Freesurfer

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30132 discussions

Qdec: problems
by Cat Chong 07 Jan '12

07 Jan '12

Hi Experts: Sorry, I forgot to attach the following error message I get when I attempt to generate stats data tables: I would be grateful if you tell me what I am doing wrong, catherine asegstats2table --common-segs --meas volume --tablefile /5000_series/5000_series/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 5002_out 5003_out 5005_out 5006_out SUBJECTS_DIR : /5000_series/5000_series Parsing the .stats files ERROR: The stats file /5000_series/5000_series/5002_out/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files fmris-Mac-Pro-2:qdec fmri$ ERROR: In /usr/pubsw/packages/KWWidgets/CVS-7Aug2010/src/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x588e8d0): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /5000_series/5000_series/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 5002_out 5003_out 5005_out 5006_out Stack trace: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /5000_series/5000_series/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 5002_out 5003_out 5005_out 5006_out while executing "vtkTemp2 GenerateStatsDataTables"

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tksurfer only showing a 'corner' of the brain
by Sasha Rayshubskiy 07 Jan '12

07 Jan '12

Hi, I downloaded and installed freesurfer on RHEL5 recently. I'm following instructions for testing the installation for 'tksurfer bert rh pial' to get a surface rendering, and only seeing a corner of the 'brain'. When I click with the mouse in the display area it leaves marks as if there's data behind a veil. I'm new to using freesurfer and wondering what mistake I'm making. Screenshot of what I'm seeing is attached. Thanks, -Sasha -- Sasha Rayshubskiy, M.Eng. Research Assistant Laboratory for Functional Optical Imaging Department of Biomedical Engineering Columbia University New York, NY 10027 Tel: 917 697 3841

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Fw : Re: get_4dfp_dimoe problem
by LAOUCHEDI MAKHLOUF 07 Jan '12

07 Jan '12

--- En date de : Ven 6.1.12, LAOUCHEDI MAKHLOUF <laoumakhl(a)yahoo.fr> a écrit : De: LAOUCHEDI MAKHLOUF <laoumakhl(a)yahoo.fr> Objet: Re: [Freesurfer] get_4dfp_dimoe problem À: "AviSnyder" <avi(a)npg.wustl.edu> Date: Vendredi 6 janvier 2012, 15h28 hi everyone i just remind you of my problem of the file name which was too long on our cloud; you advised us to download the endianio.c module, we did this and we installed it then we've run recon-all but we still have an error message : $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ Getifh: /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mnone.4dfp.ifh read error, imgfile='/var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mnone.4dfp.img' Segmentation fault ERROR: 'imgreg_4dfp /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2C_as_mni_average_305 /var/spool/pbs/tmpdir/171598.gridgate.scg.nuigalway.ie/https_3a_2f_2falbalonga.cnaf.infn.it_3a9000_2ff_5f9HZFcSVMqQu-a5r7O6fQ/ws28210/.tmp/d924f86d-ff81-451c-9d0b-f655f3361f66/systemExecTask5971557784595886118/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=139 ERROR: mpr2mni305 execution aborted i've attached the recon-all.log contained in the scripts dir and the log file contained in mri/transforms dir thank you very much --- En date de : Mer 4.1.12, Snyder, Avi <avi(a)npg.wustl.edu> a écrit : De: Snyder, Avi <avi(a)npg.wustl.edu> Objet: Re: [Freesurfer] get_4dfp_dimoe problem À: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> Cc: "LAOUCHEDI MAKHLOUF" <laoumakhl(a)yahoo.fr>, "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> Date: Mercredi 4 janvier 2012, 1h31 I don't think there are any special env variables. It may be that the environment in which FreeSurfer is being run simply generates huge pathnames. A few months ago I revised the module containing get_4dfp_dimoe() to double the size of filename buffers. This module (endianio.c) is attached. Theoretically, compiling with this revised source could fix the problem. Avi ----------------------------- On 1/3/12 6:04 PM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >Hi Avi > >just running recon-all I think. Is there an env variable you use to >specify >a tmp dir or something? > >thanks >Bruce > >On Tue, 3 Jan 2012, Snyder, Avi wrote: > >> It looks like both the command (imgreg_4dfp) and argument >> (.../711-2B_as_mni_average_305_mask.4dfp.img) fields are garbled. >> Evidently, operating system paths have not been correctly set. >> The 4dfp suite of tools is available and probably could be installed but >> I'm not sure that is what is wanted. >> I don't understand what LAOUCHEDI MAKHLOUF is trying to do. >> >> AZS >> ----------------------------------------------------- >> On 1/3/12 10:40 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >> >>> this is actually not part of FreeSurfer proper, but rather something >>>that >>> Avi Synder (ccd) was kind enough to contribute. Avi: can you comment? >>> >>> thanks >>> Bruce >>> On >>> Tue, 3 Jan 2012, LAOUCHEDI MAKHLOUF wrote: >>> >>>> hi everyone >>>> we run recon-all on a cloud and we obtained this error: >>>> >>>> mpr2mni305 failed, see transforms/talairach_avi.log >>>> >>>> The log says the file name is too long perhaps because of the tmp dir >>>> file >>>> names: >>>> >>>> >>>> >>>>get_4dfp_dimoe:/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/h >>>>tt >>>> ps_3a_2f_2fwms01. >>>> >>>> >>>>ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-4 >>>>7e >>>> 5- >>>> >>>> >>>>ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/ >>>>71 >>>> 1- >>>> 2B_as_mni_average_305_mask.4dfp.img filename too long >>>> ERROR: >>>> >>>>'imgreg_4dfp/var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.ie/http >>>>s_ >>>> 3a_2f_2fwms01. >>>> >>>> >>>>ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws15158/.tmp/8d3aa62d-5994-4 >>>>7e >>>> 5- >>>> >>>> >>>>ba6d-031806ec9ffb/systemExecTask8201883777111446775/freesurfer/average/ >>>>71 >>>> 1- >>>> 2C_as_mni_average_305 >>>> /var/spool/pbs/tmpdir/169536.gridgate.scg.nuigalway.i >>>> >>>> >>>>e/https_3a_2f_2fwms01.ihep.ac.cn_3a9000_2fM72N6GZlEC95pE7rgch5YQ/ws1515 >>>>8/ >>>> .t >>>> >>>> >>>>mp/8d3aa62d-5994-47e5-ba6d-031806ec9ffb/systemExecTask82018837771114467 >>>>75 >>>> /f >>>> reesurfer/average/711-2B_as_mni_average_305_masktalsrcimg_g11 none >>>> talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=255 >>>> >>>> >>>> knowing that it is difficult for us to do things differently (to >>>>change >>>> the >>>> path); is it possible to do something in freesurfer to work with >>>>thesse >>>> filenames ? >>>> >>>> thanks for your help >> >> >> >> > > >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. >

