Freesurfer

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30132 discussions

qdec analysis sequence
by Jenny Liu 20 Jun '12

20 Jun '12

Hello, I am attempting to use the Qdec Analysis for longitudinal data. Specifically, each subject has two timepoints, and belongs to one of two groups. Each subject has an accompanying age and painUnpleasantness rating. I do not have a 'time in years' variable, and instead listed the timepoint as baseline = 0, and post=1. Thus far, what is done is the PREPROCESSING (listed below as step #3). Thus, every subject has a directory labeled "WB101_1.long.WB101_template", and another labeled "WB101_template". I am on the POSTPROCESSING (listed as step #4). I would like to confirm that this is the correct sequence of events to use the Qdec Analysis tool to do a mixed linear effects models analysis or mixed ANOVA analysis. #1. INITIALIZATION freesurfer tksurfer 005 brainmask.mgz #2. SET SUBJECT DIRECTORY export SUBJECTS_DIR=/study/NCCAM/Data/MRI/processed/structural/freesurfer cd /study/NCCAM/Data/MRI/processed/structural/freesurfer/ #3. PREPROCESSING LONGITUDINAL recon-all -base ${subject}_template -tp ${subject}_1 -tp ${subject}_2 -all recon-all -long ${subject}_1 ${subject}_template -all recon-all -long ${subject}_2 ${subject}_template -all #4. POSTPROCESSING LONGITUDINAL BY CREATING QDEC TABLE #Example file named: long.qdec.table.dat fsid fsid-base group age painUnp tp WB101_1 WB101_template MNP 65.72 11.7 0 WB401_1 WB401_template LTM 59 11.6 0 WB101_2 WB101_template MNP 65.72 8.6 1 WB401_2 WB401_template LTM 59 1 #5. OPEN QDEC TABLE gedit qdec/long.qdec.table.dat #6. CREATE a qdec/measures.Qdecrc file in the qdec directory that contains the following line, so that the QDEC analysi know about new files. #Example file named: measures.Qdecrc MEASURE1 = long.thickness-avg MEASURE2 = long.thickness-rate MEASURE3 = long.thickness-pc1 MEASURE4 = long.thickness-spc #7. CREATE file for each discrete (categorical) factor #Example file named: group.levels MNP LTM #8. Pre-smooth fsaverage surfaces #Qdec needs each subject to have pre-computed smoothed data for the target surface (fsaverage is the default) for each measure (thickness, sulc, area, curv, etc.). Your SUBJECTS_DIR should contain either a link or a copy of the 'fsaverage' subject found in your $FREESURFER_HOME/subjects directory. Presmoothing the data onto the target surface is not part of the normal recon processing stream, but you can easily create this data with recon-all, using the command: recon-all -s <subject> -qcache #9. Shrink qdec table from a longitudinal form to a cross sectional form, in order to run the QDEC group analysis. long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat #10. PREPARE DATA QCACHE long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time tp --qcache fsaverage #11. Open pial surface of left hemi on average subject. Open symmetrized percent change. #--qcache flag of long_mris_slopes has been registered and mapped all results to the average subject tksurfer fsaverage lh pial -overlay $SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-spc.fwhm15.fsaverage.mgh -aparc #12. Run the QDEC analysis on the qdec table: qdec --table ./qdec/cross.qdec.table.dat #13. Use GUI as indicated by http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis

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Re: [Freesurfer] Recent paper on FreeSurfer reliability
by Gregory Kirk 20 Jun '12

