Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

registering subject pial to fsaverage
by Trisanna Sprung-Much 21 Jul '16

21 Jul '16

Hi there I tested registering a subject's pial surface to fsaverage and compared the original pial (from recon-all) with this registered pial surface. It turns out that they are almost identical in nature, and I am wondering how this is possible if recon-all does not alter the input data. Below is the command that I ran. Is there something I am missing here? many thanks Trisanna trisanna@kaplan:~$ mri_surf2surf --srcsubject icbm-102 --sval-xyz pial --trgsubject fsaverage --tval-xyz --tval lh.pial.icbm102 --hemi lh srcsubject = icbm-102 srcval = (null) srctype = trgsubject = fsaverage trgval = lh.pial.icbm102 trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /data-01/trisanna/freesurfer/icbm-102/surf/lh.sphere.reg Loading source data Reading surface file /data-01/trisanna/freesurfer/icbm-102/surf/lh.pial Reading target surface reg /data-01/trisanna/freesurfer/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (169941) Reverse Loop had 44416 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 131435, nTrgMulti = 32407, MnTrgMultiHits = 2.37057 nSrc121 = 140014, nSrcLost = 0, nSrcMulti = 29927, MnSrcMultiHits = 2.28035 Saving target data -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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'Cerebral Exterior' label in Freeview but not tkmedit
by Uquillas, Federico D'Oleire 21 Jul '16

21 Jul '16

Dear FreeSurfer community, Despite tkmedit being discontinued, I am still using this to make surface edits to my T1s. The main reason is that when I use Freeview and erase skull/dura, Freeview creates this blue label wherever I erase outside of the brain surface. The label is called left (or right) ‘-Cerebral-Exterior’. If I edit in tkmedit, this label is not created. I fear that this label may cause problems if the list of labels in FreeSurfer (particularly 5.1) does not contain this ‘Cerebral Exterior’ label. I suppose this has been addressed in the more recent developments, and theoretically if I use FreeSurfer 6 to process and Freeview to edit then this wouldn’t be a concern. Wondering if anyone has encountered this, and whether it was a problem or not for you. Thank you so much as always for any thoughts or recommendations you may be able to provide. Best, Fred

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Subtracting overlays
by Granberg, Erik Tobias 21 Jul '16

21 Jul '16

Hi, Is there a way to subtract one surface overlay from another (for example in fsaverage) and still having the output being an .mgh overlay file? I saw that mis_calc does a similar procedure but automatically outputs the result as out.mgz. Thank you for the help! Kind regards, Tobias _________________________________________ Tobias Granberg, MD, PhD Post-doctoral research fellow A.A. Martinos Center for Biomedical Imaging Massachusetts General Hospital | Harvard Medical School Resident in Radiology Karolinska Institutet | Department of Clinical Science, Intervention and Technology Karolinska University Hospital | Department of Radiology

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mri_convert : ERROR: cannot unpack mosiacs without ASCII header
by Koubiyr, Ismail 21 Jul '16

21 Jul '16

Hi everyone, I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. I looked for other topics with people having the same kind of problem but couldn’t find an answer. Each time I run mri_convert on my DICOMs I get the following error : WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header Here are the following DICOMs informations : Identification NumarisVer syngo MR D13 ScannerModel Skyra PatientName xxxxx Date and time StudyDate 20140918 StudyTime 121037.203000 SeriesTime 123450.600000 AcqTime 123257.367500 Acquisition parameters PulseSeq ep_b0 Protocol AX DTI no angle MS NEX 4 2 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 96 InversionTime -1 RepetitionTime 4700 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 990 NImageCols 990 NFrames 64 SliceArraylSize 0 IsMosaic 1 ImgPos 1075.1575 1069.8385 -48.6769 VolRes 2.1818 2.1818 2.0000 VolDim 0 0 0 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 Then I try using mri_convert -it dicom, it converts the files but not as it is expected, you could notice the difference when I run mri_info on my output : Volume information for output.nii.gz type: nii dimensions: 990 x 990 x 1 x 64 voxel sizes: 2.1818, 2.1818, 2.0000 type: SHORT (4) fov: 2160.000 dof: 0 xstart: -1080.0, xend: 1080.0 ystart: -1080.0, yend: 1080.0 zstart: -1.0, zend: 1.0 TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 64 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -4.8425 : x_a = -0.0000, y_a = -1.0000, z_a = -0.0000, c_a = -10.1615 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -47.6769 Orientation : LPS Primary Slice Direction: axial voxel to ras transform: -2.1818 -0.0000 -0.0000 1075.1575 -0.0000 -2.1818 -0.0000 1069.8385 0.0000 0.0000 2.0000 -48.6769 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 9.52066 ras to voxel transform: -0.4583 0.0000 0.0000 492.7805 0.0000 -0.4583 0.0000 490.3426 -0.0000 -0.0000 0.5000 24.3384 0.0000 0.0000 0.0000 1.0000 I would really appreciate your help, thank you. Best, Ismail

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Freesurfer build stamps do not match
by Lee Subin Kristine 21 Jul '16

21 Jul '16

Hi FreeSurfer Team, After I have downloaded the FreeSurfer dev version, I get the following error whenever I use the recon-all comand: mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied mkdir: cannot create directory '/usr/local/freesurfer/subjects/NYS': Permission denied cp: cannot create regular file '/usr/local/freesurfer/subjects/NYS/scripts/build-stamp.txt': No such file or directory cat: /usr/local/freesurfer/subjects/NYS/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6 /usr/local/freesurfer/subjects/NYS/scripts/patchdir.txt: No such file or directory. recon-all used to work fine when I used the stable 5.3 version. I think it may have something to do with the fact that I previously ran recon-all in v.5.3, and so the current subject directory's stamp is still 5.3 (or blank..) and it does not match the current stamp of the dev version? I am not sure.. Could anyone tell me how I can fix this problem? Thanks in advance, Subin

