Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Problem with mri_surf2surf
by Jürgen Hänggi 15 Apr '10

15 Apr '10

Dear FS experts I tried to run mri_surf2surf on parcellations produced by mris_divide_parcellation but there is the following problem: [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% mri_surf2surf --srcsubject fsaverage_divide_parc --sval-annot /Application/freesurfer/subjects/fsaverage_divide_parc/label/lh.divide100.an not --trgsubject GCS_con_01 --tval lh.divide100.annot --hemi lh Setting mapmethod to nnf srcsubject = fsaverage_divide_parc srcval = (null) srctype = trgsubject = GCS_con_01 trgval = lh.divide100.annot 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) Reading source surface reg /Applications/freesurfer/subjects/fsaverage_divide_parc/surf/lh.sphere.reg Loading source data Reading surface file /Applications/freesurfer/subjects/fsaverage_divide_parc/surf/lh.orig reading group avg surface area 750 cm^2 from file Reading in average area /Applications/freesurfer/subjects/fsaverage_divide_parc/surf/lh.orig.avg.are a.mgh could not read annot file /Application/freesurfer/subjects/fsaverage_divide_parc/label/lh.divide100.an not No such file or directory [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% When I load the annotation with tksurfer, everthying looks fine. I run the following command to produce the annot file mris_divide_parcellation fsaverage_divide_parc lh aparc.a2005s.annot 100 lh.divide_100 Any idea why mri_surf2surf does not read this parcellation. The annot file was too big to attach. Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ---------------------------------------------------------------------------- ------ Ende der weitergeleiteten Nachricht

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Longitudinal -uselongbasectrlvol
by Lars Tjelta Westlye 15 Apr '10

15 Apr '10

Dear all, I'm encountering the following error in the otherwise excellent longitudinal scheme when adding the -uselongbasectrlvol flag: Command: recon-all -long ${s}_tp1 ${s} -all -uselongbasectrlvol -- #-------------------------------------------- #@# Intensity Normalization Wed Apr 14 18:12:12 CEST 2010 /usit/psi-brain/u1/Felles/labdata/lab-data/intensity/recon/OAS2_0017_MR1.long.OAS2_0017/mri Recompute intensity norm to create OAS2_0017 ctrl_vol.mgz Too many ('s. -- Please confirm that adding \ to the end of line 1093 in recon-all is a valid fix. Thanks, Lars bugr: --------------------------------------------------------------------- FREESURFER_HOME: /psyklab/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 RedHat release: Red Hat Enterprise Linux Client release 5.5 (Tikanga) Kernel info: Linux 2.6.18-164.15.1.el5 x86_64 ---------------------------------------------------------------------

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mris_make_face_parcellation
by Diana Wotruba 15 Apr '10

15 Apr '10

Dear FS experts We used mris_make_face_parcellation to get a finer parcellation of the cortical surface. The labels of the resulting parcellations are consecutively numbered, but there is no information about the anatomical location of these parcellations. In a first step, we would like to know which of the new parcellations are located within a particular brain structure (label), e.g. within the central sulcus as defined in the aparc.a2009s.annot. In a second step, we would like to extract the MNI coordinates of the centroids of these new parcellations. All suggestions are appreciated. Thanks in advance Best regards Diana

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Re: [Freesurfer] PROBLEMS WITH SEGMENTATION
by Leonardo Chesi 15 Apr '10

15 Apr '10

Hi Bruce, thank a lot for your attention. I'll post to you the DICOM header so you will found all the information. We have a GE, Signa 3.0 T with a phased array coil at 8 channel and I haven't any access to other coil. Follow the DICOM header Format: 'DICOM' FormatVersion: 3 Width: 256 Height: 256 BitDepth: 16 ColorType: 'grayscale' FileMetaInformationGroupLength: 200 FileMetaInformationVersion: [2x1 uint8] MediaStorageSOPClassUID: '1.2.840.10008.5.1.4.1.1.4' MediaStorageSOPInstanceUID: '1.2.840.113619.2.244.6945.200562.26819.1268038798.688' TransferSyntaxUID: '1.2.840.10008.1.2.1' ImplementationClassUID: '1.3.6.1.4.1.19291.2.1' ImplementationVersionName: 'OSIRIX001' SourceApplicationEntityTitle: 'OSIRIX' SpecificCharacterSet: 'ISO_IR 100' ImageType: 'ORIGINAL\PRIMARY\OTHER' SOPClassUID: '1.2.840.10008.5.1.4.1.1.4' SOPInstanceUID: '1.2.840.113619.2.244.6945.200562.26819.1268038798.688' StudyDate: '20100308' SeriesDate: '20100308' AcquisitionDate: '20100308' ContentDate: '20100308' StudyTime: '171316.000000' SeriesTime: '173901.000000' AcquisitionTime: '173901.000000' ContentTime: '173901.000000' Modality: 'MR' Manufacturer: 'GE MEDICAL SYSTEMS' InstitutionName: 'Fondazione G Monasterio CNR PIsa' StationName: 'hdx_3t' StudyDescription: 'ANGIO TSA' SeriesDescription: 'SPGR ISOVOXEL' ManufacturerModelName: 'Signa HDxt' ReferencedStudySequence: [1x1 struct] ReferencedPerformedProcedureStepSequence: [1x1 struct] ReferencedImageSequence: [1x1 struct] PatientName: [1x1 struct] PatientID: 'kTEJ0' PatientBirthDate: '20100310' PatientSex: '0000' PatientAge: '036Y' PatientWeight: 0 ScanningSequence: 'GR' SequenceVariant: 'SS\SP\SK' ScanOptions: 'FAST_GEMS\EDR_GEMS\ACC_GEMS' MRAcquisitionType: '3D' AngioFlag: 'N' SliceThickness: 1 RepetitionTime: 10.6760 EchoTime: 4.8640 InversionTime: 450 NumberOfAverages: 1 ImagingFrequency: 127.7624 ImagedNucleus: '1H' EchoNumber: 1 MagneticFieldStrength: 3 SpacingBetweenSlices: 1 EchoTrainLength: 1 PercentSampling: 100 PercentPhaseFieldOfView: 100 PixelBandwidth: 122.1090 DeviceSerialNumber: '000000000000GEHC' SoftwareVersion: '15\LX\MR Software release:15.0_M4_0910.a' ProtocolName: 'ENCEFALO ROUTINE/12' HeartRate: 0 CardiacNumberOfImages: 0 TriggerWindow: 0 ReconstructionDiameter: 256 ReceiveCoilName: 'HDNV Head' AcquisitionMatrix: [4x1 uint16] InPlanePhaseEncodingDirection: 'ROW' FlipAngle: 13 VariableFlipAngleFlag: 'N' SAR: 0.4075 PatientPosition: 'HFS' StudyInstanceUID: '1.3.6.1.4.1.19291.2.1.1.2899125572002100004' SeriesInstanceUID: '1.2.840.113619.2.244.6945.200562.27402.1268038650.858' StudyID: '218' SeriesNumber: 7 AcquisitionNumber: 1 InstanceNumber: 1 ImagePositionPatient: [3x1 double] ImageOrientationPatient: [6x1 double] FrameOfReferenceUID: '1.2.840.113619.2.244.6945.200562.27402.1268038650.844' ImagesInAcquisition: 162 SliceLocation: 97.5057 StackID: '1' InStackPositionNumber: 3 SamplesPerPixel: 1 PhotometricInterpretation: 'MONOCHROME2' Rows: 256 Columns: 256 PixelSpacing: [2x1 double] BitsAllocated: 16 BitsStored: 16 HighBit: 15 PixelRepresentation: 1 SmallestImagePixelValue: 0 LargestImagePixelValue: 900 WindowCenter: 450 WindowWidth: 900 PerformedProcedureStepID: 'MR1268068762' PerformedProcedureStepDescription: 'ANGIO TSA' I attend your reply. Thanks a lot LEONARDO

