Freesurfer December 2006

freesurfer@nmr.mgh.harvard.edu

49 participants
59 discussions

Re: about label file
by Bruce Fischl 07 Dec '06

07 Dec '06

you can save individual labels by selecting the annotation unit you want and saving it, or you can do them all using mri_annotation2label. The vertices should be identical across the various surfaces as they all have the same topology (except the *.nofix ones) On Thu, 7 Dec 2006, Tao Song wrote: > > Hi Bruce: > > I have a question regarding the label file. How do I generate individual > label files corresponding to differenct anatomical structure specified by > .annot file? Currently, I can save them one by one in Tksurfer, after I > load annotation, is there a convenient way to do that? > Another question is: is the vertex index order in pial, smoothwm, and > inflated surface identical? > Thanks! > > Tao > > > >

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Re: [Freesurfer] Freesurfer and Grid computing
by U. Hasson 07 Dec '06

07 Dec '06

At The Uni. of Chicago, we've been playing around with parallelizing freesurfer on a 128 node grid (256 processors). Developers have parallelized procedures (scripts) by unpacking "for" loops that rotate across left and right hemispheres [i.e., they fork the independent processing of left and right hemispheres to different nodes running in parallel, whenever possible]. The main point of this work is to acquire provenance records and therefore Freesurfer scripts are "wrapped" or expressed using a virtual data system language (VDS/VDL). The freesurfer implementation, AFAIK, is in its baby steps, but the general workflow model is pretty well established http://www.ci.uchicago.edu/wiki/bin/view/VDS/VDSWeb/WebMain Best, Uri On 12/6/06, Uri Hasson <uhasson(a)gmail.com> wrote: > Here (Uni. of Chicago), we've been playing around with parallelizing > freesurfer on a 128 node grid (256 processors), and developers have > parallelized procedures (scripts) by unpacking "for" loops that > rotate across left and right hemispheres [i.e., they fork the > independent processing of left and right hemispheres to different > nodes running in parallel, whenever possible]. > > The main point of this work is to acquire provenance records and > therefore Freesurfer scripts are "wrapped" or expressed using a > virtual data system language (VDS/VDL). The freesurfer implementation, > AFAIK, is in its baby steps, but the general workflow model is pretty > well established > http://www.ci.uchicago.edu/wiki/bin/view/VDS/VDSWeb/WebMain > > Best, > Uri > > > On 12/6/06, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> wrote: > > Andries, > > > > I am not aware of usage of Freesurfer in a (Sun) Grid Engine environment > > (such as that used by the Cohen group at UCLA). > > > > However, here at the MGH/MIT/HMS Martinos Center we use a cluster of > > some 100+ nodes configured with Linux Centos 4, and governed by PBS > > (Portable Batch System). Researchers here often conduct studies with > > dozens to hundreds of brains, and for each subject, an instance of > > Freesurfer's 'recon-all -s <subject> -all' script is submitted to the > > batch system, which, under the hood, gets submitted to one computing > > node. Thus, several dozen brains can be processed in a day (and a > > half). > > > > Freesurfer does not currently support fine-grain parallelism. Some > > coarse-grain parallelism, whereby each brain hemisphere is processed > > independently (benefiting multiprocessor nodes) is possible, but not > > currently implemented in our 'recon-all' script, as the error handling > > and logging for doing so is somewhat tricky (and so this feature is in- > > the-works-but-not-anytime-soon). > > > > In short, if you plan on using Freesurfer in studies with large numbers > > of subjects, I would recommend some kind of computing cluster, and some > > fairly simple batch software (like PBS) should be sufficient. For > > instance, I know of one group that has successfully run Freesurfer on > > their Altix Itanium Linux cluster. > > > > Groetjes, > > > > Nick > > > > > > On Wed, 2006-12-06 at 18:44 +0100, Andries van der Leij wrote: > > > > > > > > > > > > > > > > > > ______________________________________________________________________ > > > > > > From: Andries van der Leij > > > Sent: Wednesday, December 06, 2006 5:59 PM > > > To: 'freesurfer(a)nmr.mgh.harvard.edu' > > > Subject: Freesurfer and Grid computing > > > > > > > > > > > > > > > Dear Freesurfer community, > > > > > > > > > > > > I'm a PHD student at the university of Amsterdam and I'm currently > > > investigating the possibilities to streamline our MRI data processing > > > stream. Next summer we'll obtain a research-only scanner. I'm trying > > > to push the group to also invest in computing power and am currently > > > investigating the applications that researchers will most probably > > > use. > > > > > > > > > > > > I came across a project of the group of Cohen at UCLA. They have > > > configured a Apple (unix) grid and have proposed a more or less > > > standard setup specially designed for MRI analyses: > > > > > > > > > > > > http://airto.bmap.ucla.edu/mt- > > > static/NICluster/archives/2005/06/welcome.html > > > > > > > > > > > > It is my understanding that one of the members has rewritten the FSL > > > code which allow distributed parallel processing in a Grid. See the > > > benchmarks here: > > > > > > > > > > > > http://airto.bmap.ucla.edu/bmcweb/bmc_bios/MarkCohen/Apple/Benchmarks.htm > > > > > > > > > > > > My question is fairly simple: Are similar steps taken in the > > > Freesurfer community? I have no experience with this app myself, but > > > it is my understanding that Freesurfer consumes a lot of resources. > > > > > > > > > > > > Thank you very much in advance, > > > > > > > > > > > > Andries van der Leij > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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mri_concat
by Lars M. Rimol 07 Dec '06

