Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

manually run freesurfer longitudinal processing
by Xie, Hong 08 Sep '08

08 Sep '08

Hello, group, I am running longitudinal process step by step following the wiki page of 12 differences between longitudinal and recon-all process. But some needed files are not generated by these 12 steps, for example, brain.mgz, wm.seg.mgz, wm.asegedit.mgz, aseg.auto_noCCseg.mgz, wm.mgz, fill.mgz, brain.finalsurfers.mgz, ?h.smoothwm, ?h.inflated, ?h.sulc, and ?h.aparc.annot. Should I use recon-all commands to create these files or just copy ( or transform) them from tp1 to tp2? Thank you for help. Hong

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version for windows- a simple tool
by asaf achiron 08 Sep '08

08 Sep '08

Dear Sir I am a student in Tel-Aviv University and i work on MRI data of Multiple Sclerosis we would like to use freesurfer to find out cortical thickness. do you have a version that can run on windows (we have it in the hospital). i have mac at home but i don't know how to script- maybe do you have a gui version? we are medical student with no knowledge of all the hardware-we would like a simple tool to measure the cortex. can you help me? thank you Asaf A

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tkregister2
by jake＠nmr.mgh.harvard.edu 08 Sep '08

08 Sep '08

Hello, I am running the following command in the standard environment: tkregister2 --targ orig.mgz --mov /space/amaebi/35/users/ablood/DMRF_ASL/CD_DMRFASL_pat3_sess1/bold/021/fmcsm4.bhdr --reg /space/amaebi/35/users/ablood/DMRF_ASL/CD_DMRFASL_pat3_sess1/bold/register.dat this command has shown that the registration (created from autoreg-sess) has warped the functional data. I would like to run tkregister2 without the register.dat file, so I can use the orignal unwarped data. Is there a simple way to do so? Thanks in advance , Jake

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Coregistrtion Siemens DICOM data
by Alexander Gussew 05 Sep '08

05 Sep '08

Dear Sir or Madam, In our institution we try to implement an automatic routine for the co-registration of MRI images and 3 dimensional MR spectroscopic metabolic maps acquired on SIEMENS MR Scanner. We try to realize it by using the Dicom reading function as implemented in MATLAB. To evaluate the transformation matrix extracted from the DICOM header tag “ImageOrientationPatient” we compared it with the matrix extracted by tool “tkregister2”contained in the freesurfer package. Because of some observed obscurities we would like to ask you following questions: 1) How does tkregister2 rebuild the transformation matrix of the corresponding Nifti-file (inversion?) which is used in the freesurfer-tool “flirt” for the coregistration (the matrix in the file with the extension .fsl)? 2) Is the order of rotations performed by the data acquisition relevant for the several steps of matrix construction? If so is there a general way how ‘tkregister2’ extract this order and consider for the further calculations? 3) By the reading and plotting the 3D DICOM image data sets with MATLAB we figured out, that directions of several spaces axes are changing (negativepositive; positivenegative) depending on the image orientation using during the acquisition (sagital, coronar, transversal). We guessed that we should at first correct our data by flipping some axes (e.g. in sagital case LR-axis) and then apply the matrix extracted from DICOM-header to the corrected data set. If it is correct how ‘tkregister2’ tool perform this correction for several orientation cases? With best regards, Alexander Gussew Medical Physics Group Instut for Diagnostic and Interventional Radiology Hospital of Friedrich-Schiller-University Jena, Germany Dipl.-Ing. Alexander Gussew Institut für Diagnostische und Interventionelle Radiologie AG Medizinische Physik Klinikum der Friedrich-Schiller-Universitaet Jena Philosophenweg 3 D-07743 Jena Germany Tel. +49 (0)3641 935361 Fax +49 (0)3641 936767 e-mail: alexander.gussew(a)med.uni-jena.de ____________________ Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Walter Bauer-Wabnegg; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777

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(no subject)
by Christian Scheel 05 Sep '08

05 Sep '08

Dear FS-Experts, While checking the results of the autorecon2 process and editing the brainmask.mgz and wm.mgz I regularly encounter quite a few spots per brain where - in my eyes - the red pial line seems to get far too close to the yellow line making the calculated cortex appear too thin in these regions (see the three examples attached). Sometimes the lines get so close that hardly any room for the cortex is left. I wonder what might be the best way to deal with these spots. Can I simply ignore them or should I try to remove some parts of the white matter in the wm.mgz (which will of course add another subjective factor into the analysis) or is there another way of handling them that i did not think of? Any help is greatly appreciated. Best wishes, Christian Scheel -- Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer

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Excluded Gray Matter
by antonio cerasa 05 Sep '08

05 Sep '08

Hi, Is there any way to fix this intensity normalization error regarding gray matter (figure attached). Thanks Antonio Cerasa, ISN-CNR Italy

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Talairach_with_skull.lta accuracy
by Jeff Sadino 04 Sep '08

04 Sep '08

Hello all, According to aseg.stats, our ICV values fluctuate on the same subject across scans, sometimes by up to 10% I have been validating the talairach_with_skull.lta accuracy by comparing the nu_neck.mgz to the RB_all_withskull_2006-02-15.gca template. I read on the boards that it is not all that necessary that the brains match, that it is more important for the skulls to match. The RB is blurred (I don't fully understand where the RB comes from, I think from 22 subjects that the freesurfers combined into one?), so am I matching up the whitest areas of the RB to the skull on the nu_neck image? I noticed also that the bottom of the brains rarely match at all to the RB image...is this normal? Are there any other parts of the image that need to be checked for validity? I attached two nu_noneck.mgz files, one was good and the other bad. Are these images typical? Thank you for your help, Jeff _________________________________________________________________ See how Windows Mobile brings your life together—at home, work, or on the go. http://clk.atdmt.com/MRT/go/msnnkwxp1020093182mrt/direct/01/

