Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

No intensity command
by Sabrina Yu 29 Jun '16

29 Jun '16

Hello, I have a question about taking out the intensity normalization commands in recon-all. I want to eliminate all normalization steps so that the WM will not be set at an average of 110. Using the ReconAllDevTable (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable <https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable>), I took out all command flags related to intensity normalization. Are these commands correct? 1) I copied orig.mgz to generate nu.mgz, T1.mgz, norm.mgz. 2) recon-all -i <.nii file> -motioncor -talairach -skullstrip -s SUBJECT 3) recon-all -skullstrip -s SUBJECT 4) recon-all -gcareg -careg -calabel -maskbfs -segmentation -fill -tessellate -smooth1 -inflate1 -qsphere -fix -white -smooth2 -inflate2 -s SUBJECT 5) recon-all -autorecon3 -s SUBJECT I hope that my question makes sense. Thank you in advance for your time. Sabrina

2 2

Re: [Freesurfer] Question about FreeSurfer
by Dorsa Haji Ghaffari 29 Jun '16

29 Jun '16

Hi, I am graduate student at the University of Michigan and I am performing research on deep brain stimulation. I want to warp an anatomical brain atlas to individual patient MRIs to get the patient specific brain models out of it. I chose FreeSurfer to do this and I have installed it on my computer. I realized that it takes 10-20 hrs to reconstruct the image. I wanted to ask if that is the time for one image? or the whole series of images? I also wanted to ask if there is a step by step tutorial on how to do this. Thank you > > Dorsa Ghaffari >

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Motion values during structural run
by Rodriguez-Thompson, Anais 29 Jun '16

29 Jun '16

Hi Freesurfer Experts, Is there a way to calculate average displacement during a T1_MEMPRAGE scan (similar to using fmcpr.nii to calculate avg displacement during functional runs)? Thank you, Anais Rodriguez-Thompson Clinical Research Coordinator Brain Genomics Laboratory Martinos Center for Biomedical Imaging Massachusetts General Hospital Phone: (617) 643-3215

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Tracula : ERROR: cannot unpack mosiacs without ASCII header
by Koubiyr, Ismail 29 Jun '16

29 Jun '16

Hi everyone, I’m reposting my problem if someone could help me I would really appreciate it. I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I tried to unpack the mosaics with gdcmtar, but I got the same error. P.S : DTIFIT works on FSL (FDT) but gives a poor quality in the reconstruction not as the one expected with Tracula. Thank you in advance for your help, Ismail

1 0

tutorial_data
by bruno fraccini pastorello 29 Jun '16

29 Jun '16

Dear freesurfer support,I'm trying to download the freesurfer data to learn freesurfer, but i can't it. Do you know why? Could you help me? I tried use this link ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz and I obtain this error: Safari cant open the page ftp://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz because Safari can't load any data from this location. Thanks in advanceBruno Pastorello PS: I tried use this link too :https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data using curl command on terminal and it has failed too

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checking freesurfer output
by Gabor Perlaki 29 Jun '16

29 Jun '16

Sorry to repost my question. I would appreciate any reply. Best Regards, Gabor 2016-06-13 10:51 GMT+02:00 Gabor Perlaki <petzinger.gabor(a)gmail.com>: > Dear all, > > I've a lot of patients and we are looking for the fastest solution to > check the output of Freesurfer. On the troubleshooting page ( > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) > there are a lot of steps to check, but I think not all of that should be > done to find out whether there is error in the final segmentations. > I think, but I am not sure, that checking the surfaces (white and pial) > and checking the subcortical segmentations (aseg) is enough to realize if > something is wrong. After an error is detected based on the checked outputs > (surfaces and aseg), we can find out the exact nature of the error and > correct it based on the troubleshooting page. Is it a good solution for > verifying the performance of Freesurfer by checking only these two things > (surfaces and aseg) or I need to check all of the steps listed on the > troubleshooting page anyway? > > > Best Regards, > Gabor > > <petzinger.gabor(a)gmail.com> > -- Gabor Perlaki research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-30-2084367 E-mail: petzinger.gabor(a)gmail.com

