Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] propagating labels to gray matter
by Douglas N Greve 02 Nov '11

02 Nov '11

Hi David, an easy way is to load the segmentation as both a segmentation and as the auxiliary volume (not aux segmentation). When you click on a point, you'll see the number of the segmentation in the aux field of the control window. doug David Grayson wrote: > Hi Doug, > > I made good progress based on your suggestion of using mri_aparc2aseg. The last piece is that I need to understand what the index values of my output volume file correspond to. Here's the command I used: > > mri_aparc2aseg --s subID --annot myaparc --o TEST.nii.gz > > Although I did notice that the index values in TEST.nii.gz for the cortical ROIs in the RH are just above 2000, and just above 1000 for the LH, the values don't seem to match the labels in FreeSurferColorLUT.txt. Then again, that makes sense, because this is a custom label set, so they don't really exist in FreeSurferColorLUT.txt. > > How can I learn more about how the index values are being assigned? > > Thanks very much for your help, > > David > > P.S. I don't know if it will work, but I attached the aparc and volume files if it's necessary for you to look that those > > -----Original Message----- > From: Douglas Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Monday, October 31, 2011 7:40 PM > To: David Grayson > Cc: 'freesurfer(a)nmr.mgh.harvard.edu' > Subject: Re: [Freesurfer] propagating labels to gray matter > > Hi David, you can use mri_label2vol with the --proj option. This works > ok, but it is often not great. Another way (the way that aparc+aseg) is > created is to convert your label into an annotation, then use > mri_aparc2aseg. > > doug > > On 10/31/11 7:22 PM, David Grayson wrote: > >> Hi Doug, >> >> Although in principle, yes this is the idea, we have a set of labels that aren't actually in the aparc+aseg file (basically a set of high-density subdivisions of those regions). The only problem is that the labels I have are just in "surface-land." I am wondering, once I have the surface labels, is there a way to re-propagate them back into the gray matter? >> >> Thanks again, >> >> David >> >> -----Original Message----- >> From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] >> Sent: Monday, October 31, 2011 2:38 PM >> To: David Grayson >> Cc: 'freesurfer(a)nmr.mgh.harvard.edu' >> Subject: Re: [Freesurfer] propagating labels to gray matter >> >> Do you just want the label in the orig volume space? If so, just use the >> labels in aparc+aseg.mgz >> doug >> >> David Grayson wrote: >> >>> Hi Doug, >>> >>> /path/to/FREESURFER/label/regenerated_lh_36$ mri_label2vol --label lh.bankssts.label --temp ../../mri/orig.mgz --identity --o TEST.nii.gz >>> >>> Thanks, >>> >>> David >>> >>> -----Original Message----- >>> From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] >>> Sent: Monday, October 31, 2011 2:04 PM >>> To: David Grayson >>> Cc: 'freesurfer(a)nmr.mgh.harvard.edu' >>> Subject: Re: [Freesurfer] propagating labels to gray matter >>> >>> what was your label2vol command line? >>> doug >>> >>> David Grayson wrote: >>> >>> >>>> Hi freesurfer experts, >>>> >>>> >>>> >>>> I currently have a set of cortical labels that are the result of a >>>> high-resolution parcellation of the standard aparc.annot labels (via >>>> the ‘connectomemapper’ software). I would like to extract the gray >>>> matter ROIs that correspond to these labels, and I understand that >>>> this requires a method to ‘propagate’ these labels through the gray >>>> matter. I have so far been unsuccessful – ‘mri_label2vol’ seems to >>>> only give me that pial or white surfaces, as opposed to the gray >>>> matter bodies. Does anyone know how to accomplish this? >>>> >>>> >>>> >>>> Thank you very much, >>>> >>>> >>>> >>>> David Grayson >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> 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. > -- 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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pial area surface - correcting for size of brain
by Tetiana Dadakova 02 Nov '11

02 Nov '11

Dear FreeSurfer experts, I have a question regarding pial area analysis. What is commonly used as a nuisance variable to correct for brain size difference between groups (e.g men vs women)? Can you suggest any article where this is discussed or has been done? Thank you, Tanja.

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surface normals
by Oya, Hiroyuki (UI Health Care) 01 Nov '11

01 Nov '11

Dear Sir, Can the surface normals be loaded in matlab? Is there a code for that and what variable should I look at in surf dir? Thank you. HIroyuki ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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VGL error
by Jason Tourville 01 Nov '11

01 Nov '11

Hello FreeSurferers, I run tksurfer remotely from a linux machine running CentOS (Boston University) using Virtual GL/TurboVNC. I have been able to do this successfully for years but have recently encountered the following error when calling tksurfer: surfer: tkoInitWindow(RMAUT015) [VGL] ERROR: OpenGL error 0x0502 [VGL} ERROR: in readpixels - - [VGL] 624: Could not Read Pixels The error occurs after the tksurfer image window is started but before a brain surface is displayed. I have confirmed that the error does not depend upon what ssh tunneling tool I am using nor on what time of machine I am using locally. Does anyone have experience with this problem? Suggested solutions? Cheers, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-6181 Fax: (617)353-7755

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Topology correction - segmentation fault
by Sindhuja Tirumalai Govindarajan 01 Nov '11