20 Jun '12

bottom line is can we trust freesurfer cortical thickness results and a recent paper my group published seems to give very strong positive answer to the question. paper - cortical thinning in psychopathy, it's on the wiki publication list. All of the areas reported overlap with the areas that have been found in a number of other reports of different modalities in psychopathy,but freesurfer found them all in one dataset,recent high quality publication from kings college on psychopathy ( spm-vbm) found all the same areas except bilateral face and hand motor area ( the exact face and hand areas bilaterally that are associated with emotional binding), i would think the chances of getting this by random error are astronomically low!!!). The ```LEFT``` anterior insula and ```LEFT``` caudal anterior cingulate, again exactly the areas that are consistantly nailed in seperate studies of empathy and they are thinned in psychopaths. the spatial specificity ( the ability to look at the surfaces and tell exactly where the differences are is vastly superior in our freesurfer paper. and this is a study with a group that is not grossly sick, so smaller differences would be expected than a neurodegenerative disease for example. only heuristic validation but my studies with freesurfer always find areas that make sense. the exact value of the cortical thickness are not as important it's the statistical differences in a consitantly processed ( same everything, version etc. ) study well done Bruce & company, i know which software i am using for structural analysis, *freesurfer* my 2 cents Greg Kirk University of Wisconsin Madison On 06/20/12, Nick Schmansky wrote: > Peter, > > Thanks for this info. The Mac OS versions compared in the paper were 10.5 > and 10.6 (Leopard and Snow Leopard). One of the major changes between > these two versions was the switch from a 32b kernel to a 64b kernel > (whereas Snow Leopard and Lion both use a 64b kernel). I havent been able > to definitely say that the math libs changed, but it would seem to account > for the differences in Mac OS version results in the paper. A 32b build > of freesurfer (for the Mac) was used in both tests so kernel differences > might not matter but are suspect. > > Nick > > > We run things on an Xgrid cluster that is now a mixture of Macs running > > Snow Leopard (10.6.8) and Lion (10.7.x). We found the results given from > > asegstats2table and aparcstats2table are identical after running 100 > > subjects on both Mac OS X 10.7.4 and 10.6.8 with Freesurfer 5.1. I also > > ran a few subjects on the cluster and on individual computers (not on the > > cluster so to speak) and the results are identical. > > > > Best, > > Peter > > > > > >> Hi, > >> > >> The paper entitled > >> > >> The Effects of FreeSurfer Version, Workstation Type, > >> and Macintosh Operating System Version on Anatomical > >> Volume and Cortical Thickness Measurements, > >> PLoSONE, Vol 7(6), e38234 (2012) > >> > >> may be of interest to all of you. It can be found at: > >> > >> http://dx.plos.org/10.1371/journal.pone.0038234 > >> > >> Cheers, > >> Ed > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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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Qdec pre-smoothed
by mdkruepke＠uwalumni.com 20 Jun '12

20 Jun '12

Freesurfers- For pre-smoothing subject surfaces for qdec using: recon-all -s <subjid> -qcache Is it necessary to have all the variations of smoothing done (ie - fwhm 0,5,10,15,20,25) or is it possible to run with only a subsection of these? Best- Michael -- Michael D. Kruepke PhD - University of Illinois at Urbana-Champaign BA - Psych - University of Wisconsin-Madison mdkruepke(a)gmail.com (262)-483-7449

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Allen Brain Institute to Freesurfer Labels
by MCLAREN, Donald 20 Jun '12

20 Jun '12

Does anyone have a mapping of the Allen Brain Institute labels to the freesurfer parcellations? Just the labels would be sufficient for these purposes. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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Re: [Freesurfer] Recent paper on FreeSurfer reliability
by Peter J. Molfese 20 Jun '12

20 Jun '12

We run things on an Xgrid cluster that is now a mixture of Macs running Snow Leopard (10.6.8) and Lion (10.7.x). We found the results given from asegstats2table and aparcstats2table are identical after running 100 subjects on both Mac OS X 10.7.4 and 10.6.8 with Freesurfer 5.1. I also ran a few subjects on the cluster and on individual computers (not on the cluster so to speak) and the results are identical. Best, Peter > Hi, > > The paper entitled > > “The Effects of FreeSurfer Version, Workstation Type, > and Macintosh Operating System Version on Anatomical > Volume and Cortical Thickness Measurements”, > PLoSONE, Vol 7(6), e38234 (2012) > > may be of interest to all of you. It can be found at: > > http://dx.plos.org/10.1371/journal.pone.0038234 > > Cheers, > Ed

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Assigning cluster index
by John Richey 20 Jun '12

20 Jun '12

Dear Freesurfer experts, I have a fairly simple question, but it is not immediately clear to me how to solve it. I have a statistical parameter map representing the results of a group-level analysis. After thresholding the map (p<.05), several significant clusters remain, and I want to assign each cluster a unique index number (e.g. 1,2,3 etc). This unique index will be useful to me later, but it is not clear how I could do this using freesurfer tools. Thanks in advance, John

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MNI coordinates of all the vertices of fsaverage
by Yolanda Vives 20 Jun '12

20 Jun '12

Dear Freesurfer experts, How could I know the MNI coordinates of the 163.842 vertices of the left hemisphere of fsaverage? Best regards, Yolanda

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mris_label2annot mislabeling
by Arno Klein 20 Jun '12

20 Jun '12

hello! i have saved a couple of .label files and am trying to convert them to a .annot file with: mris_label2annot --h lh --s MMRR-21-1 --l lh.superiorfrontal.label --l lh.superiorparietal.label --ctab FreeSurferColorLUT.txt --a output the stdout is: ColorTable atlas_colortable.txt AnnotName output nlables 2 LabelThresh 0 0.000000 Loading /usr/local/freesurfer/subjects/MMRR-21-1/surf/lh.orig 1 11829830 Left-Cerebral-Exterior 2 16119285 Left-Cerebral-White-Matter Mapping unhit to unknown ... clearly the anatomical names assigned are incorrect, and when i view the output with tksurfer, the labeled patches are in the right places but are assigned these same incorrect anatomical names. i have tried renaming the .label files to no avail. what am i doing wrong? cheers, @rno

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Editing Putamen Segmentation
by Kristin Javaras 20 Jun '12

20 Jun '12

Dear all, For a number of my participants, Freesurfer's automated segmentation of the putamen appears to include brain matter that isn't putamen - this problem persists across 5-6 slices, on average. I was wondering what people would recommend - should I edit the aseg? Thank you in advance for any advice, Kristin Javaras _______________________________ Kristin N. Javaras, PhD Waisman Laboratory for Brain Imaging and Behavior University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Telephone : +1 (608) 890-1407

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Re: [Freesurfer] -inter error
by Anastasia Yendiki 20 Jun '12

20 Jun '12

Oops, that's a typo, meant "is unavailable". In any case something like this should show up early in the logs. On Wed, 20 Jun 2012, Bruce Fischl wrote: > "not unavailable"???? > > On Wed, 20 Jun 2012, Anastasia Yendiki wrote: > >> >> Hi Maria - Do you at any point get the following warning? >> "WARN: CVS template is not unavailable in the current version" >> >> Thanks, >> a.y >> >> On Wed, 20 Jun 2012, Maria Gemzicka wrote: >> >> > Hi, >> > I run -corr and -intra with no errors. -inter finishes without errors if >> > does not use doregcvs. >> > When I want to use cvs for registration, I get error: >> > >> > iterating >> > >> > done with candidates >> > >> > Active BCs = 91494 >> > >> > Total BCs = 548640 >> > >> > no-eqs = 245610 >> > >> > surf2vol(26656) malloc: *** mmap(size=295714816) failed (error code=12) >> > >> > *** error: can't allocate region >> > >> > *** set a breakpoint in malloc_error_break to debug >> > >> > [0]PETSC ERROR: --------------------- Error Message >> > ------------------------------------ >> > >> > [0]PETSC ERROR: Out of memory. This could be due to allocating >> > >> > [0]PETSC ERROR: too large an object or bleeding by not properly >> > >> > [0]PETSC ERROR: destroying unneeded objects. >> > >> > [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 >> > >> > [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. >> > >> > [0]PETSC ERROR: Memory requested 295714444! >> > >> > >> > >> > trac-all.error in scripts: >> > >> > >> > ...... >> > >> > PROCESSOR x86_64 >> > >> > OS Darwin >> > >> > Darwin shemp.mri.yorku.ca 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr >> > 9 >> > 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 >> > >> > $Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $ >> > >> > /Users/Maria/Applications/freesurfer/bin/trac-preproc >> > >> > PWD /Users/Maria >> > >> > CMD mri_cvs_register --mov mgFS6 --template cvs_avg35 --outdir >> > /Users/maria/Desktop/mgFS/mgFS6/dmri/xfms/cvs >> > >> > >> > Thank you. >> > >> > >> >

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