Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

ERROR: mpr2mni305 failed
by Barbara Kreilkamp 31 May '16

31 May '16

Dear FSL experts, I am running freesurfer-Darwin-lion-stable-pub-v5.3.0 on MAC 10.10.5. Could you please help me with this error message? I think it relates to the library, this is what it states in talairach_avi.log. But I am unsure how to solve this issue. Any help is greatly appreciated, Thank you very much, Barbara #@# Talairach Sat May 28 14:18:53 CEST 2016 /Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 recon-all -s REF088c exited with ERRORS at Sat May 28 14:19:12 CEST 2016 For more details, see the log file /Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting talaraich_avi.log output /Users/barbarakreilkamp/projects/Pipelines_ExampleData/REF088c/T1w/REF088c/mri /Applications/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Darwin iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 2016; root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64 Sat May 28 13:27:28 CEST 2016 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from orig_nu.mgz... crypt_gkey = FSaWN44YqKOYA TR=8.21, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to talsrcimg.img... crypt_gkey = FSaWN44YqKOYA Analyze Output Matrix -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -146.00000; 0.00000 -1.00000 0.00000 148.00000; 0.00000 0.00000 0.00000 1.00000; -------------------- INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Sat May 28 13:27:29 CEST 2016 /Applications/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Sat May 28 13:27:30 2016 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- dyld: Library not loaded: /usr/local/gfortran/lib/libgcc_s.1.dylib Referenced from: /Applications/freesurfer/bin/gauss_4dfp Reason: image not found Trace/BPT trap ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133 ERROR: mpr2mni305 execution aborted

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Manual segmentation issues
by Saturne Fox 31 May '16

31 May '16

[image: Inline image 3][image: Inline image 1][image: Inline image 2][image: Inline image 4] Dear freesurfer community, These days I am manually editing some data and this subject is giving me such a hard time. In fact I would like the near-to-cortexartefacts at the top right hand corner to be excluded from the surface but even after changing the intensity of the wanted part to 255 and the one of the excluded parts to 1 (which is nevertheless not visible on these images) the surface is still not what I would like it to become. In adition to editing the wm.mgz file, I also modified the aseg.presurf file to exclude these parts and I re-runned the -normalization2 and -maskbfs flags to generate new brain.mgz and brain.finalsurfs.mgz files. Any idea why these modifications are not affecting the surface ? Best regards, Antoine

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ERROR with pial-lgi for one subject
by Vikas Bandalli 30 May '16

30 May '16

Hello FS experts, I am currently running an analysis for pial_lgi between control and patient group. But when I try to run the analysis using qdec for Right Hemisphere (rh),I get the following error with one particular subject Error in Analyze: Couldn't open /Applications/freesurfer/subjects/HC122/surf/rh.pial_lgi.fwhm0.fsaverage.mgz or .mgh file. However,the analysis works fine for Left Hemisphere (lh) without errors. I tried running the command recon-all -s HC122 -qcache -measure pial_lgi -hemi rh But output was #@# Qdec Cache rh pial_lgi fsaverage Mon May 30 20:19:32 IST 2016 INFO: File rh.pial_lgi does not exist! Skipping creation of smoothed data for rh.pial_lgi But trying to run '-localGI' did not create 'surf/rh.pial_lgi' btu it creates 'surf/lh.pial_lgi' I checked the euler number for the surface it is 2. Any suggestions to correct the error is highly appreciated . Regards, Vikas Bandalli -- Vikas B. R. Medical student Bangalore Medical College and Research Institute (BMCRI), Bangalore,India, Ph : +918904286825

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CfP - SESAMI MICCAI Workshop - Shape & Spectral Analysis
by Martin Reuter 27 May '16

27 May '16

For your information: This is a call for papers for our MICCAI Workshop on Shape and/or Spectral Analysis (SESAMI) Oct. 21, Athens, Greece ! It would be great if you could *disseminate our call-for-papers* among your students and colleagues. Looking forward to seeing you, maybe in Athens. Thank you and best regards, Martin, Christian and Hervé ****************************************************************** *MICCAI SESAMI** **Workshop on Spectral & Shape Analysis in Medical Imaging* Athens, Oct 21st, 2016 https://sites.google.com/site/sesami2016/ ****************************************************************** *Description* We gladly announce the workshop for *Spectral & Shape Analysis in Medical Imaging* (SESAMI, https://sites.google.com/site/sesami2016/) held in conjunction with the conference on Medical Image Computing and Computer Assisted Interventions (MICCAI) in Athens, Greece, on October 21st, 2016. *Aim and Scope* Today's image data often represents complex phenomena, usually with a geometric structure. Shape and geometry processing methods are receiving increased attention, for example, due to their higher sensitivity to local variations relative to traditional markers, such as the volume of a structure. Both Spectral and Shape Analysis provide a wealth of opportunities for studying complex data. This workshop targets *theoretical contributions* and *exciting applications* in medical imaging, including (but not limited to): - Spectral Shape Analysis - Spectral Image and Mesh Segmentation - Spectral Classification and Dimensionality Reduction - Shape Representation, Processing and Modeling - Shape Segmentation and Registration - Statistical Shape Analysis - Longitudinal Shape Analysis and Processing - Medical applications focused on Spectral and/or Shape Analysis This workshop will provide an invaluable opportunity for researchers to present recent work on spectral and shape analysis in medical imaging. Interactions among fellow researchers will foster a deeper understanding of the underlying concepts and will provide insights on the benefits of *incorporating spectral or shape analysis into medical imaging applications*. Researchers with no or little prior experience in spectral and shape analysis can especially profit from introductory talks that will cover basic background and give an overview of the field. *** IMPORTANT DATES *** - Deadline for paper submission: *** June 15th, 2016, 23:59PST *** - Notification of Acceptance: Mid July, 2016 - SESAMI Workshop on: October 21st, 2016 *Advisory Panel* Stanley Durrleman, Inria Guido Gerig, NYU Ender Konukoglu, Harvard Medical School Julien Lefevre, Université Aix-Marseille Diana Mateus, Technische UniversitÃ¤t MÃ¼nchen Washington Mio, Florida State University Marc Niethammer, UNC Chapel Hill Stephen Pizer, UNC Chapel Hill Robert Pless, Washington University Kilian Pohl, SRI Yonggang Shi, University Southern California Martin Styner, UNC Chapel Hill Ross Whitaker, University of Utah & More to be announced For more information, contact the organizers directly: - Martin Reuter <mreuter(a)nmr.mgh.harvard.edu>, - Christian Wachinger <wachinger(a)csail.mit.edu>, - Herve Lombaert <herve.lombaert(a)inria.fr>

