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30079 discussions

how/where is talairach.xfm used?
by Michael Harms 12 Oct '07

12 Oct '07

Hello, We are running FS v3.0.5 on some elderly brains, and the talairach transform (as assessed via tkregister2 with fstal flag) is inaccurate in an appreciable number of the scans we have examined so far. Frequently, the inaccuracies involve primarily scaling or translation, although in one instance the rotation was way-off (such that the cardinal axes were basically swapped). However, even for this worst case, the white and pial surfaces, as well as the aseg, look reasonable. (I haven't run autorecon3 to create the surface parcellations yet). To what extent is talairach.xfm important for the autorecon2 & 3 stages? If surfaces and aseg look ok, can an inaccurate talairach.xfm just be ignored if we are not going to be averaging functional data? Will the surface parcellations perhaps be affected somehow? Looking at ReconAllDevTable it appears that talairach.lta and talairach.m3z are the primary inputs to stages 2 and 3. So, I'm wondering how the .xfm relates to the .lta and .m3z files...? Lastly, the particularly bad .xfm under v3.0.5 looks fine when created using v4.0.1. If we need or want accurate .xfm's would it be appropriate to run autorecon1 under v4 but then switch to v3 for autorecon2 & 3 so as to maintain compatibility with other subjects processed under v3? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

