Freesurfer October 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
170 discussions

Issues processing brain hemispherectomized patients
by Halbertsma, HN (ohk) 12 Oct '16

12 Oct '16

Dear all, I’m having troubles getting a good Freesurfer output from a hemispherectomised brain using recon-all. I was wondering whether there’s someone that has experience with running Freesurfer on such an unusual brain? The first couple of issues I bumped into were failures regarding the talaraich alignment which I solved using registration matrices from FSL. The issue I’m having now regards the labeling of subcortical structures. Apparently Freesurfer cannot deal with the fact that there’s just one hemisphere, and the fact that there is no clear corpus callosum. It looks like it’s trying to divide one hemisphere into two, which obviously messes up the subcortical labelling. Any ideas on how to work around this issues? Is there maybe a way to mirror the intact hemisphere pretending to form a full brain? Or are there any flags I can use to make sure the subcortical labelling works fine? Thanks in advance Hinke N. Halbertsma, MSc PhD Student University Medical Center Groningen (UMCG) Department of Ophthalmology NeuroImaging Center (Antonius Deusinglaan 2, 9713 AW Groningen), room 124 T. (+31) 050 363 4431 E. h.n.halbertsma(a)umcg.nl<mailto:h.n.halbertsma@umcg.nl> ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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Hippocampal subfield analysis in FS 6.0
by Synne Aanes 12 Oct '16

12 Oct '16

Hello, I am about to start my project on hippocampal subfield analysis and realise that this function is highly improved in FS version 6.0. I have run my data in FS 5.3 before this came to my knowledge, and I am now wondering when version 6.0 will be released to the public so I can run them again? Sincerely, Synne Aanes

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Quantifying volumes
by Josue Luiz Dalboni Da Rocha 12 Oct '16

12 Oct '16

Dear Douglas, I have a segmented gyrus curvature file (.curv or .w) and I would like to calculate the volume (and other statistics) of this gyrus. I currently only know mris_anatomical_stats to perform that, but requiring a '.label' file. Can I extract statistics directly from the ".curv" file? Or can I convert directly from .curv to .label in order to extract these statistics? As another option, is it feasible to convert the '.curv' file to nifti volume (mri_surf2vol), binarize it (mri_binarize), and then convert to label (mri_cor2label)? What does the output nifti file from 'mri_surf2vol' contain? Does it contain the complete volume behind the surface? Or does it only contain the surface over the 3D space? Thank you very much in advance for your help! Best regards, Josue

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Segmentation editing
by firetech＠web.de 12 Oct '16

12 Oct '16

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Fw: freeview: command not found
by Mageshwar Selvakumar 12 Oct '16

12 Oct '16

Dear All, I'm trying to start on with freeSurfer. I have a Mac running Mac OS Sierra. I downloaded the file "freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwi…>" and installed it. I have setup the license file and also configured free surfer. Once I tried running the examples provided to check the software, the first example ran without errors but the second example that uses Freeview returned a error: command not found. On looking for a solution in the archives, I found someone had a similar problem using tkmedit, Freeview on a linux machine. When I tried tkmedit it works without errors, giving a long list of commands it supports. So, the problem command not found is only when I use Freeview. I also tried using only the freeview command and still the error remained. Kindly let me know if someone had a similar problem, or if someone is running free surfer successfully on Mac OS Sierra. PS: I had given read and write rights to the entire free surfer folder as well. Thank you for your help. Kind Regards Mageshwar Selvakumar

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Use Atlas (Binary ROIs) made in 3DSlicer in as parcellation atlas in Freesurfer
by Daya P 11 Oct '16

11 Oct '16

Hi All, We made an average subject for a non-human species and made ROI in nifiti format in Slicer, it's basically an atlas were each region corresponds to a different number. My question is if there is any way to import this into Freesurfer and be able to use this as any other parcellation atlas that comes with Freesurfer? What would be the process for that? Thank you, Daiana

1 0

Volume to Surface
by Crawford, Anna 11 Oct '16

11 Oct '16

Hello, I am trying to take nay volume that is registered and create an inflated surface. I am trying to use mri_vol2surf. I am having problems with the registration source. From the examples I could fine, it should be --srcreg *.dat. The only *.dat file I have is segment.dat which does not work. I also tried using the white matter volume which also didn't work. My input and output is below. Could you offer some guidance on the registration file? Thank you, Anna mri_vol2surf --src /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz --out /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/surf/wmparcSlh --srcreg /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat --hemi lh --surf white --out_type paint INFO: output format is paint srcvol = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/wmparc.mgz srcreg = /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume regio_read_register(): Success Error reading betplaneres from /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/segment.dat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

4 27

FreeSurfer 6 beta and mac osx el capitan
by Damien MARIE 11 Oct '16

11 Oct '16

Hi, I would like to install the FreeSurfer 6 beta on my macbook pro (OS X El capitan 10.11.6, XQuartz 2.7.9 installed). I allowed applications downloaded from Anywhere in privacy and settings, and disabled csrutil (the System Integrity Protection, a security feature that hobbles some of the capabilities of root since this OS release). No matter what I try, I cannot decompress the archive. Using the terminal and sudo : tar: Error opening archive: Failed to open '/Users/dmarie2/Applications/freesurfer-Darwin-OSX-dev.tar.gz’ Or by double clicking : Unable to expand “freesurfer-Darwin-OSX-dev.tar.gz (Error 1 - Operation not permitted). I was wondering if somebody experienced this issue and would eventually have a solution. Thank you and best, Damien

1 1

Subcortical segmentation
by Ankita Sharma 10 Oct '16

10 Oct '16

Hi, Does anyone know if subthalamic nuclei and substantial nigra are part of the automated sub-cortical segmentation (aseg) in Freesufer? Thanks, Ankita!

2 1

Subcortical Segmentation
by Raghav Mehta 10 Oct '16

10 Oct '16

Hi, I am new to freesurfer. I would like to know the command for subcortical segmentation of brain MRI volume. I read on freesurfer wiki page the recon-all -autorecon2 stage is useful for this. *My question is what exact command should I use for this purpose.* I am familiar with FSL. In FSL 'FIRST' command is useful for this and it gives you segmentaion in approimately 7-10 minutes. But in freesurfer it is written that recon-all -autorecon2 stage can take upto 12 hours for segmentation of one volume. I would like to know if there is any other option for this apart from autorecon2 stage which can give me segmentation in less time. Thank you for your help. Regards, Raghav Mehta MS by Research (ECE) Center for Visual Information Technology International Institute of Information Technology - Hyderabad +91 9712990393

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Freesurfer October 2016