Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30087 discussions

two vol fields for retinotopic analysis?
by Jason Connolly 09 Feb '11

09 Feb '11

Dear freesurfer experts: I noticed that there are two 'vol' fields when I use MRIread. 1) mri.vol 2) mri.analyzehdr.vol My question is: I have two arrays, one with 3D coordinates and a second 1 dimensional array with corresponding phase values. Which 'vol' field do I put the 3D coordinates in and which do I put the phase values in? Many thanks! -jason.

2 1

Abblocked Setup
by Chindhuri Selvadurai 09 Feb '11

09 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

3 6

Three starting questions
by Tetiana Dadakova 09 Feb '11

09 Feb '11

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.

2 1

reg-feat2anat: a problem!
by Agnieszka Burzynska 09 Feb '11

09 Feb '11

Dear all, I am using the command reg-feat2anat to transform functional data pre-processed in FSL to the anatomical image in Freesurfer. As suggested, I check the registration with reg-feat2anat --feat run2.feat manual. I have 3 runs of functional data for each subject. Surprisingly, some runs are registered well but others not (even of the same subject, so using the same reference anatomical images: see the attached image. Upper row: bad registration of one run and lower row: good registration of another run). I have no problem to manually correct the registrations, it works well, but as I have many subjects, I wonder if there may be a way to change some options of reg-feat2anat to make it work better? Can you see from the attached image what is the problem with my images? (I viewed the functional and anatomical data of a few subjects, some woth good and some with bad registration and see no difference or flip) Thanks a lot for your help! Aga

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Re: [Freesurfer] FreeSurfer TrackVis Transforms
by pablo maturana 09 Feb '11

09 Feb '11

Dears expert, I would like to know how can i get the transformation from trackvis to a space Freesurfer?. I have here a link http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms But i don't understand what mean this command, how I could load the file .dtk trk_verts_crs.xyz = trk_verts.xyz / (trkHeader.voxel_size[0], trkHeader.voxel_size[1], trkHeader.voxel_size[2]) and then I have a problem with this command trk_verts_tkreg = CRS2XYZtkreg * trk_verts_crs Could you give an example using a file .dtk? Many thanks Pablo >

2 1

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

2 1

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??

1 0

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.

1 0

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

1 0

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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