Freesurfer February 2008

freesurfer@nmr.mgh.harvard.edu

71 participants
87 discussions

Calling mri_convert from Java code
by Alexander Zaitsev (CNI) 26 Feb '08

26 Feb '08

Hello: I need to call mri_convert utility from Java code. The problem is when I am making a system call, I am getting the following error : >>>>> FreeSurfer license file /Application/freesurfer/.license not found. If you are outside the NMR-Martinos center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos center, make sure to source the standard environment. <<<<<< The mri_convert runs from the shell without problem and the .license file is in the right directory. I am including the following env variables into the system call: >>> String[] env = {"FREESURFER_HOME=/Application/freesurfer", "FSFAST_HOME=/Applications/freesurfer/fsfast", "SUBJECTS_DIR=/Applications/freesurfer/subjects", "MNI_DIR=/Applications/freesurfer/mni", "GSL_DIR=/Applications/freesurfer/lib/gsl", "FSL_DIR=/Applications/freesurfer/fsl", "FUNCTIONALS_DIR=$FREESURFER_HOME/sessions", "FSLOUTPUTTYPE=NIFTI_GZ", sPATH, "DISPLAY=:0.0", "HOME=/tmp", "DYLD_LIBRARY_PATH=/Applications/freesurfer/lib/gsl/lib", "MINC_BIN_DIR=/Applications/freesurfer/mni/bin", "MINC_LIB_DIR=/Applications/freesurfer/mni/lib", "MNI_DATAPATH=/Applications/freesurfer/mni/data", "LOCAL_DIR=/Applications/freesurfer/local", "FMRI_ANALYSIS_DIR=/Applications/freesurfer/fsfast", "MNI_PERL5LIB=/Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6", "PERL5LIB=/Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6", "LD_LIBRARY_PATH=/Applications/freesurfer/lib/gsl/lib", "FSLDIR=/Applications/freesurfer/fsl", "FSL_BIN=/Applications/freesurfer/fsl/bin", "FSLTCLSH=/Applications/freesurfer/fsl/bin/tclsh", "FSLWISH=/Applications/freesurfer/fsl/bin/wish", "FSLGNUPLOT=/Applications/freesurfer/fsl/bin/gnuplot", "FSLDISPLAY=/Applications/freesurfer/fsl/bin/display", "FSLCONVERT=/Applications/freesurfer/fsl/bin/convert", "FSLBROWSER=/Applications/freesurfer/fsl/tcl/fslwebbrowser", "FSLCONFDIR=/Applications/freesurfer/fsl/config" }; <<< Am I missing something? Yes, the mri_convert runs fine when called from the shell. And I don't see any other env variables related to the free surfer. Thank you, Alex

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inflation and registration to a sphere
by Mishkin Derakhshan 26 Feb '08

26 Feb '08

Hi, After reading the wiki and the references on the wiki, specifically [1] and [2], I'm still a little confused about how the inflation and registration to a sphere occurs. ie. what energy functions are being minimized at each step. I think it is a 3 step process, where 1. Surfaces are inflated by minimizing the energy function Js. This creates ?h.inflated. Js = 1/2V (EE ||xi-xn||^2) + lambda-d*Jd (8) in [1] 2. The inflated surfaces are then projected to a sphere by minimizing the energy function J. This creates ?h.sphere J = ??? 3. The sphere is registered to the average by minimizing the energy function J. This creates ?h.sphere.reg. J = Jp + lambda-d*Jd + lambda-a*Ja (5) in [2] Is there a step I am missing? Are my energy functions correct? thanks, mishkin [1] Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System, Fischl, B., Sereno, M.I., Dale, A.M., (1999). NeuroImage, 9(2):195-207. [2] High-resolution inter-subject averaging and a coordinate system for the cortical surface, Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). Human Brain Mapping, 8:272-284(1999).

