Freesurfer December 2006

freesurfer@nmr.mgh.harvard.edu

49 participants
59 discussions

surface coil intensity normalisation and 3.0.4
by Sebastian Moeller 12 Dec '06

12 Dec '06

Hi Doug, hi list, recently you implemented a version of mri_nu_correct.mni for me that allows for better settings for surface coil recordings. I dragged your change from 3.0.3 into 3.0.4 and just now realised, that it did not do anything ;), as the recon-all script in 3.0.4 does not process xopts for mri_nu_correct.mni. I guess in 3.0.3 I used the hacked version of nu_correct to hide the fact that recon-all dropped the xopts on the floor, oh my. Anyway recon-all of 3.0.4 only requires the following two edits: line 520 insert: set xopts = `fsr-getxopts mri_nu_correct.mni $XOptsFile`; and then replace the original line 521, now line 522 with the following: --o nu.mgz --n $NuIterations $xopts) (basically this adds "$xopts to the creation of cmd"). then it works like it expected. Thanks for all the tools & the support Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

2 2

Run Freesurfer on a supercomputer
by Juergen Haenggi 12 Dec '06

12 Dec '06

Dear Freesurfer user because Freesurfer is so processor and memory intensive, we intented to run Freesurfer parallely on a supercomputer (called Matterhorn Cluster http://www.id.unizh.ch/dl/wissrechnen/HPC-Supercomputing-Main.html) Does Freesurfer is able to run on such a machine without modifying it? What are potential problems that could occur? Thanks in advance Best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

2 1

problem after moving data
by Nicolas Cherbuin 12 Dec '06

12 Dec '06

Dear Freesurfers, I processed a large number of scans with autorecon-all on a linux cluster. I then moved the data to a usb drive for further analysis. I had no problem viewing the analysed scans with tkmedit although it seemed to search for talairach.xfm on the old path before trying in the current directory. However, tksurfer does not work and gives the error "Couldn't create output file .xdebug_tksurfersurfer". How do I fix this problem? I have tried to copy one subject to the local hard drive and view it from there but it did not help. Thanks for your help Regards Nic

3 2

version 3.0.2
by Chacko Cherian 10 Dec '06

10 Dec '06

Hello all, I'd like to know whether the good_output and bert, analysis were done on version 3.0.2? If so could anyone please pass me a link to that version? Thanks Chacko. ____________________________________________________________________________________ Have a burning question? Go to www.Answers.yahoo.com and get answers from real people who know.

2 1

how to extract a piece of cortical surface...
by Shahabuddin Ansari 09 Dec '06

09 Dec '06

Hello, I am working on nonlinear registration of cortical surface and subcortical volumes. I am able to extract individual subcortical objects from the freesurfer segmentation for registration, but don't know how to extract a patch from cortical surface. Could somebody guide me please? Thanks Shahab --------------------------------- Access over 1 million songs - Yahoo! Music Unlimited.

2 1

talairach log file
by Paul Greenberg 08 Dec '06

08 Dec '06

Hi all, In each subject's /mri/transforms/talairach.log file, there are 6 instances of output for the "Final objective function value", which one reflects the quality of the final output? The last one? Thanks, Paul Greenberg

2 1

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 ***********************

2 1

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

2 1

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 > > >

2 1

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 >>> >>> >>> >>> >> > > > >

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer December 2006