Freesurfer

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Job Opening: Research Technician in Brain Imaging
by Schiel, Matthew 07 Feb '11

07 Feb '11

The Solodkin/Small Brain Circuits Laboratory at the University of California, Irvine, will soon have an opening for a research technician in image processing. This job would be ideal for someone interested in applying basic skills in signal processing or applied mathematics to a variety of functional and structural neuroimaging studies related to human language processing and motor control, including healthy adults and children, and adults and children with neurological injuries or disease. Job tasks include: analyzing functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) data, performing statistical analyses of processed human data, working with cortical surface maps, managing and updating our imaging database, and helping to improve our processing procedures, including our use of high-performance cluster and grid computers. The ideal candidate will have a B.A. or B.S. degree in engineering, physics, mathematics, or computer science; knowledge of the UNIX operating system; programming experience; interest in biomedical applications; coursework in signal analysis and/or statistics. Variations from these ideals will certainly be entertained in an otherwise highly qualified candidate. Although this position is not yet formally posted, we are interested in hearing from qualified candidates now. If interested, please forward your CV/resume to mschiel(a)uci.edu. This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

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abblocked Setup
by Chindhuri Selvadurai 07 Feb '11

07 Feb '11

Hello, We are trying to set up the analysis for a periodic design alternating between 30s rest and 30s active condition. Because abblocked doesn't require a paradigm file, how do we specify which condition comes first (rest or active)? We understand that abblocked expects that the conditions will be alternating. Also, how do we set up the -a and -c weighting conditions if we are using abblocked, since it doesn't have a paradigm file? How do we specify the arguments for this command? Should we instead be using the -ncond and -wcond commands? Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307

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Problem running recon-all with option -qcache
by Ed Gronenschild 07 Feb '11

07 Feb '11

Hi, A serious error was encountered in running recon-all with option -qcache. The error occurred during execution of mri_surf2surf and the message was: number of vertices in ....../subjectID/surf/lh.thickness does not match surface (141969,131763). It means the number of vertices in lh.sphere.reg does not match the number in lh.thickness. I traced the course of this error and that is causing me serious troubles. What happened? I edited the wm voxels and then invoked another call to recon-all by issueing the command recon-all -autorecon2-wm. Looking at the dates of the files in the surf directory I noticed that the file lh.sphere.reg was not updated, so it was still the same file as before editing the wm voxels. The lh.thickness was correctly updated as expected. What can I do to use the -qcache option? Ed

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mri_convert with lists and orientations
by Reza Farivar 07 Feb '11

07 Feb '11

Hello, I'm encountering a strange problem with mri_convert. Basically, if I just ask it to convert a set of dicoms into a 4D NIFTI, it does this fine, but if I specify anything about the input and/or output orientation (using --in_orientation or --out_orientation), it only spits out 1 image, not the entire time series. Am I doing something wrong? Thanks, Reza |||||||||||||||||||||||||||||||||||||| Reza Farivar, Ph.D. Research Fellow Harvard Medical School Massachusetts General Hospital Dept. of Radiology Building 149, Room 2301 13th Street Charlestown, MA 02129

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vertex-wise nuisances
by Thesen, Thomas 06 Feb '11

06 Feb '11

Dear Freesurfer experts, Is there a way using the existing statistical tools in Freesurfer to control for a variable that changes across vertices? For example, looking at the correlation of performance measure X with thickness at each vertex, while correcting for curvature at that specific vertex (as opposed to using a set overall mean curvature that is computed across all vertices of the entire hemisphere)? Thanks a lot, Thomas </PRE> <html> <body> ------------------------------------------------------------<br /> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> ================================= </body> </html> <PRE>

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possible tkregister2 bugs on OSX 10.6
by Jason Webster 05 Feb '11

