Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

fsaverage vertex index to talairach
by Cesar Echavarria 25 Jun '13

25 Jun '13

Hello, Anyone know of a fast way to get the talairach coordinates of a vertex index in fsaverage. A function or script is best since I want to do this for a large number of vertices. Thank you for any help you guys can provide. Cesar

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Fwd: DTI questions
by Rotem Saar 24 Jun '13

24 Jun '13

Hi there, Long time:). Well I wrote to the list several times regarding high FA values I got when performing DTI analysis. Today we know that the problem was an additional direction (we had 17 directions instead of 16 - we used a Philips scanner,1.5T). So we deleted the additional slices and the high values indeed disappeared, but then another problem came up (tried several subjects so the problem is not specific to a subject) - I noticed an artifact that I can't explain - please see the attached pictures. This artifact existed even before I deleted the additional slices, also - I see the artifact also when loading the masked volume...It is cyclic - run over all slices... any ideas ? I'm using version 5.2 and I know the command lines are correct (send it to u in the past). Thanks for your help Rotem

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Multiple inputs into recon-all -i
by ye tian 24 Jun '13

24 Jun '13

Dear David, I wonder whether there is a short cut for recon-all -s Barbara -i /path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i /path_to_data/scan100.dicom Recon-all -i takes only a single file as an input. A typical user, however, has hundreds of files for a particular subject. For example, the directory Barbara may have 100 scans. Therefore, the above command is necessary to include all the scans. I understand that I can write loops to a text file and then copy and paste to command line. However, I wonder whether there is a simpler way to input several files or even a directory to recon-all. Thank you very much! Sincerely, Ye

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HCP Releases Second Quarter of Brain Connectivity Data
by Jennifer Elam 24 Jun '13

24 Jun '13

June 13, 2013 (repost to Freesurfer list June 24, 2013) The Human Connectome Project (HCP) WU-Minn consortium is pleased to announce our second quarterly (Q2) release of HCP image and behavioral data. What’s in the HCP Q2 data release? The Q2 data include multimodal MRI and behavioral data collected from 68 healthy young adults scanned in winter 2012-2013. The current release expands the total (Q1+Q2) number of released healthy participant data for imaging and/or behavioral measures to 148, including 40 datasets that include the complete HCP protocol (T1w and T2w MRI, rfMRI, tfMRI, dMRI, and behavioral measures) and an additional 60 that include all modalities other than dMRI. The Q2 release also includes: · New preprocessing pipelines - Along with the newly processed Q2 datasets, the Q2 release also includes a complete regeneration of the minimally preprocessed data from Q1. We strongly encourage all investigators to update their existing Q1 data to stay current with HCP's latest and greatest. · More behavioral data, physiological data - Most of the collected behavioral/individual difference assessments and physiological data for functional MRI scans of Q1/Q2 participants is now available for a majority of subjects. · Restricted Data - Qualified investigators who are approved for restricted access will be given access to restricted data through the ConnectomeDB interface. · 40 dMRI datasets - Diffusion MRI data is being released for 40 unrelated Q1/Q2 subjects only because HCP has recently implemented an improved image reconstruction algorithm for dMRI data. Unprocessed and minimally preprocessed datasets based on these improved reconstructions for all Q1, Q2, and Q3 subjects will be included in the Q3 data release scheduled for August 2013. Access Q2 data on the HCP website. Explore, download, or order the entire HCP Q1+Q2 dataset (~3.5TB of data!) via the ConnectomeDB database ( http://humanconnectome.org/data/) Most HCP image and behavioral data is openly accessible to investigators worldwide who register and accept a limited set of Open Access Data Use Terms. Note: Please clear your browser cache before logging in to ConnectomeDB. Want more information? Check out the HCP Q2 Data Release Reference Manual ( http://humanconnectome.org/documentation/Q2/) for a comprehensive guide that includes details on imaging protocols, behavioral measures, and information that will help users obtain and analyze the Q2 data. Detailed descriptions of many HCP methods are available in eight papers now in press for a special issue of NeuroImage in 2013 (Van Essen et al., 2013, Ugurbil et al., 2013, Glasser et al., 2013, Smith et al., 2013, Barch et al., 2013, Sotiropolous et al., 2013, Marcus et al., 2013, and Larson-Prior et al., 2013). For those who choose to download the HCP data and begin to analyze it, we encourage you to join and be active in the hcp-users discussion group ( http://www.humanconnectome.org/contact/#subscribe) so that you can tune in to technical discussions on issues that may be of interest. Please send us your questions and comments anytime to info(a)humanconnectome.org. Best, The WU-Minn HCP Consortium Jennifer Elam, Ph.D. Outreach Coordinator, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elamj(a)pcg.wustl.edu www.humanconnectome.org