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Combined parcellation of the left and right hemispheres
by varshas＠cns.iisc.ernet.in 21 Jul '16

21 Jul '16

Hi, I've been working on getting a finer parcellation of the Desikan-Killiany atlas using mris_divide_parcellation. I was able to generate two annotation files; one each for the left and right hemisphere. I want to create a volume similar to aparc+aseg.mgz, containing the labels and indices of the ROIs from both hemispheres. I tried using mri_label2vol. However, this gives me two separate volumes for the left and right hemispheres. Is there a way to combine these volumes into one? Alternatively, can one generate such a volume form an annotation file that has information of both hemispheres? Any help is greatly appreciated! Regards, Varsha

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tkmedit issue - image too bright in tkmedit after running gcut
by Uquillas, Federico D'Oleire 20 Jul '16

20 Jul '16

Hi fellow FreeSurfer users, I just did a gcut procedure and now that I'm opening it up again to check out how it went the brain is so bright I can't see white matter and gray matter contrast. Anybody ever experience this before? I tried exiting the terminal, and opening it again, but that doesn't do the trick. I'm opening up the image in tkmedit. If I use Freeview, the image looks fine and is not super bright as when I open it up in tkmedit. Not sure what is going on. Any thoughts? Best, Fred

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Beta-Zero Correction - No Phase File
by Afzal, Afsana 20 Jul '16

20 Jul '16

Hi, I'm working with a dataset that outputs only one file (not two separate mag and phase files) for the fieldmap. The data was also collected on non-Siemens scanners: Philips Ingenia and GE SIGNA HDx (not sure if this is the reason the fieldmaps are unpacking differently). I've attached the .dat file for one of the fieldmaps in this email. If there a way to separate out the mag and phase from the single fieldmap file so I can use epidewarp.fsl? Thanks, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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Re: [Freesurfer] Fwd: question about voxel size
by Dorsa Haji Ghaffari 20 Jul '16

20 Jul '16

Hi Bruce, that is a 3TS T1 weighted image and is taken after the patients have taken the contrast medium. I have played with the intensities in Analyze and this is the best I could get. Do you have any suggestions for getting better contrast? Thank you Dorsa On Tue, Jul 19, 2016 at 4:29 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > also, please post to the list so that others can answer! > thanks > Bruce > On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: > > Here it is. Also can you explain why the algorithm works best with 1mm^3 >> voxel size? >> >> Thank you! >> >> >> >> >> >> >> > > 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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Fwd: Connectome Research Coordinator (Senior), University of Pennsylvania
by Jeff Phillips 20 Jul '16

20 Jul '16

Dear colleagues, The Penn Frontotemporal Degeneration Center at the University of Pennsylvania (http://ftd.med.upenn.edu/) is seeking a research coordinator for the multi-site FTD Connectome study. Please see the details below; applications should be directed to http://jobs.hr.upenn.edu/postings/18756. Thanks, Jeff Phillips Postdoctoral Fellow Penn FTD Center University of Pennsylvania Duties: The primary responsibility of the successful candidate will be the coordination of a multi-site consortium using a novel approach to neuroimaging of neurodegenerative diseases. The lead site is Penn, and participating sites include Mayo Clinic, UCSF, MGH and Northwestern. All sites have specialized neuroimaging equipment, and we will be using advanced neuroimaging tools developed locally and in collaboration with the Human Connectome Project (HCP) to analyze the acquired data. The successful candidate also will be responsible for managing the Penn site. This project is coordinated with two other multi-site registries involving these same sites that are recruiting participants for this neuroimaging project (and other studies). Participants will include: 1. healthy control subjects; 2. individuals who have a frontotemporal degeneration (FTD) spectrum disorder such as primary progressive aphasia, progressive supranuclear palsy, or FTD with amyotrophic lateral sclerosis; and 3. individuals who are carrying a mutation that has resulted in an FTD spectrum disorder or are at risk for developing a FTD-spectrum disorder. Coordination will include weekly meetings with project coordinators at the other participating sites, developing reports for monthly meetings with NIH and principal investigators at other sites, monitoring imaging data flow to our coordinating site, monitoring the database that tracks participants, monitoring data flow from Penn to the HCP coordinating center, and managing requests for data from investigators. Other administrative responsibilities will include help managing the consortium budget. Local site responsibilities will include assistance with on-going recruitment processes, helping to collect imaging data, managing the local budget, supervising local technical and research staff, and participating in imaging analyses. Also included are implementation of Connectome imaging analysis and operation of the Prisma MRI scanner. Position is contingent on continued funding. Qualifications: A Bachelor’s degree and to 3 to 5 years of experience, or equivalent combination of education and experience, are required. Masters degree or PhD in neuroscience, psychology, linguistics, biology, biomedical engineering or related fields and 2 years to 3 years of experience strongly preferred. Past research and project coordination experience working in a similar lab setting is highly desirable. Experience with the following is preferred: Linux/Unix, brain imaging data analysis, MATLAB, computer programming, statistical analysis, research project management, or neuropsychological assessment. The candidate must be able to work independently and have strong organizational and interpersonal skills. Apply at http://jobs.hr.upenn.edu/postings/18756

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Freesurfer