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Internal Capsule White Matter Volumes
by Lakhani, Bimal 27 May '16

27 May '16

Hello, I would like to extract white matter volume from both anterior and posterior limb of the internal capsule, but the wmparc lists these regions as ‘unsegmented white matter’. They appear in the ColorTableLUT as regions 155-158, but do not actually appear in any of the outputted parcellations. Is there any other way to get internal capsule volumes? Thanks very much, Bimal Bimal Lakhani, PhD | Postdoctoral Fellow Department of Physical Therapy |The University of British Columbia T142A - 2211 Wesbrook Mall, Vancouver, BC, Canada V6T 1Z3 604.827.3369 |bimal.lakhani(a)ubc.ca | www.brain.rehab.med.ubc.ca<http://www.brain.rehab.med.ubc.ca/>

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Intensity Thresholding
by Daya P 27 May '16

27 May '16

Hi all, As a process a subject through recon-all I get the brainmask.mgz, norm.mgz too bright. the white matter turns out to be 150 or higher. instead of normalization and normalization2 I tried to do mri_normalize -gentle which helps a bit but when I run autorecon2-wm it just makes it very bright again. There seems to be a threshold adjusting problem. This of course messes up the segmentation of the white matter. Is there any way I can change the normalization part of recon-all? How can I change normalization parameters? The scans that go into the SUBJ have the white matter already close to 110 and the normalization part makes it too bright. Thanks for your help, Daiana

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recon-all deprecated error
by Tamara Tavares 27 May '16

27 May '16

Hello All, I am currently using Freesurfer version 5.1 and when I run the recon-all command I get the following warning message: Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer/mni/bin/sharpen_volume line 153. Recon-all continues to run and finishes completely without any errors. Should be worried about this error? Thank you in advance for your help, Best, Tamara

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Creating a new atlas
by Daya P 27 May '16

27 May '16

Hi all, I created a custom template using a few subjects and have two tif. files for lh and rh. I am trying to create a cortical/surface atlas from scratch. My understanding is that I must use mris_ca_train. mris_ca_train [options] <hemi> <canonsurf> <annotfile> <subject1> [subject2 ...] <outputfile> the canonsurf is mentioned to be lh,sphere,reg. I assume this is the file that was created using mris_register during the template creation process. I am not sure what the annotfile -> name of per subject annotation file to input from every subject means. Say, I create a label on each subject delineating primary auditory cortex, and a different label delineating primary visual cortex for each individual. First, on what surface do I draw the labels on? lh,sphere.reg? lh.pial? Secondly, after having drawn the surface labels do I make them into annotation files and save them under the same name for each subject and then input then in mris_ca_train? I couldnt find information on this in the mail archive.. Thank you for your help! Daiana R.P

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Re: [Freesurfer] Connectivity design ill-conditioned
by Zimmerman, Jared Perry 27 May '16

27 May '16

Thanks Doug, this worked. Misconfigured my nuisance regressor seeds. Matrix still has 47 columns, but it seems to be appropriately designed. Best, Jared Message: 2 Date: Thu, 26 May 2016 12:14:27 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Connectivity design ill-conditioned To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <574720E3.30603(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed It is strange that it has 47 columns, I would have expected 48, however, the current problem is caused by the wm.dat and vcsf.dat having the same content. Probably it was an error when you set up the command line for fcseed-config On 05/25/2016 06:40 PM, Zimmerman, Jared Perry wrote: > Hi, I'm having a problem running first level connectivity analysis on > my resting-state data. When I run selxavg3-sess I keep getting a > notice that my design is ill-conditioned but I can't figure out why. > I am trying to run analysis on two 124 volume rsfMRI runs in my fsd > and the design matrix looks fine to me with dimensions 248x47 > (although should ncols be an even number since I'm doing two runs?). > > Poking around the Xtmp.mat I noticed a few things that are confusing. > Notably, flac.funcfspec points only to one of my runs in the fsd, and > flac.X is a 124x24 matrix which appears to be the design matrix for > just one of my runs (and if there are 24 columns in that, should there > be 28 columns in the design matrix for combining both runs?). Any > help figuring out why this design is ill-conditioned would be great. > > I've attached my Xtmp.mat, selxavg3.log and analysis design file to > this email, but it's unclear to me if the mailing list will scrub them > off. If so I can make them available some other way. > > > Thanks, > Jared > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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mri_cc
by Arash Nazeri 27 May '16

27 May '16

Dear all, mri_cc does not seem to be working properly to parcellate corpus callosum. As per one of the previous posts, there is a bug in the current release of mri_cc. However, the link provided in the same thread for an updated version of mri_cc is no longer existent. Our cluster runs on 64bit Ubuntu 14.04 systems. I'd be grateful if someone can post a new link for the corrected mri_cc. Thanks in advance. Cheers, Arash

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