Freesurfer February 2011

freesurfer@nmr.mgh.harvard.edu

103 participants
152 discussions

best orientation of t1 images for recon-all
by simon maier 09 Feb '11

09 Feb '11

Dear all, we acquired mprage images of a Siemens tim-Trio scanner and converted the DICOMs into nifti-Format for VBM and manual Morphometry. Nifti images were automatically co-registered with the MNI Standard brain in SPM8 by changing the header information. No reslicing was performed. We noticed differences in volumes in the aseg_stats_tables depending on the initial orientation of the individual brain. Is there a standard procedure to optimally reorient the images before processing the recon-all analysis? Is it better to use reoriented images that have been resliced or is it sufficient to change only the header information? Is it advisable to reorient the anatomical images manually to AC-PC before running recon-all? Thanks in advance for your help, Simon

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mesh_vertex_nearest and white matter segmentation
by Gabriele Arnulfo 09 Feb '11

09 Feb '11

Hi list, I've got to questions: 1) mesh_vertex_nearest matlab script takes the vertices from a surface a matrix of points in 3D Cartesian coordinates system. Is it correct if I choose points in the Scanner RAS Space as input for this script? I cannot figure out by the description of the tool. 2) I've some points in the brain volume and I'd like to understand if they belongs to white or to grey matter is it possible to classify them (white against grey) using some freesurfer tool? I can find anything in previous email in the list. I'm sorry if the questions has been previously answered. Cheers, g. -- In a world without wall, how needs WINDOWS??

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Re: [Freesurfer] Three starting questions
by Ed Gronenschild 09 Feb '11

09 Feb '11

Dear Tanja, Concerning your question 3 do the following: In the System Preferences -> Keyboard & Mouse you should select the buttons as follows: left one: primary button, right one: secondary button top on: Button 3 You will now have a 3-button mouse that works fine with FreeeSurfer. Ed On 09 Feb, 2011, at 00:07, tetiana.d(a)gmail.com wrote: > Dear FreeSurfer community, > > You were very helpful for my last question, thank you. > > Now I have three basic questions. > > 1. I would like to check the segmentation by loading T1.mgz and > aseg.mgz as an -aux volume, so that I can switch between them. How can > I do this? (<tkmedit subject T1.mgz -aux aseg.mgz> gives some king of > black and white segmentation instead of colorful one). > > 2. When I press View -> View configuration, I have three options there > (Single view, Multiple orientations, and Mosaic). How can I view just > 3 orientations or 2 (e.g. sagittal and transverse)? > > 3. Do MacOS users have problems with mouse? When I try to edit > segmentation or surfaces with Edit Tools, my mouse doesn't seem to > work. I mean, when I click on the pixel with any of three buttons, > nothing changes. I saw similar problem on the mailing list, but there > was no answer. > > Thank you for your time, > Tanja.

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about option -show-edits in version 5.0.0
by binod thapa chhetry 08 Feb '11

08 Feb '11

Hi, I am trying to develop a custom software to run freesurfer, make edits if necessary(user intervention) and rerun the freesurfer from appropriate staring point and also, track/record the user interventions. My prime concern is the tracking of user intervention part, and I came across -show-edits option. But I could not find proper documentation on how we can retrieve desired info using this option. Is it possible to track any sort of user intervention by running -show-edits option with recon-all? If so how can one perform that? Thanks in advance. Binod

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tksurfer error
by Evan Luther 08 Feb '11

08 Feb '11

Dear freesurfer community, I am currently trying to view one of the surfaces generated by recon-all command in tksurfer but when I enter the command: tksurfer LuceHR_FS_SURF lh inflated.nofix I receive a series of errors that look like this: Received X error! Error code : 1 Request code : 147 Minor code : 181 Error text : 'BadRequest (invalid request code or no such operation)' Subsequently the surface window does not display what I would believe is the surface I am trying to view and then the only way I can exit the tksurfer environment is by exiting the terminal that I invoked it in. Any ideas or solutions? Thank you very much, Evan Luther

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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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Freesurfer February 2011