Freesurfer July 2011

freesurfer@nmr.mgh.harvard.edu

129 participants
195 discussions

Nipype 0.4 release
by Chris Filo Gorgolewski 11 Jul '11

11 Jul '11

Dear all, I am delighted to announce release of Nipype version 0.4. Nipype, an open-source, community-developed initiative under the umbrella of NiPy, is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL, FreeSurfer, Camino, AFNI, Slicer), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems. This release brings plenty of improvements. Among the most important are: new modular executions system (direct support for PBS, SGE, and multi-processing), support for Camino, Camino2Trackvis and Connectome Viewer, improved parallel performance of MapNode, and growing collection of ready to use pipelines (have a look at nipype.workflows). Grab it from https://github.com/nipy/nipype/tarball/0.4 For support please use our mailing list: nipy-users(a)googlegroups.com Full changelog: * API: Timestamp hashing does not use ctime anymore. Please update your hashes by running workflows with updatehash=True option NOTE: THIS IS THE DEFAULT CONFIG NOW, so unless you updatehash, workflows will rerun * API: Workflow run function no longer supports (inseries, createdirsonly). Functions used in connect string must be pickleable * API: SPM EstimateContrast: ignore_derivs replaced by use_derivs * API: All interfaces: added new config option ignore_exception * API: SpecifModel no longer supports (concatenate_runs, output_specs). high_pass_filter cutoff is mandatory (even if its set to np.inf). Additional interfaces SpecifySPMModel and SpecifySparseModel support other types of data. * API: fsl.DTIFit input "save" is now called "save_tensor" * API: All inputs of IdentityInterfaces are mandatory by default. You can turn this off by specifying mandatory_inputs=False to the constructor. * API: fsl FILMGLS input "autocorr_estimate" is now called "autocorr_estimate_only" * API: fsl ContrastMgr now requires access to specific files (no longer accepts the result directory) * API: freesurfer.GLMFit input "surf" is now a boolean with three corresponding inputs -- subject_id, hemi, and surf_geo * ENH: All commandline interfaces display stdout and stderr * ENH: All interfaces raise exceptions on error with an option to suppress * ENH: Supports a plugin interface for execution (current support for multiprocessing, IPython, SGE, PBS) * ENH: MapNode runs in parallel under IPython, SGE, MultiProc, PBS * ENH: Optionally allows keeping only required outputs * ENH: New interface: utility.Rename to change the name of files, optionally using python string-formatting with inputs or regular expressions matching * ENH: New interface: freesurfer.ApplyMask (mri_mask) * ENH: New FSL interface -- SwapDimensions (fslswapdim) * ENH: Sparse models allow regressor scaling and temporal derivatives * ENH: Added support for the component parts of FSL's TBSS workflow (TBSSSkeleton and DistanceMap) * ENH: dcm2nii interface exposes bvals, bvecs, reoriented and cropped images * ENH: Added several higher-level interfaces to the fslmaths command: - ChangeDataType, Threshold, MeanImage, IsotropicSmooth, ApplyMask, TemporalFilter DilateImage, ErodeImage, SpatialFilter, UnaryMaths, BinaryMaths, MultiImageMaths * ENH: added support for networx 1.4 and improved iterable expansion * ENH: Replaced BEDPOSTX and EddyCurrent with nipype pipelines * ENH: Ability to create a hierarchical dot file * ENH: Improved debugging information for rerunning nodes * ENH: Added 'stop_on_first_rerun' option * ENH: Added support for Camino * ENH: Added support for Camino2Trackvis * ENH: Added support for Connectome Viewer * BF: dcm2nii interface handles gzipped files correctly * BF: FNIRT generates proper outputs * BF: fsl.DTIFit now properly collects tensor volume * BF: updatehash now removes old result hash file Enjoy! Chris Gorgolewski on behalf of Team Nipype ( https://www.ohloh.net/p/nipype/contributors )

