Freesurfer

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30132 discussions

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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How do we obtain the .license file from registration e-mail and put it in the Freesurfer home directory?
by Sinem Burcu Erdoğan 09 Aug '11

09 Aug '11

Dear FreeSurfer Users; I am quite new to FreeSurfer and have just downloaded the full package. However; I do have a serious problem with introducing the license file to the system. The Freesurfer registration e-mail doesnot have any attachments but tells me to 'Place the three lines between the CUT HERE markers in a file named ".license" in the directory pointed to by the $FREESURFER_HOME environment variable' Am I supposed to cut and copy the three lines into the LICENSE file (I tried but was not allowed to make changes in it)? Or am I supposed to create a new file with an extension .license and copy it into the freesurfer folder? ( May seem irrelevant but I copied the LICENSE file to desktop; delete everything and put only the three lines between CUT HERE markers and saved the file with a .license extension and put it in the freesurfer directory- but it didnot help.) Your help is greatly appreciated. Thank you Here is your FreeSurfer license. Place the three lines between the CUT HERE markers in a file named ".license" in the directory pointed to by the $FREESURFER_HOME environment variable (see the FreeSurfer documentation). #---------------CUT HERE--------------- berdogan83(a)gmail.com 11403 *CQmdQSakwEaM #---------------CUT HERE--------------- The information you submitted was: title=Ms firstname=Sinem Burcu lastname=ERDOGAN institution_name=Bogazici University institution_type=nonprofit_education_research user_email=berdogan83(a)gmail.com address1=Bogazici Universitesi Biyomedikal Muh. Enstitusu Kandilli Kampus Cengelkoy address2=Kandilli Kampus rasathane cengelkoy city=Istanbul state=Uskudar zipcode=34684 country=turkey telephone=+905333965220 fax= OS/Platform=Darwin/Mac ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- Sinem Burcu ERDOĞAN Research Assistant Bogazici University Biomedical Engineering Institute Kandilli Kampüs 34684 Çengelköy / İSTANBUL TURKEY Tel :+90-216-5163433 Fax :+90-216-5163479 e-mail: burcu.erdogan(a)boun.edu.tr

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Using FreeSurfer with 6-14 year olds
by Felipe Picon 08 Aug '11

08 Aug '11

Dear FreeSurfer experts, I'm starting to recon-all the MPRAGE volumes of a large sample of 6-14 year olds So far I haven't had any errors (only 15 subjects runned so far) My questions are: - Should I make a template from the subjects of my whole sample, considering their age range? - Or FreeSurfer template would work just fine with this sample? If I should make a average from my whole sample, should I make it separating the sample in age ranges? Any suggestions are welcome Thank you!! -- *Felipe Picon, MD* Child and Adolescent Psychiatrist Master's Degree Student - Department of Psychiatry of Federal University of Rio Grande do Sul - UFRGS - www.ufrgs.br Adult ADHD outpatient research program - PRODAH-A - http://www6.ufrgs.br/prodah/prodah/equipe.html Hospital de Clinicas de Porto Alegre - HCPA - www.hcpa.ufrgs.br Member of the World Psychiatric Association (WPA) Early Career Psychiatrists Council Area Coordinator for the Americas - http://www.wpanet.org/detail.php?section_id=22&content_id=120 Web based CV: http://lattes.cnpq.br/3896757276389918 felipepicon(a)gmail.com

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kvlThresholdImage fails MacOSX 10.6.8
by Carl Anderson 08 Aug '11

08 Aug '11

Dear Freesurfer, I am using a 2 x 2.66 Ghz 6-Core Intel Xeon with 24Gb RAM and MacOSX 10.6.8 I tried running kvlThresholdImage from /subject/mri/ which resulted in the following error: ------------------ kvlThresholdImage orig.mgz /Applications/freesurfer/subjects/repeats/n10a/mri/orig/002.mgz X Error of failed request: BadWindow (invalid Window parameter) Major opcode of failed request: 2 (X_ChangeWindowAttributes) Resource id in failed request: 0x2dc00ad0 Serial number of failed request: 7 Current serial number in output stream: 9 0 255 ERROR: In /usr/pubsw/packages/vtk/5.6.0/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 542 vtkXOpenGLRenderWindow (0x31b8080): bad X server connection. DISPLAY=:0 Bus error _________ FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Kernel info: Darwin 10.8.0 x86_64 Thanks, -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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