01 Nov '11

Hi all, I got the following error while running recon-all on a patient dataset. Kindly let me know how to proceed. Thanks! Sindhuja Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 13 iterations marking ambiguous vertices... 129422 ambiguous faces found in tessellation segmenting defects... 51 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 0 -merging segment 2 into 0 -merging segment 8 into 0 -merging segment 5 into 7 -merging segment 28 into 12 -merging segment 35 into 31 -merging segment 47 into 43 44 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/mscat/users/caterina/3T/recons-04082011/MS_pt20_recon/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5482 (-4.7741) -vertex loglikelihood: -6.9824 (-3.4912) -normal dot loglikelihood: -3.5307 (-3.5307) -quad curv loglikelihood: -5.9945 (-2.9973) Total Loglikelihood : -26.0558 CORRECTING DEFECT 0 (vertices=50712, convex hull=8198) Segmentation fault recon-all -s MS_pt20_recon exited with ERRORS at Wed Oct 26 18:49:31 EDT 2011

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recon-all error
by Chindhuri Selvadurai 01 Nov '11

01 Nov '11

Hello, I am having trouble doing a recon-all of my data. pbsubmit -m chinsel -c 'recon-all -s DODASD001 -all -i /cluster/archive/295/siemens/TrioTim-35006-20111026-155248-065000/364000-000015-000001.dcm -mail chinsel(a)nmr.mgh.harvard.edu' Here is the error: ERROR: no run data found in /autofs/cluster/manoach/dod/subjects/DODASD001/mri. Make sure to have a volume called 001.mgz in /autofs/cluster/manoach/dod/subjects/DODASD001/mri/orig. If you have a second run of data call it 002.mgz, etc. I usually do the recon all through launchpad first before any other preprocessing, and hadn't had a problem before? Not sure why this is the case this time. What step should be done before this to get the data in the mri? My subjects_dir is /cluster/manoach/dod/subjects Thanks so much!

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Hippocampal Sub-Field Segmentation -Appropriate Scan Protocol to Use
by Joshua Lee 01 Nov '11

01 Nov '11

Dear Experts, I've been collecting hi-res hippocampal scans with a 32 ch coil on a 3T Siemens Trio to manually segment hippocampal subfields. However, I wonder whether the protocol is appropriate for use with the new Freesurfer subfield segmentation tool. Specifically, our hi-res scan does not capture the entire brain, rather it acquires slices perpendicular to the long axis just for the length of the long axis axis. Can this scan be used for the new subfield auto-segmentation? Or does it require a whole-brain acquisition? We do acquire a 1 mm isotropic whole brain MPRage, but... Thanks for any info, Joshua

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Fwd: Position available: Postdoc in System and Cognitive Neuroscience - Beijing Normal University, China
by Zhen Zonglei 31 Oct '11

31 Oct '11

---------- Forwarded message ---------- From: Zhen Zonglei <zonglei.fsl(a)gmail.com> Date: Tue, Nov 1, 2011 at 11:13 AM Subject: Position available: Postdoc in System and Cognitive Neuroscience - Beijing Normal University, China To: FSL - FMRIB's Software Library <FSL(a)jiscmail.ac.uk> Postdoctoral positions are available to study the neural mechanisms of visual perception and cognition in the State Key Laboratory of Cognitive Neuroscience and Learning (SKLCNL), Beijing Normal University, Beijing, China. The SKLCNL (http://psychbrain.bnu.edu.cn) is one of the most influential institutes for brain research in China. The institute receives ample annual funding from multiple sources, including the Ministry of Science and Technology and the Ministry of Education of China; it also offers state-of-the-art research facilities incorporating new technologies, such as behavioral and molecular genetics, 3T fMRI, multielectrode recordings in awake behaving monkeys, optical imaging, TMS and EEG. Well-established PIs recruited overseas form a multidisciplinary research team covering the fields of cognitive neuroscience, psychology, neurobiology, computational neuroscience, information sciences and education. Dr. Jia Liu (http://psychbrain.bnu.edu.cn/teachcms/liujia.htm) studies the neural mechanism of object recognition and its heritability and experience dependency using multiple approaches such as psychophysics, fMRI and behavioral and molecular genetics. Dr. Wu Li ( http://psychbrain.bnu.edu.cn/teachcms/liwu.htm) studies intermediate-level visual processing, including top-down modulation and perceptual learning, in both humans and behaving monkeys. Candidates should have a doctoral degree related to neuroscience (including cognitive neuroscience and computational neuroscience) or psychology, and should have the ability to design and conduct experiments independently as well as to analyze fMRI or electrophysiological data. Strong computer skills including programming (MATLAB, Python, and C) are preferred. The SKLCNL offers competitive salaries depending on candidates’ previous training and experiences. If interested, please send a cover letter, a cv, a summary describing research accomplishments and interests, and the names and addresses of three references to Dr. Jia Liu (liujia(a)bnu.edu.cn) or Dr. Wu Li ( liwu(a)bnu.edu.cn) Zonglei Zhen

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files in surf and label subfolders in a subject's folder
by Forrest Sheng Bao 31 Oct '11

31 Oct '11

hi, I wonder whether there is a document describing files in surf and label subfolders in a subject's folder. I wanna know what kind of information is stored in each of those files. Cheers, Forrest

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internal capsule
by Vaidya, Jatin G 31 Oct '11

31 Oct '11

Hi, We recently processed some T1 data through Freesurfer but I did not see any labels for the internal capsule. Does Freesurfer still create a label for this region? Thanks, Jatin ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ________________________________

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