Freesurfer February 2011

freesurfer@nmr.mgh.harvard.edu

103 participants
152 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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Re: [Freesurfer] I/O performance mitigation
by Bruce Fischl 26 May '11

26 May '11

Hi David, I'm surprised you didn't have to do this in the past. We always space our jobs out. Glad there's an easy workaround cheers Bruce On Fri, 3 Sep 2010, David Mischel wrote: > We took the suggestion of staggering the launch of Freesurfer 5.0 recon-all > jobs. The attached Word doc (I don't know how to contribute this information > other than attaching the image and text using Word) shows a load graph on > our file server. When 20 FS jobs began at once (all processing servers using > a single file server) the load on the file server bulged up. When we spaced > out the launch of each job by 15 seconds the load hardly budged. > > > > We have not had to do this in the past with earlier versions of Freesurfer > but this is an obvious work around to the problem we encountered. > > > > < david > > > > > > David Mischel > > Manager of IT > > Center for Imaging of Neurodegenerative Diseases (CIND) > > <http://www.cind.research.va.gov/> http://www.cind.research.va.gov/ > > VA Medical Center > > 4150 Clement Street, 114M > > San Francisco, CA 94121 > > voice: 415-221-4810 x3864 > > fax: 415-668-2864 > >

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Slice Order
by Rita Loiotile 07 Apr '11

07 Apr '11

If my BOLD scan has 30 slices in "interleaved" series, can I assume the slice order is 1,3,5,7,9...29,2,4,6,8..30? In other words, 1:2:30,2:2:30?

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LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

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retinotopy manual?
by Michelle Umali 05 Apr '11

05 Apr '11

Dear All, I was wondering if anyone knows of a step-by-step guide on how to do retinotopic analysis with freesurfer. Thanks. Michelle

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Re: [Freesurfer] Interpreting results from Qdec
by Nick Schmansky 05 Apr '11

05 Apr '11

Courtney, if i understand your question, i think one way to do that is to use qdec to draw a label on the blob of interest, and the run 'map label to subjects', which creates a label file in each subjects label dir, then you can run stats on that with mris_anatomical_stats. (btw, i'm putting this answer on the list, as others may have better ideas.) n. On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) [F] wrote: > Hi Nick > > Thanks for the prompt reply. Sorry if my questions seem a bit naïve--this is my first time using Freesurfer. > > A follow up question to your answer for question 1. I see that the group data will be plotted in Qdec for significant blobs, but say there is a significant interaction between two variables and it's not entirely apparent what is driving this interaction. > Is there a way to extract the mean of this blob for each individual (i.e., treat it as an ROI or something similar) to determine what's driving the significance? > > Thanks in advance! > Courtney > > -----Original Message----- > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: Thursday, December 30, 2010 2:44 PM > To: Gallen, Courtney (NIH/NIDA) [F] > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Interpreting results from Qdec > > ans. 1. - the easiest way is to Ctrl- left mouse click on a blob, and a > plot of the data at that surface vertex will appear. the group will be > apparent from that (say, demented group is thinner than non-demented > group). this data is significance data (log p, so '2' is 0.01), so mean > and stdev wouldnt apply in that case. the file 'y.mgh' is the raw data > of all subjects in the analysis, so you could extract mean and stdev > from that. > > ans. 2. - slide the 'annotation' opacity slider to show the annotation > data (cortical parcellation). the ctrl left click will also put the > region info for that vertex on the lower left of the display. > > see also: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis > > n. > > On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) [F] > wrote: > > Hi, > > > > > > > > I’m currently running analyses in Qdec and have identified areas that > > show significant effects in my contrasts. I have two questions related > > to interpreting these results. > > > > > > > > 1. How can you interpret the effect in each “blob?” (i.e., which > > group has a greater cortical surface area, etc.). Right now, all I > > know is that there is an effect in certain areas. Can you export this > > data to get means and standard errors? > > > > 2. Is there a way to localize where these effects are? E.g., a > > tool that tells you this effect is located in __ area of the brain? > > > > > > > > Thanks in advance > > > > Courtney > > > > > > > > Courtney Gallen > > > > Post-baccalaureate IRTA > > > > Neuroimaging Research Branch > > > > National Institute on Drug Abuse (IRP) > > > > 251 Bayview Blvd > > > > Suite 200 > > > > Baltimore, MD 21224 > > > > Tel: (443) 740-2631 > > > > > > _______________________________________________ > > 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. > >

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Bad orientation/registration in the motion correction step
by Nikolas Borrel-Jensen 30 Mar '11

30 Mar '11

Hi! I am having some trouble with the motion correction step when having two volumes (NIFTI files). The average volume has not been determined correctly due to a wrong orientation/registration of the two original volumes (see http://freesurfer.nikolasborrel.com/bad_registration.tif) Is the problem caused by wrong information in the qform matrix in the header of the NIFTI file or by a bad registration in the mri_robust_template or mri_convert functions in the motion correction step? Kind regards Nikolas Borrel-Jensen

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clusterwise correction ocn.annot missing and ICV in aseg.stats
by Pieter van de Vijver 02 Mar '11

02 Mar '11

Dear Freesurfer experts, I’m doing a longitudinal study on cortical thickness and subcortical volumes and got some questions. I used the longitudinal stream for the preprocessing 1. On cortical thickness, I’m doing a paired analysis as described in https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis, and then a cluster-wise correction as described in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis, with 5000 simulations instead of 5, and a vertex-wise threshold of 3 . But I don’t get the ocn.annot map, instead I get a ocn.mgh and ocn.lut. The CSD file also looks weird (constantly about 150 clusters with max size one or 2) and the resulting cluster.summary also gives a huge list of very small but significant clusters. Am I doing something wrong? How should I go about this? I’m using FS 4.5. Files are included (jpg for sig.mgh and cluster.mgh for negative simulation, and csd (zipped), summary and simulation log) 2. For the subcortical volumetric analysis I use the aseg.stats. Is the ICV a reliable measure to correct for overall brain size? I heard ICV measurements are not very reliable on T1’s (I get a mean of 2,4% decrease over 16 months...). Are other methods preferable to this one. 3. Is there a logic or rule of thumb for choosing the vertex-wise threshold? Thanks for your help! Pieter

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Freesurfer February 2011