Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

selxavg-sess outputs
by Yang Liu 10 Aug '11

10 Aug '11

Hi all, I want to plot the hemodynamic response of a voxel after my analysis finishes. I hope I can get the hemodynamic response of each voxel for each session, so I can see the statistics by myself. My analysis.cfg is below: -gammafit 0 8 -gammaexp 0.3 -timewindow 40.0000 -prestim 0 -polyfit 2 -TER 2.0000 -autowhiten 40 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 After I ran selxavg-sess, I got the following volumes: h0.nii, h0-offset.nii, h.nii, h-offset.nii, rstd.nii, rvar.nii. How can I get a response from these volumes? Yang

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[freesurfer] FS5.1 talairach issue
by Myriam Siefert 10 Aug '11

10 Aug '11

Hi freesurfers, I'm currently re-processing with FS5.1 some data that i had already processed with FS5.0 and am experiencing some unexpected issues with the linear talairach transform. - While manually checking with Tkregister, I noticed that some off the subjects had quite unsatisfying transforms , while no talairach failure was detected on the log - The transforms looked ok for those subjects in FS 5.0 - I re-run autorecon1 using the -use-mritotal flag - While still no error in the log file, the transforms usually then look acceptable in Tkregister but completely wrong when talairach.xfm is loaded in tkmedit : transformation in the top or bottom left corners, coronal and transversal views interverted, sagittal views rotated by 90 degrees... This happens for a few (not all) of the subjects that I've re-processed with FS5.1 so far. I'm probably doing something wrong but can't figure out what nor what to do about it. Any advice would be highly appreciated. Thanks in advance Myriam Siefert, MD, MS candidate Visiting scholar in SACNlab Northwestern University

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mne_analyze not dispalying surfaces
by Vema Krishnamurthy, Santosh 10 Aug '11

10 Aug '11

Hello, I'm trying to display the inflated surfaces through mne_analyze and all I see is only few pixels of the surfaces. I'm assuming this is a problem with graphics, so I think I have Matrox Graphics (MGA G200ew WPCM450 rev 0a) installed on my host machine and I'm accessing this machine through VNC. Thanks and Regards, --------------------------------------------------- Santosh Vema KrishnaMurthy, M.A.Sc Medical Devices Engineer NRC Institute for Biodiagnostics (Atlantic) Elekta/IWK MEG Research office Ph: (902) 470-3984 ---------------------------------------------------

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FMRI Hemispheric Asymmetry Analyses
by Andy Mayer 09 Aug '11

09 Aug '11

Hello- I would like to directly compare asymmetries in FMRI activation in surface space based on the Greve et al pipeline presented at HBM this year. All of our anatomical data have been processed with FS v4.5, but the FMRI data is in AFNI volumes. I am very new to the freesurfer program so any corrections on how to achieve cross-hemisphere registrations would be greatly appreciated. 1) We transformed the functional data to anatomical space using bbregister. 2) We then registered each subject’s T1 data to the contralateral hemisphere of fsaverage and made templates of the contra (?h.con.sphere.reg ) and ipsilateral (?h.sphere.reg ) registrations Registration step mris_register -curv surf/rh.sphere {$FREESURFER_HOME}/average/lh.average.curvature.filled.buckner40.tif surf/rh.CON.sphere.reg mris_register -curv surf/lh.sphere {$FREESURFER_HOME}/average/rh.average.curvature.filled.buckner40.tif surf/lh.CON.sphere.reg template step make_average_subject --out CON_TEMPLATES --surf-reg CON.sphere.reg --subjects M87150222_20110311 M87138477_20080429 .. make_average_subject --out IPS_TEMPLATES --surf-reg sphere.reg --subjects M87150222_20110311 M87138477_20080429 .. 3) I then re-registered RH data to the new contralateral template (study-specific) and LH data to the new ipsilateral template to get everything in the same sphere space mris_register -curv surf/rh.sphere CON_TEMPLATES/rh.reg.template.tif surf/rh.finalTEM.sphere.reg mris_register -curv surf/lh.sphere IPS_TEMPLATES/lh.reg.template.tif surf/lh.finalTEM.sphere.reg 4) Finally, I apply the final registration template to aux data (thickness, FMRI) to bring everything into a common space that can be directly tested for hemispheric asymmetries mris_preproc --hemi rh --target CON_TEMPLATES --surfreg finalTEM.sphere.reg --meas thickness --out final.thickness.nii --s ${subject} mris_preproc --hemi lh --target IPS_TEMPLATES --surfreg finalTEM.sphere.reg --meas thickness --out final.thickness.nii --s ${subject} Please let me if this pipeline makes sense and follows what was proposed at the HBM meeting. Also are the iterations mentioned in the poster necessary (ie make additional templates and re-reregister) when the sample is relatively large (N = 100)? Thanks! Andrew

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Functional Data Hippocampus
by Sunil Patel 09 Aug '11

09 Aug '11

Hello, I'm wondering how to obtain the functional data for the hippocampus between specific slices. Is there a command I can run to do this? If not, what would be the best course of action? Best, Sunil I Patel

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mri_watershed for generating scalp surfaces
by Vema Krishnamurthy, Santosh 09 Aug '11

