Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

fsfast tkmedit-sess problem
by Mike Angstadt 12 Apr '05

12 Apr '05

Hi, I've just started to look at fs-fast for analyzing data and was following along with the tutorial data using the fs-fast documentation from the website. My problem arises when I try to view the data with tkmedit: > tkmedit-sess -sf sessid -df sesspar -a sem_assoc -c omnibus -map fsig -------------------------------------------------------------- tkmedit-sess logfile is /data/freesurfer/scratch/bert/log/tkmedit-sess.log -------------------------------------------------------------- INFO: Found session in: /data/freesurfer/Sessions//bert-functional INFO: Found session in: /data/freesurfer/Sessions//bert-functional ERROR: cannot find /data/freesurfer/scratch/bert//data/freesurfer/Sessions//bert-functional/bold/register.dat I don't understand why it's adding the current directory to the beginning of the path where it should be looking for the register.dat file. The path should just be /data/freesurfer/Sessions//bert-functional/bold/register.dat, where the registration file is located. Any thoughts? Also, as a side note... has the tutorial data been updated since the documentation was made? Because following alone with exactly the commands given in the documentation does not yield the same visual results for me as the example images. -Mike

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question
by Paul Aparicio 11 Apr '05

11 Apr '05

Hello list, I had a question about unpacksdcmdir. I am trying to get freesurfer/fs-fast up and running on my off-site linux box. It goes through the motions until I try to unpack my raw allegra data, then it stops on me and gives the following error: error: reading ../...path to raw data.../125000-1-2.dcm tag 28 30 Any help would be greatly appreciated! thanks, Paul

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Functional Overlay in 2004 freesurfer
by Ruth Smans 08 Apr '05

08 Apr '05

Hi, We are having problems with freesurfer 2004 to overlay the functional .w or .bfloat files onto the volume. It is not a problem to load the data onto the surfaces eg flat map, but we cannot set the functional onto the volume images. Does someone know how to do this in freesurfer version 2004. Your help is greatly appreciated. Thanks Ruth Smans KU Leuven

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.bhdr file questions
by Nicole Aucoin 08 Apr '05

08 Apr '05

Hello, I'm trying to orient bfloat and bshort volumes in 3D Slicer, and to do that, need to calculate the corners of the volumes to calculate an RAS to IJK transform matrix. The .bhdr files that I have contain the top left, top right and bottom right corners, which I'm using as is with the assumption that they are on the first slice, and are in relation to an origin of (0,0,0). I also need a point on the last slice, so I'm using those corners to create vectors that will give me a cross product pointing to a corner on the last slice. I then scale that vector by slice_thick * nslices and add it to the top left corner point. It's almost but not quite right at this point, so I'd like to check my assumptions: - are the top_left_?, top_right_?, bottom_right_? points on the first slice? - is the origin (0,0,0)? if not, how do I find it? What do the .bhdr file entries normal_? and image_t? denote? thanks, Nicole -- Nicole Aucoin nicole(a)bwh.harvard.edu Surgical Planning Laboratory, Brigham and Women's Hospital Rm 245, 1249 Boylston St., Boston, MA 02215 http://www.slicer.org

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job announcement: MIT fMRI lab technical assistant
by Nick Knouf 07 Apr '05

07 Apr '05

(apologies for the cross-posting) feel free to distribute widely. informal enquiries about the position can be directed to me. ======================================================================== ========== TECHNICAL ASSISTANT, McGovern Institute, to join Professor Nancy Kanwisher's cognitive neuroscience lab and assist with all phases of functional MRI and behavioral studies of high-level vision. This includes maintenance and administration of a network of servers, workstations, external storage, and tape backup systems; implementation of experiments; design, implementation, and maintenance of analysis software; technical support for lab personnel; and basic administrative duties such as procurement. This position is ideal for anyone considering future graduate study in cognitive neuroscience. REQUIREMENTS: a bachelor's degree in psychology, cognitive science, neuroscience, or math. Experience with a heterogeneous computing environment (Linux/UNIX, Macintosh, and Windows) and programming languages (C, python/perl/shell scripting, Matlab) a must. Knowledge of any of the following helpful: RAID arrays, tape backup systems, psychological experiment software (Psychtoolbox, Vision Egg, presentation, etc.), and web development and design. Demonstrable preexisting interest in cognitive neuroscience a must. Knowledge of visual cognition, neuroanatomy, or statistics helpful. Must be self-motivated and able to work in a fast-paced and changing environment. MIT-00001825 MIT is an Equal Opportunity / Affirmative Action employer. ======================================================================== ========== Please apply through the following website: http://sh.webhire.com/servlet/av/jd?ai=631&ji=1534980&sn=I thanks, nick knouf lab manager, kanwisher lab

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mri_convert with IMA files
by mperry＠ucsd.edu 07 Apr '05

