Freesurfer August 2012

freesurfer@nmr.mgh.harvard.edu

110 participants
170 discussions

Problems with ICV calculations in fs5.1.0?
by Cheryl McCreary 20 Aug '12

20 Aug '12

Dear fs Experts, In the most recent Freesurfer Digest (vol102, Issue13), a question regarding ICV calculations in version 5.1.0 was raised (message 4). Can you please expand on the problems with this? I am using version 5.1.0 and the estimate of ICV is of interest. Thanks, Cheryl McCreary

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More problems created when adding WMCP
by Mark Fletcher 20 Aug '12

20 Aug '12

Dear FreeSurfers, I have been working on cross-sectional MRI's of healthy older adults (55-88), and have been correcting the FreeSurfer 5.1 output using the instructions given here ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) to correct the FreeSurfer errors that we have found. For the majority of the subjects, we have been able to fix the errors as described by your website. However, for about 7 of our subjects, whenever we attempt to add WMCP to non-traced white matter regions (especially noticed in the anterior region of the temporal lobe), the new "main surface" and "Pial" tracings end up much worse than they were originally (thus, new problems that never previously existed are created). At this point we have tried a variety of things. We have tried going back to the original FreeSurfer Output to add WMCP differently, yet a variety of new problems are consistently being created (on some of these subjects we have tried over 10+ different ways of adding WMCP in order to fix the brains). After this has occured, we simply tried fixing the "new problems" as well, but it has created a never ending loop of new problems (upon fixing the new problems, even newer problems were created). For some of our subjects (besides these 7), this eventually leads to a correct segmentation. However, for these 7, we have been unable to ever end up at an adequate tracing?? I would love you send you images and or the files themselves to figure out how to proceed (however, when I tried to send it as an attachment my message was rejected due to size issures). Is there a way I can directly send you the FS output (via a ftp site, or dropbox) so you can look at the problem directly? The IRB has approved our "sharing" of this data if it helps us in our processing. Also, do you have any suggestions on how we might proceed? Is there a way besides adding WMCP to assist our fixing of the anterior temporal regions? Thanks in advance. Sincerely, Mark Fletcher

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Talairach transform error
by Alexandra Tanner 20 Aug '12

20 Aug '12

Dear Doug, As I mentioned in a previous email, I'm currently working with T1 DICOM files from the Clinical PACS System that I'd like to pull into the freesurfer stream to get cortical thickness. I've unpacked the data, converting the DICOM files to mgz format, and successfully ran the first recon-all command: "recon-all -i <input> -s <subject> -force". I then proceeded to run the "recon-all -autorecon-all -s <subject>" command on my subject, but the command terminated about 5 minutes in and I received the following error message: #-------------------------------------------- #@# Talairach Failure Detection Mon Aug 20 13:53:21 EDT 2012 /autofs/cluster/roffman/users/Stable5_PerRun/Subject2/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux compute-0-35 2.6.32-220.23.1.el6.x86_64 #1 SMP Mon Jun 18 18:58:52 BST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Subject2 exited with ERRORS at Mon Aug 20 13:53:21 EDT 2012 I tried viewing the talairach.xfm file in tkregister2, as I saw someone else who received the same error message was instructed to do, but no image would load (in the coronal and horizontal views the screen remained black and had one thin strip of grey in the center; the sagittal view brought up a blank white screen). We know that our data is intact because Dr. Roffman is able to view images of this subject on his computer using the mi2b2 software, so do you think it is possible that somewhere earlier, either in the recon or the dcmunpack stages, there was an error with the data that wasn't recognized until doing the talairach transformation? Also, something else I noticed when looking at our subject's data, the talairach.xfm and talairach.auto.xfm files are different, even though for all other subjects I've run recons on they are the same -- could this be a contributing factor? I'm unsure how to proceed with the unpacking since I'm currently unable to perform any edits to the talairach registration to try and fix the error, so any suggestions would be very helpful and greatly appreciated! Thanks, Alex

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Clinical DICOM files
by Alexandra Tanner 20 Aug '12

20 Aug '12

Dear Doug, We're getting T1 DICOM files from the Clinical PACS System (via mi2b2) and would like to pull them info the freesurfer stream to get cortical thickness. In order to run the standard unpacking commands, do we need any other files besides the DICOM files themselves? Of note, these scans were acquired on a variety of clinical scanners at MGH. Any suggestions you have would be greatly appreciated! Thanks, Alex

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Re: [Freesurfer] Projection of FMRI data onto Cortical Surface in FS5.1: interpolation method
by Douglas N Greve 20 Aug '12

20 Aug '12

By default, it uses nearest neighbor. There is an option to use trilinear. doug On 08/19/2012 04:23 AM, Xinian Zuo wrote: > Dear Dr. Greve, > > Hope all is well. I am writing to ask if you can give me some > references or details on the interpolation method used in FS (version > 5.1) cmd mri_vol2surf, which I used for the surface-based R-fMRI > computation. Thanks for your time! > > Warm Regards, -- 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

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Re: [Freesurfer] 3d Gaussian filter on volume
by Douglas N Greve 20 Aug '12