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Using the T2 pial flag for pial refinement
by Michael Kranz 24 Jun '13

24 Jun '13

Hi all, I'm having trouble determining whether or not to use our T2 images for the new pial refinement feature. *Most importantly, I'm wondering if our T2 image parameters are sufficient for the T2 pial refinement. The parameters of our T2 images are as follows:* T2 TSE overlay with a voxel size of 1.1x1.1x3.5 mm (slice thickness). A couple other studies in our lab have a voxel size of 0.9x0.9x4.0 mm. Note that our MPRAGE voxel size is .9x.9x.9mm. In your release notes, it states we should uaround a 1x1x1mm (let me know if you need additional specifications such as geometry bandwidth etc): "T2/FLAIR used for pial surface refinement: if you have T2 or FLAIR scans ~1mm^3, then they can be used by the recon-all stream to refine the pial surfaces". I have experienced about 1/4 of our subjects with errors using the T2 pial flag. As a next step, if you think the parameters are acceptable, then I can send you some screen shots different errors that I have encountered wit these subjects. Best, Mike

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infant .tiff templates
by Mark Plantz 24 Jun '13

24 Jun '13

Hello freesurfers, I am currently attempting to create my own .tiff templates for a series of infant fMRI's (neonates, 1 yr olds, and 2 yr olds). I currently have the templates in .nii.gz, .mgz, and .img/.hdr formats. Is there any easy way to convert from one of these formats to a .tiff image to use as an actual template for reconstruction with FreeSurfer? If so, would the conversion distort/ruin the template? Thank you! - Mark Plantz

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[FreeSurfer] Freeview: Invalid drawable
by ye tian 24 Jun '13

