Freesurfer September 2011

freesurfer@nmr.mgh.harvard.edu

119 participants
181 discussions

Re: [Freesurfer] Problem writing talairach.m3z in mri_ca_register
by Lauge Emil Borch Laurs S0rensen 22 Sep '11

22 Sep '11

On Tue, Sep 20, 2011 at 15:00, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > what other information would you like? Can you remind me: are you running > on a cluster? Does this happen if you run on your local workstation? Do you > have limits on # of open files? Yes, I am running on a cluster with Gentoo (Linux imageserver1 2.6.20-gentoo-r8 #2 SMP Fri May 25 10:23:59 CEST 2007 x86_64 Intel(R) Xeon(R) CPU X5355 @ 2.66GHz GenuineIntel GNU/Linux) I runs without problems on the same data on a MAC The limits in the cluster are: ulimit -a core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 155648 max locked memory (kbytes, -l) 32 max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 8192 cpu time (seconds, -t) unlimited max user processes (-u) 155648 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited Still haven't resolved the problem. I was wondering, is there some way of forcing mri_ca_register to finish fast (to make error tracing easier)? I have tried using -tol [some large numer], but still it takes many hours before reaching the part where talairach.m3z is written (the part that fails). Best, Lauge

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manual editting problem
by Jing Ming 21 Sep '11

21 Sep '11

Hi Bruce and Sita: Thanks for your relay. And Here are the images. Jing From: Jing Ming [mj_coming(a)hotmail.com] Sent: Thursday, September 15, 2011 7:31 PM To: Vy Dinh Subject: FW: [Freesurfer] manual editting problem > CC: mj_coming(a)hotmail.com; jennifer_g_goldman(a)rush.edu; vydinh(a)rush.edu; freesurfer(a)nmr.mgh.harvard.edu > From: fischl(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] manual editting problem > Date: Thu, 15 Sep 2011 20:07:41 -0400 > To: sita(a)nmr.mgh.harvard.edu > > Can you send an image? > > > > On Sep 15, 2011, at 6:38 PM, Sita Kakunoori <sita(a)nmr.mgh.harvard.edu> wrote: > > > > > How does the wm.mgz look. Correcting the white surface will correct the > > pial surface as well. > > > > Sita. > > > > > > On Thu, 15 Sep 2011, Jing Ming wrote: > > > >> > >> Hi Surfers: > >> We have been coming > >> across several gray matter regions that are not included within the pial > >> surface (red line) when it should be (e.g., very anterior parts of the > >> temporal lobe). From my understanding of similar posts on the forum, it > >> seems that there isn't a way to add this region to the pial surface so > >> that the missing brain matter is included. We have tried using the clone > >> tool to fill in this region, as per the tutorial and have experimented > >> with this tool using the tutorial data. I followed the steps in the > >> tutorial but could not observe any changes when the middle button was > >> selected. Does anyone have any ideas on how to troubleshoot this > >> issue? Can someone please explain to me why this is not possible? Also > >> how does Freesurfer determine what regions to include within the pial > >> surface? If there is a way that has been developed recently, please > >> enlighten me. > >> > >> -Jing > > _______________________________________________ > > 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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Re: [Freesurfer] please help, unsupported slice timing
by Greg Burgess 21 Sep '11

21 Sep '11

We've had a similar issue when using MRIconvert (mcverter) to convert dicom to nifti. Our anatomical images have this slice timing pattern 5, which isn't part of the Nifti standard. Also, mcverter outputs a blank sform matrix, which causes other problems. The easiest fix is to run the following magic: fslmaths /PATH/TO/IMAGE.nii /PATH/TO/IMAGE.nii A potentially better long-term fix is to switch dicom to nifti converters. We've been having success with dcm2nii, which is part of mricron. Good luck, --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Email: burgessg(a)pcg.wustl.edu

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freesurfer problem?
by Nick Dery 21 Sep '11

21 Sep '11

Hi, I just downloaded the new version of freesurfer (5.1.0) with the hopes of completing hippocampal subfield segmentation. After running my data through the appropriate streams and trying to visualize it, ie: deryn(130)freeview nu.mgz \ -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt I get the following feedback: freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory Any help would be appreciated. Thanks, Nick

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Partial brain scanning and registeration
by SHAHIN NASR 20 Sep '11

20 Sep '11

Hi I want to know if there is any limit for the automatic registration of functional scans on structural ones when we are scanning activity just in a specific part of the brain (e.g. occipital cortex).

