Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

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 --------------------------------------------------------------------

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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

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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

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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

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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

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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

preproc-sess failure on Mac
by Shigeaki Nishina 08 Oct '07

08 Oct '07

I'm trying to use freesurfer/fsfast on Mac Pro and found preproc-sess fails in mcparams2etreg. The problem seems actually in Mac version of MATLAB, which does not terminate properly when it finishes processing the piped code without an explicit 'exit' at the end of it (I asked Mathworks and confirmed this is a bug existing in all MATLAB versions for Mac OS X). Because the MATLAB process does not quit, mcparams2etreg can not continue processing the rest. A workaround for this problem is to put a wrapper script that calls matlab after adding 'exit' at the end of the piped code, with the name of 'matlab' in the shell path. Is this a known issue? -- Shigeaki Nishina

1 0

Question on fs-fast
by lan lin 08 Oct '07

08 Oct '07

I'm trying to use fs-fast to analysis the PET data, but found that the first level analysis is specially designed for fmri. Is there any way to use fs-fast to analysis the PET data?

1 0

selxavg-sess error
by raij＠nmr.mgh.harvard.edu 08 Oct '07

08 Oct '07

Hi Doug, selxavg-sess -analysis group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat -sf sessid7 -df sesspar -noomnibus exits with the error: ... Saving offset to group7_ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat/h-offset_000.bfloat Slice 1, 77.2438 -------------- ??? Error using ==> minus Matrix dimensions must agree. Error in ==> fast_selxavg at 439 extreg = extreg - repmat(mean(extreg), [ntrs 1]); >> ??? Undefined function or variable 'r'. >> quiting matlab ------------------------------------------ ERROR: fast_selxavg() failed\n ERROR (/autofs/space/cuzco_014/users/raij/avml_fmri_mctogether/avml10_session_BRISI04): selxavg failed I suspect this may have to do that, for each of the seven subjects, there are three runs with an unequal number of TRs. Oddly enough, the same analysis worked in March 07. Is there a way to make this analysis work again? I am only interested in BOLD% signal change (FIR waveforms) so comparing runs with different numbers of TRs should be legal. What I would like to do is to calculate a single fixed effects group analysis where each of the three run types is output as its own category (the paradigm files are coded to allow that). Only runs that have the same number of TRs are collapsed across subjects. (Running three separate analyses, one for each run type, would not help, as we need the output to be in a single block with multiple categories, just as in our earlier analysis) Or maybe the error has to do with something else... my matlab setup.m should be fine to my knowledge. machine: cuzco nmr-dev-env (same error with the standard edition) cd /space/cuzco/14/users/raij/avml_fmri_mctogether setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage Thanks!!! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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