Freesurfer April 2005

freesurfer@nmr.mgh.harvard.edu

25 participants
35 discussions

Vncviewer
by Jonathan Wisco 13 Apr '05

13 Apr '05

Hi Kevin, I'm not able to use vncviewer in this environment. I get the message: VNC server supports protocol version 3.3 (viewer 3.3) VNC authentication succeeded vncviewer: VNC server closed connection Thanks, Jon -- Jonathan J. Wisco, Ph.D. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Building 149, 13th St. Charlestown, MA 02129 E-mail: jjwisco(a)nmr.mgh.harvard.edu Tel: 617-851-8492 Fax: 617-726-7422

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parcellation
by Wan Park 13 Apr '05

13 Apr '05

Hello, after parcellating some brains, I have noticed that the program "get confused" and label the occipital as frontal and viceversa. I started with img/hdr images. I suspect that this occurs because of a "wrong" direction of the original image before doing mri_convert. Is it true? How can I solve this? Thanks, Wan

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TR Units
by Doug Greve 12 Apr '05

12 Apr '05

Hi All, I just wanted to let you know about a change to the units that the TR is reported in for SOME data when converting from Siemens DICOM to analyze or bshort using unpacksdcmdir or mri_convert. I expect that this will have no effect on anyone, but I think it's a good idea to let people know, just in case. First, this does not effect functional data, which is generally the only time software would automatically read and use the TR. For analyze and bshort functional data, the TR has been and will be stored in seconds. There will be a change for non-functional data -- specifically, data whose images are not stored as mosaics in the Siemens DICOM file, but only when this data are stored in analyze or bshort formats. For these data the TR value was stored in milliseconds. It will now be stored in seconds (again only in analyze and bshort). This will have no effect on FreeSurfer reconstructions. For those in the NMR Center, this change has already been incorporated into the NMR standard and development environments. Those who run FreeSurfer and unpacking externally will be affected by the next release. Like I said, I don't think this will affect anyone, but if you think it affects you or need clarification, please let me know. thanks Doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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Re: [Freesurfer] fsfast tkmedit-sess problem
by Mike Angstadt 12 Apr '05

12 Apr '05

Yeah... I figured there might be minor differences... however, I've attached tutorial.jpg which is a picture from the fs-fast documentation that is says is the output of the command: sliceview-sess -contrast omnibus -analysis sem_assoc -sf sessid -df sesspar -map fsig -slice mos -nohdr and also myresult.jpg which is what I get from the same command, after having followed all the commands in the tutorial in sequence. The other results like motion correction parameters/automatic registration/etc come up with similar numbers to theirs, though not exact which makes sense if the binaries have changed. However these two pictures appear very different. -Mike At 12:39 PM 4/12/2005 -0400, Brian T. Quinn wrote: >hi Mike- > >in response to your 2nd question, the manual was created a few years ago >and the binaries have changed since then, so the images won't look exactly >the same, but should not be drastically different. > >thanks, >brian t. quinn > >On Tue, 12 Apr 2005, Mike Angstadt wrote: > >>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 >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >brian t. quinn

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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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Freesurfer April 2005