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Re: [Freesurfer] cortical thickness value of each pixel
by Bruce Fischl 01 Jun '09

01 Jun '09

use -l lh.cortex.label or rh.cortex.label to exclude the non-zero regions On Mon, 1 Jun 2009, Feng-Xian wrote: > > Hi, > From your response, I thick that if I want to get the global thickness > statistics (mean +/- SD) without any regions where the thickness is 0, I > would consider these regions where the thickness is 0. But, I donÿÿt know > what can I do? Would you teach me? > > First, I get the global thickness statistics with all regions by the > following command: > mris_anatomical_stats -t subjid/surf/lh.thickness -b subjid lh > And, I get the following information: > table columns are: > number of vertices > total surface area (mm^2) > total gray matter volume (mm^3) > average cortical thickness +- standard deviation (mm) > integrated rectified mean curvature > integrated rectified Gaussian curvature > folding index > intrinsic curvature index > structure name > 155006 103166 299737 2.608 1.022 0.121 0.041 2632 > 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_0 > /surf/lh.white > > Then, I get the global thickness statistics with some regions where the > thickness is 0 by the following command: > mris_anatomical_stats -t subjid/label/lh.cortex.label -b subjid lh > And, I get the following information: > table columns are: > number of vertices > total surface area (mm^2) > total gray matter volume (mm^3) > average cortical thickness +- standard deviation (mm) > integrated rectified mean curvature > integrated rectified Gaussian curvature > folding index > intrinsic curvature index > structure name > > 155006 103166 0 0.000 0.000 0.121 0.041 2632 > 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_ > 0/surf/lh.white > > Thank you in advance! > > Feng-Xian > > > > > On Mon, 1 Jun 2009 10:47:19 -0400 (EDT), Bruce Fischl wrote >> that's right, but it will average over the whole surface including >> e.g. the callosum where the thickness is 0. If you specify the >> ?h.cortex.label file it will exclude these regions Bruce On Mon, 1 >> Jun 2009, Feng-Xian wrote: >> >>> >>> Hi, >>> From your suggestion, I get the global thickness statistics (mean +/- > SD) >>> by the following command: >>> mris_anatomical_stats -t subjid/surf/lh.thickness -b subjid lh >>> >>> Then, I get the following information: >>> table columns are: >>> number of vertices >>> total surface area (mm^2) >>> total gray matter volume (mm^3) >>> average cortical thickness +- standard deviation (mm) >>> integrated rectified mean curvature >>> integrated rectified Gaussian curvature >>> folding index >>> intrinsic curvature index >>> structure name >>> 155006 103166 299737 2.608 1.022 0.121 0.041 2632 >>> > 269.2 /usr/local/freesurfer/subjects/analysis/noise_analysis/noise/noise0.5_0 >>> /surf/lh.white >>> >>> So, I think 2.608 & 1.022 is the global thickness statistics (mean +/- > SD) >>> for this subject. Do I have something wrong? >>> >>> Thank you in advance! >>> >>> Feng-Xian >>> >>> >>> >>> On Mon, 1 Jun 2009 07:29:46 -0400 (EDT), Bruce Fischl wrote >>>> Hi Feng-Xian, >>>> >>>> the ?h.thickness files in each subject's surf dir contain the vertex- >>>> wise thickness, and mris_anatomical_stats will compute the average. >>>> Make sure to give it -l ?h.cortex.label so it only computes them >>>> over the cortial region of the surface >>>> >>>> cheers, >>>> Bruce >>>> >>>> On Mon, 1 Jun 2009, Feng-Xian wrote: >>>> >>>>> >>>>> Hi, >>>>> I want to calculate the global thickness statistics (mean +/- SD) for >>> all >>>>> my subjects. And, I could calculate the global thickness statistics by >>> some >>>>> information about cortical thickness values of each pixel. But I canÿÿt >>> find >>>>> any files regarding cortical thickness values of each pixel. >>>>> Could you suggest me how to calculate the global thickness > statistics >>> or >>>>> tell me where to get the file regarding cortical thickness values of > each >>>>> pixel? >>>>> >>>>> Thank you in advance! >>>>> >>>>> Feng-Xian >>>>> >>>>> >>>>> ------------------------------------------------- >>>>> Chang Gung University Mail Server Web Mail system >>>>> By Chang-Gung University Information Center >>>>> (http://www.cgu.edu.tw/ic/) >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>> >>> >>> ------------------------------------------------- >>> Chang Gung University Mail Server Web Mail system >>> By Chang-Gung University Information Center >>> (http://www.cgu.edu.tw/ic/) >>> >>> >>> > > > ------------------------------------------------- > Chang Gung University Mail Server Web Mail system > By Chang-Gung University Information Center > (http://www.cgu.edu.tw/ic/) > > >