4 7

problem with dt_recon
by Dirk Dettmering 11 Oct '07

11 Oct '07

Hello, after I figured out how to prepare the dt_recon command with the correct input (which was a long struggle to find the correct dicom input) I got now stuck as dt_recon always stops before finishing the run with the same error message: brainmask not found I attach the log file with the relevant parts. The complete log and subject dir is available upon request. Does somebody know whats wrong? I created the complete directory tree under the subjects dir with mksubjdirs. The dicom input was created with unpacksdcmdir -src 02171336/ -targ mri -run 2 dicom dicom 002 after I copied the content of the dicom data directory from cd to disk. And thats exactly the stage where I was stuck a long time as it wasn't obvious to me to prepare dicom data with unpacksdcmdir to dicom format to satisfy dt_recon. Thanks for any hint or help in advance Dirk -- Dirk Dettmering DV-Koordinator - Klinik für Neurologie Universitätsklinikum Gießen und Marburg GmbH, Standort Marburg Baldingerstraße D-35043 Marburg Telefon (+49) 06421 - 286 5354 Telefax (+49) 06421 - 286 5208 Pager 142 69684 E-Mail: dirk.dettmering(a)med.uni-marburg.de url: http://www.med.uni-marburg.de Aufsichtsratsvorsitzender: Wolfgang Pföhler Geschäftsführung: Gerald Meder (Vors.), Prof. Dr. Werner Seeger (stv. Vors.), Dr. Hans-Jürgen Hackenberg, Prof. Dr. Martin Hansis, Dr. Peter Mein, Manfred Wiehl Sitz der Gesellschaft: Gießen Amtsgericht Gießen HRB 6384 dt_recon logfile Do Okt 11 18:09:09 CEST 2007 VERSION $Id: dt_recon,v 1.6.2.2 2007/08/23 19:17:46 greve Exp $ setenv SUBJECTS_DIR /mrt-daten/dt_recon/0001_DTI_RLS2 cd /mrt-daten/dt_recon/0001_DTI_RLS2 /usr/local/freesurfer/bin/dt_recon --i mri/dicom/002/29265430 --o maps --s . ixneurol247.med.uni-marburg.de surfer /usr/local/freesurfer/fsl/bin/eddy_correct #@#------------------------------- Converting input Do Okt 11 18:09:09 CEST 2007 cd /mrt-daten/dt_recon/0001_DTI_RLS2 mri_convert /mrt-daten/dt_recon/0001_DTI_RLS2/mri/dicom/002/29265430 /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi.nii mri_convert /mrt-daten/dt_recon/0001_DTI_RLS2/mri/dicom/002/29265430 /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi.nii $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from /mrt-daten/dt_recon/0001_DTI_RLS2/mri/dicom/002/29265430... Getting Series No INFO: Found 2103 files in /mrt-daten/dt_recon/0001_DTI_RLS2/mri/dicom/002 INFO: Scanning for Series Number 2 Scanning Directory INFO: found 2100 files in series INFO: loading series header info. RunNo = 1 INFO: sorting. INFO: (128 128 60), nframes = 35, ismosaic=0 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; This looks like an MGH DTI volume MGH DTI SeqPack Info 0 ep_b0#0 0.000000 0 1 ep_b0#1 0.000000 1 2 ep_b0#2 0.000000 2 3 ep_b0#3 0.000000 3 [snip] #@#------------------------------- Eddy/Motion Correct Do Okt 11 18:15:26 CEST 2007 cd /mrt-daten/dt_recon/0001_DTI_RLS2/maps/ectmp eddy_correct /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi.nii /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii 0 processing vol0000.nii processing vol0001.nii processing vol0002.nii processing vol0003.nii processing vol0004.nii processing vol0005.nii processing vol0006.nii processing vol0007.nii processing vol0008.nii processing vol0009.nii processing vol0010.nii processing vol0011.nii processing vol0012.nii processing vol0013.nii processing vol0014.nii processing vol0015.nii processing vol0016.nii processing vol0017.nii processing vol0018.nii processing vol0019.nii processing vol0020.nii processing vol0021.nii processing vol0022.nii processing vol0023.nii processing vol0024.nii processing vol0025.nii processing vol0026.nii processing vol0027.nii processing vol0028.nii processing vol0029.nii processing vol0030.nii processing vol0031.nii processing vol0032.nii processing vol0033.nii processing vol0034.nii #@#------------------------------- Fitting Tensors Do Okt 11 18:57:54 CEST 2007 cd /mrt-daten/dt_recon/0001_DTI_RLS2 mri_glmfit --y /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii --glmdir /mrt-daten/dt_recon/0001_DTI_RLS2/maps --dti /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-infodump.dat $Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $ cwd /mrt-daten/dt_recon/0001_DTI_RLS2 cmdline mri_glmfit --y /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii --glmdir /mrt-daten/dt_recon/0001_DTI_RLS2/maps --dti /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-infodump.dat sysname Linux hostname ixneurol247.med.uni-marburg.de machine i686 user surfer FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii logyflag 1 X /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-infodump.dat usedti 1 glmdir /mrt-daten/dt_recon/0001_DTI_RLS2/maps DoFFx 0 Creating output directory /mrt-daten/dt_recon/0001_DTI_RLS2/maps Loading y from /mrt-daten/dt_recon/0001_DTI_RLS2/maps/dwi-ec.nii Using DTI bValue = 1000 nB0 = 5 nDir = 30 GradFile /usr/local/freesurfer/diffusion/mgh-dti-seqpack/gradient_mgh_dti30.gdt Matrix condition is 27.8204 Pruning voxels by frame. Found 972044 voxels in mask Saving mask to /mrt-daten/dt_recon/0001_DTI_RLS2/maps/mask.nii search space = 9.33162e+06 Computing natural log of input DOF = 28 Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Fit completed in 1.75672 minutes Writing results Saving DTI Analysis Computing fa Computing ra Computing vr Computing adc Computing ivc Computing dwisynth Computing dwires Computing dwi rvar mri_glmfit done #@#------------------------------- Registration Do Okt 11 19:02:55 CEST 2007 setenv SUBJECTS_DIR /mrt-daten/dt_recon/0001_DTI_RLS2 cd /mrt-daten/dt_recon/0001_DTI_RLS2 fslregister --s . --mov /mrt-daten/dt_recon/0001_DTI_RLS2/maps/lowb.nii --reg /mrt-daten/dt_recon/0001_DTI_RLS2/maps/register.dat Log file is /mrt-daten/dt_recon/0001_DTI_RLS2/maps/register.dat.fslregister.log Do Okt 11 19:02:55 CEST 2007 --s . --mov /mrt-daten/dt_recon/0001_DTI_RLS2/maps/lowb.nii --reg /mrt-daten/dt_recon/0001_DTI_RLS2/maps/register.dat $Id: fslregister,v 1.16 2007/07/26 16:52:54 greve Exp $ ixneurol247.med.uni-marburg.de Linux ixneurol247.med.uni-marburg.de 2.6.17-1.2142_FC4smp #1 SMP Tue Jul 11 22:57:02 EDT 2006 i686 i686 i386 GNU/Linux ERROR: /mrt-daten/dt_recon/0001_DTI_RLS2/./mri/brainmask not found

2 1

New UserContributions page on the wiki
by Kevin Teich 11 Oct '07

11 Oct '07

Noticing that many FreeSurfer users have developed their own scripts for automating various tasks, somebody had the idea of adding a user contributions section to our documentation. I've added this page to the Wiki: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions Please use it to add your scripts and check out what other people are doing. If you have anything else you'd like to add, such as tips or techniques, that might be useful to others, please feel free to do so. To edit a Wiki page, you'll need to create an account; instructions on how to do this can be found on the front page, or here: http://surfer.nmr.mgh.harvard.edu/fswiki/GettingAccess -- Kevin Teich

1 0

midline parcellation bug fix
by Michael Harms 11 Oct '07

11 Oct '07

Hello, The Release Notes of v4.0.0 indicate that one of the bug fixes was "Corrected midline parcellation". Is this a fix that affects the volume segmentation (aseg) or the surface parcellation (aparc)? Is that the fix for what was described in the "Known Issues" of v3.0.5 as "During cortical parcellation, areas of the anterior cingulate cortex (rostral anterior cingulate in the parcellation atlas), are mislabelled as corpus callosum or "unlabelled subcortical". A fix for this is in the works, possibly for the next release." thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

