Freesurfer September 2010

freesurfer@nmr.mgh.harvard.edu

93 participants
127 discussions

Re: [Freesurfer] preproc-sess failing
by Adam Nitenson 27 Sep '10

27 Sep '10

Hi Doug, My original email was sent to the freesurfer list. Here is the more detailed terminal info: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.5 (Final) Kernel info: Linux 2.6.18-194.8.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: audrey SUBJECTS_DIR: /cluster/roffman/users/MTH_Study PWD: /cluster/roffman/users/MTH_Study ssh audrey setenv SUBJECTS_DIR /cluster/roffman/users/MTH_Study cd /cluster/roffman/users/MTH_Study I had already ran all of the unpacking commands through recon-all without fail (see old email below for first subject; MTH20007AA). These were done using the SUBJECTS_DIR /autofs/space/seymour_001/users/MTH_Study. After that, we had bought a TB in the new cluster, and I copied all of the seymour 1 data there. So, I then switched to SUBJECTS_DIR: /cluster/roffman/users/MTH_Study, as running the preproc-sess for the other subject using the directory /cluster/roffman/users/folate_subjects worked fine. The failed command was: preproc-sess -s MTH20007AA -fwhm 5 with the error: niiRead(): error reading from 012/fmc.nii ERROR: Read 40, expected 64 ERROR: mri_fwhm failed ERROR: spatialsmooth-sess failed -Adam > Hi Adam, what is the command line you ran and the directory you ran it > from? What was your SUBJECTS_DIR? In general, you should send this > information each time you write. You might want to look at > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for other ways to improve > your bug reports. Also, please start to send these kinds of things to > martinos-tech or the freesurfer list. > > thanks > > doug > > > Adam Nitenson wrote: >> Hi Doug, >> >> Using the new storage cluster with extra space allows the second >> subject, FB0011060AA to preprocess, but I'm still having issues with >> the first MTH20007AA. I'm getting the following error now: >> >> niiRead(): error reading from 012/fmc.nii >> ERROR: Read 40, expected 64 >> ERROR: mri_fwhm failed >> ERROR: spatialsmooth-sess failed >> >> Again, the raw data source is >> /cluster/archive/288/siemens/TrioTim-35101-20100916-143244-437000 >> >> -Adam >> >> >> >> >>> Ah, yea, it's probably space issues. Let me know if more space does >>> not fix the problem. >>> >>> doug >>> >>> On 9/23/10 7:37 AM, Adam Nitenson wrote: >>> >>>> Sure. I would also like to note that after I sent that email, I >>>> realized >>>> that I only had 508 KB left in Seymour 1, so I don't know if these >>>> errors >>>> could have been generated due to a lack of space. We just purchased a >>>> block of space on the new storage cluster, but haven't used it yet. >>>> >>>> If you think it might still be something else....here are the commands >>>> (after sourcing, etc). >>>> >>>> FIRST SUBJECT >>>> >>>> unpacksdcmdir -src >>>> /cluster/archive/288/siemens/TrioTim-35101-20100916-143244-437000 >>>> -targ >>>> /autofs/space/seymour_001/users/MTH_Study/MTH20007AA -run 5 MPRAGE COR >>>> blah >>>> >>>> unpacksdcmdir -src >>>> /cluster/archive/288/siemens/TrioTim-35101-20100916-143244-437000 >>>> -targ >>>> /autofs/space/seymour_001/users/MTH_Study/MTH20007AA -fsfast -run 12 >>>> bold >>>> nii f.nii -fsfast -run 13 bold nii f.nii -fsfast -run 14 bold nii >>>> f.nii >>>> -fsfast -run 15 bold nii f.nii -fsfast -run 16 bold nii f.nii -fsfast >>>> -run >>>> 17 bold nii f.nii >>>> >>>> cd $SUBJECTS_DIR >>>> >>>> recon-all -i >>>> /autofs/space/seymour_001/users/MTH_Study/MTH20007AA/MPRAGE/005 -s >>>> MTH20007AA -force >>>> >>>> recon-all -autorecon-all -s MTH20007AA >>>> >>>> preproc-sess -s MTH20007AA -fwhm 5 (FAILED) >>>> >>>> >>>> SECONDS SUBJECT >>>> >>>> unpacksdcmdir -src >>>> /cluster/archive/288/siemens/TrioTim-35101-20100917-142812-643000 >>>> -targ >>>> /autofs/space/seymour_001/users/folate_subjects/FB0011060AA -run 5 >>>> MPRAGE >>>> COR blah >>>> >>>> unpacksdcmdir -src >>>> /cluster/archive/288/siemens/TrioTim-35101-20100917-142812-643000 >>>> -targ >>>> /autofs/space/seymour_001/users/folate_subjects/FB0011060AA -fsfast >>>> -run >>>> 13 bold nii f.nii -fsfast -run 14 bold nii f.nii -fsfast -run 15 bold >>>> nii >>>> f.nii -fsfast -run 16 bold nii f.nii -fsfast -run 17 bold nii f.nii >>>> -run >>>> 18 bold nii f.nii >>>> >>>> cd $SUBJECTS_DIR >>>> >>>> recon-all -i >>>> /autofs/space/seymour_001/users/folate_subjects/FB0011060AA/MPRAGE/005 >>>> -s >>>> FB0011060AA -force >>>> >>>> recon-all -autorecon-all -s FB0011060AA >>>> >>>> preproc-sess -s FB0011060AA -fwhm 5 (FAILED) >>>> >>>> Let me know if you need any more info. >>>> >>>> Thanks, >>>> >>>> Adam >>>> >>>> >>>>> Adam, can you send a pointer to the data to me? >>>>> >>>>> doug >>>>> >>>>> Adam Nitenson wrote: >>>>> >>>>>> Hello freesurfers, >>>>>> >>>>>> I am trying to unpack a couple of recent subjects in Stable 4. I ran >>>>>> all >>>>>> steps through recon-all without error. However, when I try to run >>>>>> the >>>>>> next >>>>>> step, preproc-sess, it keeps failing. >>>>>> >>>>>> This is the command I enter: >>>>>> >>>>>> preproc-sess -s FB0011060AA -fwhm 5 >>>>>> >>>>>> It works for about 30 seconds, and then I get the following in >>>>>> return >>>>>> >>>>>> niiRead(): bad number of dimensions (0) in >>>>>> 013/tmp.mc-afni2.15211/outvol.nii.gz >>>>>> reading info from 013/f.nii... >>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>>> reading from 013/tmp.mc-afni2.15211/outvol.nii.gz... >>>>>> ERROR: converting output >>>>>> Invalid null command. >>>>>> ERROR: mc-sess failed >>>>>> >>>>>> the error for the other subject was slightly different: >>>>>> >>>>>> niiRead(): error reading from 013/tmp.mc-afni2.15452/outvol.nii.gz >>>>>> reading info from 012/f.nii... >>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>>> reading from 013/tmp.mc-afni2.15452/outvol.nii.gz... >>>>>> ERROR: Read 14, expected 64 >>>>>> ERROR: converting output >>>>>> Invalid null command. >>>>>> ERROR: mc-sess failed >>>>>> >>>>>> Any idea what might be going on? I've done these same steps many >>>>>> times >>>>>> for >>>>>> processing data and have not before received this error. >>>>>> >>>>>> Thanks! >>>>>> >>>>>> Adam Nitenson, B.S. >>>>>> Brain Genomics Lab >>>>>> Massachusetts General Hospital >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve(a)nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> >>>>> >>>>> >>>>> >>>> Adam Nitenson, B.S. >>>> Brain Genomics Lab >>>> Massachusetts General Hospital >>>> >>>> >>>> >>> >>> >> >> >> Adam Nitenson, B.S. >> Brain Genomics Lab >> Massachusetts General Hospital >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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Basal Ganglia
by Dhinakaran Chinappen 24 Sep '10