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FS-FAST mkanalysis GUI Bug. Please Read!
by Douglas N Greve 31 May '09

31 May '09

IMPORTANT! PLEASE READ! I am writing to let you know I have recently uncovered a bug in FSFAST. While I don't expect the bug to have widespread effects, the places where it does have an effect could be serious. I have set up the following web page to document the bug and help track what is being done to asses its impact and to fix it: surfer.nmr.mgh.harvard.edu/fswiki/FsFastGuiBug The bug has to do with contrasts configured with the mkanalysis Graphical User Interface (GUI). The bug is particularly bad for unbalanced contrasts, eg, comparing A to the AVERAGE of B and C. The contrast actually would compare A to the SUM of B and C. Please read the above wiki page for more details. If you have not used the GUI, then you are unaffected. I am currently developing tools to detect and fix these errors. If you are (or think you might) affected by this bug, please email me as I'd like to know exactly how widespread the problems really are. Finally, I apologize for the inconvenience that this will cause. doug ps. Thanks to Amitai Shenhav and Moshe Bar for bringing this to my attention. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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sulc and mid-surface
by Zhangyuanchao 30 May '09

30 May '09

Dear Mr or Ms, Thanks a lot for your previous help! In freesurfer wiki, I notice the description of 'sulc', that is how far removed a particular vertex point on a surface is from a hypothetical "mid-surface" that exists between the gyri and sulci." I am still not quite clear about sulc and how it is calculated, could you recommend me the revelant paper on how to calculated it? Thanks, Best Regards yczhang ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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one more question about curvature
by Zhangyuanchao 29 May '09

29 May '09

When I compare the thickness measure among subjects, I have to resample and smooth the thickness, so that each data have the same number of vertices and which are in correspondence with one another across subjects. Now I have .curv files or .sulc files for each subject and would like to make group analysis for these datasets. To compare the curvature and sulc measures, can I follow the same procedures as above ( ie I repeat the resampling and smoothing steps as I do for thickness)? If yes, how should I choose FWHM？ By the way, could you recommend me relevant papers that calculates the following indices : k1 maximum curvature k2 minimum curvature K Gaussian = k1*k2 H Mean = 0.5*(k1+k2) C Curvedness = sqrt(0.5*(k1*k1+k2*k2)) S Sharpness = (k1 - k2)^2 BE Bending Energy = k1*k1 + k2*k2 SI Shape Index = atan((k1+k2)/(k2-k1)) FI Folding Index = |k1|*(|k1| - |k2|) .sulc, .curv So that I can get a better understanding of what the above measures reflects. Thanks a lot! yczhang ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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A question about cortical foldings
by Zhangyuanchao 29 May '09

29 May '09

Dear Mr or Ms Is there any way that we can obtain curvature value of the pial surface? I am not sure whether lh.curv is the curvature file that I want. How can I calculate the mean curvature, Gauss curvature of the pial surface and the GM/WM interface? Is there any built-in function in freesurfer to calculate the above index? Is there any other measures of cortical foldings in freesurfer besides lGI and curvature? Thanks a lot! yczhang ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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brainmask.mgz recan-all and nu_correct error
by Iwo Bohr 29 May '09

29 May '09

Hello everybody, Since I was corresponding with a few persons separetly, it required resending the same information to all of them. So I am getting back to the general forum with my still unsolved problem. To recap: when I run recaon-all pipeline as below: [iwobohr@huxley FMRI]$ recon-all -autorecon1 -i NCVI-JR001TH_T1WIR_brain-conv.nii.gz -subjid test -all -force (with -autorecon1 option or without, similar situation occurs with -make option) It fails to output many necessary files, including brainmask.mgz, and the error message upon the completion of the pipeline is as follows: ERROR: nu_correct recon-all exited with ERRORS at Thu May 28 12:06:45 BST 2009 I attach a more detailed log file. I hope that now somebody will be able to help me :) Many thanks in advance, Iwo

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(no subject)
by Elina Pitri 29 May '09