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Failed to download Freesurfer from ftp, server seems empty
by C. Minos Niu 29 Jun '16

29 Jun '16

Hello, I tried to have my new students download and install Freesurfer from https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall, but all download links gave "550 Failed to change directory" error. I logged into the FTP anonymously only to find it empty under "pub/". Any idea how to proceed with the downloading? Thanks! -Minos

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Diffusion MRI Workshop, 12-16 September, 2016
by Tim Dyrby 29 Jun '16

29 Jun '16

Dear Freesurfer users, Registration is officially open for the 4th ISMRM Diffusion MRI Workshop "Breaking Barriers in Diffusion MRI" to be held September 12-16 in Lisbon, Portugal! Dates: September 12-16, 2016 Venue: Sheraton Lisboa, Lisbon, Portugal Deadline for abstracts: July 21, 2016 Facebook: https://www.facebook.com/DSGworkshop2016/ As with the first three workshops held in 2002, 2005 and 2013, the workshop has been designed as the primary scientific venue for basic scientists and clinical researchers in the diffusion MR community to learn, meet the experts, discuss the latest advances in the field, and network. There is an optional bootcamp for trainees and those new to the field of diffusion MR on September 12. The formal scientific program from September 13-16 will cover the full scope of diffusion MR topics from acquisition to microstructure and modeling, anatomy, tractography, connectomics, validation, clinical application, and future strategies for innovation. Whether you are new to the field, a PhD student, postdoc, senior researcher or physician, we hope that you will be able to participate in the workshop and interact with the leaders in the field. *Please note that the deadline for scientific abstract submission is July 21, 2016.* For physicians in practice, the ISMRM is accredited by the ACGME to provide up to 25.75 AMA PRA Category 1 credits for participation in the workshop. For additional details, please visit the workshop website: http://www.ismrm.org/workshops/Diffusion16 or contact any of the organizing committee: / Mara Cercignani, Brighton & Sussex Medical School, Brighton, England, UK Maxime Descoteaux, Sherbrooke University, Sherbrooke, QC, Canada Tim B. Dyrby, Danish Research Centre for Magnetic Resonance, Hvidovre, Denmark Christopher Hess, University of California, San Francisco, CA, USA Alexander Leemans, University Medical Center Utrecht, Utrecht, The Netherlands / -- Tim B. Dyrby Associate Professor Danish Research Centre for Magnetic Resonance (DRCMR), section 714 Center for Functional and Diagnostic Imaging and Research Copenhagen University Hospital Hvidovre Kettegård Allé 30 2650 Hvidovre Denmark Office phone: +45 38626542 Mobile:+45 40790282 web: http://dig.drcmr.dk and www.drcmr.dk & Image Analysis and Computer Graphics section Department of Applied Mathematics and Computer Science Technical University of Denmark Richard Petersens Plads, Building 324 2800 Kongens Lyngby Denmark Office Phone: +45 45253424

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Problem while using the -localGI
by Hari Guragain 28 Jun '16

28 Jun '16

Dear Freesurfer experts, I am having trouble using the -localGI option to smoothen the pial surface. When I use the command like: recon-all -s ABC -localGI I got the following error: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-OSX-dev-20160611-876a0e6 cp: /Applications/freesurfer/subjects/ABC/scripts/lastcall.build-stamp.txt: Permission denied INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer /Applications/freesurfer/subjects/ABC/scripts/recon-all.cmd: Permission denied. But when I tried to do the same reconstruction via the super user(su), it says something about the library linking like below. I am wondering if it is a problem related to Matlab or freesurfer? I am currently using the development version of freesurfer. Any help will be greatly appreciated. reading surface from lh.pial... dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Thank you all. Hari

1 0

freeview display problem
by Ramtilak Gattu 28 Jun '16

28 Jun '16

Hello , I am having strange freeview display problem. The images doesnt appear in gray scale anymore. Please have a look at the attachment. Is there a switch that was turned on that I am not aware of. Could some one help. Thanks Regards Tilak

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