07 Apr '05

Hi, I am trying to use mri_convert to convert Siemens .IMA files to COR files. I have tried a few different ways and none seem to be working. Here is what I've tried and the error messages. Do you have any advice? >mri_convert -it siemens </path/to/IMA/dir> <$SUBJECTS_DIR/subjid/mri/orig> mri_convert -it siemens </path/to/IMA/dir> <$SUBJECTS_DIR/subjid/mri/orig> reading from </path/to/IMA/dir>... ERROR: could not parse </path/to/IMA/dir> ERROR: siemensRead(): </path/to/IMA/dir> > mri_convert -it siemens_dicom </path/to/IMA/dir> <$SUBJECTS_DIR/subjid/mri/orig> mri_convert -it siemens_dicom </path/to/IMA/dir> <$SUBJECTS_DIR/subjid/mri/orig> reading from </path/to/IMA/dir>... ERROR: </path/to/IMA/dir> is not a siemens DICOM file INFO: loading series header info. Segmentation fault >mri_convert -it dicom </path/to/IMA/dir> <$SUBJECTS_DIR/subjid/mri/orig> mri_convert -it dicom </path/to/IMA/dir> <$SUBJECTS_DIR/subjid/mri/orig> reading from </path/to/IMA/dir>... no DICOM files found. Exit

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parcellation
by Wan Park 06 Apr '05

06 Apr '05

Hi, after doing the parcellation and listing the areas with mris_anatomical_stats I have noticed that in many brains (or hemispheres) there are typically two areas that are frequently missing: S_paracentral S_intracingulate is there any explanation for this? is there any way to avoid this? thanks! wan

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aseg skull strip failed
by Michele Perry 05 Apr '05

05 Apr '05

What is the best way to correct an aseg when non-brain regions (eg the skull) are labelled?

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subject averaging
by orphoebe＠polyu.edu.hk 05 Apr '05

05 Apr '05

Hi, I used the following script in the old post to do the subject averaging of the surfaces. However, the 'T1' and 'orig' sub-directory under 'mri' of the 'average' are empty. Is there any way that I can convert the surface file (e.g. rh.orig) into CORs so that I can view the corresponding brain volume using TkMedit? Thanks, Phoebe. ********************************************************** #!/bin/tcsh -ef set SUBJECTS = (031204_wwk 031204_yts 040115_llk 040219_wly) # set SUBJECTS=($SUBJECTS) set average_subject=average if (-e $SUBJECTS_DIR/${average_subject} == 0) then mksubjdirs $SUBJECTS_DIR/${average_subject} else mkdir -p $SUBJECTS_DIR/${average_subject}/surf endif foreach hemi (lh rh) foreach s (orig white pial inflated) set echo=1 mris_make_average_surface -i 7 -o $s $hemi ${s}_avg sphere.reg ${average_subject} $SUBJECTS unset echo end cd $SUBJECTS_DIR/${average_subject}/surf pwd mris_smooth -n 5 ./${hemi}.white_avg ./$hemi.smoothwm mris_inflate ./${hemi}.smoothwm ./${hemi}.inflated mris_curvature -a 10 -w ./${hemi}.white_avg cp ${hemi}.white_avg.H ${hemi}.curv cp $CSURF_DIR/average/$hemi.sphere.reg . ln -s -f $hemi.sphere.reg $hemi.sphere set echo=1 mris_average_curvature -o $average_subject curv $hemi sphere.reg $SUBJECTS ./${hemi}.curv mris_average_curvature -o $average_subject sulc $hemi sphere.reg $SUBJECTS ./${hemi}.sulc mris_average_curvature -o $average_subject thickness $hemi sphere.reg $SUBJECTS ./${hemi}.thickness end cp $SUBJECTS_DIR/$SUBJECTS[1]/mri/T1/COR-.info $SUBJECTS_DIR/${average_subject}/mri/T1 --- Phoebe Suk-tak Chan, Ph.D. Assistant Professor The Hong Kong Polytechnic University Department of Optometry and Radiography Hunghom, Kowloon Hong Kong SAR Tel: (852) 2766 6095 Fax: (852) 2764 6051

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missing aparc.annot in 'labels' directory
by orphoebe＠polyu.edu.hk 04 Apr '05

04 Apr '05

Hi, I just found out that I forgot to link average7 when I did the 'recon-all' on two subjects' brain data. Will it affect the talairach coordinates? Do I need to do the brain inflation again? Also, I found that the label files, e.g. lh.aparc.annot and rh.aparc.annot, which are expected to be in the 'labels' sub-folder of the subject directory. Is there any way that I can generate these labels files again? Thank you for your help in advance. Phoebe --- Phoebe Suk-tak Chan, Ph.D. Assistant Professor The Hong Kong Polytechnic University Department of Optometry and Radiography Hunghom, Kowloon Hong Kong SAR Tel: (852) 2766 6095 Fax: (852) 2764 6051

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