24 Sep '10

Dear all, I was wondering if there is a direct measurement to get the basal ganglia volume? I looked into the stats files but could get my hands on it. Is there a particular calculation to carry out? Thanks in advance, Dhinakaran Chinappen.

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preproc-sess in v5
by Timothy Vickery 24 Sep '10

24 Sep '10

Hi all, I noticed in the new version of Freesurfer, you now offer the option to resample raw functional data to a standard (MNI or surface) space at the preprocessing stage (preproc-sess) as opposed to after statistical maps have been computed, but I couldn't find much documentation relevant to this change. I'm just curious -- should this method be preferred for a standard functional contrast GLM analysis? Or is it preferable to follow the old fsfast routine, analyzing in each subject's native functional space and then normalize/concatenate the outputs? It's not completely clear to me that it should make any difference whatsoever in the final product (i.e., group contrast maps), except perhaps with respect to the effects of smoothing...However, I'd be interested to hear the experts' perspectives on this. Thanks, Tim

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Unstripped vtk libraries
by Chris Adamson 24 Sep '10

24 Sep '10

I noticed that the vtk libraries included with Freesurfer took up 800MB of disk space. Upon investigation of this I noticed that all the shared libraries were unstripped. After stripping them they only took up 100MB. I was thinking that if there was no compelling debugging reason to leave the symbols in the vtk libraries then stripping them should lead to a much smaller download size of the freesurfer distro. Chris Adamson. -- Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash) Research Officer Developmental and Functional Brain Imaging, Critical Care and Neurosciences Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Road Parkville Victoria 3052 Australia T 9345 4306 M XXXX XXX XXX E chris.adamson(a)mcri.edu.au www.mcri.edu.au

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Qdec 1.4 and an older version of freesurfer
by Christian Scheel 24 Sep '10

24 Sep '10

Dear all, a while ago I have processed a set of brains making use of recon-all in freesurfer version 4.02. After a longer break I have now come back to my data and wonder whether it is possible to employ qdec 1.4 (as shipped with freesurfer version 5) for the group analysis. In particular I am interested in making use of mri_glmfit-sim and the pre-cached Monte Carlo simulations. Do you think it would be appropriate to use the new qdec version for the analysis? And if so, should I run recon-all -qcache with freesurfer version 4.02 or version 5 for that? Best regards, Christian Scheel --- University of Cologne Department of Psychiatry

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Failing mri_cvs_register
by Martin Kavec 23 Sep '10

23 Sep '10

Hi, I am trying to run mri_cvs_register between a subject and another set of 10 healthy subjects (all analyzed with FS-5.0.0), but in all cases it fails on: trying to execute elastic registration -> cmd line = surf2vol -fixed_mri ......... error executing surf2vol at /opt/freesurfer/bin/elastic_registration_CVS.pl line 162 My commandline is mri_cvs_register --mov S1 --template S2 --outdir $SUBJECTS_DIR/CVS --nocleanup Thanks for suggestions, Martin

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mri_watershed Error
by Shugao Xia 23 Sep '10

23 Sep '10

Hi, I ran recon-all on one subject, and exited with errors: mri_watershed Error: GLOBAL region of the brain empty! what is the reason which caused this error? Thank you in advance Best Shugao

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Re: [Freesurfer] System requirements
by Nick Schmansky 23 Sep '10

