Freesurfer

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30080 discussions

make_average_subject v4.0.0
by Claus Tempelmann 05 Nov '08

05 Nov '08

Hello everybody, please have a look at this email from my collegue Cindy! Claus ----------------------------------------------------------- Dear freesurfers, I would like to do a cortical thickness group comparison of patients and two control groups. Therefore I already pre-processed my data with an older version of freesurfer (I think v3.05). As I tried to create an average subject I realized that there is a bug in the make_average_subject script of v3.0.5 so that no ?h.thickness cards were calculated for my average subject. I learned from the mailing list archive that I could create the thickness cards using mri_surf2surf but was not sure how to define the necessary variables. Just using a newer script (e.g. v4.04) unfortunately was not possible as the older version of freesurfer did not yield all cards necessary during the pre-processing and the resulting average brain looked kind of deformed. Now my question: does anyone still work with the freesurfer version v4.0.0 and could sent me the make_average_subject script of this version? There the mentioned bug should have been fixed... Thanks and greatings Cindy -------- Original-Nachricht -------- > Datum: Mon, 3 Nov 2008 14:35:50 +0100 (CET) > Von: Claus Tempelmann <Claus.Tempelmann(a)med.ovgu.de> > An: Cindy Eckart <Cindy.Eckart(a)gmx.de> > Betreff: Re: freesurfer average > Hallo nochmals, > > ich habe mal kurz in das log-file reingeschaut. Da taucht ja in der ersten > haelfte recht haeufig die Meldung "could not open ..." auf. Bist Du > sicher, dass das nichts mit dem Problem zu tun hat? > > Claus > > ----------------------------------------------------------------------- > Claus Tempelmann email: Claus.Tempelmann(a)medizin.uni-magdeburg.de > Clinic for Neurology II > MR department Tel.: +49-(0)391-6117183 > OvG University Magdeburg +49-(0)391-6117177 > Leipziger Strasse 44 > 39120 Magdeburg Fax: +49-(0)391-6117178 > Germany > > On Mon, 3 Nov 2008, Cindy Eckart wrote: > >> make_average_subject --subjects <subj1> >subj2> ... <subj36> --echo > --out averagesubject >> >> das "--echo"-Flag ist dabei jedoch irrelevant, weil es nur festlegt, > dass ein dokumentierendes log-file erstellt wird (das hab ich dir > vorsichtshalber auch einmal angehängt) >> >> LG Cindy >> >> -------- Original-Nachricht -------- >>> Datum: Mon, 3 Nov 2008 13:39:37 +0100 (CET) >>> Von: Claus Tempelmann <Claus.Tempelmann(a)med.ovgu.de> >>> An: Cindy Eckart <Cindy.Eckart(a)gmx.de> >>> CC: Claus Tempelmann <Claus.Tempelmann(a)med.ovgu.de> >>> Betreff: Re: freesurfer average >> >>> Hallo Cindy, >>> >>> kannst Du mir dazu noch Deine verwendete Befehlszeile schicken? >>> >>> Danke >>> >>> Claus >>> >>> ----------------------------------------------------------------------- >>> Claus Tempelmann email: Claus.Tempelmann(a)medizin.uni-magdeburg.de >>> Clinic for Neurology II >>> MR department Tel.: +49-(0)391-6117183 >>> OvG University Magdeburg +49-(0)391-6117177 >>> Leipziger Strasse 44 >>> 39120 Magdeburg Fax: +49-(0)391-6117178 >>> Germany >>> >>> On Mon, 3 Nov 2008, Cindy Eckart wrote: >>> >>>> Hallo Claus, >>>> >>>> hier die beiden Hemisphären des freesurfer average als TIFF-Datei... >>> vielleicht auch noch ganz nützlich, das average wurde anhand von 36 >>> Probanden aus 3 Gruppen erstellt... >>>> >>>> Vielen dank und liebe Grüße >>>> >>>> Cindy >>>> -- >>>> Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten >>>> Browser-Versionen downloaden: http://www.gmx.net/de/go/browser >>>> >> >> -- >> GMX Download-Spiele: Preizsturz! Alle Puzzle-Spiele Deluxe über 60% > billiger. >> > http://games.entertainment.gmx.net/de/entertainment/games/download/puzzle/i… >> -- "Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat ... Jetzt GMX TopMail testen: http://www.gmx.net/de/go/topmail

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Creating ROIs from FreeSurfer segmentation
by Barkay, Gavriel 05 Nov '08

