Freesurfer May 2009

freesurfer@nmr.mgh.harvard.edu

81 participants
126 discussions

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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problems aligning fsfast functional to anatomical..
by Srihasam, Krishna 28 May '09

28 May '09

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

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Re: Freesurfer Digest, Vol 63, Issue 48
by Sebastian Moeller 28 May '09

28 May '09

Hi Falk, On May 28, 2009, at 3:50 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 4 > Date: Thu, 28 May 2009 11:56:51 +0200 > From: Falk L?sebrink <falk.luese(a)gmx.net> > Subject: [Freesurfer] Troubleshooting > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <001501c9df7a$9fe15a40$dfa40ec0$@luese@gmx.net> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > > > Im having trouble to generate a correct aseg.mgz for one volume of > mine. > The nu_noneck.mgz is also incorrect and therefore I think the -careg > stage > of autorecon2 might fail. Is there a way to do some kind quality > check, like > the tal-check during autorecon1, to see whether the talairach.m3z is > incorrect? Are there some kind of instructions like fixing the bad > output > from the talairach registration? Or are there some parameters which > can be > adjusted to get better results? > > > > If none of this is possible in some way, would it be advisable to > use the > -noaseg flag? Im actually in no need for the subcortical > segmentation, it > would just be a plus, but the aseg.mgz is needed during the - > segmentation > stage to remove the cerebellum and brain stem. Maybe there even is > another > way to remove these structures automatically? Well, I can offer a very rough method that seems to work with my monkey data (where I always use -noaseg), I never tried it with humans. I edit the wm.mgz and delete two slices worth of midbrain above the upper connection of the cerebellum to the midbrain. It seems important that there are no connections from cerebellum left to white matter (if there are connection above the cut I always delete the cerebellar part of those, but I do not care about the cerebellum currently). Then I pick a point on the pons in the segment above the cut. I use this point, as well as a point picked somewhere in the middle of the corpus callosum to feed into further recon-all steps (see below). This probably is rather unclean, but it seems to work okay, at least with monkey data... Here my actual script for that step (replace the values in CC_string and PONS_string with your real values picked from tkmedit of wm.mgz): # set the target directory and file_name set targ_dir = ../mri set src_vol = wm.mgz #set brain = brain.mgz set targ_vol = filled.mgz set controlpoints = ../tmp/control.dat set cur_dir = `pwd` # ATTENTION please specify the cutting planes for the pons and the corpus callosum # define the raw voxel coordinates for CC and PONS set CC_string = "128 110 132" set PONS_string = "128 136 125"#"127 129 112" # do an initial filling to check the cutting planes set check_filling = 0 cd .. set tmp_subj = 0?????* cd ${cur_dir} if (${check_filling} == 1) then echo "Testing the CC and Pons coordinates, if the filled volume is okay rerun this script with set check_filling = 0" #mri_fill -CV 127 128 128 -PV 127 154 128 ${src_dir}/${src_vol} $ {targ_dir}/${targ_vol} mri_fill -a ../scripts/ponscc.cut.log -PV ${PONS_string} -CV $ {CC_string} ${src_dir}/wm.mgz ${src_dir}/filled.mgz # check the results, left and right white matter should be colored differently and the cerebellum should be excluded tkmedit -f ${src_dir}/filled.mgz -aux ${src_dir}/T1.mgz exit 0 endif # 20060224 recon-all -autorecon2-wm \ -subjid ${tmp_subj} \ -cc-crs ${CC_string} \ -pons-crs ${PONS_string} \ -noaseg \ -xopts-use > > > > > Thanks in advance, > > Regards, > > Falk I hope this helps Sebastian -- 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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Using tmpfs to speed up recon-all
by Luke Robot Hospadaruk 28 May '09

28 May '09

Hi, I've noticed recon-all (-all) doesn't really grind my cpu as intensely as it might, which makes me wonder if it might be more I/O limited, which further makes me wonder if I could get any kind of speedup using a tmpfs to store the subject's directory while running recon-all, and then copying the results back to disk when I'm done. Does anyone know how I/O limited recon-all is (I realize it consists of many tasks, but if even some of them would be significantly sped up by putting their data in memory, it'd be worth my time). Also, do all recon-all components store their scratch data (if they have it) in the subject directory? or do they go somewhere else (like /tmp or /var)? Thanks for the help --Luke Hospadaruk

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Projecting 3-D voxel data onto the cortical surface
by m.e.kirlangic＠fz-juelich.de 28 May '09

28 May '09

Dear Freesurfer Community, I am quite new in freesurfer, getting just acquainted with the tools. What I am currently trying to do is, projecting 3-D voxel data (i.e. postmortem probability maps of Prof. Katrin Amunts and Prof. Karl Zilles in Research Center Juelich -Germany) onto the cortical surface. For the time being, I assume that both types of data are registered to a reference space (e.g., Collin27-brain). Which functions I would/could need for the calculations and visualization? Which data format(s) is/are required in order to be able to make use of the available freesurfer functions? Any guidance and all tips are very welcome :-) And sorry for any inconvenience using the terminology! Thanks, Eylem Kirlangic ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

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Freesurfer May 2009