Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

Correcting Pial Surface
by Gallo, Antonio (NIH/NINDS) [F] 08 Dec '06

08 Dec '06

Hi all, Regarding pial inaccuracies, should I edit brain.mgz or brainmask.mgz ? I'm asking this because it seems to me that correcting brainmask.mgz and running autorecon2 (-cp, -wm or -pial) doesn't seem to fix the problem. Furthermore, when I was going through the tutorials it suggests using brain.mgz (according to the tutorial from January) and brainmask.mgz (according to the tutorial from May). Thanks, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 ***********************

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question about mri_vol2surf
by Emily Cooper 08 Dec '06

08 Dec '06

hi, i have been using mri_vol2surf to map individual functional data onto the fsaverage brain: mri_vol2surf --src 003/bold/03.time.intval.resam+orig.BRIK --src_type afni --srcreg 003/bold/register.dat --hemi rh --projfrac-avg 0 1 10 --trgsubject fsaverage --out 003/surf/03.time.intval.fsave.mgh each time i do this, i compare the mapping onto the curvature with the same functional mapped onto the individual brain: mri_vol2surf --src 003/bold/03.time.intval.resam+orig.BRIK --src_type afni --srcreg 003/bold/register.dat --hemi rh --projfrac-avg 0 1 10 --out 003/surf/03.time.intval.orig.mgh --out_type mgh and thus far it's always been a fantastic match. i was curious, how does the mri_vol2surf script match up the individual functionals onto the curvature of fsaverage? i had a theory that maybe it implicitly references the surf directory of the subject, so i made a new subject directory tree with the functionals of one subject (003) and the surf directory of another. vol2surf-ing the same functional in this new directory to fsaverage results in an identical mapping as to in the regular 003 directory. a similar SUMA function (mapicosahedron) maps functionals into an icosahedron space by first warping the individual anatomical. does freesurfer's mri_vol2surf work somehow without using this information? thanks, emily

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RE: [Freesurfer] Freesurfer and Grid computing
by Andries van der Leij 08 Dec '06

08 Dec '06

Nick and Uri: thank you for your replies, I'm not really into parallel processing and forgive me if I talk nonsense :). From your stories I sketch the following possible scenarios: 1. We use a sort of batch system. For instance, a Linux bash script with 10 recon-all commands or with 10 FSL feat commands. The system assigns each individual command to the node with the least load and the output data are automatically stored on a central (fi RAID) server. I guess this is the way the UCLA FSL/MAC grid works, since I can see no need to alter the software itself, if the applications are suitable to work from and write to an external computer. I'll contact the group exactly how they work. I guess we need very fast connections between the individual servers and the storage host to do this.... I don't know PBS, but I think this is exactly how the Sun grid engine works also, so maybe they are comparable. Batches are submitted to the host and are processed one at a time. In fact this is how I work myself right now sometimes when I'm in a hurry. I copy all my FSL source data to different computers and let each computer run a subset of the feat batch. By hand I group the data afterwards and I perform only the group averaging on a single computer. 2. We allow for more sophisticated parallelizing. You give the example of assigning the reconstruction of left and right hemispheres separately. This is the most elegant solution but implies rewriting the code. I think the second scenario would eventually be the most elegant but the first scenario would be less difficult to implement. In fact, I guess most applications (like FSL, freesurfer, SPM) work with batches, so if we have software that manages these batches we already have won a lot (and it saves a lot of manual work.... ;( What do you think? Thank you, Andries van der Leij PS: here's a presentation with screenshots of the sun grid: it looks fairly straightforward. http://www.sun.com/products-n-solutions/edu/whitepapers/pdf/bioinformati cs_supercomputer.pdf PS2: Nick, are you Dutch? -----Original Message----- From: uhasson(a)gmail.com [mailto:uhasson@gmail.com] On Behalf Of U. Hasson Sent: Wednesday, December 06, 2006 9:50 PM To: Nick Schmansky Cc: Andries van der Leij; Freesurfer Mailing List Subject: Re: [Freesurfer] Freesurfer and Grid computing 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.ht m > > > > > > > > > > > > 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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Re: about label file
by Bruce Fischl 07 Dec '06

07 Dec '06

I'll leave this for Doug. As for the label file, each annotation would be in a different one, but I don't think it will match since there are unknowns in the annotation and I don't think they go to a label file (do they Doug?) On Thu, 7 Dec 2006, T. Song wrote: > Thanks a lot, Bruce. > Another question is: after running mri_annotation2label, some anatomical > structure in surface_labels.txt were skipped during the mri_annotation2label. > There are 78 catogories in the a2005s.annot file, but mri_annotation2label > only create 56 .label files. I think the missing parts are in annotation > file, as they can be seen in tksurfer. Does mri_annotation2label do a fine > matching, or just roughly? And, does the summation of all the vertex in > .label file matchs the total vertex number in annotation file? > > Tao > > Bruce Fischl wrote: > >> 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: 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

2 1

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

2 1

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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