1 0

displaying time course for blocked-design
by Yuhong Jiang 14 Apr '10

14 Apr '10

Dear Freesurfer users, Is there a way to display time course information for blocked-design experiments? I have used the command tkmedit-sess, which displays time course information for event-related designs. However, it does not display anything like that for blocked design. Is it possible to change mkanalysis-sess.new to fool the program in thinking that the blocked-design experiments are event-related, and is that the right thing to do? Also, when displaying activation using surf-sess for event-related design experiments, which time point is painted on the surface? Is it 6-sec after the event onset? Is there a way to specify that? Thanks. -Yuhong

1 0

3d slicer view only the post-central gyros
by asaf achiron 14 Apr '10

14 Apr '10

hello, How can i use 3d slicer to only view the post-central gyros without the other areas, than you Asaf

1 0

Problem with tkmedit Edit Voxels Tool on Intel Mac
by Ed Gronenschild 14 Apr '10

14 Apr '10

Hi, On an Intel Mac the Edit Voxels Tool does not work, contrary to a PPC Mac. This applies both to version v4.3.1 and v4.5.0. Ed

2 2

PROBLEMS WITH SEGMENTATION
by chesi.leonardo＠alice.it 14 Apr '10

14 Apr '10

Hi, I'm Leonardo an italian student of Pisa. I'm writing to you to ask if there's any way to correct this problem: we have a 3.0T machine with a 8 channels head coil to acquire the volumetric image. we have found a big inhomogeneity in the contrast of the image particularly in the frontal lobe where, so we think, the head is influenced by a inhomogeneity of the B0. I'm going to ask to you if there's any normalization way of this image because when I execute the recon-all command I foud many segmentation errors in this zone. Thaks for your help Greetings Leonardo

2 1

recon-all with nifti
by Christophe Chênes 14 Apr '10

14 Apr '10

Hi, I'd like to launch recon-all with a nifti input file and get a nifti file in output... Do you know how can I do that? Thanks in advance! Chris'

2 1

Which way is better for mapping automatic segmentations
by liang wang 14 Apr '10

14 Apr '10

Hi FSusers, I am engaging to map automatic segmentation image (eg. aparc.a2009s+aseg.mgz) to raw functional space. According to the instructions from the FreeSurfer website, I found that there were two ways below to do it. However, the results from both methods are different and attached. Let me say BNC006 is a subject under $SUBJECTS_DIR (here /drive3/TEST). The functional data has been processed using FSL and found in bold.feat directory. *# one way* (red images in the attached picture) $ bbregister --mov example_func.nii.gz --bold --s BNC006 --init-fsl --reg register.dat $ mri_label2vol --seg BNC006/mri/aparc.a2009s+aseg.mgz --temp example_func.nii.gz --reg register.dat --fillthresh 0.5 --o BNC006 .aseg-in-fun.nii.gz *# anther way* (blue images in the attached picture) $ reg-feat2anat --feat /drive3/TEST/BOLD/bold.feat --subject BNC006 $ aseg2feat --feat /drive3/TEST/BOLD/bold.feat --aseg aparc.a2009s+aseg cd /drive3/TEST/BOLD/bold.feat/reg/freesurfer *BNC006 .aseg-in-fun.nii.gz* and *aparc.a2009s+aseg.nii.gz* are outputs from the first and second one, respectively. Does anyone give me some suggestion about which method is suitable to my situation. Best, Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

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