07 Dec '06

Hi, I am wondering if it is possible to use some kind of a list of subjects to specify input for mri_concat, like you can use --f filename, where filename refers to a list of subjects, for mri_surf2surf ? It seems that using e.g.: mri_concat subj*-lh.mgz --o allsubjs-lh.mgz is an alternative to: mri_concat subj1-lh.mgz subj2-lh.mgz ... subjN-lh.mgz--o allsubjs-lh.mgz but if you have a typical Freesurfer subjects directory where the files you want to concatenate are buried in e.g. the surf directory of each subject, it would be very useful to be able to specify a list of subjects. The mri_concat --help function doesn't seem to include any such option. Am I missing something, is there an alternative way of doing it? Thank you! -- yours, LMR

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sphere.reg curvature question
by XJ Kang 06 Dec '06

06 Dec '06

Hi, I tried to check the curvature on the inflated, sphere and registered sphere. The curvature pattern doesn't change much from inflated to sphere, but a lot from sphere to registered sphere (Please see the attached jpg files). The curvature on sphere.reg was not the pattern on inflated and sphere. This was not the case for the results from the older version of FreeSurfer. Is this normal for the new FreeSurfer (v3.03) or something is wrong with my mris_register process? Thanks. XJ Kang

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aparc+aseg.mgz
by Paul Greenberg 06 Dec '06

06 Dec '06

Hi all, Regarding measures of cortical volume output in the ?h.aparc.stats file, are all the cortical voxels contributing to these values labeled in the aparc+aseg.mgz segmentation file? Do cortical voxels (regions of the cortex bounded by the white and pial surfaces) with the aparc+aseg.mgz segmentation label "none" (as seen when viewing in Tkmedit, orig.mgz & aparc+aseg.mgz) contribute to the cortical gray matter volume estimates found in ?h.aparc.stats, or will they be overlooked in the stats output? Thanks, Paul

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Mac Release checksum failure
by Neil Killeen 06 Dec '06

06 Dec '06

Hi 1. I have downloaded the Mac Tiger release (PowerPC) freesurfer-Darwin-tiger-stable-pub-v3.0.4-full.dmg but when I try to install it i get an invalid chksum message. I have downloaded it several times, via different hosts and different ftp programs with the same result. Is the archive corrupted perhaps ? 2. All I really want is the mri_convert application. Can that be obtained separately ? thanks Neil

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.license files
by Tim Martin 06 Dec '06

06 Dec '06

Hello, I received the information for my license, but the instructions say to cut and paste into a file called .license. It isn't clear whether this means to create the file, or open a file that already exists. In either case, when I try to create this file by changing the name of a text document with the information in it, I get an error that says files beginning with '.' are reserved for the system, and I should rename the file. When I try to save the file with the name .license (using TextEdit or Word), I am told that if I do this, the file will be hidden (which I expect, since files beginning with . are indeed not visible). I proceed anyway, and get no further error, but when I attempt to check my installation of freesurfer, I'm told that there is no .license file. Since I am not an expert in Unix, I don't know how to create files beginning with '.' or see them or edit them once they are created. Any help would be greatly appreciated. Tim Martin __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Running flame on mris_preproc output
by Luetcke, Henry 06 Dec '06