3 7

func2roi, roisummary, and different paradigm files
by Cameron Ellis 10 Oct '07

10 Oct '07

Hi all, I am running in stable3 trying to finish up an old analysis. I think the problem I am running into arises because I have 2 separate analyses that are identical except for the paradigm files used but I am looking for verification. One analysis uses paradigm files that define only 3 conditions and the other defines 5 conditions (the original 3 plus 2 more). When I run func2roi-sess on each analysis, and compare the results I obtain using roisummary-sess for the 3 conditions that overlap between the 2 analyses they are very different. I guess the root of my question is: how are the condition values calculated? Are they calculated as offsets from averages of everything that isn't defined as a condition? Would this be why the condition values are different for 2 analyses using different paradigm files with overlapping conditions? I attached two roi summaries for comparison. Thanks in advance! Cameron

1 0

installed fsl with fs 4.0.1 package, but can not run it.
by Zhen Zonglei 10 Oct '07

10 Oct '07

Hi all: I have installed fsl with freesurfer 4.0.1, but some errors were reported when I run fsl: > source new_fs.csh Setting up Enviroment for NewFreeSurfer && new_subjects -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /nfs/h1/r1/new_soft_test/freesurfer FSFAST_HOME /nfs/h1/r1/new_soft_test/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /nfs/h1/r1/new_soft_test/freesurfer/subjects MNI_DIR /nfs/h1/r1/new_soft_test/freesurfer/mni FSL_DIR /nfs/h1/r1/new_soft_test/freesurfer/fsl >fsl /nfs/h1/r1//new_soft_test/freesurfer/fsl/bin/fslwish: line 17: /nfs/h1/r1/new_soft_test/freesurfer/fsl/extras/bin/fslwish8.4: No such file or directory /nfs/h1/r1/new_soft_test/freesurfer/fsl/bin/fslwish: line 17: exec: /nfs/h1/r1/new_soft_test/freesurfer/fsl/extras/bin/fslwish8.4: cannot execute: No such file or directory Can someone give some cues how to slove this problem? Thanks Zonglei Zhen

2 2

mkanalysis-sess -gui error, help!
by Zhen Zonglei 10 Oct '07

10 Oct '07

Hi, all: When I run mkanalysis-sess -gui, Matlab reported the following error, can someone help me solve the problem ? Thanks very much. Zonglei Zhen >mkanalysis-sess -gui Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] Font specified in font.properties not found [-*-standard symbols l-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific] < M A T L A B > Copyright 1984-2002 The MathWorks, Inc. Version 6.5.0.180913a Release 13 Jun 18 2002 Using Toolbox Path Cache. Type "help toolbox_path_cache" for more info. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> ??? Error using ==> load Unable to read MAT file /nfs/h1/r1/jliu/new_soft_test/freesurfer/fsfast/toolbox/mkanalysis_gui.fig See FILEFORMATS for a list of known file types and the functions used to read them. Error in ==> /nfs/h1/app/matlab/toolbox/matlab/iofun/hgload.m On line 45 ==> fileVars = load(filename,'-mat'); Error in ==> /nfs/h1/app/matlab/toolbox/matlab/graphics/openfig.m On line 89 ==> [figs, oldvis] = hgload(filename, struct('Visible','off')); Error in ==> /nfs/h1/app/matlab/toolbox/matlab/uitools/gui_mainfcn.m (local_openfig) On line 184 ==> gui_hFigure = openfig(name, singleton, 'auto'); Error in ==> /nfs/h1/app/matlab/toolbox/matlab/uitools/gui_mainfcn.m

2 1

QA tools--Permission denied??
by Pratap Kunwar 09 Oct '07

09 Oct '07

hi all I tried to use QA tools on the wiki (writen by jpacheco) at https://surfer.nmr.mgh.harvard.edu/fswiki/QATools?action=highlight&value=qa…. I got the following error saying permission denied. I could not even copy the QATOOLS to my folder. thanks pratap [galen:S4_HR_LR18_recon] (nmr-std-env) setenv QA_SCRIPTS /space/tensor/17/users/jpacheco/QAtools [galen:S4_HR_LR18_recon] (nmr-std-env) $QA_SCRIPTS/data_checker/recon_checker -nocheckasegoutliers -s rfa1410 -o QAsnap.html /space/tensor/17/users/jpacheco/QAtools/data_checker/recon_checker: Permission denied. -------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20071006 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_002/users/carl/S4_HR_LR18/S4_HR_LR18_recon/ PWD: /space/galen/2/users/carl/S4_HR_LR18/S4_HR_LR18_recon

2 1

Displaying cortical thickness
by Martin Kavec 08 Oct '07

08 Oct '07

Hi, I would really appreciate a help (steps or a link to description) on how to display cortical thinning on an inflated surface. I ran a subject through recon-all -autorecon3 and now I would basically want to see, where (s)he has abnormal thickness of the cortex. Thanks a lot in advance, Martin

3 2

how to apply transformation into other dataset?
by lan lin 08 Oct '07

08 Oct '07

I have some functional data coregistered to MRI, is it possible to apply linear and nonlinear transformation that we got at MRI recon-all to those functional data?

2 1

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