Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

bbregister
by Kushal Kapse 21 Jun '12

21 Jun '12

hi fellow FS users, i am running bbregister (bbregister --s 083010_004498 --mov 083010_004498/bbl1_frac2back1_231.nii.gz --bold --reg register.dat --init-fsl). it shows me following error: FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -27, ref det = -1 FSLDIR: Undefined variable. i did run bbregister few weeks ago and it did run fine....but i am not able to understand this problem .... please let me know if possible.... thanks kk

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Re: [Freesurfer] correcting for normal inter-cranial variability
by carl＠nmr.mgh.harvard.edu 21 Jun '12

21 Jun '12

Will you may get a quick telegraphic reply on this, these are each really separate and quite complex questions and you will likely get many answers For subcortical volumes, while dividing by TICV has become a common solution and we have done it, it is not the optimal method. Introduces fixed error for all structures in a subject. See footnote in Buckner paper on this. If you are doing between group analysis, analysis of covariance is preferable. Proc glm or mixed in SAS, easy in other packages This can handle as covariates ICV, and depending on your population, you can add handedness, gender, IQ or the kitchen sink. Another plus for covariance is that you get an interpretable group mean, a real number that can be compared to the literature instead of some weird fraction. For surface, we have used the (third root of TICV), squared, based on suggestions by Bruce Fishl, I don't see why covariance with this as the term would not be slightly preferable to diving for the same reasons as above. For thickness, two schools of thought. Some do no correction. Others use mean thickness over the whole brain of the individual or a subregion. It has been convincingly argued that what you use and whether you use it it depends again on the question you are actually asking. There are some very good and smart threads on this if you search. Mike Harms I seem to recall Carl Schwartz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> hi miro, as per me, i would suggest to divide ICV with TotalGrayVol and other aseg.stats files' global measures to remove the invariability across these measures. divide ICV to totalgrayvol,corticalwhitemattervolume,supratenorialvol,subcorticalgrayvol...this will remove any in-variability within those measures across ICV...... hope that helps kk ----- Original Message ----- From: "Miro Drahos" <miroslav.drahos(a)ucsf.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Thursday, June 21, 2012 2:21:13 PM Subject: [Freesurfer] correcting for normal inter-cranial variability Hi all, When analyzing output measures from FreeSurfer, what is the proper way to correct for normal anatomical variability before comparing between subjects? Which variable should be used to calculate normalized measures? volumetric measures -- total intra-cranial volume? total brain volume? surface measures -- total surface area? thickness measures -- mean thickness? Thank you! Miro Drahos Hi all, When analyzing output measures from FreeSurfer, what is the proper way to correct for normal anatomical variability before comparing between subjects? Which variable should be used to calculate normalized measures? volumetric measures -- total intra-cranial volume? total brain volume? surface measures -- total surface area? thickness measures -- mean thickness? Thank you! Miro Drahos

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correcting for normal inter-cranial variability
by Miro Drahos 21 Jun '12

21 Jun '12

Hi all, When analyzing output measures from FreeSurfer, what is the proper way to correct for normal anatomical variability before comparing between subjects? Which variable should be used to calculate normalized measures? volumetric measures -- total intra-cranial volume? total brain volume? surface measures -- total surface area? thickness measures -- mean thickness? Thank you! Miro Drahos

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masking ?h.curv with a label
by Ritobrato Datta 21 Jun '12

21 Jun '12

Hi, I have created a ?.cortex.label on canine brain. How do I apply this label to the ?h.curv and ?.sulc so that I get rid of the medial wall FOREVER ? Thanks a lot Ri

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color table for custom labels
by Ritobrato Datta 21 Jun '12

21 Jun '12

Hello All, I have created some labels and want to assign distinct colors to each and save it so that I can assign the same colors when I load them again. How do I do it ? Thanks Ri

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how much talairach registration affects segmentation?
by Gabor Perlaki 21 Jun '12

21 Jun '12

Dear all, I've subjects processed by freesurfer 5.1.0. We checked the talairach transformation. It seems to be not so bad, but sometimes the zoom or the roation are not the best, which may affect the TIV, however we're actually not interested in TIV. Does this "talairach transformation issue" affect the cortical and subcortical segmentation somehow? I read that this transformation is used by later algorithms as seeding point. We checked the skull stripped image, white matter segmentation, surface between white and gray (yellow line) and between gray and pia (red line). Everything seems to be fine. The subcortical segmentation also seems to be good. Does the initial talairach transformation have any influence on the volumes calculated during the subcortical/cortical segmentations? I'd appreciate any help, thnaks, Gabor

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qdec_glmfit problem
by Nicolai Grüner-Hegge 20 Jun '12

20 Jun '12

Dear FreeSurfer, I am emailing you to ask for your help with the qdec_glmfit command (I got the command from the following link: http://www.freesurfer.net/fswiki/qdec_glmfit) My issue is that I do not know how to turn my raw data into the .dat file required by the command (you used qdec.table.dat as an example). Could you please tell me how I can turn my raw data into the .dat file that is required for the qdec_glmfit command to work? Thank you for your time! Best Regards, Nicolai

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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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Freesurfer