos.j001-lh-try-ctr-dys2.csd. Thanks very much in advance, Irene -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75005 Paris tel. +33 (0)1 44 32 26 23

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vidualizing fcseed results
by Y.V. Jiang 07 Apr '11

07 Apr '11

Hi Doug, I ran fcseed-sess in Freesurfer 5.1, all the way through selxavg3-sess. How can the results be visualized, given that no contrast was specified? In the freesurfer wiki, it is said that "a contrast does not need to be made because one is automatically created with an -taskreg". But without a contrast I am not sure what the data can be visualized?? Thank you. -Yuhong

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