23 Sep '10

the memory requirements of mri_glmfit are dependent on the number of subjects given as input, the greater the subjects, the greater the ram. but generally it is not a ram hog. compiling with system specific flags might improve performance, but generally not enough to be worth the trouble. freesurfer already is compiled with maximal optimization (-O3). the GPU work is what we are targeting for substantially improved performance. n. On Thu, 2010-09-23 at 17:49 +0200, daniel geisler wrote: > Hi Nick! > > Thanks a lot for your answer. I guess that I could only benefit from > processing several subjects in parallel. Do you also have some > estimations of the resources needed by mri-glmfit? > > I notice that the source-code of freesurfer is also available. One > could suppose that compiling with system-specific optimization flags > improves performance in some way. Is it worth the trouble? > > Thank you & best wishes from Dresden, > Daniel > > On Wed, Sep 22, 2010 at 10:50 PM, Nick Schmansky > <nicks(a)nmr.mgh.harvard.edu> wrote: > the second option is best because it uses the x86 processor > (amd > opteron), which is our common distribution. the first option > uses the > Itanium processor which we dont actively support because we no > longer > have access to a build machine. > > the recon-all stream is not parallelized so you wouldnt > benefit from > multi-cores or any special parallelization hardware. runtime > on the amd > cluster would be about 25 hours per subject, and consume a > peak of about > 2.7GB of ram. each subject consumes around 400MB of hard disk > space > (budget 500MB per subject). negligible temporary hard disk > space is > used. > > n. > > On Wed, 2010-09-22 at 19:17 +0200, daniel geisler wrote: > > Dear Freesurfers! > > > > I am a new user of freesurfer and I intend to install it on > a HPC > > system. There are two different systems available (see end > of > > message). Could you please give me a hint which one is best > suited wrt > > hardware and software. > > > > In order to use these systems one also has to state some > estimations > > of the needed resources. In detail, I have to estimate: > > > > * CPU time > > * maximal number of parallel used CPUs > > * size of used RAM > > * size of permanent HDD usage > > * size of temporary HDD usage > > > > Could you share some experience how many resources are > usually used > > for the segmentation (recon-all) of a single subject? > > > > Thank you & best wishes from Dresden, > > Daniel > > > > --- > > 1.SGI Altix 4700 (Mars) > > > > * For highly parallel and memory-intensive applications > > * 2048 cores Intel Itanium II Montecito 1.6 GHz > > * 6,5 TB memory > > * One partition for interactive operation with 128 cores > > * 68 TB SAN disk storage > > * 1 PB SAN tape archive > > * SuSE Linux Enterprise Server 10, SGI ProPack 5, batch > system LSF > > * 13,1 TFlop/s peak performance > > > > 2. Linux Networx Evolocity II PC-Farm (Deimos) > > > > * For capacity computing > > * 2576 cores AMD Opteron 2,6 GHz > > * 5,4 TB memory > > * 724 nodes with 1, 2, or 4 dual-core CPUs each > > * 68 TB SAN disk storage > > * SuSE Linux Enterprise Server 10, batch system LSF > > * 13,9 TFlop/s peak performance > > > > For software specification please refer to: > > > http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/hpc/hochleis… > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > The information in this e-mail is intended only for the person > to whom it is > addressed. If you believe this e-mail was sent to you in error > and the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > -- > > > ........................................................ > Drosselstraße 8 > 02827 Görlitz, Germany > mobile: +49 (0) 174 7932227 > e-mail: daniel.geisler(a)gmail.com > ........................................................ >

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System requirements
by daniel geisler 23 Sep '10

23 Sep '10

Dear Freesurfers! I am a new user of freesurfer and I intend to install it on a HPC system. There are two different systems available (see end of message). Could you please give me a hint which one is best suited wrt hardware and software. In order to use these systems one also has to state some estimations of the needed resources. In detail, I have to estimate: * CPU time * maximal number of parallel used CPUs * size of used RAM * size of permanent HDD usage * size of temporary HDD usage Could you share some experience how many resources are usually used for the segmentation (recon-all) of a single subject? Thank you & best wishes from Dresden, Daniel --- 1.SGI Altix 4700 (Mars) * For highly parallel and memory-intensive applications * 2048 cores Intel Itanium II Montecito 1.6 GHz * 6,5 TB memory * One partition for interactive operation with 128 cores * 68 TB SAN disk storage * 1 PB SAN tape archive * SuSE Linux Enterprise Server 10, SGI ProPack 5, batch system LSF * 13,1 TFlop/s peak performance 2. Linux Networx Evolocity II PC-Farm (Deimos) * For capacity computing * 2576 cores AMD Opteron 2,6 GHz * 5,4 TB memory * 724 nodes with 1, 2, or 4 dual-core CPUs each * 68 TB SAN disk storage * SuSE Linux Enterprise Server 10, batch system LSF * 13,9 TFlop/s peak performance For software specification please refer to: http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/hpc/hochleis…

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-legacy
by Juranek, Jenifer 23 Sep '10

23 Sep '10

I'm hoping to push my legacy datasets (processed and edited in FSv4.0.5) through FSv5.0.0. After installing FSv5.0.0, I received an error that it didn't look like a legacy analysis (see below). [jjuranek@localhost subjects]$ recon-all -legacy -s SB_057_H21001 ERROR: you have specified -legacy, but this does not look like a legacy analysis. My recon-all.log file for this subjid reports the following build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 How do I convince FSv5.0.0 that I am feeding it legacy data from FSv4.0.5? Have I skipped too many versions to use this -legacy flag? Many thanks, Jenifer

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Freesurfer September 2010