29 May '09

hello, I am a bit confused. I am trying to correct defects manually but I am not sure which voxels must be corrected. I am attaching 3 pictures containing the right hemisphere with the defects loaded and a specific saved point at each view. I have tried following the instructions of the tutorial, but I can't understand what's wrong with the saved point. The images are quite similar in the few slices up and down. Similar issues are involved in most of the defects shown. Is there a possibility I did something wrong? Or is there anywhere else besides the tutorial to read more about this? I appreciate your help. Thank you, Elina

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Doubt about label
by Kelly Silva 29 May '09

29 May '09

Hi, Freesurfers I need to know how can I generate a label or ROI of one subcortical structure. Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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Odd behavior in aparcstats2table of FreeSurfer V4.3.1
by Brain Apprentice 28 May '09

28 May '09

Hello, I am trying to combine data from 2 different runs of aparcstats2table and I noticed that although all the columns are there the order of the columns are different. Has anyone else noticed this? Thanks

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Re: Freesurfer Digest, Vol 63, Issue 50
by Sebastian Moeller 28 May '09

28 May '09

On May 28, 2009, at 11:10 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 5 > Date: Thu, 28 May 2009 13:21:35 -0400 > From: "Srihasam, Krishna" <Krishna_Srihasam(a)hms.harvard.edu> > Subject: [Freesurfer] problems aligning fsfast functional to > anatomical.. > To: "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <97172F7B8A916A44BF05EA8D13905ECE4E174DC587(a)ITCCRMAIL02.MED.HARVARD.EDU > > > > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I am having trouble overlaying my functional data generate by FSFAST > stream onto the surfaces which I generated using Freesurfer. The > registration is going haywire. I used spmregister-sess and the > output registers coronal sections of the anatomical to horizontal > sections of the fMRI data. So, I tried using the original > anatomical image, not the surfaces I generated from it, the > registration looks great. I used mri_info to check the difference > between the images and my original anatomical image is 256x256x240 > in size and its resolution is 0.5x0.5x0.5mm. The data seems to be > stored as float. The brainmask.mgz in the mri directory of where I > created the surfaces has different stats: 256x256x256 ; resolution: > 1x1x1 and the data is in UCHAR. BTw, I am working on data from > monkey rain. Any help will be more that appreciated.. > > -Krishna Yeah, to which anatomical did you coregister it? hopefully to the 256x256x256 volumes as this seems to be the base for the surface. How did you create your surfaces in the first place? I think most monkey people scan at 0.5mm isotropic, but tell freesurfer the voxelresolution is 1mm isotropic, so that freesurfer does not degrade the resolution. But that means you always have to coregister functionals to the anatimcals with faked resolution (I like to pick the T1.mgz, nu.mgz or even the rawavg.mgz but that changes between sessions). This also means you will have to upscale the functionals by at least a factor of two to account for the change of the anatomical header. If its is helpful I can also send you a version of the script that finally displays activation maps over volume and surface. ahoi & good luck Sebastian This is the script I use to coregister functionals from fsfast (vfreesurfer 3.0.5) to volumes, this will not work with 4.3.1 out of the box, as it uses old formats and command line arguments, if I recall correctly. #! /bin/csh -f # prepare the necessary steps for the registration of the functionals to the structural scans # this should allow arbitrary structurals #TODO unify all register scripts (func2func func2arb_struct func2struct func2session_struct) #TODO: automagically load surface if one exists cd ../mystudy #1. create the subjectname file, # this has to point to a valid subdirectory of freesurfers $SUBJECTDIR # bail out if subjectname exists... #EDIT THIS set base_dir = /space/data/moeller/cooked # define stuff for the coregistration set redo_initial_reg = 1 # start with a fresh registration matrix baesd on the