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Editing annotations
by Pierson, Ronald K 26 Feb '08

26 Feb '08

Forgive me if this has been covered before, but I was unable to find an answer after searching for a bit. I have been considering editing the final surface parcellation for those scans that have problems in certain areas. Can these corrections then be used to correct the surface registration for the input into Qdec? Also, to test out the editing process I have been simply importing the annot file, editing the labels, then exporting it. Is this the correct thing to do, and is there a tutorial anywhere about this kind of editing? Thanks, Ronald Pierson

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surface co-ordinates
by Mishkin Derakhshan 25 Feb '08

25 Feb '08

Hi, 1. When using mris_convert lh.white lh.white.ascii, what co-oridnate system are the xyz co-ordinates reported in? ie. is it the RAS co-ordinates of the T1.mgz volume? 2. I am making the assumption that the lh.white and the lh.pial will always have the same number of indices and polygons. Can I also make the assumption that the order in which they are printed using mris_convert will be the same. ie. Will the vertex on line 54 of lh.white.ascii correspond to the same vertex on line 54 of lh.pial.ascii? thanks, mishkin

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changing tissue priors
by David Kahn 25 Feb '08

25 Feb '08

Hello, I'm a beginning FS user, and I've been working on segmenting some atypical brains. A colleague has worked out grey/white/csf tissue priors for these subjects and I wanted to insert these into freesurfer before segmentation and parcellation. Does anyone know how freesurfer stores tissue priors and how to change them? Also, I intend upon creating a new cortical parcellation atlas as well (using mris_ca_train and _label). Is swapping out the priors an unnecessary step if I am already prepared to supply the atlas? Thanks for any help, and forgive my relative inexperience with FS. David

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mri_surf2surf
by Daniel Wakeman 25 Feb '08

25 Feb '08

Hi, I have a question (I believe about mri_surf2surf). First, I'll describe my goal: I want to take a surface created with mri_tessellate and modified with mris_smooth and convert it to an isomorphic equally subdivided icosahedron (like mri_watershed creates). e.g. take the lh.smseghead created by mkheadsurf and resample it: mri_surf2surf --srcsubject $SUBJECT --srcsurfval $SUBJECTS_DIR/$SUBJECT/surf/lh.smseghead --src_type surf --trgsubject ico --trgsurfval $SUBJECTS_DIR/$SUBJECT/surf/$SUBJECT'_outer_skull' --hemi lh I get the following error: ERROR: could not determine type of /imaging/dw01/simulation/subjects/subject_02/surf/lh.smseghead If this is possible, I want to know how I can correct my command. Cheers, Dan --

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multiple runs and optseq
by Sheeba Arnold 25 Feb '08

25 Feb '08

Hi, We had a question about multiple runs and optseq. If we compute our sequence as one long 12 minute run, then we get a sequence with a VRF around 25. But of course, that's too long and we would want to split it into two. If we calculate a run half as long, then we get a VRF around 10. If we split our long run into two, how would that affect our efficiency? If we calculate the sequence as two short runs, how does the power of the two add up when you analyze them together (after concatenating the two short sessions)? Thanks and Regards, Sheeba

2 1

(no subject)
by James Olkin 25 Feb '08

25 Feb '08

Hello, I'm wondering if surfaces need to be smoothed (and if running "recon-all -s SUBJECT -qcache" performs the smoothing) when analyzing data. Thank you. -Ryan McGarry

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qcache flag on recon-all
by Gonzalo Sanchez Benavides 25 Feb '08

25 Feb '08

Dear FS experts, I have a beginner question so sorry if it is obvious for you... Is possible (and a good idea) to include the -qcache flag at the end in the recon-all -s /../ command? or I have to wait until recon-all had finished to run qcache? Many thanks -- Gonzalo Sánchez Benavides

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Vertex-wise thickness correlations
by Juergen Haenggi 22 Feb '08

22 Feb '08

Dear FS experts We would like to correlate the cortical thickness of a particular vertex or the mean thickness of a region with the thickness of all other vertices in one hemisphere. Therefore my question: Is there any tool in FS yet that is able to do that? 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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Freesurfer February 2008