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Optseq2 Null Events between every Event
by Anita Cservenka 20 Sep '11

20 Sep '11

Hi, I was wondering if it is possible to use optseq2 to get null events (e.g. fixation) between each event type. I would like to see the optimal sequence of trials for a design that involves two event types (each 0.5 sec), 60 TRs for one event, 26 TRs for the other, and a 2sec TR. I would like to have an intertrial interval lasting between 2-10 seconds (jittered) between each of the 0.5 sec long events. I can’t seem to find an option for optseq2 that would allow me to set a null event between each 0.5 sec event. Is this possible and if so what options should I use? Thanks! Anita

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Patch file to ascii issues
by Michael Waskom 20 Sep '11

20 Sep '11

Hi, Two issues related to patch files. Issue number 1: If I generate an ascii flat patch file like so: $ bin_patch=fsaverage/surf/lh.cortex.patch.flat $ mris_convert -p $bin_patch lh.cortex.patch.flat.asc And then inspect the file that gets created: $ head lh.cortex.patch.flat.asc #!ascii version of patch fsaverage/surf/lh.orig. The 1st index is not a vertex number 149297 296943 1 vno=0 -60.013611 4.446770 0.000000 2 vno=1 -56.163204 88.759064 0.000000 3 vno=2 -112.137077 -18.977211 0.000000 4 vno=3 -34.436668 -72.297958 0.000000 This is sort of annoying if I want to read it into Matlab, etc. (actually Python) using routines that expect an array of numbers. Is there any way to suppress the intercoordinate output? Issue number 2: Even if I get around the text file formatting issues, I run into some problems when I try and generate meshes with the resulting data. It seems like the triangles component of the surface makes references to vertex ids that don't exist anymore. In other words, the triangles array contains values that are larger than the number of rows in the vertices array. Obviously I'm doing things that aren't officially supported by Freesurfer there, but does that jive with your knowledge of how the patch files are written? Thanks! Michael

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How can I include 3 covariates in my GLM model
by Dalwani, Manish 20 Sep '11

20 Sep '11

Hello Freesurfer's, I am using QDEC and I have created and FSGD descriptor file with 2 groups (pts and ctrls) and three continuous variables: age, IQ and mean thickness. I have 2 questions: 1. I can only choose 2 covariates at one time? How can I choose all three covariates in one model in my design? 2. I tried group and 2 covariates combinations to check if it runs ok and found that when I select age and IQ, it runs...when I select IQ and mean thickness it runs but it fails when I try running with age and mean thickness in the model? The error in the terminal says matrix not correct, check duplicates..., etc.. What I am doing wrong? Thanks, Manish Dalwani

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please help, unsupported slice timing
by Gregory Kirk 20 Sep '11

20 Sep '11

i am trying to run tracula on a large number of subjects, tracula dies quicklyin -prep stage when mri_convert tries to copy/rename the diffusion data, the error actually comes from the data read function. the data is already in .nii format the error is 'unsupported slice timing pattern 5' this is diffusion data that is already in .nii format so the slice timing information is irrelevant, no slice timing correction is done on diffusion data, but the info was obviously encoded in the nifti header. what do i need to do to get this data to load, go edit the .nii header and 'remove' this info. i tried with the fsledithd function and just setting the 5 to 0 does not work, then i just get a 'read error' with no other information. this data is from a 1.5T siemens mobile scanner so the snr will be a little lower and the bval = 800 is lower so it is just the data that could use the helping hand of the spatial priors to find the tracts. i can run 500 of these if i can get this fixed, incarcerated psychopaths so an important data set. thank you Greg

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Re: [Freesurfer] FW: flipped orientation in tksurfer and tkmedit
by Ilana Hairston 20 Sep '11

20 Sep '11

Hi Doug, No, we had the lh loaded in tksurfer, and when saving a point it showed up on the *left* in tkmedit (i.e., the right side). thanks ilana On Tue, Sep 20, 2011 at 11:34 AM, weiland, Barbara <bweiland(a)med.umich.edu>wrote: > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto: > freesurfer-bounces(a)nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Wednesday, September 14, 2011 6:10 PM > To: Ilana Hairston > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] flipped orientation in tksurfer and tkmedit > > When you say on the "right hemi in tkmedit" do you mean on the right side > of the image (which is the left side of the brain)? > doug > > Ilana Hairston wrote: > > Hi there, > > We recently had a problem that tksurfer and tkmedit were flipped > > relative to each other. Basically, when saving a point in the left > > hemisphere in tksurfer it it loaded in the right hemisphere in tkmedit. > > Any ideas how this could have happened? > > Thanks > > ilana > > > > > > > > -- > >> ****************************** > >> Ilana Hairston ,PhD > >> Research Assistant Professor > >> 4250 Plymouth Rd. (rm 2439) > >> Psychiatry Department, Addiction Research Center University of > >> Michigan, Ann Arbor MI 48109-2700 > >> Tel: 734-232-0232; Mobile: 650-906-8449 > >> > >> ******************** > >> Reminder: Women do 66% of the work worldwide, earn 10% of the income, > >> and own 1% of the world's property > > > > > > > > ---------------------------------------------------------------------- > > -- > > > > _______________________________________________ > > 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 > > _______________________________________________ > 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. > > -- ****************************** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property

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Freesurfer September 2011