20 Aug '12

what do you mean "compute a gaussian image"? doug On 08/18/2012 05:01 PM, John Papaioannou wrote: > Hi Doug, > > Will the following compute a gaussian image? > > mri_fwhm --smooth-only --fwhm 2 --i brainmask.mgz --o > brainmasksmoothed.mgz > > Thank you in advance, > John > ___ > > JohnPapaioannou > Medical Imaging Sciences > Digital Mammography, CAD Mammography > Department of Radiology > Biological Sciences Division > The University of Chicago > 5841 South Maryland Avenue > Chicago, Illinois 60637 > 773.834.5104 voice 773.702.0371 fax > -- 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

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Fwd: How TE, TI and flip angle parameters affect the images and results?
by Daniel Ferreira 20 Aug '12

20 Aug '12

Thanks for your answers! Following your comments, I have thought to select only first two sequences, as they are the more frequent in our database and only differ on the TE parameter. We will also create balanced groups. cheers Daniel 2012/8/18 Andre van der Kouwe <andre(a)nmr.mgh.harvard.edu> > Hi Daniel, > > I agree, those flip angle differences are quite big and would make a > difference to contrast. I suspect gray/white contrast is better for the > higher TI and lower flip angles in those scans (and they could benefit from > longer TR). So if you have a balanced study/control group it's ok but I > wouldn't compare subjects with systematically different protocols like > those below. > > Cheers, > > Andre. > > > Bruce Fischl wrote: > >> Hi Daniel >> >> those are pretty big differences in flip angle. I'll cc Andre van der >> Kouwe on this so he can comment, but I would be hesitant. The increased TE >> will have a big effect on dura (darkening it), but will also reduce >> gray/white contrast. >> >> cheers >> Bruce >> >> >> On Fri, 17 Aug 2012, Daniel Ferreira wrote: >> >> Dear all, >>> We are designing a study based on clinical data. We want to work with a >>> MPRAGE sequence but subjects have been given 4 different sets of >>> parameters: >>> >>> - TR: 1900; TE: 4,38; TI: 1100; flip angle: 15 >>> - TR: 1900; TE: 3,55; TI: 1100; flip angle: 15 >>> - TR: 1900; TE: 3,39; TI: 900; flip angle: 9 >>> - TR: 1900; TE: 3,39; TI: 900; flip angle: 15 >>> >>> I wonder how these differences could affect the images and thus the >>> results. >>> Can I combine all of them or at least some of them? Are they so different >>> that I should just study them by separate? >>> >>> thank you very much on advance >>> >>> Daniel Ferreira >>> >>> >>> > > 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<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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mri_convert unsupported slice timing error
by Joshua Lee 20 Aug '12

20 Aug '12

Hi All, I tried to convert a high res T2 image using mri_convert and got this error message: nifti1Read(): unsupported slice timing pattern 5 Any advice? Complete message below: mri_convert DKA2921c_20120807_001_003_t2_ tse_hippo.img bb.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 003_t2_tse_hippo.img... nifti1Read(): unsupported slice timing pattern 5 in ./003_t2_tse_hippo.hdr Joshua

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empty CSD folder?
by lordowen 20 Aug '12

20 Aug '12

Dear experts: We performed permutation analysis (with -sim perm) for our thickness data. After 2 month calculation, the process completed but the CSD folder only contained an empty folder named "poll". No CSD file in them. So I wonder if the CSD file has been stored in another place or something wrong with them? Please advise us. -- Best regards -- 杜政昊 Cheng-Hao Tu, PhD Post Doctoral Research Fellow Integrated Brain Research Unit Department of Medical Research and Education Taipei Veterans General Hospital No.201, Sect.2, Shih-Pai Rd. Taipei Taiwan Email: lordowen(a)ms10.hinet.net or lordowentu(a)gmail.com Tel: +886-2-28712121 ext 3474 Fax: +886-2-28745182

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sub field hippo segment fault in kvlSegmentHippocampalSubfields.sh: line 18
by Knut J Bjuland 19 Aug '12

19 Aug '12

When I run recon-all for subfield segmentation I get a segmentation error? I get the error message below. Cheers Knut J Bad trial move (maximal deformation: 278.205, lambda: 12.021) Cost going from 433597 to 1.79769e+308 Transforming mesh Done transforming mesh Increasing lambda from 12.021 to 24.0421 and trying again. Transforming mesh Done transforming mesh Calculating Levenberg-Marquardt step with lambda 24.0421... Time taken to solve the Levenberg-Marquardt system of equations: 0.621659 ...done! maximalDeformation: 348.155 Transforming mesh Done transforming mesh Rasterizing Levenberg-Marquardt... Done transforming mesh Rasterizing Levenberg-Marquardt... /global/apps/freesurfer/5.1.0/bin/kvlSegmentHippocampalSubfields.sh: line 18: 21317 Segmentation fault kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt failed to do kvlSegmentWithoutGUI configurationFileSegmentationWithoutPartialVolumingButAfterUpsampling.txt Linux c4-1.local 2.6.18-194.17.1.el5 #1 SMP Wed Sep 29 12:50:31 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subject_id exited with ERRORS at Sat Aug 18 19:00:37 CEST 2012 For more details, see the log file /home/kjbjuland/freesurfer/20_ucsd_automatic/023/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Freesurfer August 2012