1 0

V1 dimensions
by Ritobrato Datta 11 Jul '11

11 Jul '11

Hello All, Is there a way to calculate the length and breadth of V1 in mm defined by the Fischl method ? How do I do it ? Thanks Ri

1 0

interpolation during conform step of oblique acquisitions
by Michael Harms 11 Jul '11

11 Jul '11

Hi guys, I'm curious why the conform step of mri_convert (in generating mri/orig.mgz) automatically interpolates oblique acquisitions. Is this a historical legacy? Something mandated by other elements of the FS pipeline? As a consequence of this behavior, if you have an oblique acquisition that was intentionally aligned to the actual anatomy of a given subject's brain (e.g., using AutoAlign to generate a AC-PC aligned acquisition), unless one manually alters the qform in the input NIFTI file to remove the "oblique" components of the xform, there will be an interpolation in the generation of the mri/orig.mgz, which brings with it blurring (i.e., the same sort of concerns that prompt one to use a single MPRAGE, rather than the average of two MPRAGEs) Just curious... thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

2 2

Brain Volume in FreeSurfer5.1
by Justin Eisenberg 11 Jul '11

11 Jul '11

Hi Fellow FreeSurfers, How do you calculate Brain Volume in FS5.1? In 4.5 there was the BrainSegNotVent statistic in aseg.stats, but I'm not seeing that in 5.1. I did find something about the SupraTentorialVol, but that would exclude the brainstem and cerebellum. I'm not sure if that also includes the ventricles, but that would need to be factored in as well. I did some math to compare values between 4.5 and 5.1. I took the SupraTentorialVol from 5.1, added Left-Cerebellum-White-Matter, Left-Cerebellum-Cortex, Right-Cerebellum-White-Matter, Right-Cerebellum-Cortex, and Brain-Stem. I then subtracted out the ventricles (Left/Right-Lateral-Ventricle, Left/Right-Inf-Lat-Vent, 3rd/4th/5th-Ventricle). The end result of my 5.1 volume is 51,429 voxels larger than the value from 4.5. Thanks in advance Justin -- Justin Eisenberg Candidate for B.A. in Biology | 2013 Washington University in St. Louis JEisenberg(a)wustl.edu 262.914.4648

1 0

fscalc size mismatch error
by Corinna Bauer 11 Jul '11

11 Jul '11

When running fscalc, I get the following error on some of my subjects but not all of them, mris_calc: Sorry, but I seem to have encountered an error. While checking on input filetype sizes, I found a size mismatch, i.e. len(input1)!=len(input2) Any suggestions? Thanks, Corinna

3 4

save label after expand boundary of region
by Keefe, Helen L 11 Jul '11

11 Jul '11

Hi Bruce, Doug, and All: Questions on a continuing problem: When I run tksurfer, the caudalanteriorcingulate is invaded by the corpuscallosum. I edited the boundary using the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit I'm then instructed to "Save the annotation: File > Label > Export Annotation. Probably choose a new name rather than writing over an existing file" I don't need a new name - I just need to save the labels for the caudalanteriorcingulate and the corpuscallosum, which both now look correct. How/where do I do that? Here are the files in the label dir: lh.cortex.label lh.aparc.annot lh.aparc.a2009s.annot rh.cortex.label rh.aparc.annot aparc.annot.ctab rh.aparc.a2009s.annot aparc.annot.a2009s.ctab Also - I previously asked what I need to do after that to ensure accurate measurements. Bruce responded, "I don't think you need recon2 since you are just changing the aparc. I believe you can just run the aparc stats step, but I'll cc Doug who might know better." Any advice on all this? Thanks, Helen ________________________________ 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. ________________________________