24 Jun '13

Dear Koen, Freeview returns 8 lines of the error message "invalid drawable" whenever executed. The messages are as follows 2013-06-24 14:24:57.930 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.931 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.944 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.945 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.957 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.958 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.971 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.972 Freeview[1937:303] invalid drawable In the $FREESURFER_HOME directory, I tried sed -i "" 's/CA2_3/CA2\/3/g' FreeSurferColorLUT.txt sed -i "" 's/CA4_DG/CA4\/DG/g' FreeSurferColorLUT.txt as you suggested in http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22276.html(co… copied at the end of this email) I checked in FreeSurferColorLUT.txt and made sure all CA2_3 was changed into "CA2\3", all "CA4_DG" into "CA4\DG", but the problem still persists. My computer is Mac OS X version 10.8.2. I downloaded freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwi…> Would you please give me some guidance on how to fix the problem? Thank you very much! Sincerely, Ye Tian Hi Ed, It seems that the 5.1.0 release for the Mac was composed two days after the one for Linux, and during exactly those two days one of us made a change to the file $FREESURFER_HOME/FreeSurferColorLUT.txt. To correct this issue, please make a back-up copy of your FreeSurferColorLUT.txt file, and execute the following commands: cd $FREESURFER_HOME sed -i "s/CA2_3/CA2\/3/g" FreeSurferColorLUT.txt sed -i "s/CA4_DG/CA4\/DG/g" FreeSurferColorLUT.txt Thanks, Koen On Wed, Apr 4, 2012 at 9:32 AM, Ed Gronenschild <ed.gronensch...(a)np.unimaas.nl> wrote: > I have downloaded the file > freesurfer-Darwin-leopard-i686-stable-pub-v51.0..dmg, > date 26/05/2011. > > Ed > > > On 4 Apr 2012, at 13:09, Koen Van Leemput wrote: > >> OK, I see why this is not working. We've been changing some name >> conventions in our internal FreeSurfer repository after the public >> release of version 5.1, and somehow you managed to get an incompletely >> updated version. >> >> It appears from >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0 that some >> versions for the Mac were updated *after* the release date (24 May >> 2011), so I'll check with the engineers what exactly happened. Do you >> remember which file you downloaded? >> >> Thanks, >> >> Koen >> >> >> >> On Wed, Apr 4, 2012 at 6:59 AM, Ed Gronenschild >> <ed.gronensch...(a)np.unimaas.nl> wrote: >>> >>> Hi Koen, >>> >>> No worries. >>> The result of grep is: >>> >>> 500 right_CA2_3 17 85 136 0 >>> 550 left_CA2_3 17 85 137 0 >>> >>> Ed >>> >>> >>> On 4 Apr 2012, at 12:41, Koen Van Leemput wrote: >>> >>>> Hi Ed, >>>> >>>> Can you please do >>>> >>>> "grep _CA2 $FREESURFER_HOME/FreeSurferColorLUT.txt" >>>> >>>> and let me know what the result is? >>>> >>>> Thanks, and sorry this seems so difficult to sort out. >>>> >>>> Koen >>>> >>>> >>>> On Wed, Apr 4, 2012 at 6:14 AM, Ed Gronenschild >>>> <ed.gronensch...(a)np.unimaas.nl> wrote: >>>>> >>>>> >>>>> Hi Koen, >>>>> >>>>> As already mentioned, I'm using v5.1.0, Mac Intel >>>>> Leopard version. >>>>> The voxel values of posterior_left_CA2-3.mgz and >>>>> posterior_right_CA2-3.mgz are between 0 and 255, >>>>> if that is what you mean by "results". >>>>> By the way: I always get the 8 lines with "invalid >>>>> drawable" messages from freeview. >>>>> >>>>> Ed >>>>> >>>>> >>>>> On 3 Apr 2012, at 21:29, Koen Van Leemput wrote: >>>>> >>>>>> Hi Ed, >>>>>> >>>>>> What version of the FreeSurfer build are you using? >>>>>> >>>>>> Also, could you please let me know what the result is of "ls >>>>>> posterior_left_CA2*"? >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Koen >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Mar 27, 2012 at 8:29 AM, Ed Gronenschild >>>>>> <ed.gronensch...(a)np.unimaas.nl> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I followed the instructions to visualize the hippocampal subfield >>>>>>> segmentation >>>>>>> by entering the command (in the subject's mri directory) >>>>>>> >>>>>>> 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 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> and got the following messages: >>>>>>> >>>>>>> 2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable >>>>>>> 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable >>>>>>> 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable >>>>>>> 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable >>>>>>> 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable >>>>>>> 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable >>>>>>> 2012-03-27 11:54:37.182 freeview.bin[34414:907] invalid drawable >>>>>>> 2012-03-27 11:54:37.184 freeview.bin[34414:907] invalid drawable >>>>>>> QObject::connect: Connecting from QAbstractButton::toggled(bool) to >>>>>>> COMPAT slot (QGroupBox::setShown(bool)) >>>>>>> QObject::connect: Connecting from QAbstractButton::toggled(bool) to >>>>>>> COMPAT slot (QGroupBox::setShown(bool)) >>>>>>> CTABrgbAtIndexi: index -1 was OOB >>>>>>> CTABrgbAtIndexi: index -1 was OOB >>>>>>> Can not find index for color name left_CA2-3 >>>>>>> CTABrgbAtIndexi: index -1 was OOB >>>>>>> CTABrgbAtIndexi: index -1 was OOB >>>>>>> CTABrgbAtIndexi: index -1 was OOB >>>>>>> Can not find index for color name right_CA2-3 >>>>>>> CTABrgbAtIndexi: index -1 was OOB >>>>>>> >>>>>>> Nothing was shown on top of nu.mgz. All the left and righ posterior >>>>>>> files >>>>>>> are present. >>>>>>> >>>>>>> (Mac OS X 10.6.8, FreeSurfer version 5.1.0) >>>>>>> >>>>>>> Cheers, >>>>>>> Ed >>>>>>> _______________________________________________ >>>>>>> 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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retinotopy betas
by dgw 24 Jun '13