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Newbie problem...
by Feuerstein Philippe 04 Sep '08

04 Sep '08

Hello, I am evaluating FreeSurfer, installed and runned the tutorial without major troubles. Now, we have set up the MPRAGE sequence as stated here: http://www.nmr.mgh.harvard.edu/~andre/Sequences/SagMPR8Min.html and we have also a problem, surely a newbie and trivial one (sorry about that...). We had a series from a test patient, but initial stage of recon-all fails (in mri-convert) with the cause "ERROR: VolSS2MosSS: number of columns in the mosaic (192) is not an integer multiple of the number of columns in the image (200)" Here is the detailed log: ------------------------------------------------------------------------------------------- servux:~/freesurfer/subjects/ghca> recon-all -i C0001 -s test INFO: SUBJECTS_DIR is /home/philfeu/freesurfer/subjects Actual FREESURFER_HOME /home/philfeu/freesurfer Linux servux 2.6.24-19-generic #1 SMP Wed Aug 20 17:53:40 UTC 2008 x86_64 GNU/Linux /home/philfeu/freesurfer/subjects/test mri_convert /home/philfeu/freesurfer/subjects/ghca/C0001 /home/philfeu/freesurfer/subjects/test/mri/orig/001.mgz mri_convert /home/philfeu/freesurfer/subjects/ghca/C0001 /home/philfeu/freesurfer/subjects/test/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /home/philfeu/freesurfer/subjects/ghca/C0001... Getting Series No INFO: Found 250 files in /home/philfeu/freesurfer/subjects/ghca INFO: Scanning for Series Number 2 Scanning Directory INFO: found 128 files in series INFO: loading series header info. RunNo = 1 WARNING: Run 1 appears to be truncated Files Found: 128, Files Expected (lRep+1): 1 FileName /home/philfeu/freesurfer/subjects/ghca/C0001 Identification NumarisVer syngo MR A30 4VA30A ScannerModel Symphony PatientName TEST Date and time StudyDate 20080828 StudyTime 165725.921000 SeriesTime 171106.578000 AcqTime 170220.252481 Acquisition parameters PulseSeq *tfl3d1_ns Protocol MPRAGE VOLUM 8MIN PhEncDir ROW EchoNo 0 FlipAngle 7 EchoTime 3.48 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 192 NImageCols 192 NFrames 128 SliceArraylSize 1 IsMosaic 1 ImgPos 85.7703 164.3475 80.1092 VolRes 1.2800 1.2800 1.3300 VolDim 200 200 1 Vc 0.1097 -0.9940 -0.0000 Vr -0.1091 -0.0120 -0.9940 Vs -0.9880 -0.1091 0.1097 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (200 200 1), nframes = 128, ismosaic=1 Numaris Version: syngo MR A30 4VA30A Maj = 4, Min=3, MinMin = 0 Repetition Time = 2730, TR = 2730 ms AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /home/philfeu/freesurfer/subjects/ghca/C0001 Identification NumarisVer syngo MR A30 4VA30A ScannerModel Symphony PatientName TEST Date and time StudyDate 20080828 StudyTime 165725.921000 SeriesTime 171106.578000 AcqTime 170220.252481 Acquisition parameters PulseSeq *tfl3d1_ns Protocol MPRAGE VOLUM 8MIN PhEncDir ROW EchoNo 0 FlipAngle 7 EchoTime 3.48 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 192 NImageCols 192 NFrames 128 SliceArraylSize 1 IsMosaic 1 ImgPos -0.0636 171.2637 83.8372 VolRes 1.2800 1.2800 1.3300 VolDim 200 200 1 Vc 0.1097 -0.9940 -0.0000 Vr -0.1091 -0.0120 -0.9940 Vs -0.9880 -0.1091 0.1097 VolCenter -0.6357 42.4228 -43.3169 TransferSyntaxUID 1.2.840.10008.1.2.1 ERROR: VolSS2MosSS: number of columns in the mosaic (192) is not an integer multiple of the number of columns in the image (200) Linux servux 2.6.24-19-generic #1 SMP Wed Aug 20 17:53:40 UTC 2008 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Sep 2 15:06:32 CEST 2008 ------------------------------------------------------------------------------------------- Any clue about what we have done wrong? TIA. ----------------------------------------------------------------------------------------------------------------------------------- Dr Philippe Feuerstein Radiologie Groupe Hospitalier du Centre Alsace Hôpital Albert Schweitzer 201, Avenue d'Alsace - BP 20129 68003 Colmar Cedex France Tél: +33 3 89 21 25 74 mailto: philippe.feuerstein(a)ghca.fr<mailto:philippe.feuerstein@ghca.fr>

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Recon-all-long
by Juergen Haenggi 04 Sep '08

04 Sep '08

Dear FS experts I tried to run recon-all-long, but there is no such command. I use FS 4.0.5 on a MacIntel. Where can I find this command and is there any documentation about a longitudinal FS analysis? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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Cerebellum Segmentations
by Jeff Sadino 03 Sep '08

03 Sep '08

Hello, I am processing a large number of scans with the goal of segmenting the cerebellum into subregions, particularly the Vermis. Without editing each scan individually using tkmedit, what is the best way to achieve this subregion segmentation for a large number of subjects? Thank you in advance, Jeff Sadino JABSOM University of Hawaii at Manoa _________________________________________________________________ Want to do more with Windows Live? Learn “10 hidden secrets” from Jamie. http://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!5…

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Freesurfer