Freesurfer January 2007

freesurfer@nmr.mgh.harvard.edu

51 participants
74 discussions

FS-FAST: problem with extracting BOLD time courses with a tksurfer tcl script
by raij＠nmr.mgh.harvard.edu 05 Jan '07

05 Jan '07

Hi, I am trying to extract numerical values for BOLD time courses of (a large number of) ROIs. For this purpose I use a tksurfer tcl script. Everything works fine when I only have a small number (~6) of contrasts/stimulus categories (as defined in the paradigm files), but if I increase the number of stimulus categories to 14-18, the script dies without producing anything. I am able to produce the numerical tables semi-manually with the GUI/tcl shell even for the large number of stimulus categories so I do not quite figure what gives. However, doing this manually for all our data would be impossible. Any suggestions how I could circumvent this problem? (The visualization part in the script below, that draws the actual time course display, is not necessary for producing the numerical tables, but removing that part of the script does not help - it still dies.) Any suggestions much appreciated! Also if anyone needs the full script I am happy to send you a copy - however notice that currently one of the command lines only works in the developmental environment (nmr-dev-env). Cheers, Tommi Specs: on machine ai nmr-dev-env cd /space/cuzco/12/users/raij/avml_fmri_mctogether/ setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage #Here is the part of the subroutine that does the extraction (to run the whole thing from the master script that sets the variable values, launch run-label-FIR-h.csh in the same directory): # Set curvature for lh set curv lh.curv read_binary_curv set curvflag 1 # Clear earlier labels labl_remove_all # Clear earlier timecourses func_clear_selection # Load new label (use actual path to label file instead of $lname if running the script by itself) labl_load $lpath/$lname.label # Load new timecourse. 3 = No registration needed. # (use actual path to time course file [e.g., bold/<analysisname>/h-lh.bhdr] instead of $timecourse if running the script by itself) func_load_timecourse $timecourse 3 # Set timecourse to show average value across all vertices included in the label set gaLinkedVars(func_graph_avg_mode) 2 # Some draw command, dunno what it does really SendLinkedVarGroup graph # Select only some of the contrasts for display. Specifically, here turn off contrasts 4-6 # General format: set gGraphSetting(<color>,visible) <0|1> # where <color> is: Red/Green/Blue/Purple/Brown/Pink/Gray/LightBlue/Yellow/Orange # "Red" is condition zero (NULL), "Green" is condition one, etc. set gGraphSetting(Brown,visible) 0 set gGraphSetting(Pink,visible) 0 set gGraphSetting(Gray,visible) 0 # Adjust amplitude (y-axis, % BOLD signal change) scale from -1 to +2 .wwGraph.gwGraph.gwGraph axis config y -min -1 -max 2 # Pre-stimulus baseline correction (to turn OFF, use 0) set gbPreStimOffset 1 # Draw time course display (this command works only in nmr-DEV-env version!) Graph_SelectVerticesFromMode # Save text file listing the numerical time course values for all categories func_print_timecourse_selection $lpath/$lname-$aname-h.xls # Save time course display as postscript Graph_SaveToPS $lpath/$lname-$aname-h.ps

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control points and white matter edits
by Paul Greenberg 05 Jan '07

05 Jan '07

Hi all, I'm having trouble getting accurate white and pial surfaces in inferior temporal regions on a few lower quality scans with significant intensity variation. I've added hundreds of control points and drawn in white matter in these regions when control points failed to recover unlabeled cortex, but when re-running the scripts with either -autorecon2-wm, or -autorecon2-cp, followed by -autorecon3 the surfaces are still not accurate. Are there other interventions I can to to get more accurate surfaces? If you manually add white matter why will the regenerated white matter surfaces not always extend around the hand drawn parts? Thanks, Paul

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Coloring problem after autorecon2
by Niels Bergsland 05 Jan '07

05 Jan '07

Hi list, After completing autorecon1, I found the cerebellum missing and I manually editted for this case. But I found after autorecon2, the cerebellum were not filled with appropriate color at all. I have uploaded a picture to my webspace. Please see: http://www.lucidthoughts.org/download/color_failure.png I can also upload the dicoms to the drop box if this would help. Thanks! Niels Bergsland

