Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30061 discussions

Some FS input questions
by Graham Wideman 02 Jun '06

02 Jun '06

Most likely to Nick S, unless anyone else would like to chime in... I'm gearing up for some extensive use of FS... it's downloaded, installed, and initial tests run OK... so far with minimum of pain (yay team!). Now... I need to discover how to feed in data other than raw scanned files, because we want to try several alternatives to the initial processing, which we have in AFNI format, ac-pc aligned with iso-sided voxels but not 1 mm. I suspect I'll end up scouring the recon-all script, but a few hints would be helpful, mainly aimed at (a) taking advantage of processing that we have done by other methods, (b) minimizing resampling and (c) winding up with surfaces and segmentations that are most readily overlayed with our other processed data, tracings etc. 1. If we want to feed in already ac-pc aligned, brain-extracted input, at what stage of recon-all should we be looking to supply it? (I can figure out where in the directories to put the data, but not sure on the stage of processing to start at). 2. It used to be that FS's surface pipeline didn't insist on Talairaching the voxel data, and skipping that resulted in output that is true to original space. Is that still the case? 3. Does current FS proper require 256x256x256 1mm data, or can it take any shape "brick" and voxel size (ie: without resampling) these days? 4. If FS *does* want to work with 1mm voxels only: It used to be that though FS wanted 1mm input voxels, you could feed in some other sizes by do-it-yourself creation of the COR images, and FS was fine... is that still the case (but now with mgz format)? 4. Is it the case that the subcortical voxel-based parcellation *does* require the Talairaching step for correspondence with the probability atlas? 5. The surface and voxel-based pipelines are separate, not even sharing the white segmentation step, right? Thanks in advance, Graham

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mris_anatomical_stats problem
by adam walczak 02 Jun '06

02 Jun '06

Hello, I am trying to run mris_anatomical_stats using a label that I have created in tksurfer, but I get a strange error when I run the command. mris_anatomical_stats -mgz -a label/rh.aparc.annot -l label/rh_stg.label -b wraw_KH_MAE3_4 rh inflated INFO: assuming MGZ format for volumes. computing statistics for each annotation in label/rh.aparc.annot. limiting computations to label label/rh_stg.label. reading volume /cajal/public/programs/freesurfer/subjects/wraw_KH_MAE3_4/mri/wm.mgz... zcat: /cajal/public/programs/freesurfer/subjects/wraw_KH_MAE3_4/mri/wm.mgz.gz: No such file or directory mghRead(/cajal/public/programs/freesurfer/subjects/wraw_KH_MAE3_4/mri/wm.mgz, -1): read error mris_anatomical_stats: could not read input volume /cajal/public/programs/freesurfer/subjects/wraw_KH_MAE3_4/mri/wm.mgz Did I do something wrong on the command? It works when I don't include the label flag. Thanks, Adam adam __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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downloading freesurfer- sha1sum
by d.g.lawyer＠medisin.uio.no 02 Jun '06

02 Jun '06

Hi, yes, bundling all of the other librarys (mni, fsl, etc) with Freesurfer does make installation much easier. Thanks, team! I'm wondering if it wouldn't be too much trouble to also put up the sha1sums with the downloads? This allows a simple check that the download didn't get corrupted. I bring this up because I just tried to install ver 3.0.3 on a laptop, and "tar" had some cowardly complaints about the files being corrupted - end result, no FreeSurfer on that machine. (or at least not until Monday when I get another shot at it). +glenn

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New doc: FS processes vs input/output tabulated
by Graham Wideman 02 Jun '06

02 Jun '06

Folks: In the interests of getting a grand overview of all the moving parts in FS 3.x, I've distilled the Wiki's "ReconAllDevTable"... https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable ... into a Files vs Processes table here: http://grahamwideman.com/gw/brain/fs/fsunderstanding2006/processvsdata2006.… (Note there's also an Excel version if you wish to print it.) Hopefully this might be of some use to others as well. Graham

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How to disable jumping tool windows? Environment variables?
by Graham Wideman 01 Jun '06

01 Jun '06

Folks: Both tkmedit and tksurfer have tool windows which jump to a location below their respective main image windows whenever the image windows are moved or adjusted. This prevents the image windows from being enlarged to full screen height, because the tool windows then jump to bottom of screen, and behind the main window. Is there some way to signal these two apps not to move the tool windows? Also, if there is such a setting I'm suspecting it would be an environment variable. I looked at the Wiki, but didn't find a listing of useful environment variables -- is there one to be had? Thanks, Graham

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Re: Re: [Freesurfer] error in 'create surface'
by Joongnam Yang 01 Jun '06

01 Jun '06

Thanks, Nick, If I install a new version of FS, would it be too much of hassle? Because I am in the middle of data analysis for a project using the old version, and I remember I had a big trouble installing different libraries for Freesurfer for the old version, which was a daunting job. Nam. >>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 06/06/01 오후 2:54 >>> Nam, The csurf application is no longer supported (and has been removed from the newest release). The recon-all script now performs all processing stages, where the three main stages are -autorecon1, -autorecon2 and - autorecon3 (-stage1 is a deprecated option). You may want to see our new tutorial, here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial to learn what sorts of problems can occur during the various stages. It's hard to say from your email what the problem may be, but it could be a bad Talairach alignment. The tutorial discusses this. Note: you should not see the brain stem after the image has been skull-stripped (which occurs during the -autorecon1 stage). Nick On Thu, 2006-06-01 at 14:40 -0400, Joongnam Yang wrote: > Hi all, > > I posted a question, but for some reason, I didn't get any response. > Please help me on this. > Here is the question. > > I ran 'process volume' and 'create surface' on csurf. > The created surface (left inflated) has brain stem attached to it. > So, I editted 'wm' slices to get rid of it, and ran 'create surface' again. > No change took place. > I tried commandline 'recon-all -stage1 -subjid ID', with no luck. > > Would someone suggest any comment on this? > > Nam. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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eTIV bug
by Sasha Wolosin 01 Jun '06

01 Jun '06

Dear all, I have processed all my data using Stable v3.0.1. Does the eTIV bug effect any other volume measures? If I want to compute eTIV for my data, should I install the lates version and re-run mri_label_volume -eTIV ? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Recon error
by Frederick Powell 01 Jun '06

01 Jun '06

gunzip: /Users/frederickpowell/freesurfer/subjects/011106RJ/nu.mgz.gz: No such file or directory mghRead(/Users/frederickpowell/freesurfer/subjects/011106RJ/nu.mgz, -1): read error I went into my subjects directory and to the subject that I ran with the error and received the above. -- Frederick G. Powell Boston University School of Medicine MD/PhD candidate 617-593-7183

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directional cosine error?
by Nguyen, Thang Q 01 Jun '06

01 Jun '06

Hello all, I get a directional cosine error when I try to register data or extract values from them so I tried mri_info and get this message: mri_info subj1.img matfile: only read 256 bytes of name (810698068 specified) MatlabRead: readHeader returned NULL WARNING: analyzeRead(): matfile subj1.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. ----------------------------------------------------------------- INFO: could not find subj1.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in subj1.mat file ----------------------------------------------------------------- Volume information for subj1.img type: analyze4d dimensions: 79 x 95 x 68 voxel sizes: 2.0000, 2.0000, 2.0000 type: FLOAT (3) fov: 79.000 xstart: -39.5, xend: 39.5 ystart: -47.5, yend: 47.5 zstart: -34.0, zend: 34.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 0.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 0.0000 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.0000 0.0000 0.0000 79.0000 0.0000 2.0000 0.0000 -95.0000 0.0000 0.0000 2.0000 -68.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -8 ras to voxel transform: -0.5000 -0.0000 -0.0000 39.5000 0.0000 0.5000 0.0000 47.5000 0.0000 0.0000 0.5000 34.0000 0.0000 0.0000 0.0000 1.0000 Here is the mat file: Subj1 2.000000 2.000000 200.000000 1.054861e+00 -2.348376e-02 -1.086195e-01 7.747378e-01 9.350572e-02 -3.302234e-01 1.067427e+00 -3.124532e+01 -4.640190e-02 -9.299399e-01 -3.056859e-01 -7.546637e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 round What does the matlab error mean? Why can't it read the directional cosine? -Thang

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error in 'create surface'
by Joongnam Yang 01 Jun '06

01 Jun '06

Hi all, I posted a question, but for some reason, I didn't get any response. Please help me on this. Here is the question. I ran 'process volume' and 'create surface' on csurf. The created surface (left inflated) has brain stem attached to it. So, I editted 'wm' slices to get rid of it, and ran 'create surface' again. No change took place. I tried commandline 'recon-all -stage1 -subjid ID', with no luck. Would someone suggest any comment on this? Nam.

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