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SPGR compressed files
by Cat Chong 07 Jan '12

07 Jan '12

Hi Experts, We wanted to run clinical scans that underwent some compression at the scanner through freesurfer. I just wanted to seek confirmation that SPGR sequences that have undergone slight compression can not be run through freesurfer, is that correct? thank you, catherine

2 3

What effect will it give if software is used to change flip angle on a dicom image? Can Freesurfer change flip angle?
by Knut J Bjuland 07 Jan '12

07 Jan '12

Hi I have problem with two dataset processed with different version of Freesurfer but with the same subject. I am able to import the data set proceed with Freesurfer 4.30 into Freesurfer 5.1. But there was used some proprietary programs at FS 430 data for motion correction and contrast enhancement before the dicom files was input into Freesurfer. These proprietary programs change the flip angle from 7 degrees to 401.07 degrees. I am able to replicate findings that survive FDR but I get quite different result for findings that do not survive FDR. My theory is that the proprietary programs change the dicom in such manner that it gives a new dicom files. Is this correct? I do not have access to these programs anymore. What effect will it give if software is used to change flip angle on a dicom image? Can I use Freesurfer to force the flip angle back to 7 degree? I converted the files from Freesurfer 4.30 to Freesurfer 5.1 using recon –make all –s {subject}. I am enclosing the mri_info of the first files in Freesurfer pipeline. The vox to ras and ras to voxel is also changed. What effect will this have? Knut J

2 1

SPGR gadolinium contrast
by Cat Chong 05 Jan '12

05 Jan '12

Hello Experts: Is is possible to run 3D SPGR's with contrast (gadolineum) through freesurfer? Also, in a separate dataset, we have 3D SPGR's that have unfortunately been compressed. Can they still be run? Thanks, catherine

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QDEC:/ problems with generating stats Data Tables
by Cat Chong 05 Jan '12

05 Jan '12

HI Experts: Using Qdec, I have tried to generate Stats Data Tables, but below is the error message I received. .I get this error message for all subjects but the aseg.stats files are there and seem ok... any ideas of what I am doing wrong? cheers, catherine asegstats2table --common-segs --meas volume --tablefile /5000_series/5000_series/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 5002_out 5003_out 5005_out 5006_out SUBJECTS_DIR : /5000_series/5000_series Parsing the .stats files ERROR: The stats file /5000_series/5000_series/5002_out/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats file

1 0

Segmentation Problem
by Markus Savli 05 Jan '12

05 Jan '12

2 1

Re: [Freesurfer] Freesurfer Courses
by Allison Player 04 Jan '12

04 Jan '12

Hi Cat, Anyone who is interested in receiving emails about upcoming FreeSurfer courses should sign up for the mailing list here: http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi Registration is not yet open but an announcement about when it will open will go out to that list. Allison On Wed, 4 Jan 2012, Cat Chong wrote: > Hi Allison, > that would be great, is there a website I can check to register? > Cat > > ____________________________________________________________________________ > From: Allison Player <astevens(a)nmr.mgh.harvard.edu> > To: Cat Chong <cavecreekcutter(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Wednesday, January 4, 2012 10:29 AM > Subject: Re: [Freesurfer] Freesurfer Courses > > Hi Catherine, > We hope to have a course in Boston in April. > Allison > > On Wed, 4 Jan 2012, Cat Chong wrote: > > > Hi all, > > > > Just checking.. is the Freesurfer course in New Zealand this May the only > > course offered this year, or are there others? > > would love to go.... but New Zealand may be a stretch... > > cheers, > > catherine > > > > > _______________________________________________ > > 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. > > > >

1 0

Freesurfer Courses
by Cat Chong 04 Jan '12

04 Jan '12

Hi all, Just checking.. is the Freesurfer course in New Zealand this May the only course offered this year, or are there others? would love to go.... but New Zealand may be a stretch... cheers, catherine

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