Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

research position in San Francisco, CA
by Brian Roach 27 Jun '08

27 Jun '08

FreeSurfer users, We are looking for new and experienced brain imagers wanting to work in our UCSF-affiliated research lab. Please apply at the following link if interested: http://www.ncire.org/positions.php?id=145 thank you, Brian

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Sulcal CSF in aseg
by Juergen Haenggi 27 Jun '08

27 Jun '08

Dear FS experts In the aseg file there are several CSF labels. Does the term "csf" mean sulcal CSF of both cerebral hemispheres, and does the term "restCSF" mean CSF in cisterns? 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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Deflate compression support
by Jan Kalkus 27 Jun '08

27 Jun '08

Hi, I'm using mris_make_template to create a template with some monkey data. At the very end I get this message: Deflate compression support is not configured. TiffWrite: TIFFWriteScanline returned error I've recompiled libtiff with the #define COMPRESSION_SUPPORT option in the tifconf.h file, but I keep getting the same message. Does anyone have any suggestions? - Jan Kalkus

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make_average_subjects & FS v4.0.5
by antonio cerasa 27 Jun '08

27 Jun '08

Dear Freesurfers I am trying to build an average subject (dataset with 38 subjects) under FS v4.0.5 (freesurfer-Linux-rh9-stable-pub-v4.0.5-full.tar.gz). It seems to work fine. But, when I click the Analyze button of Qdec, the error show as below: Writing to /usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh reading group avg surface area 828 cm^2 from file Reading in average area /usr/local/freesurfer/subjects/fsaverage/surf/rh.white.avg.area.mgh reading group avg surface area 990 cm^2 from file Reading in average area /usr/local/freesurfer/subjects/fsaverage/surf/rh.pial.avg.area.mgh reading group avg surface area 828 cm^2 from file Couldn't find file /usr/local/freesurfer/subjects/fsaverage/surf/rh.curv I don't know how to deal with this problem. Could you tell me how to resolve this? Thanks in advance. Antonio -------------------------------------------------------------------------- Antonio Cerasa PhD Part-time lecturer: University of Calabria UNICAL & University "Magna Graecia" UNICZ. Laboratory of Neuroimaging Institute of Neurological Sciences National Research Council (CNR) C/Da Burga 44, 87050 Cosenza, Italy. Phone: +39 0984.9801270 Fax: +39 0984.969306 Phone mob: +39 333/9633511 http://www.isn.cnr.it/public/pagine_ita/settori_neuroimg.asp

2 1

qdec
by Judith Segall 26 Jun '08

26 Jun '08

Hi. I am running qdec on freesurfer v 4.0.5. I am getting the following error messages: WARNING: Marker for class Main was invalid. WARNING: Color for class Main was invalid. My two two classes (male and female) are not being configured. I know from reading the freesurfer support lists that this was a problem in earlier versions of qdec, so is there a patch that I can install to remedy this? Thanks. Judith S.

2 1

What's wrong in fmc.nii data?
by Zhen Zonglei 26 Jun '08

26 Jun '08

Hi all: When I run selxavg3-sess on a analysis with 'fmc' as 'funcstem', the program report the following error, but when I did the same analysis on the same data with 'fmcsm6' as 'funcstem', the program could run successfully. our data was preprocessed with the command 'preproc-sess -sf cm_sess -df sesspar' and our freesurfer version is stable 4.0.1. We hope our analysis can do on the data with no smoothing to keep the resolution of the data. What's wrong in fmc.nii data? Thanks very much. ERROR: cannot find slice 000 for /nfs/h2/r5/data2/cm1/bold/407/fmc ??? Error using ==> fmri_bfiledim Could not find any slices with stem /nfs/h2/r5/data2/cm1/bold/407/fmc Error in ==> MRIread at 126 [nrows ncols ntp fs ns endian bext] = fmri_bfiledim(fstem); Error in ==> flac_customize at 65 mri = MRIread(fstem,1); Error in ==> fast_selxavg3 at 97 flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Best regards Zonglei Zhen

2 1

Tutorial Example Data
by Yuan Xu 26 Jun '08

26 Jun '08

2 1

brainmask.mgz vs. brain.mgz
by p.s.bjerkan＠studmed.uio.no 26 Jun '08

26 Jun '08

Hi! Have a couple of questions regarding manual edits correcting the pial-surface. Have found out, in some of our data sets, that the brain.mgz file has been used instead of the brainmask.mgz during edits to correct the pial surface. Seems that this protocol has been inherited from pre-version 3.0 work-ups. Therefore; 1) What does this imply for the data? Generally, when we have inspected the surfaces after recon2 is rerun it seems that the corrections are taken into account. Have tried to analyze the process stream in order to localize what the implications would be, but I am not sure I understand it. 2) What should we do when we have more data in the same study that is not controlled yet, keep on doing the same thing or switch? Yours sincerely, Petr Szulc Bjerkan Dept. of psychiatry University of Oslo

2 1

GTCA
by Daniel H Choi 26 Jun '08

26 Jun '08

Does anyone know if GTCA is part of the freesurfer commands? My protocol requires that I use a "GTCA" command to create a better surface image for stg. If not, can anyone direct me towards a resource to explain what it is and how to use it? Thanks. -- Daniel Horim Choi Northwestern University Class of 2009 dhchoi(a)u.northwestern.edu or dchoi1024(a)gmail.com

1 0

significance thresholds and multiple comparisons corrections
by Judith Segall 26 Jun '08

26 Jun '08

Hi FreeSurfer groupers. I have been using FreeSurfer since v3.0.2, but still have some questions about the group analysis pipelines. I have used both QDEC and the previous manual method using glm_fit. Questions about QDEC: 1. What are the guidelines for setting significance thresholds, by adjusting the color thresholds? 2. Should the FDR correction for multiple comparisons that is is the GUI be used? Previously, we used mri_glmfit to correct for multiple comparisons, using the mc-z-z- monte carlo simulation method. We would then report the p-values obtained from the clustering. My main question is what is the best direction to take after using QDEC, i.e. how to correct for multiple comparisons? Also, are there any advantages/disadvantages to using QDEC/glm_fit, for example circumstances where one would be better to use. (For instance, you can have more factors when using glm_fit) I appreciate any help or suggestions that anyone has to give, for I am trying to finish two papers using freesurfer. Also, thanks for developing QDEC, for it makes second level analysis easier to set up. Thanks, - Judith S.

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