Freesurfer June 2011

freesurfer@nmr.mgh.harvard.edu

118 participants
168 discussions

Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
by Xue, Feng 19 May '12

19 May '12

Sorry, I didn't notice that the reply address was not the list, I've done re-post it. Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings. It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script. On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > can you post this to the list? There are others better qualified to say > what's going on. But if everything finished ok is there really a problem? > Maybe this is just a warning? > On Sun, 14 Mar 2010, Xue, Feng wrote: > >> Hi Bruce, >> >> Thanks for your reply. The recon-all.log said it finished without >> error. please find the whole scripts root in the attachment. >> I'm also running a raw testing with one subject and without SGEяяMaybe >> I can report the result the day after tomorrow. >> >> BTW, I found in my 64bit Debian nodes, I repeated got the error as below >> (standard_in) 2: Error: comparison in expression >> but in 32bit, I met both. >> >> for the GMail security restriction, I changed recon-all.cmd in the >> attachment to recon-all.cmds. >> >> On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>> what does the recon-all.log say? Did the recon finish correctly? Does >>> this >>> happen if you just run it on the command line? >>> Bruce >>> >>> On Sat, 13 Mar 2010, Xue, Feng wrote: >>> >>>> Dear Bruce & FS experts, >>>> >>>> Please forgive my re-post, for I havn't got any response from last post. >>>> I do appreciate if anyone could give me a hint or suggestion. >>>> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>> >>>> We are running freesurfer with Sun GridEngine. Currently, we >>>> repeatedly got this error in SGE's job error log file on some data >>>> when doing recon_all: >>>> >>>> $ cat recon_xf.e437 >>>> (standard_in) 2: Error: comparison in expression >>>> $ cat recon_xf.e431 >>>> (standard_in) 2: comparison in expression >>>> >>>> I also checked the recon-all-status.log file, but not error was found. >>>> >>>> Has anyone met this problem? Is it critical? >>>> Thanks in advance. >>>> >>>> -- >>>> Best Regards >>>> >>>> Xue, Feng Phd. candidate >>>> Major in Developmental Cognitive Neuroscience >>>> >>>> National Key Laboratory of Cognitive Neuroscience and Learning >>>> Beijing Normal University >>>> Beijing, China. 100875 >>>> Tel: +86-13810154455 >>>> web: http://psychbrain.bnu.edu.cn >>>> ============================================== >>>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University >>>> telnet://bbs.mdjs.org >>>> http://bbs.mdjs.org >>>> _______________________________________________ >>>> 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. >>> >>> >> >> >> > -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org

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Re: [Freesurfer] Freesurfer Digest, Vol 75, Issue 15
by Sebastian Moeller 19 Jan '12

19 Jan '12

Hi Fred, yu probably checked the following already, but on the off chance you have not... Maybe you have set X11 to 256 color mode? Start X11.app (from /Applications/Utilities) go to the X11 menu, select Preferences..., switch to the tab called output and see what is selected for Colors. If it is set to 256 Colors you have your root cause, just switch to something higher and all should be fine. best Sebastian On May 9, 2010, at 9:00 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. tksurfer/tkmedit display color fix in OSX 10.6? (Fred Dick) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 9 May 2010 15:34:35 +0100 > From: Fred Dick <fdick(a)crl.ucsd.edu> > Subject: [Freesurfer] tksurfer/tkmedit display color fix in OSX 10.6? > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <873B33F2-3339-4871-9395-1EFEEC1EFAAB(a)crl.ucsd.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear all > > This is a pretty minor issue (except for figure making) - but has anyone experienced and then fixed a display problem in tksurfer/tkmedit in OSX 10.6 (possibly also 10.5) where graphics seem to be drawn only with 256 colors, thereby giving images a kind of contour-plot look? (See attached image below). [Running 10.6.3, i686-apple-darwin10-gcc-4.2.1, tksurfer 1.309 (yes, older), tkmedit v 1.330] > > I looked around the mail archives but didn't see anyone else commenting on this, but do know someone else having the same issue, so would be happy for any suggestions. > > Thanks, > Fred > > >

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downsampling 4D volume
by ythomas 10 Jan '12

10 Jan '12

Hi, I am trying to downsample a 4D volume using mri_convert. However, it seems to be killing the 4 dimension. For example, if I do mri_convert -voxsize 4 4 4 tmp.mgz tmp444.mgz The original volume which is 256 x 256 x 256 x 120 becomes 64 x 64 x 64. Thanks, Thomas

