Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

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>

4 4

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) -----------------------------------------------------------

2 1

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…

1 0

WM intensity < CSF intensity?
by Juranek, Jenifer 03 Sep '08

03 Sep '08

Hi, I'm running fsv405 on RHEL5. I received the following message and reviewed the input images, but could not spot the problem. Any suggestions about where I should be looking in the T1.mgz? Many Thanks, Jenifer White matter intensity 0 is lower than CSF intensity 14. Please examine input images. Will terminate ... *********************************************** *********************************************** *********************************************** ********************************************************** MRIstripSkull failed. ************************************************************

2 4

Surface area measurement
by Barkay, Gavriel 03 Sep '08

03 Sep '08

Can I do surface area measurement using freesurfer? -- Gavriel Barkay M.D. M.Sc. Psychopharmacology Fellow Office: 317-433-1771 Pager: 317-312-2448

2 1

about white matter segmentation
by abel cruz vadell 02 Sep '08

02 Sep '08

Hi Checking the white matter segmentation of a subject I found the problem atacched (blue arrow in the axial, sagital and coronal views). I used controls points but the problem remains. Any idea? Thanks Abel

2 2

Statistic in Freesurfer
by Massimiliano Calabrese 02 Sep '08

02 Sep '08

Dear Freesurfer users, probably this is for you a very simple question: we would like to know if it has been implemented a tool based on permutation test to compare thickness and volume of different regions. we know that there are similar tools for voxels scale, but we did not know anything of similar for regional anlaysis.(and if this could be useful ) Thank you Massimiliano Calabrese Multiple Sclerosis Centre University of Padova Italy Marco Battaglini Quantitative Neuroimaging Laboratory University of Siena _________________________________________________________________ Stanco della solita finestra? Personalizza la tua Hotmail! http://www.messenger.it/personalizza.html#sfondi

1 0

convert point from anatomical- to functional space
by Steinmann, Iris 01 Sep '08

01 Sep '08

Dear Freesurfers, I have a question concerning the register.dat. In Freesurfer-Wiki I found that sentence: 'The last four lines of register.dat have the values of the registration matrix that converts a location in anatomical space to a location in functional space' I want convert one special point from my high resolution anatomical space (256x256) to my low resolution functional space (64x64). So I want apply the register.dat-Matrix to the Vektor from this point in anatomical space. But why is it an 4x4 Matrix? I supposed that I need an 3x3-matrix for an translation in x,y,z-direction. How can I get this anatomical point in my functional space? Thanks for your answer

2 1

definition of metric distortion
by Patrick Schikowski 31 Aug '08

31 Aug '08

I am wondering how the percent distance error you present in fig.11 in "Cortical Surface-Based Analysis - II: Inflation, Flattening, and a Surface-Based Coordinate System" [Fischl et al, 1998] was exactly determined? In "6. ERROR ANALYSIS" you just mentioned "Finally, we present the errors of the flattening and spherical transformation on a set of 10 human hemispheres.All percentages in this section are computed using an L1 norm as it is less sensitive to outliers than the L2 norm." Could you please give me some details about the process of measuring the errors, maybe an equation? thanks a lot, patrick

1 0

mri_glmfit error while following tutorial
by N. Eiji Nawa 31 Aug '08

31 Aug '08

Hi: I am doing the freesurfer tutorial (http://surfer.nmr.mgh.harvard.edu/ fswiki/FsFastTutorial), but got an error while running the Random Effects Surface-based Group Analysis section. The command line was: mri_glmfit --y lh.ces.nii --osgm --mask ../lh.mask.nii --glmdir lh.rfx.osgm --nii --surf fsaverage lh and this is the terminal output: Reading source surface /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial//fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /Applications/freesurfer/subjects/ buckner_data/tutorial_subjs/fsfast-tutorial//fsaverage/surf/ lh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $ cwd /Applications/freesurfer/subjects/buckner_data/tutorial_subjs/ fsfast-tutorial/fb1-analysis-study/group-analysis-tut/sm-gamma-fwhm5/ odd-v-0 cmdline mri_glmfit --y lh.ces.nii --osgm --mask ../lh.mask.nii -- glmdir lh.rfx.osgm --nii --surf fsaverage lh sysname Darwin hostname cerezo.cis.atr.jp machine Power Macintosh user eiji FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Applications/freesurfer/subjects/buckner_data/tutorial_subjs/ fsfast-tutorial/fb1-analysis-study/group-analysis-tut/sm-gamma-fwhm5/ odd-v-0/lh.ces.nii logyflag 0 usedti 0 mask ../lh.mask.nii maskinv 0 glmdir lh.rfx.osgm DoFFx 0 Creating output directory lh.rfx.osgm Loading y from /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial/fb1-analysis-study/group-analysis-tut/ sm-gamma-fwhm5/odd-v-0/lh.ces.nii ERROR: Read 819210, expected 41943552 niiRead(): error reading from /Applications/freesurfer/subjects/ buckner_data/tutorial_subjs/fsfast-tutorial/fb1-analysis-study/group- analysis-tut/sm-gamma-fwhm5/odd-v-0/lh.ces.nii ERROR: loading y /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial/fb1-analysis-study/group-analysis-tut/ sm-gamma-fwhm5/odd-v-0/lh.ces.nii I am not quite sure what is in 'lh.ces.nii' - from the file's time stamp it looks like it was not generated during the tutorial (Jun 19 2007). Any help or comment will be very helpful - I am basically clueless... Thanks a lot in advance!!! Eiji (below is the summary of my environment and problem) -- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v4.0.5 Kernel info: Darwin 8.11.0 Power Macintosh (Mac OS 10.4.11 on a G5) SUBJECTS_DIR: /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial/ which mri_glmfit: /Applications/freesurfer/bin/mri_glmfit pwd: /Applications/freesurfer/subjects/buckner_data/tutorial_subjs/ fsfast-tutorial/fb1-analysis-study/group-analysis-tut/sm-gamma-fwhm5/ odd-v-0 command line: /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial/fb1-analysis-study/group-analysis-tut/ sm-gamma-fwhm5/odd-v-0 error message: ERROR: Read 819210, expected 41943552

2 2

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer