Freesurfer June 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
107 discussions

memory limitations
by Don Hagler 04 Jun '06

04 Jun '06

Running recon-all with the v3.0.2 release, I have noticed recently that the process will run into seg faults at various stages (e.g. topology correction, sphere reg, or cortical parcellation). This seems somewhat random, but judging from some other posts, and the fact that it happenened when I was running multiple jobs at once but didn't (for the same subject) when it was the only job, it seems to be memory dependent. That is, when there is not enough available memory, things crash without warning or relevant error messages (e.g. not enough memory). Does that seem like an accurate assessment of things? Aside from hardware solutions (e.g. more RAM or bigger swap space), is there anything that can be done to the software to allow the user to balance speed with memory usage? And die in a less mysterious way?

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question about distortion from flattening
by adam walczak 03 Jun '06

03 Jun '06

Hello, I was wondering if there is a more intutive way than guess-and-check to help me to eliminate the distortion on the flattened surfaces. I know that it is due the the placement/length of the cuts, but I am not sure how to alter the cuts so that the images won't be distorted. This seems like a problem that has been encountered before, so I was wondering if anyone had a method. Thanks for any help you give, Adam adam __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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measures of folding
by Sasha Wolosin 02 Jun '06

02 Jun '06

Dear All, We are interested in degree of cortical folding within our subject populations. Would someone please help me to better understand what the measures "MeanCurv", "GausCurv", "FoldInd" and "CurvInd" in the ?h.aparc.stats files mean? Also, are whole brain stats reported elsewhere? 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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statistics without mri_glmfit
by Lars M. Rimol 02 Jun '06

02 Jun '06

Hi, I would like to analyse my data without using the mri_glmfit, because it is not flexible enough for my current purposes. But I would like to use mris_preproc and surf2surf in order to get the data into common space. However, when executing the mris_preproc I am required to specify a FSGD file, i.e. a design (variables, regressors etc.). I am wondering if that influences the processing of the data in any way - before mri_glmfit of course. So, what I am doing is just loading the ?h.FSGDF.thickness.10.mgh file that is the output of the surf2surf script, into Matlab and doing the statistics there. However, I am worried that the mris_preproc script may be using the information from the FSGD file to alter the measurements in any way. Of course, I turn of the reshape that is default in surf2surf. Are there any other options I should turn off or change? Thank you! -- yours, LMR

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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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Freesurfer June 2006