Freesurfer December 2013

freesurfer@nmr.mgh.harvard.edu

107 participants
197 discussions

Re: [Freesurfer] Fwd: white matter and pial surface don't track sulcus
by Darren Gitelman 06 Dec '13

06 Dec '13

Yes. That's it. I tried editing the wm.mgz earlier and deleting all voxels labels as ventricle (250) but that didn't solve the problem. Do I edit the aseg.mgz file and just label it as none in this region? Would I use the command tkmedit <subjid> brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt When done do I run recon-all -autorecon2-noaseg -autorecon3? Thanks, Darren On Sun, Sep 16, 2012 at 4:38 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Check the aseg and see if it was labeled ventricle (and make sure it > really isn't). You may need to edit the aseg > > > > On Sep 16, 2012, at 5:19 PM, Darren Gitelman <d-gitelman(a)northwestern.edu> > wrote: > > Hi > > I have run into an issue that I'm not sure how to correct. What happens > is that in some subjects the surfaces don't seem to properly track sulci > coming off the medial part of temporo-occipital cortex. Please see green > arrows on the attached image. > > In fact the tutorial on topological defects shows an image with a > similar issue, but fixing it is not discussed. > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect?actio… > > I have checked and these are sulci and not the occipital extent of the > lateral ventricle. > > Perhaps it is not a problem, or if it is then how to approach fixing it? > > Thank you, > Darren > -- > Darren Gitelman, MD > Northwestern University > 710 N. Lake Shore Dr. > Abbott 11th Floor > Chicago, IL 60611 > Ph: (312) 908-8614 > Fax: (312) 908-5073 > > <3809-error.png> > > _______________________________________________ > 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. > -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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trac-all version 5.3 crash
by Jon Wieser 06 Dec '13

06 Dec '13

Hi freesurfer experts, I've recnetly upgraded to freesurfer 5.3 (lion) 64bit version on our Mac Pro when I run trac-all -prep, I get the following error: writing to /Studies/MJMRI/MJ0030/freesurfer/dmri/dwi_orig.nii.gz... mri_probedicom --i /Studies/MJMRI/MJ0030//s1869/i1560627.MRDC.1 > /Studies/MJMRI/MJ0030/freesurfer/dmri/dcminfo.dat Trace/BPT trap Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Dec 6 11:20:50 CST 2013 I've included the trac-all.log and trac-all.error file the trac-all log indicates in incompatible library version: Reason: Incompatible library version: mri_probedicom requires version 10.0.0 or later, but libX11.6.dylib provides version 9.0.0 Darwin psy-blackbird.ad.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 I have reinstalled Xquartz and rebooted, but I still get the same error. what else can I do? system info: mac pro 6-core intel Xeon MAc OS 10.6.8 snowleopard Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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bad skull strip but pial and white matter borders ok
by krista kelly 06 Dec '13

06 Dec '13

Hi, I have one subject with a poor skull strip - much of the skull and neck are left over. I have used one of the automated processes to remove the problems areas and I now the skull strip is fine. If the talarairching, pial and white matter borders, and labels were fine, do I need to rerun any of the recon-all steps? Thanks! Krista

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Freeview question
by Alan Francis 06 Dec '13

06 Dec '13

Hi Bruce et al, Is it possible to load just the Hippocampal mask/ROI from the ASEG onto a brain in Freeview? thanks, Alan

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empty norm.mgz file {Disarmed}
by Adam Mezher 06 Dec '13