06 Dec '06

Hi all, I used mris_preproc to generate a surface file from 4 feat directories, as described in the tutorial: mris_preproc --out lh.cope1.nii.gz --target fsaverage --hemi lh \ --iv fbert1.feat/stats/cope1.nii.gz fbert1.feat/reg/freesurfer/anat2exf.register.dat --iv fbert2.feat/stats/cope1.nii.gz fbert2.feat/reg/freesurfer/anat2exf.register.dat --iv fbert3.feat/stats/cope1.nii.gz fbert3.feat/reg/freesurfer/anat2exf.register.dat --iv fbert4.feat/stats/cope1.nii.gz fbert4.feat/reg/freesurfer/anat2exf.register.dat I would now like to feed the resulting lh.cope1.nii.gz into fixed-effects analysis with flame and tried the following: flame -cope=lh.cope1.nii.gz -dm=design.mat -cs=design.grp -tc=design.con -fe However, flame complains that not all compulsory arguments have been provided. I guess I need a varcope file and a mask file. How can I generate these, given that I am dealing with a surface format file? Thanks very much in advance for your help. Best regards, Henry ________________________________ Henry Lütcke Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone: +49-(0)551-201 1735 Mobile: +49-(0)176-20808069 Mail: hluetck(a)gwdg.de

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Icosahedron nodes
by Emily Cooper 05 Dec '06

05 Dec '06

Dear FreeSurfer gurus, We are trying to conduct a simple group analysis, employing freesurfer. However, our aim is to use the software only up to the point where the functional data is projected to a common space, and from that point on export the data to a text file and conduct the analysis using an external mathematical package (R, http://www.r-project.org) We have received very useful information from this message board in the last 2 weeks assisting us in this endeavor, but are still stumped by part of the workflow. At this point, we have succeeded in projecting our functional files (AFNI format) to the FreeSurfer surface representation so that each individual functional data is project to the individual registered surface. Given that each individual surface has a different number of surface nodes, we reasoned that to conduct a group analysis, it would be necessary to project the functional data not to the individual surface of each participant, but instead, to the registered icosahedron representation. The documentation of mri_vol2surf states that using the "icoorder" option, will result in mapping to an icosahedron with *prespecified* sizes. Specifically, we have tried projecting to an ico with order 7 (documentation states 163842 nodes in this reprsentation). However, when using this option and outputting to a "paint" (.w) file, we do not get this number of nodes for the icosahedron. Instead, different subjects' icosahedrons have different numbers of nodes. This is evident when the paint file is converted to and ".asc" file via mris_convert. Before we continue, we would like to know if this is a bug in mri_vol2surf, in mris_convert, or perhaps not a bug at all (i.e., different icosahedrons may indeed have different number of nodes by design). Now that we find ourselves with no way to equate the number of nodes in each participants' surface representation we are faced with a quandary: How do we conduct the group analysis? It has been suggested to us that we use the surf2surf utility. The documentation of that utility mentions that both the src and target surfaces may be icosahedrons. If we do indeed need to use this utility, should we map data between icosahedrons, or would it be better to cut down one stage of interpolation and just directly project the surfaces of all subjects to one reference subject (e.g., subject b -> subject a, subject c ->subject a, and so on). Thanks for any assistance, Emily

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(no subject)
by Lichen Liang 05 Dec '06

05 Dec '06

Dear All, I tried to extract a surface from a MRI scan (T1, 1.5T) using Freesurfer 3.0.3 on a Linux computer. I just run "recon-all" script for the same scan 6 times (same computer, no human interaction). To my supprise, I got 6 different results ( different #triangles, #vertices). Go back to check the intermediate results, all T1.mgz, WM.mgz are identical, but lh.origdifferent. Can someone tell me why my results are not consistent? Thanks very much for your help. Li-Chen

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Freesurfer December 2006