05 Nov '08

Dear All, I am using FreeSurfer version 4.0.5 I need to create an ROI mask from aseg.mgz using specific labels (e.g. lt hippocampus). What is the best way to do that? What would be the best way to convert the resulting mask to NIFTI? Thanks, Gabi Barkay

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wmparc.stats
by david felps 05 Nov '08

05 Nov '08

Hi dear freesurfer, my wmparc.stats file contains 815 rows but for many structures listed there, the computed values belonging to the different columns are just null. can somebody please tell me how should i interpret this, or is it just a failure that happened while computing this values?. thank you. _________________________________________________________________ MSN Mobile: Die neuesten Infos aus der Welt der Stars und Sternchen zum Mitnehmen! http://redirect.gimas.net/?n=M0811xMobileDE

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Image deidentification
by Keller, Corey J. 05 Nov '08

05 Nov '08

Hi freesurfers, I have been unable to find a program/method to view the header file on some nifty files made from mri_convert with MPRAGE scans. I want to make sure the files we are creating do not have patient information in the headers. Is there an easy way to check this? Thanks. Best, Corey -------------------- Corey Keller Epilepsy Unit Clinical Research Coordinator Massachusetts General Hospital Wang 735, 55 Fruit Street Boston, MA 02114 Phone 802.578.6292 Email cjkeller(a)partners.org ckeller(a)nmr.mgh.harvard.edu

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mri_ca_normalize
by Nurunisa Neyzi 04 Nov '08

04 Nov '08

Hi, I am getting an error with the command: mri_ca_normalize -mask /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/brain.mgz -seg /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/cma_seg_noAA.mgz /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/nu.mgz -noatlas -noxform /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/norm_trn1.mgz using MR volume /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/brain.mgz to mask input volume... using segmentation volume /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/cma_seg_noAA.mgz to generate control points... reading 9 input volumess reading atlas from '8'... reading input volume from /Users/Nurunisa/Documents/MLS_STUDY/cma_segs/10281/mri/nu.mgz... reading input volume from -noatlas... mri_read(): couldn't determine type of file /Users/Nurunisa/Documents/MLS_STUDY/-noatlas mri_ca_normalize: could not read input MR volume from -noatlas end Is the flag -noatlas not valid? Or am I doing something wrong here?

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thickness measurement
by asaf achiron 04 Nov '08

04 Nov '08

Dear Group, in the lh.aparc.stats i can find this variables: SurfArea GrayVol ThickAvg MeanCurv GausCurv what is the difference between them? for the thickness is use the thick avg, right? thank you Asaf

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Monte carlo simulation for multiple comparison on a surface
by Zhangyuanchao 04 Nov '08

04 Nov '08

Dear Mr or Ms, How can I do Monte carlo simulation for multiple comparison correction on a surface. which command should I launch? I also want to know about permutation test. could you tell me how to use them? yczhang --------------------------------- 雅虎邮箱，您的终生邮箱！

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Monte carlo simulation and permutation test
by Zhangyuanchao 04 Nov '08

04 Nov '08

Dear Mr or Ms, How can I do Monte carlo simulation for multiple comparison correction? I also want to know about permutation test. could you tell me how to use them? yczhang --------------------------------- 雅虎邮箱，您的终生邮箱！

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Subcortical Segmentation
by Alexa Nardelli 03 Nov '08

03 Nov '08

Hi, I am new to freesurfer and to automated segmentation in general and I am having a problem using tkmedit's segmentation. I am able to open my images with freesurfer but I am having problems with the segmenation function. I am not sure I am even properly using it? I have gone through the tutorial with the tutorial data however I cannot do the same things with my own data. Any hints or procedures to follow? Thanks Alexa

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diffusion unpacksdcmdir error-wrong run!
by jake＠nmr.mgh.harvard.edu 03 Nov '08

