Freesurfer April 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
147 discussions

recon-all error: _FindFacePath
by muet0005＠umn.edu 17 Apr '10

17 Apr '10

Hello, I am getting the following error in the $subjid/scripts/recon-all.log: ERROR: _FindFacePath: could not find path! Linux blade279 2.6.5-7.322-smp #1 SMP Mon Feb 8 09:14:05 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Apr 16 08:23:35 CDT 2010 The recon-all-status.log shows the process ended prematurely here: #@# Fix Topology lh Fri Apr 16 04:28:28 CDT 2010 Linux blade279 2.6.5-7.322-smp #1 SMP Mon Feb 8 09:14:05 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Apr 16 08:23:35 CDT 2010 I've tried running recon-all on this subject two separate times from scratch, getting the same result (thinking perhaps the first time was a random error with our system/software). The image is of good quality --- little motion, good contrast. The brainmask.mgz and aseg.mgz look OK. The inflated surface is very rough (lots of "spikes" coming out of it), but I am not sure if that is just because of how early on in the processing this is. I saw a post related to this from 2008 (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13371.html) but I am not sure if the problem for that user was resolved? Let me know if you have any ideas/suggestions for us to try! Best, Ryan Cut-and-paste the following info into your FreeSurfer problem report: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer/freesurfer-binary-distribution/freesurfer-centos4_x86_64-stable-pub-v4.5.0/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Kernel info: Linux 2.6.5-7.322-smp x86_64 ---------------------------------------------------------------------

2 1

QDEC question about covariates
by Manabu Kubota 17 Apr '10

17 Apr '10

Dear FreeSurfer experts, Hello, I started to use FreeSurfer recently. I want to do group analysis with QDEC in order to compare 2 groups (control group and patient group), regressing out age and gender. When I include 2 discrete factors (diagnosis and gender) and 1 continuous factor (age), and run QDEC, there appear a question of "Does the average thickness, accounting for Gender, differ between Controls and Patients?", but there NOT appear a question of "Does the average thickness, accounting for Gender *AND AGE*, differ between Controls and Patients?". So, it seems that age cannot be regressed out in this way. However, when I include 1 discrete factor (gender only) and 2 continuous factors (age and also diagnosis *dummy parameterized: Controls = 1, Patients = 0*), and run QDEC, there appear a question of "Does the correlation between thickness and Diagnois, accounting for Age and Gender, differ from zero?", and the result seems OK. My question is; 1) Is it right to do the (above-mentioned) latter way to compare difference of thickness between the 2 groups, regressing out age and gender? 2) Why couldn't age regressed out in the former way? 3) In this way, generally is it OK if I enter simple "discrete" factor as a continuous factor in QDEC (for example, gender:male=1, female=0)? This time I want to ask, since I couldn't find an answer in the past archives. Thanks a lot, Manabu Kubota kubotajp(a)kuhp.kyoto-u.ac.jp Graduate School of Medicine, Kyoto University

1 0

Reference for Insula delineation in standard parcellation
by Laluz, Victor 16 Apr '10

16 Apr '10

Hello Freesurfer-ers, I tried to look up a reference for the delineation of the insula label in the standard parcellation and came up empty. Does anyone have a published article, or some form of citation that explains how Freesurfer defines the insula? This is in reference to the insula label starting in version 4.3.0 (I believe). Thanks, Victor

2 1

Multi-echo MPRAGE on GE 3T?
by Kippenhan, Shane (NIH/NIMH) [C] 16 Apr '10

16 Apr '10

Dear FreeSurfers, Does anyone know if a GE implementation of MEMPR (as described in van der Kouwe et all '08) exists anywhere? Thanks, Shane Kippenhan --------------------------------------------------------------- J. Shane Kippenhan, Ph.D. Contractor Imaging Scientist Section on Integrative Neuroimaging CBDB/GCAPP/NIMH/NIH Voice 301 496 9656 Fax 301 496 7437 ----------------------------------------------------------------

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selxavg3-sess error "design is ill-conditioned"
by Ben Letham 15 Apr '10

15 Apr '10

Hello, I'm trying to run selxavg3-sess for an analysis with TER < TR, and it errors with "design is ill-conditioned". I searched the mailing list archive, and the only past problem of this sort that I found was associated with a faulty tpef file, which I am not using. The details: There is only one run. TR is 1.2s, and stimuli were presented at intervals of 1/3 TR (0.4s) (the desired TER). The paradigm file reflects this, it is of the form: 0 0 0.4 1 0.8 0 1.2 2 1.6 1 2 0 I loaded it into matlab and verified that the time points all have a difference of 0.4s. The analysis is, mkanalysis-sess -analysis analysis_name -TR 1.2 -TER 0.4 -paradigm 03TR.par -designtype event-related -nconditions 2 -timewindow 19.2 -prestim 2.4 -mcextreg -funcstem fmcstcsm6 -polyfit 2 -runlistfile runlist_03TR -noautostimdur -force I define two contrasts, mkcontrast_sess -analysis analysis_name -rmprestim -contrast AV-REST -a 1 -c 0 mkcontrast_sess -analysis analysis_name -rmprestim -contrast AVT-REST -a 2 -c 0 And then selxavg3-sess, selxavg3-sess -analysis analysis_name -sf subjectname -df sessdir -overwrite And this errors. Like I said, the only thing I found in the mailing list was a problem with tpef, and so I left it out altogether (as above), and the problem persists. If I change TER to equal TR (1.2), then it works. So the problem has something to do with TER being less than TR. Perhaps something in the par file then? I checked it in matlab, and diff(par(:,1)) = 0.4 for all of the events. Any thoughts would be very appreciated! Ben.

2 3

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

2 1

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 ---------------------------------------------------------------------

2 1

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

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Freesurfer April 2010