24 Jun '13

Hi, I am examining the affect a metal artifact has on fMRI data, and I am using Eccentricity mapping with the retinotopy analysis in FSFast. I was recently asked to switch from examining the difference in the fsig to examining the difference in the betas. I opened up beta.nii.gz and I can see that it has a size of: 1 #of vertices 1 39 Can you explain to me, how I figure out where each of the 39 come from (and possibly point me to which of these might be appropriate to use?)? Thank You, Dan

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lme issues + failure to converge
by Catherine Bois 24 Jun '13

24 Jun '13

Dear Jorge/freesurfer group, I am using the scripts you sent me that do not require the newer version of matlab, and now using a computer that has the Statistics toolbox. I can get the scripts (with the suffix 1) to run with; lhstats = lme_mass_fit_vw(X[1 2],ni,lhcortex);) however it "fails to reach convergence" at most vertices. We have tried simplifying the model to include only one random effect at a time, however the problem persists. Our design matrix is as follows; X = [ones(length(M),1) M(:,1) Mat(:,1) Mat(:,1).*M(:,1) Mat(:,2) Mat(:,2).*M(:,1) Mat(:,3) Mat(:,3).*M(:,1) M(:,3)-1 M(:,4)]; I have read on the mailing list that non-convergence at some vertices is normal, however what we are getting far exceeds 10%. Any help on this matter would be greatly appreciated! Best Wishes, Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Re: [Freesurfer] retinotopic mapping selxavg3-sess error
by Bianca van Kemenade 24 Jun '13

24 Jun '13

Sorry for the delay. I'm new to FSL, Freesurfer, and VB, so maybe I'm doing it wrong, but I have the impression I cannot run FSL from the VB: - Typing 'fsl' yields 'fsl: Command not found'. - Checking the environment with 'echo $FSLDIR' yields 'FSLDIR: undefined variable' - Checking the path with 'flirt -version' yields 'flirt: Command not found' However, typing 'fsl' + tab shows the following available commands: - fsl2par - fsl_label2voxel - fslmaths.fsl - fslorient.fsl - fslregister - fslregister -sess - fsl_rigid_register - fslsfonts - fsl_sub_seychelles - fslswapdim.fsl So it seems there are some FSL-related files installed, but apparently not all. I did download the virtual disk image for Freesurfer, so I assumed a complete FSL version would be included? I'm sorry if there's an obvious solution, but I can't seem to find it... Thanks again, Bianca On Fri, Jun 21, 2013 at 6:16 PM, Douglas Greve <greve(a)nmr.mgh.harvard.edu>wrote: > > Can you run FSL at all in your VB? > > > > > On 6/21/13 7:49 AM, Bianca van Kemenade wrote: > > Dear Freesurfers, > > I'm setting up freesurfer to do retinotopic mapping. I use a PC with > Windows XP, so I installed Freesurfer using the VirtualBox (with Xubuntu). > I managed to get through the initial steps for retinotopic mapping, but I > get stuck at the actual analysis. > > The point where I get stuck is: > > selxavg3-sess -a rtopy.self.lh -s P2_BK > > It starts the analysis, but runs into problems at the stage "Using FSL's > BET to extract brain" and gives the following error output: > > # ---------- Using FSL's BET to Extract Brain------------------ # > /home/virtualuser/freesurfer/ > shared/P2_BK/bold > bet.fsl /tmp/mkbrainmask_4425/in.nii /tmp/mkbrainmask_4425/brain -m -f 0.1 > /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found > /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found > /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found > [: 158: =: unexpected operator > /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found > /bin/rm: cannot remove `_tmp*': Protocol error > ERROR: bet failed > > I tried updating FSL in case that is the problem, but it is only > available for Ubuntu 10.04 and up, whereas the Ubuntu system that is > provided to install the Freesurfer virtual disk image is 9.04. If anyone > has an idea how to proceed let me know, any help is much appreciated. > > Thanks, > Bianca > > > > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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. > > -- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/ -- Bianca van Kemenade, MSc Doctoral Candidate, Berlin School of Mind and Brain Klinik für Psychiatrie und Psychotherapie Campus Charité Mitte Charitéplatz 1 10117 Berlin http://www.mind-and-brain.de/

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Freesurfer June 2013