Freesurfer July 2011

freesurfer@nmr.mgh.harvard.edu

129 participants
195 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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Error while loading qdec project file
by Tetiana Dadakova 18 Aug '11

18 Aug '11

Dear experts, When I try to load a saved Project File, I get an error: Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat Error loading the project file. I do not have any /tmp subdirectory. Should it appear when I save the Project File? Should it be in /qdec directory? Thank you, Tanja.

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Defining the Calcarine and distances from it in the Hinds et al. V1 label
by Krish Singh 08 Aug '11

08 Aug '11

Dear All, I've been trying out the automatic V1 labelling using the Hinds et al. (NeuroImage, 2008 vol. 39 (4) pp. 1585-99) and, as far as I can tell it seems to work pretty well on our anatomical scans (In general I'd be interested in the opinions/experiences of others who've tried it). I have a couple of questions: 1) Is it possible to automatically label just the calcarine itself? I know there is a pericalcarine label, but I am hoping to essentially label the line of the calcarine itself. 2) Is it possible to automatically find the occipital pole of the calcarine? The reason I want to do this is that it would then enable me to calculate the distance down the calcarine and the lateral distance away from the calcarine for each patch in the Hinds-V1 label. That potentially could be really useful in terms of sub-dividing the Hinds label into foveal and eccentric zones (although without retinotopy individual differences in M-scaling, for example, might limit interpretability). Would mris_divide_parcellation be useful here? Thanks in advance, Krish -- Prof. Krish Singh CUBRIC School of Psychology / Ysgol Seicoleg Cardiff University / Prifysgol Caerdydd Park Place / Plas y Parc Cardiff / Caerdydd CF10 3AT, UK Tel / Ffôn: 02920 874690 / 870365 Fax / Ffacs: 02920 870339 Email / Ebost : singhkd(a)cardiff.ac.uk

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dmri_train malloc error
by Dabbs (Kevin) 05 Aug '11

05 Aug '11

Freesurfer users, I have ran into a malloc error running trac-all. Looks like the same error that Stijn posted to the list on 17 Jun 2011. I did not see a solution posted. It occurs in dmr_train using trac-all -prep –c dmrirc.txt. Also tried using trac-all –prior –c dmrirc.txt with the same results. Reset the tcsh limits for datasize, …. ********* Loading segmentation from /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz dmri_train(54615) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 26th slice Cannot allocate memory ********** My system Model Name: Mac Pro Model Identifier: MacPro3,1 Processor Name: Quad-Core Intel Xeon Processor Speed: 2.8 GHz Number Of Processors: 2 Total Number Of Cores: 8 L2 Cache (per processor): 12 MB Memory: 18 GB System Version: Mac OS X 10.5.8 Thanks for any advice or suggestions! Kevin Dabbs SMPH/Neurology UW-Madison

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isxconcat-sess missing dof file
by Chindhuri Selvadurai 03 Aug '11

03 Aug '11

Hi all, When I run isxconcat-sess, I am experiencing an error finding a 'dof' file in my analysis directories within the FSD files. subjects directory: /cluster/manoach/milton/subjects command line: isxconcat-sess -sf sessid_all -analysis mstmct_v_base -c type_v_rest_vol -o /cluster/manoach/milton/subjects/group_analysis/volume/ output: /cluster/manoach/milton/subjects/group_analysis/volume//mstmct_v_base/log/isxconcat.log ERROR: cannot find /autofs/cluster/manoach/milton/subjects/PAMST02/bold/mstmct_v_base/dof Did I miss a step before the isxconcat? Thank you!

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Re: [Freesurfer] Poor Intensity or Image Resolution?
by Bruce Fischl 02 Aug '11

02 Aug '11

Hi Antonella Are the sequence parameters the same? The way you convert should have no effect Bruce On Jul 27, 2011, at 11:51 AM, Antonella Kis <atorok9(a)yahoo.com> wrote: > Hi Bruce, > > I highly appreciate your great help/advice. > > Unfortunately, today I have another question: I finished running the recon-all for the new subjects for which I converted the dicom files in the NIFTI format as you advised me, using mri_convert. I was telling you that the .nii.gz file for this new subjects are very big , around 38 MB. Today I was analysing the volumes and I see there is a poor image in comparison with my other brains that were converted in a NIFTI format (having just 4 MB size) by someone else before me. > > My question is: is this poor image due to a different conversion way (I understood the other person used Mricron to convert the files) OR I need to do manually corrections adding control points for the intensity normalization. > > What is your suggestion/advise? > > Many thanks. > Antonella > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Tuesday, July 26, 2011 5:53 PM > Subject: Re: [Freesurfer] Loading atlases > > Hi Antonella > > the atlas is not guaranteed to be correct. If it were we would just take the labels from it :) The only way to tell if it is correct is to look at the segmentations on top of the MR and see if they follow the visible boundary > > To get the surfaces you should do > > tkmedit SUBJECT1 brainmask.mgz lh.white \ > -aux T1.mgz -surfs \ > -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt > > cheers > Bruce > > > > On Tue, 26 Jul 2011, Antonella Kis wrote: > > > Hi, > > > > I would like to check if my subcortical segmentation is correct so I was running: > > > > tkmedit SUBJECT1 brainmask.mgz \ > > -aux T1.mgz -surfs \ > > -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt > > > > 1). Pial (red line), and white (yellow line) surfaces are shown and I wonder how I can add a green lie for my orig surface? > > 2). After I load the aparc+aseg.mgz is theer a way to load and overlay the original/correct atlas so I can see if my segmentation is correct? > > > > Thank you very much. > > Antonella > > > > > > > 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. > > > <P27.tiff>

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Need help to run MRI data using Freesurfer in Mac OSx
by joanna floria 01 Aug '11

01 Aug '11

Hello Everyone, We just installed Freesurfer on Mac and the software got installed successfully. But when I am running my data, it just gets stuck in between and shows me the error. The command I used was: /Applications/freesurfer/bin/recon-all-s 002 -i /Users/kashou/Desktop/fMRI/Anesthetics/002/SPGR/MR000000 -all -notal-check The error: /Applications/freesurfer/subjects/002/mri \n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin Nasser-Kashous-iMac.local 10.4.1 Darwin Kernel Version 10.4.1: Fri Jul 16 23:04:20 PDT 2010; root:xnu-1504.7.51~1/RELEASE_I386 i386 recon-all -s 002 exited with ERRORS Can anyone please help me out with the error? Thanks, Joanna

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Retinotopy Registration to Anatomical
by Michelle Umali 31 Jul '11

31 Jul '11

Dear Freesurfers, During my retinotopy analysis, I was getting very strange fieldsign data (blue and red speckles) and my polar and eccentricity data was limited to the occipital pole. It was suggested that I check registration between the functional and anatomical. I was looking up tkregister2 help to figure this out but am still unsure how to register the polar and eccentricity data to the anatomical. Any help would be most appreciated. -Michelle Umali

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Freesurfer July 2011