05 Feb '11

I couldn't get either of the built-in functions to work to check the registration between two volumes which should have been the same. I also noticed that the tkregister2 wiki page<http://surfer.nmr.mgh.harvard.edu/fswiki/tkregister2>contains no info about the command, though it does have a link to the TkRegister2 Guide <http://surfer.nmr.mgh.harvard.edu/fswiki/TkRegister2Guide>, which does not exist. --------------------------------------------------------------------- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 Kernel info: Darwin 10.6.0 i386 --------------------------------------------------------------------- swi> tkregister2 --targ SWI1.nii.gz --mov SWI2.nii --identity tkregister_tcl /Applications/freesurfer/lib/tcl/tkregister2.tcl ERROR: no registration file specified swi> tkregister2 --targ SWI1.nii.gz --mov nsLGH_26Aug10_10.nii --check-reg tkregister_tcl /Applications/freesurfer/lib/tcl/tkregister2.tcl target volume SWI1.nii.gz movable volume SWI2.nii reg file /tmp/reg.tmp.1297311621.dat LoadVol 1 ZeroCRAS 0 $Id: tkregister2.c,v 1.117.2.1 2010/08/02 17:42:03 greve Exp $ Diagnostic Level -1 regio_read_register(): No such file or directory Could not open /tmp/reg.tmp.1297311621.dat ERROR: reading /tmp/reg.tmp.1297311621.dat

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freeview and control points
by Mehul Sampat 04 Feb '11

04 Feb '11

Hi Folks, We used to use tkmedit to add control points and recently started using freeview. I have a few basic questions about saving controls points created with freeview. 1. I noticed that in tkmedit edit controls points were saved as "control.dat" in the "subject_dir"/tmp (e.g. bert/tmp). When I use freeview I assume I should also save the control points in the same location ? 2. If so, is there a way to configure freeview so that it saves it to "subject_dir"/tmp ? (currently the default location where freeview saves the control points in the current subject directory.) 3. Also I believe tkmedit saved the control points as "control.dat" but for freeview one has to specify the name manually. Is there a command line argument to set the name of the file as "control.dat" by default ? Thanks Mehul

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right hippocampus bad segmentation...
by Gonzalo Rojas 04 Feb '11

04 Feb '11

Hi: I processed the T1 volume of a patient... I got bad segmentation of the right hippocampus (see attached images)... How can I correct the segmentation ?... Sincerely, Gonzalo Rojas Costa

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problem with spmregister on mac
by Maryam Vaziri Pashkam 04 Feb '11

04 Feb '11

Hi, I am new to freesurfer and I am analyzing fmri data on a Mac OSX 10.5.8 computer using freesurfer 4.5. I have SPM 8 and FSL also installed. I have two versions of matlab (matlab R2009b & R2008a) on my computer. I think spm runs through the R2009b on my computer. I have added the SPM path to the startup.m of both matlabs by adding the following line (they both point to the same startup.m ): path(path,'/Applications/spm8'); I run preprocessing on the data using the following command: preproc-sess -nosmooth -sf retino-sess -df retino.dir then I run automatic registration with the following command: spmregister-sess -sf retino-sess -df retino.dir It runs smoothly and there seems to be no errors. But when I try to check the registration with this command: tkregister-sess -sf retino-sess -df retino.dir -inorm what I see is not a good registration. Isn't spm register supposed to do a good job in automatic registration? The one that I get still needs a lot of manual adjustment. Am I doing something wrong? I have attached the log files for spmregister and tkregister and a screen shot of the image that I get after running tkregister. I would appreciate any help in this matter. Thanks, Maryam

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Variables meaning -White matter hypointensities vs. non-WM-hypointensities?
by San Jung 03 Feb '11

03 Feb '11

Hi. I'm visiting researcher for Behavior neurology. I'm trying to compare pathology and MRI image data in ischemic vascular disease patients. In our group, there are a lot of image researchers and they already made MRI free surfer DATA. My PI advised me to use free surfer data for my study. Using those files, I hope to know the volume of white matter lesion on MRI. In subcortical volume data, there are 2 variables for white matter volumes. One is "Volume (white matter parcellation) of non-WM-hypointensities region in mm3" and the other is "Volume (white matter parcellation) of WM-hypointensities region in mm3". I think hypo-intensity region means the lesion area in T1 sequence. However I am not sure the meaning of non-white matter hypointensities region in subcortical volume data. Can you help me to define two variables? . San Jung MD

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