03 Nov '08

Hi, Running the following command line : unpacksdcmdir -src /media/AJB_CERV1A/07311357 -targ /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti -run 015 dti NII ajb_cerv_1a_dti.nii -unpackerr I encountered an error of the wrong run being unpacked. Instead of 15 as designated, 13 appears to have unpacked. This is data from our CD backup. This does not seems to be related to environment, because I originally tried to unpack in STD environment with same results, though all the original analysis was done in stable3 in 2004 when the scans were collected. The logfile is following after bugr. Thanks in advance! Jake BUGR: FREESURFER_HOME: /usr/local/freesurfer/stable3 Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 NMR Center info (/space/freesurfer exists): machine: striatum SUBJECTS_DIR: /space/sake/3/users/inverse/subjects PWD: /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti ------------------------------------------------ Log file created by unpacksdcmdir $Id: unpacksdcmdir,v 1.12 2006/01/24 18:04:33 greve Exp $ /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/unpack.log /autofs/space/amaebi_035/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti Mon Nov 3 14:19:09 EST 2008 -src /media/AJB_CERV1A/07311357 -targ /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti -run 015 dti NII ajb_cerv_1a_dti.nii -unpackerr dicomdir /media/AJB_CERV1A/07311357 Scanning source directory ... INFO: summary file is /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dicomdir.sumfile INFO: status file is /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/parse.status INFO: scanning path to Siemens DICOM DIR: /media/AJB_CERV1A/07311357 INFO: Found 1758 files in /media/AJB_CERV1A/07311357 INFO: counting Siemens Files $Id: mri_parse_sdcmdir.c,v 1.13.2.1 2006/05/15 21:42:35 greve Exp $ cwd /autofs/space/amaebi_035/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti cmdline --sortbyrun --d /media/AJB_CERV1A/07311357 --o /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dicomdir.sumfile --status /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/parse.status sysname Linux hostname striatum machine i686 user jake INFO: found 1756 Siemens Files INFO: scanning info from Siemens Files INFO: status file is /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/parse.status 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 INFO: found 1756 Siemens files syngo MR 2004A 4VA25A Sorting Assigning Run Numbers RunNo = 0 RunNo = 1 RunNo = 2 RunNo = 3 RunNo = 4 RunNo = 5 RunNo = 6 RunNo = 7 RunNo = 8 RunNo = 9 RunNo = 10 RunNo = 11 RunNo = 12 RunNo = 13 RunNo = 14 WARNING: Run 11 appears to be truncated Files Found: 78, Files Expected (lRep+1): 126 FileName /media/AJB_CERV1A/07311357/58851927 Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Allegra PatientName ajb_cerv_1a Date and time StudyDate 20040731 StudyTime 121222.984000 SeriesTime 130908.562000 AcqTime 130848.812487 Acquisition parameters PulseSeq epfid2d1_64 Protocol ge_functionals PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 30 InversionTime 30 RepetitionTime 2500 PhEncFOV 200 ReadoutFOV 200 Image information RunNo 10 SeriesNo 11 ImageNo 1 NImageRows 384 NImageCols 384 NFrames 78 SliceArraylSize 30 IsMosaic 1 ImgPos 581.7606 607.9159 80.1682 VolRes 3.1250 3.1250 5.0000 VolDim 64 64 30 Vc -0.9896 -0.0181 -0.1426 Vr 0.0368 -0.9909 -0.1294 Vs -0.1389 -0.1333 0.9813 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 WARNING: Run 15 appears to be truncated Files Found: 70, Files Expected (lRep+1): 1 FileName /media/AJB_CERV1A/07311357/58844259 Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Allegra PatientName ajb_cerv_1a Date and time StudyDate 20040731 StudyTime 121222.984000 SeriesTime 134037.953000 AcqTime 134005.220012 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 83 InversionTime 83 RepetitionTime 7900 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 14 SeriesNo 15 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 70 SliceArraylSize 64 IsMosaic 1 ImgPos 993.7068 1043.8300 171.7054 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 64 Vc -0.9896 -0.0181 -0.1426 Vr 0.0300 -0.9962 -0.0813 Vs -0.1405 -0.0848 0.9864 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 Done scanning Mon Nov 3 14:24:42 