06 Dec '13

Hi all, I'm having a similar issue to the one described below - the mri_cc step seems stuck and goes on for days (still going); I'm using FreeSurfer version 5.1 as well. Like Bruce said in another thread, this could be due to an empty norm.mgz file. This seems like it is my exact problem, as that file is empty. Is there a way to skip this step, or to re-run from autorecon1 and ensure the norm.mgz file is created? Thanks, Adam *Adam Mezher* Staff Research Associate II Center for Imaging of Neurodegenerative Diseases San Francisco VA Medical Center 4150 Clement St. (114M) San Francisco, CA 94121 Tel: 415-221-4810 Ext. 4629 Fax: 415-668-2864 If someone can send us and example of this behavior I will fix it Cheers Bruce On Feb 20, 2013, at 12:23 PM, Matt Glasser <matt at ma-tea.com <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> wrote: >* I've noticed this at well when something goes wrong before mri_cc. It gets stuck in some kind of infinite loop. You might check that the linear and nonlinear registration worked correctly. *> >* Peace, *> >* Matt. *> >* From: Dawei Liu <ldw70171 at gmail.com <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> *>* Date: Wednesday, February 20, 2013 10:49 AM *>* To: <freesurfer at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> *>* Subject: [Freesurfer] unusually long running time in autorecon2 *> >* Dear Freesurfer experts, *> > > >* I am running autorecon2 using Freesurfer verion 5.1.0 on Linux. For some subjects, it looks that the pipeline stucked in the middle of mri_cc and keeps running for days (without any error message). Last time when it occurred I thought it may be caused by some hardware-related problem, so I killed these jobs and re-launched recon-all -autorecon2 on a different machine. Now these jobs have been running for over 40 hours and they are still running. Do you know why they take so long? For your reference, I copied the most recent processing information below: *> > > >* mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/transforms/cc_up.lta 0057_34479 *> > > >* will read input aseg from aseg.auto_noCCseg.mgz *> >* writing aseg with cc labels to aseg.auto.mgz *> >* will write lta as /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/transforms/cc_up.lta *> >* reading aseg from /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/aseg.auto_noCCseg.mgz *> >* reading norm from /Experiments/20120801.SubjectOrganized_Results/20121213_RAW_T1_ONLY/0057_34479/mri/norm.mgz *> >* 24076 voxels in left wm, 23641 in right wm, xrange [73, 130] *> >* searching rotation angles z=[65 79], y=[-54 -40] *> >* searching scale 1 Z rot 75.6 global minimum found at slice 103.0, rotations (-50.09, 68.60) *> >* final transformation (x=103.0, yr=-50.093, zr=68.597): *> >* 0.234 -0.931 -0.280 230.831; *> >* 0.597 0.365 -0.714 75.219; *> >* 0.767 -0.000 0.642 3.440; *> >* 0.000 0.000 0.000 1.000; *> > > >* Thanks in advance for your help! *> > > >* Dawei*

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Significance of value in sig.nii file under 'polar' directory
by Cesar Echavarria 06 Dec '13

06 Dec '13

Hi freesurfers, I conducted a retinotopic analysis for one of my subjects. I was wondering if any of you knew what is represented by the values in the sig.nii file under the 'polar' directory that the process puts out. I appreciate your help! Cesar

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label to curv .mgh
by Gregory Kirk 06 Dec '13

06 Dec '13

hello, trying to convert a medial wall label to a curv format .mgh file running mris_convert --label lh.Medial_wall.label lh.white foo.mgh tried a few things but not getting there, what does it want ? thank You

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refeventdur in mkanalysis-sess
by 王晗 06 Dec '13

06 Dec '13

Hi, I am making an analysis in freesurfer 5.1 using mkanalysis-sess and I am a bit confused about the flag refeventdur. In the help it is said that it should be set to the event duration if the events have similar durations. But I have two conditions with different durations that one lasts for 1.6 second and another lasts 0.8s in a event-related design paradigm, and my fixation condition lasts for 8 second. What should I set the refeventdur to? How does this value influence the design matrix? Thanks, WangHan

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Fwd: Re: Fwd: Some problems of the brain image after recon-all
by Xiaojun.Huang 06 Dec '13