headers... set try_fsl_rigid_registration = 1 # use flirt for the initial matrix set check_reg = 1 # if set to 1 display the registration in tkregister2, otherwise skip set edit_string = "--noedit" set flirt_opts_string = #"-maxangle 15 -dof 6" # sometimes flirt needs constraints... set reg_id = #".chamber"#".electrode" # allow registation labels # TREAT AS MAIN REGISTRATION? set reg_2_main_struct = 1 # if one treat the structural as the main structural (and create bold/register.dat) # Napoleon face localiser, chamber coordinates #set structural_session = 061119Napoleon set structural_session = 080110QX90 #set targ_dir = ${base_dir}/${structural_session}/mri set targ_dir = ${SUBJECTS_DIR}/${structural_session}/mri set targ_vol = T1.mgz#rawavg.mgz ## Monchichi face localiser, chamber coordinates #set structural_session = 070123Monchichi #set targ_dir = ${base_dir}/anatomicals/${structural_session}/mri #set targ_vol = nu_electrode.mgz #set targ_dir = $targ_dir # the volume to be moved set mov_sess = `cat ./sf` set mov_dir = ../t1epi set mov_vol = fmc_000.bshort echo $mov_sess #2. create the t1epi directory for the registration # and copy the first functional average into it # why not simply symlink ../bold/101/001 to t1epi ??? set in_dir = ../bold/901/001 set out_dir = ../t1epi set out_vol = tmp_fsl_rotated.${mov_sess}_2_${structural_session}$ {reg_id} if !(-e ${out_dir}) then mkdir ${out_dir} cp ${in_dir}/fmc*.* ${out_dir}/ endif #3. set the in_register.dat file (do not overwrite existing files) set out_reg = ${mov_sess}_2_${structural_session}${reg_id}.register.dat set out_reg_dir = ../t1epi # create the initial registration... if (!(-e ${out_reg_dir}/${out_reg}) || (${redo_initial_reg} == 1)) then echo "Initial step, header creation..." # the monkey structurals' scanned at 0.5mm have been imported into freesurfer with the resolution forced to be 1.0mm # so the functionals have to be scaled by the same factor of 2 to allow the registration... (--noedit does not apply --movescale 2, so skip this) tkregister2 --sd ${targ_dir} --s ${structural_session} --targ $ {targ_dir}/${targ_vol} --mov ${mov_dir}/${mov_vol} --reg $ {out_reg_dir}/${out_reg} --regheader #--movscale 2 #--noedit endif # try to coregister the volumes using fsl's flirt... if (${try_fsl_rigid_registration} == 1) then if (!(-e ${out_reg_dir}/${out_reg}.done_by_fsl) || ($ {redo_initial_reg} == 1)) then # now convert the initial registration matrix into fsl format, to seed the registration... set fs2fslreg = initxfm.fslmat tkregister2 --targ ${targ_dir}/${targ_vol} --mov ${mov_dir}/$ {mov_vol} --s ${structural_session} --reg ${out_reg_dir}/${out_reg} $ {edit_string} --fslregout ${out_reg_dir}/${fs2fslreg} echo "using FLIRT for registration... might take a while" fsl_rigid_register -r ${targ_dir}/${targ_vol} -i ${mov_dir}/$ {mov_vol} -o ${out_dir}/${out_vol} \ -regmat ${out_reg_dir}/${out_reg} -initxfm ${out_reg_dir}/$ {fs2fslreg} ${flirt_opts_string} #tkmedit -f ${out_dir}/${out_vol} -aux ${targ_dir}/${targ_vol} touch ${out_reg_dir}/${out_reg}.done_by_fsl endif endif if ((${%check_reg} > 0) & (${check_reg} == 1)) then # actually register the session averages.. if ((-e ${targ_dir}/../surf/lh.white) && (-e ${targ_dir}/../surf/ lh.white)) then tkregister2 --s ${structural_session} --targ ${targ_dir}/$ {targ_vol} --mov ${mov_dir}/${mov_vol} --reg ${out_reg_dir}/${out_reg} --surf white else tkregister2 --sd ${targ_dir} --s ${structural_session} --targ $ {targ_dir}/${targ_vol} --mov ${mov_dir}/${mov_vol} --reg $ {out_reg_dir}/${out_reg} #--surf white endif endif #6. copy register.dat into fsd (bold) set reg_targ_dir = ../bold set targ_reg = $out_reg #cp ${out_reg_dir}/${out_reg} ${reg_targ_dir}/${targ_reg} if !(-e ${reg_targ_dir}/regs) then mkdir ${reg_targ_dir}/regs endif cp ${out_reg_dir}/${out_reg} ${reg_targ_dir}/regs/${targ_reg} if (${reg_2_main_struct} == 1) then echo "treating as main registration (creating bold/ register.dat)..." cp ${out_reg_dir}/${out_reg} ${out_reg_dir}/$ {structural_session}.register.dat cp ${out_reg_dir}/${out_reg} ${out_reg_dir}/register.dat cp ${out_reg_dir}/${out_reg} ${reg_targ_dir}/register.dat endif # auto registration supposedly requires same session anatomicals... #autoreg-sess –sf sessid –df sesspar # last line follows... -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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