Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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. ________________________________

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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

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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

Rejoindre mon réseau sur LinkedIn
by Jamaan Alghamdi via LinkedIn 09 Jul '11

09 Jul '11

LinkedIn ------------ Jamaan Alghamdi souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Jamaan Alghamdi http://www.linkedin.com/e/-qq80um-gpx7oboi-9/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59… Voir l'invitation de Jamaan Alghamdi http://www.linkedin.com/e/-qq80um-gpx7oboi-9/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59… ------------------------------------------ SAVEZ-VOUS que vous pouvez utiliser votre profil LinkedIn comme page Web personnelle ? Personnalisez l'adresse Web de votre profil et utilisez-la sur vos cartes de visite, comme signature d'e-mail, sur votre site, etc. http://www.linkedin.com/e/-qq80um-gpx7oboi-9/ewp/inv-21/ -- (c) 2011, LinkedIn Corporation

1 0

Rejoindre mon réseau sur LinkedIn
by Jamaan Alghamdi via LinkedIn 09 Jul '11

09 Jul '11

LinkedIn ------------ Jamaan Alghamdi souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Jamaan Alghamdi http://www.linkedin.com/e/-qq80um-gpx7h7cg-28/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Jamaan Alghamdi http://www.linkedin.com/e/-qq80um-gpx7h7cg-28/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ SAVEZ-VOUS que vous pouvez utiliser votre profil LinkedIn comme page Web personnelle ? Personnalisez l'adresse Web de votre profil et utilisez-la sur vos cartes de visite, comme signature d'e-mail, sur votre site, etc. http://www.linkedin.com/e/-qq80um-gpx7h7cg-28/ewp/inv-21/ -- (c) 2011, LinkedIn Corporation

1 0

Optseq with Sparse Sampling
by Sam Norman-Haignere 08 Jul '11

08 Jul '11

Hi, I'm planning to run an auditory experiment using a pseudo-sparse sampling design. Something like: 4 sec stim period + 2 sec acquisition + 4 sec stim period + 2 sec acquisition ... So for example, I'd like to find an optimal sequence for a design with a TR of 6 seconds but where the stimulus presentations can only occur in specific 4 second intervals after acquisition. There is room for jittering either in which 4-sec periods are NULL or alternatively in which part of the 4 seconds is occupied by stimulus (e.g. 3 sec stim + 1 sec NULL). Is there a way to use optseq for this type of design? For example, maybe you could specify when half of the NULL conditions occur. Thanks, Sam Norman-Haignere

1 0

muliple fressurfer instance and cuda
by Knut J Bjuland 08 Jul '11

08 Jul '11

Hi When I have ran two or more Freesurfer instance in pc with one geforce gtx 460. I usually get a abort or memory corruption when running two or more Freesurfer instance. I usually get trouble when two ore more Freesurfer instance is in autocon3 phase of the recon-all protocol. Cheers Knut J

3 3

Freesurfer and VBM
by Ahmed, F, Me <fahmed＠sun.ac.za> 08 Jul '11

08 Jul '11

Hello, I'm wondering if anyone could help me out with a question I had. For a study I'm working on, I'm comparing the regional brain volumes in adolescents with and without PTSD. I ran VBM analysis and Freesurfer on my subjects and I found some significant results on VBM (however, only using uncorrected p values) and on Freesurfer, I found no group differences in brain regions. Is there an explanation for that? If anyone has any thoughts I'd really appreciate it. Thank you kindly! Fatima

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