06 Dec '13

hi all, I am processing the 3D PD patients brain now . After recon-all running, the segmentations of the GM and WM is not accurate although the original data is normal. additionally, when I use the TKSurfer Tools to review the 3D brain,it is reverse. More informations and images as follows: -------- 原始消息 -------- 主题: Re: [Freesurfer] Fwd: Some problems of the brain image after recon-all 日期: Thu, 05 Dec 2013 12:45:10 +0800 发件人: Xiaojun.Huang <lvdosha(a)gmail.com> 收件人: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Hi Bruce, Sorry for reply late. The data were provided by a hospital and the input data were 3D images.Some image informations as followed(eg.PDSub_02): 0008,103E,Series Description=Ax 3D VBM 0008,1090,Manufacturer's Model Name=SIGNA EXCITE 0018,0000,Acquisition Group Length=484 0018,0020,Scanning Sequence=GR 0018,0021,Sequence Variant=SS\SP\SK 0018,0022,Scan Options=FAST.GEMS\EDR.GEMS\FILTERED.GEMS 0018,0023,MR Acquisition Type=3D 0018,0025,Angio Flag=N 0018,0050,Slice Thickness=1 0018,0080,Repetition Time [TR, ms]=7.652 0018,0081,Echo Time [TE, ms]=3.312 0018,0082,Inversion Time=0 0018,0083,Number of Averages=1 0018,0084,Imaging Frequency=127.755675 0018,0085,Imaged Nucleus=1H 0018,0086,Echo Number= 0018,0087,Magnetic Field Strength=3 0018,0088,Spacing Between Slices=1 0018,0091,Echo Train Length=1 0018,0093,Percent Sampling=100 0018,0094,Percent Phase Field View=100 0018,0095,Pixel Bandwidth=97.6562 0018,1020,Software Version=12\LX\MR Software release.12.0.M5A.0819.a 0018,1030,Protocol Name=PDD-YANGWANQUN/4 0018,1310,Acquisition Matrix=0, 256, 228, 0 0018,1312,Phase Encoding Direction=ROW 0018,1314,Flip Angle=13 0018,1315,Variable Flip Angle Flag=N 0028,0010,Rows=512 0028,0011,Columns=512 It comes up in the proper orientation in tkmedit in three orientations as attachment(eg.coromaland saggital view). Tanks, Xiaojun. 于 2013/12/4 22:45, Bruce Fischl 写道: > Hi Xiaojun > > we need more details in order to help you. What was your input data? > What format was it in? Does it come up in the proper orientation in > tkmedit? What kind of acquisition (resolution, type, etc...) did you use? > > cheers > Bruce > On Wed, 4 Dec 2013, Xiaojun.Huang wrote: > >> >> >> >> -------- 原始消息 -------- >> 主题: >> Some problems of the brain image after recon-all >> 日期: >> Tue, 03 Dec 2013 21:33:41 +0800 >> 发件人: >> Xiaojun.Huang <lvdosha(a)gmail.com> >> 收件人: >> Freesurfer(a)nmr.mgh.harvard.edu >> >> >> Hi, >> >> I am processing the 3D PD patients brain now . After recon-all >> running, the segmentations of the GM and WM is not accurate >> although the original data is normal. additionally, when I use the >> TKSurfer Tools to review the 3D brain,it is reverse. (eg. >> PDSub_02 in the attach files) >> >> It is the first time for me to use Freesurfer.I'm sorry for the >> trouble I'm giving you.And looking forward your reply. >> >> Thanks, >> Xiaojun >> >> 2013.12.3 >> >> >> >> >> > > > 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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infant template
by Supreet kaur 06 Dec '13

06 Dec '13

Dear Freesurfer experts, I'm involved in the neonatal research (infants less than 1 year of age). I tried running the recon-all command, however it fails and I get error messages at the Talriach registration step. Is there any way in which I can incorporate our own custom infant atlas or template in place of the Talriach space, which is for adults. I'd really appreciate your help and fedback on this. Thanks in advance, Sincerely, Supreet kaur, Biomedical research engineer, Nationwide Childrens Hospital, Columbus, OH <%28614%29355-3509>

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Freesurfer December 2013