Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08
by Arkadiy Maksimovskiy 29 Jun '16

29 Jun '16

Thank you for catching this. Really appreciate your help. - Arkadiiy

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Re: [Freesurfer] Freesurfer Digest, Vol 148, Issue 28
by Arkadiy Maksimovskiy 29 Jun '16

29 Jun '16

Thank you!!

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longitudinal tracula
by Harms, Michael 29 Jun '16

29 Jun '16

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Announcement: fsurf, a command line tool for running freesurfer on the Open Science Grid
by Krieger, Donald N. 29 Jun '16

29 Jun '16

Dear FreeSurfer community, The Open Science Grid (http://www.opensciencegrid.org) is a federation of university and laboratory HPC facilities which share computing capacity to support science. We have developed a command line tool "fsurf" you can use from your laptop or desktop computer to submit scans for FreeSurfer processing on these clusters. In the initial release it is capable of executing "recon-all -all -i SubjectName.mgz" using FreeSurfer 5.3. No allocation is required. We only request that you cite the OSG in publications that benefit from its use. Instructions for getting started are found here: http://bit.ly/freesurferopensciencegrid. Please post questions and problems to OSG user support at user-support(a)opensciencegrid.org<mailto:user-support@opensciencegrid.org>. We hope you find it useful. Best regards, The OSG fsurf support team

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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

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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

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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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