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label
by Ran Tao 05 Jan '07

05 Jan '07

Hi All, When I ran mri_annotation2label --subject UNC_4 --hemi rh --labelbase ./labels/aparc-rh --table $FREESURFER_HOME/surface_labels.txt Some labels are always skipped such as 6,7... I also tried on tutorial data, the same thing happened. Any ideas? Is surface_labels.txt a complete label list I should use? I also want to add some own labels(not extract them from annot), and cannot figure it out. How can I do this? Thank you, Ran

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ages of subjecs in buckner_data-raw_dicoms.tar.gz
by Jose Luis Cantero 05 Jan '07

05 Jan '07

Hi there, we are trying to determine small atrophy changes based on novel analytic approaches. At this point of our project MPRAGE sequences were adquired in a group of MCI patients (65-85 yrs.) but we do not have healthy controls of the same age interval. For this purpose, I decided to download the file buckner_data-raw_dicoms.tar.gz, but I am unable to figure out the ages of each subject within the file. I was wondering if you wouldn´t mind to provide me with the ages for the 40 subjects contained in this file in order to test my algorithms by combining Freesurfer and Matlab functions. Thanks in advance. Best, Jose L. Cantero -- Jose Luis Cantero (Lorente), Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 Seville (Spain) Phone: +34 95 4348366 Fax: +34 95 4349151 email: jlcanlor(a)upo.es

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Cortical thickness group analyses
by Dziobek, Isabel 04 Jan '07

04 Jan '07

Dear All, I have some questions in regard to the FreeSurfer group analyses (I am using the 3.0 Version), for which I would appreciate your help. I am trying to compare a patient to a control group with respect to cortical thickness (regressing out variables such as age and IQ) and also to see if associations exist in specific ROIs between cortical thickness and cognitive variables (for the groups separately). I started constructing a group descriptor file containing the two classes (patient and control) and the variable age. First, I wanted to compare the groups disregarding any other variable and so I constructed the following contrast vector: (1 -1 0), assuming doss and thinking that the ³0² meant that this column of the design matrix would not be taken into account in the model. However, this yielded the same result as running (1 -1 1). Do I have to construct a separate fsgd file only containing the classes and then a contrast vector (1 -1)? What about regressing out more than 1 variable (e.g. age and IQ), how does the contrast vector have to look like then? Also, how do I look at correlations between those variables and cortical thickness for the groups separately? When loading the scatter plots of the fsgd, the regression line for the separate groups seems to run always parallel, which does not seem very likely (see attached jpg). Are these regression lines at all? Where can I obtain the Rs in numbers? Can I, alternatively, stream out the numbers for the cortical thickness of a defined ROI to then run correlations in SPSS. Where would I find those numbers? I was also wondering about corrections for intracranial vault. Does the registration to the group¹s average brain takes care of differences in overall head size or is it advisable to put icv as a separate regressor (as is done in very few studies)? Thanks a lot for your help and happy holidays, Isabel ************************************** Isabel Dziobek, PhD Postdoctoral Research Fellow Independent Junior Research Group Neurocognition of Decision-Making Max-Planck Institute for Human Development Lentzeallee 94 14195 Berlin Phone: +49 30 82406 619 Fax: +49 30 82406 616 dziobek(a)mpib-berlin.mpg.de

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mri_surf2surf resampling error
by Julien 04 Jan '07

04 Jan '07

Hello there, I'm trying to resample some thickness difference maps using mri_surf2surf. Unfortunately, I keep getting the following error: ------------------------------------------------------------------- [engram:Multispect] (nmr-std-env) mri_surf2surf --srcsubject 002_MEF_A \ --sval $SUBJECTS_DIR/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff.w \ --src_type curv \ --trgsubject 001_MEF_A \ --tval $SUBJECTS_DIR/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff_resampled_to_001_MEF_A.w \ --trg_type paint \ --hemi lh \ --surfreg sphere.reg Registration surface changed to sphere.reg srcsubject = 002_MEF_A srcval = /space/engram/1/users/Multispect/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff.w srctype = curv trgsubject = 001_MEF_A trgval = /space/engram/1/users/Multispect/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff_resampled_to_001_MEF_A.w trgtype = paint surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /space/engram/1/users/Multispect/002_MEF_A/surf/lh.sphere.reg Loading source data Reading curvature file /space/engram/1/users/Multispect/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff.ÔC MRISreadCurvature: could not open /space/engram/1/users/Multispect/thickness/002_MEF_A-002_MPRAGE_A/surf/lh.thickness_diff.ÔC No such file or directory ERROR: reading curvature file ------------------------------------------------------------------- From the initial command output, it appears as though the paths are input correctly, but upon reading the file it appears to be trying to open "lh.thickness_diff.ÔC" instead of "lh.thickness_diff.w" and subsequently failing. Am I doing anything incorrectly here? Thanks, Julien -- Julien Wonderlick Research Assistant, Behavioral Neuroscience Laboratory Department of Brain and Cognitive Sciences, MIT Building 46-5127 617.253.7437 jswonder(a)mit.edu