09 Aug '11

Hello Everyone, I have an application outside freesurfer where I need the scalp/face surface from the MRI file so I'm trying to use mri_watershed algorithm to generate the scalp surface, but when I read the subject-outer_skin.surf file in matlab using the read_surf command I see that the facial features (nose, eyes, lips, chin) are not clear. But when I viewed the MRI file using mrilab I can see the facial features clearly. So I was wondering if there are parameters I can change while running the mri_watershed alrgorithm so that I can get good face shape. I'm also up for any suggestions/hints. Here is the command I used to run the mri_watershed: mri_watershed -atlas -useSRAS -surf /../../bem/watershed/subject /../..subject/T1.mgz /../../bem/watershed/ws/ Thanks and Regards, --------------------------------------------------- Santosh Vema KrishnaMurthy, M.A.Sc Medical Devices Engineer NRC Institute for Biodiagnostics (Atlantic) Elekta/IWK MEG Research office Ph: (902) 470-3984 ---------------------------------------------------

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Functional Data Hippocampus
by Sunil Patel 09 Aug '11

09 Aug '11

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Code changes to use Compiled Matlab?
by Bill Taylor 09 Aug '11

09 Aug '11

Mathworks loves their parallel toolbox. We love using Condor. I won't go into the reasons. http://www.cs.wisc.edu/condor/ We have negotiated an unlimited license of for Matlab and I have freesurfer recon-all broken into the three phases. This gives us currently 1700 dedicated cores where we can process brain scans for groups on the Madison, WI campus. We are contractually prevented from running anything but compiled Matlab on any cluster on the UW-Madison campus. I have had to modify "mris_computer_lgi" to call compiled matlab entry points after setting up a Matlab runtime within the Freesurfer 5.1.0 staged executable. What I ran into was a type mismatch from the way I now call the matlab functionality. Is there a known solution for this or do I have to change the matlab entry points to do initial type changing? We are working on a work flow to not only process the brains but also do FSL and matlab post processing at the same time and/or take preprocessed subjects and do either FSL or Matlab processing. I automate researchers on campus and don't actually program Matlab though I can work my way through this. As a computer Scientist I don't really want to be changing the code base in an unmanaged way. *********************************************************************Change in call # # make_outer_surface.m # # create the outer surface from the filled volume set MLF = /tmp/mos"_$$_".m set arg1 = ${tmpdir}/${input}.filled.mgz set arg2 = ${closespheresize} set arg3 = ${tmpdir}/${input}-outer rm -f ${arg3} # bt commented out for converting to compiled echo "Calling compiled matlab make_outer_surface" echo "make_outer_surface('${arg1}',${arg2},'${arg3}')" make_outer_surface ${arg1} ${arg2} ${arg3} #echo "make_outer_surface('${arg1}',${arg2},'${arg3}'); exit" > $MLF #echo "=================" #echo "`cat $MLF`" #echo "=================" #if ($RunIt) then #cat $MLF | ${MATLAB} -display iconic -nojvm -nosplash #endif ********************************************************************* ERROR BELOW Calling compiled matlab make_outer_surface reading filled volume... closing volume... ??? Error using ==> iptcheckinput Function STREL expected its second input, R, to be one of these types: double Instead its type was char. Error in ==> strel>ParseInputs at 1308 Error in ==> strel>strel.strel at 143 Error in ==> make_outer_surface at 41 ^G Images:strel:invalidType ********************************************************************* -- Bill Taylor 608-263-2656 (cell 608-219-4430) Center for High Throughput Computing(CHTC) Condor project Computer Sciences University of Wisconsin, Madison

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Modifying Regression Analysis
by Adam Nitenson 09 Aug '11

09 Aug '11

Hi Doug and Freesurfers, I am currently analyzing data acquired from the Sternberg memory task, which involves memorizing sets of 1, 3, 5, and 7 letters. I have created an analysis (see attached analysis.info and paradigm example) which allows me to create maps of the load-based activation when going from 1 to 3 to 5 to 7 letters, which accounts for the analysis' single "contrast". My PI was hoping that, for some subjects, we could look at the regression from JUST 1 to 3 to 5, since they have poor 7-letter data. >From looking at the analysis setup, it looks like I would have to make this change at the paradigm level since subjects have already been run with the current analysis with just the 1,3,5,7 regression contrast. I would probably have to change the "2"s in the paradigm file to "1"s for the 7-letter sets (since the contrast is 2vFix, and this alteration would essentially "ignore" the 7-letter condition), but a change at the paradigm file level, I believe, would essentially necessitate the formation of a new analysis entirely, which would then have to be run again individually on subjects, which can be a time consuming process. I was wondering if there was a way I could bypass this step and modify the analysis to suit these newer needs, or will I have to essentially make a new analysis based on my current one for this to work? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

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Segmentation of hippocampal subfilelds
by mohan boddu 09 Aug '11

09 Aug '11

I have completed the segmentation of hippocampal subfileds, but now I would like to know the generated images are in probability map or label map? If they are in label map what would be the best upper and lower thresholds to generate the ROI mask images. Could you please also tell me the way to do so. -- --Mohan Boddu-- Research Assistant Department of Radiology and Imaging Research II Building Indiana University School Of Medicine Indiana University-Purdue University Indianapolis Indianapolis, IN 46202

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Freesurfer August 2011