EST 2008 ------------------------------------------ 1 circle_localizer ok 256 256 3 1 58867961 2 AAScout ok 128 128 128 2 58867988 3 t1_mprage_sag ok 256 256 128 1 58865756 4 t1_mprage_sag ok 256 256 128 1 58863603 5 ep2d_t1w ok 64 64 30 1 58859483 6 t2_HI_RES ok 448 444 30 1 58859933 7 AAScout ok 128 128 128 2 58860380 8 circle_localizer ok 256 256 3 1 58855710 9 ge_functionals ok 64 64 30 174 58855738 10 ge_functionals ok 64 64 30 174 58852366 11 ge_functionals err 64 64 30 78 58851927 12 ge_functionals ok 64 64 30 126 58850048 13 ge_functionals ok 64 64 30 126 58848889 14 ge_functionals ok 64 64 30 174 58844698 15 DIFFUSION_HighRes err 128 128 64 70 58844259 sortmethod fsfast unpacking config ------------------ {015 dti NII ajb_cerv_1a_dti.nii} ----------------------------------- --------------------------------------------------------- Run 015 ----------------------------------------- Mon Nov 3 14:24:43 EST 2008 015 dti NII ajb_cerv_1a_dti.nii Files In Run: --------------- 58848889 58848904 58848919 58848934 58848949 58848964 58848979 58848994 58849009 58849024 58849039 58849054 58849069 58849084 58846067 58846082 58846097 58846112 58846127 58846142 58846157 58846172 58846187 58846202 58846217 58846232 58846247 58846262 58846277 58846292 58846307 58846322 58846337 58846352 58846367 58846382 58846397 58846412 58846427 58846442 58846457 58846472 58846487 58846502 58846517 58846532 58846547 58846562 58846577 58846592 58846607 58846622 58846637 58846652 58846667 58846682 58846697 58846712 58846727 58846742 58846757 58846772 58846787 58846802 58846817 58846832 58846847 58846862 58846877 58846892 58846907 58846922 58846937 58846952 58846967 58846982 58846997 58847012 58847027 58847042 58847057 58847072 58847087 58847102 58847117 58847132 58847147 58847162 58847177 58847192 58847207 58847222 58847237 58847252 58847267 58847282 58847297 58847312 58847327 58847342 58847357 58847372 58847387 58847402 58847417 58847432 58847447 58847462 58847477 58847492 58847507 58847522 58847537 58847552 58844518 58844533 58844548 58844563 58844578 58844593 58844608 58844623 58844638 58844653 58844668 58844683 ----------------------------- VolRes: 3.125 3.125 4.9999980646632 ------- mri_convert ------------- mri_convert /media/AJB_CERV1A/07311357/58848889 /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/ajb_cerv_1a_dti.nii --sdcmlist /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom ----------------------- mri_convert /media/AJB_CERV1A/07311357/58848889 /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/ajb_cerv_1a_dti.nii --sdcmlist /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/flf -ot nii --nspmzeropad 3 --in_type siemens_dicom reading from /media/AJB_CERV1A/07311357/58848889... INFO: found 126 files in list file INFO: loading series header info. RunNo = 12 INFO: sorting. INFO: ( 64 64 30), nframes = 126, ismosaic=1 Numaris Version: syngo MR 2004A 4VA25A Maj = 4, Min=2, MinMin = 5 Repetition Time = 2500, TR = 2500 ms FileName /media/AJB_CERV1A/07311357/58848889 Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Allegra PatientName ajb_cerv_1a Date and time StudyDate 20040731 StudyTime 121222.984000 SeriesTime 132256.718000 AcqTime 132234.949990 Acquisition parameters PulseSeq epfid2d1_64 Protocol ge_functionals PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 30 InversionTime 30 RepetitionTime 2500 PhEncFOV 200 ReadoutFOV 200 Image information RunNo 12 SeriesNo 13 ImageNo 1 NImageRows 384 NImageCols 384 NFrames 126 SliceArraylSize 30 IsMosaic 1 ImgPos 105.3537 103.3935 -55.8230 VolRes 3.1250 3.1250 5.0000 VolDim 64 64 30 Vc -0.9896 -0.0181 -0.1426 Vr 0.0368 -0.9909 -0.1294 Vs -0.1389 -0.1333 0.9813 VolCenter -0.3464 -7.5104 -9.4246 TransferSyntaxUID 1.2.840.10008.1.2.1 sagrev = 0, correv =0, trarev = 0 Vs = -0.138915 -0.133327 0.981288 INFO: no Siemens slice order reversal detected (good!). TR=2500.00, TE=30.00, TI=30.00, flip angle=90.00 i_ras = (-0.98962, -0.0181386, -0.142559) j_ras = (0.0368061, -0.990906, -0.129423) k_ras = (-0.138915, -0.133327, 0.981288) writing to /space/amaebi/35/users/ablood/OLD_cerv_data/ajb_cerv_1a_fsl_dti/dti/013/ajb_cerv_1a_dti.nii... StartTime: Mon Nov 3 14:19:09 EST 2008 EndTime: Mon Nov 3 14:24:54 EST 2008 unpacksdcmdir Done

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