Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

eTIV measures
by d.g.lawyer＠medisin.uio.no 08 Sep '08

08 Sep '08

Hi, Given the recent debate on the accuracy of the eICV in FS, I am wondering what to cite when using these measures. Do you prefer Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Fischl, B., D.H. Salat, E. Busa, M. Albert, M. Dieterich, C. Haselgrove, A. van der Kouwe, R. Killiany, D. Kennedy, S. Klaveness, A. Montillo, N. Makris, B. Rosen, and A.M. Dale, (2002). Neuron, 33:341-355. or is there a better choice? ------------------------------------ Here miracles become marvels, and marvels recurring wonders. -- William Beebe Dr. Glenn Lawyer +352 661 967 244 Instituttgruppe for psykiatri Seksjon Vinderen PB 85 Vinderen 0319 Oslo http://folk.uio.no/davidgl

4 3

Optseq2
by Matt Dixon 08 Sep '08

08 Sep '08

Hello, I would be very grateful if someone could help me with a few questions I have regarding optseq 2: 1) If presenting a given stimulus multiple times (a la repetition reduction experiments), can Optseq2 optimize stimulus presentation and if so, what is the command to specify the number of repetitions per stimulus? 2) Should each run of my experiment use the same or different optimization outputs from Optseq2. And if they should use different outputs, what is the command to specify the number of runs in my experiment? Thanks so much for your time! Matt

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Problem to run FreeSurfer for under one year old baby subject
by Yuan Xu 08 Sep '08

08 Sep '08

4 3

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

2 1

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

2 1

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

2 1

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

2 1

(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

3 2

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

2 1

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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