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6 participants
30076 discussions

qdec
by Feng-Xian Yan 27 Feb '08

27 Feb '08

hi, I have a problem. I analysis my data using qdec. But, after runing the command (recon-all -s subject1 -qcache) I can't find the qdec.table.dat and the discrete factor files. The following commands that I type to run. First, I set SUBJECTS_DIR to a directory. setenv SUBJECTS_DIR $SUBJECTS_DIR/group_analysis cd $SUBJECTS_DIR Then, I run the pre-smoothed fsaverage surfaces recon-all -s subjects1 -qcache Could you tell me what's wrong? Thank you~~

2 1

Re: [Freesurfer] autorecon1 errors
by Jenni Pacheco 26 Feb '08

26 Feb '08

Hi Mike, I've run into the same problem you see in number 1 - the SPLINE_CUBIC_SET - Fatal Error!, with a fine talaraich. I was able to fix this by using the -no1d flag in mri_normalize. You can add this as an xopt to that subject so that it is always run: http://surfer.nmr.mgh.harvard.edu/fswiki/recon_2dall#head-25c704d7d03b1c22e… I think this occurs when there is a bigger bias field in left-right direction than in the anterior-posterior direction (although, maybe it's I/S, I forget now). I'll leave the other two problems for someone more qualified! Jenni -- Learning and Memory Lab The University of Texas at Austin Department of Psychology 1 University Station A8000 Austin, TX 78712 phone: (512) 471-2727 fax: (512) 471-5935 email: jpacheco(a)mail.utexas.edu > On Tue, Feb 26, 2008 at 3:29 PM, Michael Harms <mharms(a)conte.wustl.edu> > wrote: > > > > > Hello, > > We recently just ran 80 elderly brains through -autorecon1 using FS > > v4.0.2, and encountered 3 different types of errors that we are not > > entirely sure how to handle: > > > > (1) During mri_normalize of 1 subject we encountered: > > SPLINE_CUBIC_SET - Fatal error! > > The number of data points N must be at least 2. > > The input value is 1. > > > > The FS archive indicates to check the talairach transform given this > > error, but the talairach.xfm appears fine for this subject (as assessed > > using tkregister2). > > > > (2) During mri_watershed of 1 subject: > > Sorting... > > mri_watershed Error: > > Problem in the COG calculation > > > > This subject had a slightly warped talaraich.xfm, but I think more > > relevantly, its talairach_with_skull.lta was way off. > > > > (3) During mri_watershed of 5 subjects: > > mri_watershed Error: > > GLOBAL region of the brain empty ! > > > > For all 5 of these subjects, the talairch_with_skull.lta also had > > obvious problems. > > > > RE (1): Any insight would be appreciated. > > > > RE (2) and (3): I suspect that we should try running with the -no- > > wsgcaatlas flag, so that talairach_with_skull.lta is longer used by > > mri_watershed. Should we then substitute the -wsatlas flag instead? > > (Its not clear to me which atlas is used when that particular flag is > > included). > > > > Last, I thought you might be interested in these errors, because they > > directly relate to my recent question regarding the robustness of > > talairach_with_skull.lta. At least during the -autorecon1 (i.e., > > initial) creation of this lta file, it appears that there is some > > possibility of a bad talairach_with_skull registration (6 of 80 in this > > particular subject set). > > > > 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 > > -------------------------------------------------------------------- > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

1 0

autorecon1 errors
by Michael Harms 26 Feb '08

26 Feb '08

Hello, We recently just ran 80 elderly brains through -autorecon1 using FS v4.0.2, and encountered 3 different types of errors that we are not entirely sure how to handle: (1) During mri_normalize of 1 subject we encountered: SPLINE_CUBIC_SET - Fatal error! The number of data points N must be at least 2. The input value is 1. The FS archive indicates to check the talairach transform given this error, but the talairach.xfm appears fine for this subject (as assessed using tkregister2). (2) During mri_watershed of 1 subject: Sorting... mri_watershed Error: Problem in the COG calculation This subject had a slightly warped talaraich.xfm, but I think more relevantly, its talairach_with_skull.lta was way off. (3) During mri_watershed of 5 subjects: mri_watershed Error: GLOBAL region of the brain empty ! For all 5 of these subjects, the talairch_with_skull.lta also had obvious problems. RE (1): Any insight would be appreciated. RE (2) and (3): I suspect that we should try running with the -no- wsgcaatlas flag, so that talairach_with_skull.lta is longer used by mri_watershed. Should we then substitute the -wsatlas flag instead? (Its not clear to me which atlas is used when that particular flag is included). Last, I thought you might be interested in these errors, because they directly relate to my recent question regarding the robustness of talairach_with_skull.lta. At least during the -autorecon1 (i.e., initial) creation of this lta file, it appears that there is some possibility of a bad talairach_with_skull registration (6 of 80 in this particular subject set). 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 --------------------------------------------------------------------

1 0

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

2 1

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).

2 1

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

2 1

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

2 3

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

2 1

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 --

2 5

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

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