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Tracula - error in pre-proc
by phoebe＠nmr.mgh.harvard.edu 14 Jul '11

14 Jul '11

Hi, I do the pre-processing with the following command: trac-all -prep -c ./scripts/dmrirc_single_subject THe process exits with error when it comes to fslroi (attached pls find the log file). I try to re-run the fslroi command as follow: fslroi /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi.nii. gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz 0 25 It works and the lowb.nii.gz looks normal. In case if I have the same problem with another dataset, how can I incorporate the number of frames (25) in the trac-all command for the fslroi? Can I continue the remaining procedures of trac-all from this point? Thank you. Phoebe. -- ___________________________________ Phoebe Suk-tak Chan, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Bldg. 149, 13th St., mailcode 149-2301 Charlestown, MA 02129 phoebe(a)nmr.mgh.harvard.edu

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interpolation during conform step of oblique acquisitions
by Michael Harms 11 Jul '11

11 Jul '11

Hi guys, I'm curious why the conform step of mri_convert (in generating mri/orig.mgz) automatically interpolates oblique acquisitions. Is this a historical legacy? Something mandated by other elements of the FS pipeline? As a consequence of this behavior, if you have an oblique acquisition that was intentionally aligned to the actual anatomy of a given subject's brain (e.g., using AutoAlign to generate a AC-PC aligned acquisition), unless one manually alters the qform in the input NIFTI file to remove the "oblique" components of the xform, there will be an interpolation in the generation of the mri/orig.mgz, which brings with it blurring (i.e., the same sort of concerns that prompt one to use a single MPRAGE, rather than the average of two MPRAGEs) Just curious... thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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mri_cvs_register version for CentOS4 and CentOS5
by tulu＠ms36.hinet.net 06 Jul '11

06 Jul '11

Dear FS experts I download CentOS5 x86-64 version (not CentOS4) of FS 5.1. should I need to upgrade the mri_cvs_register and applyMorph for correction ? best JLH

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Re: [Freesurfer] mri_cvs_register update
by Peter J. Molfese 06 Jul '11

06 Jul '11

Is this significant enough that we should re-run data processed using the standard recon-all stream in version 5.1? Thanks, Peter On Jun 10, 2011, at 3:28 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Fri, 10 Jun 2011 12:59:34 -0400 (EDT) > From: Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] mri_cvs_register update > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <Pine.LNX.4.62.1106101257120.4547(a)gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi, > > We found a bug in the mri_cvs_register script after the > release. Please, download the new version of applyMorph and > mri_cvs_register from one of the below links for Linux Centos4, > Linux Centos4 x86 64 and Mac Leopard respectively: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4 > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/mac-leopard-intel > > --Lilla

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stats on masked functional data
by Ritobrato Datta 05 Jul '11

05 Jul '11

Hello All, I have a functional beta value overlay as a .mgh file and a label file and I want to compute the average value within that mask for each subject. Is there a program to do that ? Thanks Ri

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Trac-all: using bvecs/bvals from FSL folder
by Jared Saletin 01 Jul '11

01 Jul '11

Hi Freesurfer experts, I was wondering if you all had some advice for getting trac-all up and running. I'm trying to work up a trac-all configuration file for a group of subjects, previously processed in FSL. We extracted the Siemens bvec and bval files for the FSL pipeline when importing the dicoms through dicom2nii. I know FSL bval and bvec files are organized in a different matrix shape from what Trac-all wants. Has anyone had sucess with transforming these files? Should/do I need to worry about whether to flip the orientation on bvec files as the images seem to get flipped in the early steps of Trac-all? Also is it possible to feed the configuration file a list of bvec files (for each subject) similar to how we feed it the dicom directory for each subject, or should I create a configuration script for each subject pointing to their bvec file specifically. Thanks in advance for help! Cheers, Jared

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error in qdec design analyze
by Sophy Zhu 01 Jul '11

01 Jul '11

Hi Freesurfers, There existed an error "Error in Analyze: Couldn't open file /usr/local/freesurfer/subjects/PD1/surf/lh.thickness.fwhm10.fsaverage.mgh", when I clicked on the button "Analyze" in qdec design. I have only done "recon-all" with my data (PD-MPR group and Controled-MPR group). Did I miss one step before qdec analysis? Thanks

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Freesurfer June 2011