2 1

using mri_convert with multiframe dicom
by Timothy Brown 11 Jul '11

11 Jul '11

Hi All, Can mri_convert be used with multiframe dicom? In attempting to use the command that was successful on non-multiframe dicom I receive the following error: /usr/local/freesurfer/bin/mri_convert -it dicom -ot analyze 401/GL.MR.Project.401.1.20100923.103636.ench9 h.0502265032.dcm ANALYZE/Target $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 401/GL.MR.Project.401.1.20100923.103636.ench9h.0502265032.dcm... Starting DICOMRead2() dcmfile = 401/GL.MR.Project.401.1.20100923.103636.ench9h.0502265032.dcm dcmdir = 401 WARNING: tag image orientation not found Ref Series No = 401 Found 3 files, checking for dicoms WARNING: tag image orientation not found Found 1 dicom files in series. /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficien t by 2 WARNING: tag image orientation not found First Sorting Computing Slice Direction Vs: 0 0 0 Vs: nan nan nan Second Sorting Counting frames nframes = 1 nslices = 1 ndcmfiles = 1 PE Dir = UNKNOWN (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr<T>::solve() : matrix is rank-deficien t by 2 MRIresample(): error inverting matrix; determinant is nan, matrix is: TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -0, 0) j_ras = (-0, -0, 0) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation -0.000 -0.000 nan nan; -0.000 -0.000 nan nan; 0.000 0.000 nan nan; 0.000 0.000 0.000 1.000; Thanks. -Timothy Timothy Brown email: timothy(a)cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Science fax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218

2 1

Multiple frames error
by Antonella Kis 11 Jul '11

11 Jul '11

Good morning Bruce, 1). My LNX3 the only one which is working is a Fedora Linux, Kernel Linux 2.6.32.23-170.fc12.x86_64, GENOME 2.28.2 LNX2 where I get the weird surface display is a Linux CENTOS x86_64, GENOME 2.16.0 The Analyst computer where I got the multiple frames error is a Linux, Kernel Linux 2.6.35.13-91.fc14.x86_64, GENOME 2.32.0 2). Also, when I am doing my data analysis after running the recon -all and qcache -all for my subjects, what is the best steps order to be followed. While reading the FreeSurfer Troubleshooting Reconstruction Work suggests the user to run all these steps at once before beginning to inspect the data since this allows the user to see the final complete output before deciding on any interventions.But this steps are in a different order that the one in the tutorial and also in a different order that the one described in the attached document. FreeSurfer Troubleshooting Reconstruction Work Flow:1. Source the correct version of FS 2. Set your SUBJECTS_DIR variable to your subjects directory 3. Import your data and create a subject data directory 4. Run the all the steps of recon-all 5. Check the talairach transform 6. Check the skull strip: - After adding control points run the steps -autorecon-cp (this will run -normalization, using control points, and everything else through the end of -autorecon2) and -autorecon3 (this will update all your stat tables with the new changes). - After adjusting the skullstrip, run the steps -autorecon2 and -autorecon3. 7. Check the white and pial surfaces - After editing the wm.mgz volume run the steps -autorecon2-wm (this will run -fill, using new wm.mgz volume, and everything else through the end of -autorecon2) and -autorecon3. - After editing the brainmask.mgz volume to adjust the pial surface, run the steps -autorecon-pial (this will run -finalsurfs, using new brainmask.mgz volume, and everything else through the end of -autorecon3.) 8. Check the segmentations - After editing the wm.mgz volume run the following steps: -normalization -maskbfs -segmentation -autorecon2-wm -autorecon3. 3). Sorry for the silly question: It is possible in order to save time to do all the corrections ones at the time and then run all the autorecon in one step? Thank you for your help! Antonella

1 0

MRI book
by Adil Javed 11 Jul '11

11 Jul '11

Hi, Is there any good MRI book that teaches the basics of MRI acquisition and various types of sequences or maybe another that teaches basics of image analysis? Thanks, AJ

2 1

how to get high resolution atlas on the Freesurfer ?
by 刘继欣 11 Jul '11

11 Jul '11

2 1

← Newer
1
...
10
11
12
13
14
15
16
...
20
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer July 2011