Freesurfer

freesurfer@nmr.mgh.harvard.edu

9 participants
30092 discussions

.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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Re: [Freesurfer] missing aparc.annot in 'labels' directory
by orphoebe＠polyu.edu.hk 04 Apr '05

04 Apr '05

Hi Bruce, I would like to read the anatomical labels with the corresponding Tal coordinates on tksurfer. However, the aparc.annot files are missing in the 'labels' sub-directory of each of the subjects. How can I regenerate them again? Thanks, Phoebe ---- Original message ---- >Date: Mon, 4 Apr 2005 14:39:04 -0400 (EDT) >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] missing aparc.annot in 'labels' directory >To: orphoebe(a)polyu.edu.hk >Cc: freesurfer(a)nmr.mgh.harvard.edu > >Hi Phoebe, > >you shouldn't have to redo any of that stuff. Average7 is only used as a >domain for visualizing group data, although you are better off making an >average of the subjects in your study and using it instead (in which case >you shouldn't need average7 at all) > >cheers, >Bruce > > >On Tue, 5 Apr 2005 orphoebe(a)polyu.edu.hk wrote: > >> 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 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > --- 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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Talaraich Problems
by Calabrese Massimiliano 30 Mar '05

30 Mar '05

Thank you very much Kevin for your help! Now I have fixed my problem on Lib.glut libraries Unfortunately , I have another problem ( I hope is the lastone) If I run recon-all -stage1 the computer freezes as the following point: writing to orig/orig.mnc... Outputting Volume: ............................................................ -------------------------------------------- mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm At this point, the machine needs to be rebooted because the process never finishes. The software MNI seems to be correctly installed, but maybe there is some other line to add in order to config correctly. Thanks a lot for your help Massimiliano Calabrese Neuroimmunology Branch NINDS, NIH

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Freeglut problem
by Calabrese Massimiliano 30 Mar '05

30 Mar '05

Hi all I've installed Freesurfer and when I open csurf to edit segmentation on images, I get the following error: /usr/local/freesurfer/bin/Linux/tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory Now, I've installed Freeglut and still get the above error. I can see the libglut.so.3 library in /usr/local/lib and this is in my $PATH. Any ideas why the error exists? Thanks a lot for your help Massimiliano Calabrese Neuroimmunology Branch, NINDS, NIH and Willy Calderon NINDS, NIH.

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