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question about strange results after talairach transform
by Bum Seok Jeong 03 Jan '07

03 Jan '07

Hi! I use axial LAS system 3D nifti and analyze format images to perform autorecon1 process. Skull stripping results looked fine. However, when I checked talairachs transform results (tkregister2 --mgz --s C1 --fstal), a part of original image was just shown at left upper corner and talairach template did not appear with white background. So I can not perform a manual registration. The message appeared as follows Thanks in advance bsJeong <259> fs/tmp% tkregister2 --mgz --s C1 --fstal INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 %Wed Jan 3 12:24:29 2007>>> /bin/freesurfer/mni/bin/minctracc -clobber -debug /tmp/mritotal_16322/src_8_dxyz.mnc /bin/freesurfer/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc transforms/talairach.auto.xfm -transformation /tmp/mritotal_16322/src_8tmp2c.xfm -lsq9 -xcorr -model_mask /bin/freesurfer/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -191.589493 222.719711 194.588959 -step 4 4 4 -tol 0.004 -simplex 2 talairach.xfm --------------------- 1.053 -0.003 -0.046 212.831; 0.006 1.123 0.061 -264.791; 0.045 -0.057 1.036 -186.491; 0.000 0.000 0.000 1.000; INFO: loading target /tmp/C1/mri/orig.mgzINFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 -62.500; 0.000 0.000 1.000 91.141; 0.000 -1.000 0.000 347.141; 0.000 0.000 0.000 1.000; INFO: loading movable /bin/freesurfer/average/mni305.cor.mgz INFO: changing move type to float Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.053 -0.003 -0.046 212.831; 0.006 1.123 0.061 -264.791; 0.045 -0.057 1.036 -186.491; 0.000 0.000 0.000 1.000; subject = C1 Zoom Factor = 2 FOV = 256 Opening window C1 Setting scale tkregister2: interface: /bin/freesurfer/lib/tcl/tkregister2.tcl tkregister.tcl: startup done tkregister.tcl: default macro interface (to change: macro,mini,micro) tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}

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free surfer installation questions
by Andrew Bolstad 03 Jan '07

03 Jan '07

Hi, We are trying to install Freesurfer on a Linux Fedora Core 6 platform. We downloaded the CentOS 4 platform and the FC 5 upgrade of tksurfer. We have two questions: 1. When we rename tksurfer_fc5 to tksurfer and move it into the Freesurfer directory, it is an executable file, whereas the old tksurfer was an executable text file. Do we need to do something to change the file type? In its current state, the tksurfer upgrade does not appear to work. We tried the command: tksurfer bert rh pial and got a "permission denied" message (we are logged in as root). The message was: /usr/share/freesurfer/bin//tksurfer: Permission denied. By the way, we have the freesurfer directory in /usr/share/. 2. We seem to be missing a library file of some kind. We ran these two commands to test freesurfer: tkmedit bert norm.mgz tkmedit bert orig.mgz and get this error message both times: /usr/share/freesurfer/bin/tkmedit.bin: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory Do we need to download libglut.so.3? If anyone on this list can answer these questions, please let us know what we need to do. Thanks, Andrew Bolstad

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mri_nu_correct: how to maintain original geometry?
by Stephen Towler 03 Jan '07

03 Jan '07

Hi all, Is there a way to get mri_nu_correct to output geometry identical to the input scan, with no interpolation? For example: if I run mri_nu_correct (only) on a T1 scan that is 124x256x256 (1.2mm x .9375 mm2), the output is 256x256x256 (.9375 mm3). Not desirable for my current application. Thanks! Stephen -- Stephen Towler stowler(a)mbi.ufl.edu 352-294-0048 office 352-258-6409 mobile 352-392-8347 fax Leonard Lab Department of Neuroscience PO Box 100244 University of Florida HSC Gainesville, FL 32610

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Freesurfer January 2007