Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Postdoctoral Fellowship in Memory
by Aneesha Nilakantan 11 Dec '16

11 Dec '16

*Full-Time Postdoctoral Fellowship in Memory * *Laboratory for Human Neuroscience Northwestern University* *Feinberg School of Medicine * http://www.lhn.northwestern.edu/Postdocsearch2017.pdf One full-time postdoctoral fellowship is available in The Laboratory for Human Neuroscience at the Northwestern University Feinberg School of Medicine, directed by Dr. Joel Voss (www.lhn.northwestern.edu) The research focus for this position is the effects of transcranial magnetic stimulation (TMS) on cortical networks of the human hippocampus and their contributions to learning and memory. The successful candidate would work with a large, longitudinal fMRI dataset collected from individuals participating in multi-week TMS experiments, including both young and elderly adults (supported by NIH grants R01MH106512, R01MH111790, and R01AG049002). The successful candidate would also be encouraged to develop an independent research focus, and would be provided with access to laboratory resources including equipment for TMS, high-density EEG, and eye-movement tracking studies of memory, a research registry of individuals with circumscribed neurological injuries, and excellent fMRI scanning facilities (www.cti.northwestern.edu) The Northwestern University Feinberg School of Medicine is a large academic medical center in the heart of downtown Chicago. It is home to a vibrant neuroscience community, structured around a multi-departmental neuroscience program (www.nuin.northwestern.edu) Position requires a Ph.D. or M.D./Ph.D. in a neuroscience-related field, broadly specified. We are seeking candidates with strong computational abilities, substantial experience in fMRI or EEG data analysis, and excellent written and verbal communication abilities. To apply, please send a cover letter, C.V. (or NIH-style biographical sketch), and the names of at least three individuals who could provide references if required. Contact name: Jonathan O’Neil Contact email: lhn(a)northwestern.edu

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Free surfer mri_convert and subjdir problems
by anand iyer 10 Dec '16

10 Dec '16

I wonder if anybody could help please? 1. I have converted DICOM to NIFTI and then when I try to apply mri_convert command to change it to .mgz; i cant locate the converted file! 2. When I try and create directories of the patient within subjects subfolder; it says ‘permission denied’. I then used the sudo command to prepare directories.But then i cant move .mgz file (which is not found) into the mri subfolder of the patient. 3. Thus i cannot apply the command recon-all. Is there any easy way to get the DICOM to load on to freesurfer without all this hassle? I am grateful for your help. Anand

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Freesurfer on Centos 7?
by Caspar M. Schwiedrzik 09 Dec '16

09 Dec '16

Hi! I was wondering whether there is an update from the 2014 thread on Freesurfer's compatibility with Centos 7? The old thread is here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38466.html I have also come across this website mentioning some changes in the installation related to Perl and MNI tools: http://miconsult.weebly.com/blog/freesurfer-running-on-centos-7 Any insights would be appreciated. Thanks, Caspar

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Freesurfer software in stroke study
by Frank Robert 09 Dec '16

09 Dec '16

Dear Freesurfer experts I am curious whether Freesurfer segmentation tool is good at segment and quantify the stroke lesion size in T2 FLAIR image, GRE images, DWI images and Perfusion (DSC/ASL) images? If have a good tool, is there instructions how to use it? Many thanks Best Regards Frank Yu

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poor segmentation and skull-strip = due to talairach?
by Rizvi, Batool 09 Dec '16

09 Dec '16

Hi FreeSurfer team, We have a couple of subjects that have really poor segmentation and skull-strip as well, that seem beyond fixing with just control points or WM edits. I'm wondering if this occurred because of earlier in the stream, there was a bad talairach transform? I went back to see the talairach, and it also looked irreparable. So this time, I tried using the other method of producing a talairach transform (mritotal), but this only made it much worse than before. How can I regenerate the talairach so that it will at least cleanly fit the lines of at least the target volume? Thanks very much! Batool

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Infant brain atlas
by Axelson, Eric D 09 Dec '16

09 Dec '16

Does the infant brain atlas mentioned in this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/ exist yet or will it be included in version 6? Thanks Eric Axelson Research Specialist Department of Psychiatry University of Iowa eric-axelson(a)uiowa.edu<mailto:eric-axelson@uiowa.edu> ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of 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 you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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STRING type
by Melvin Robinson 09 Dec '16

09 Dec '16

I'm trying to build Freesurfer from developer sources and am running into this error: mriio.c:3692:27: error: 'STRING' undeclared (first use in this function) status = output_volume((STRING)fname, nc_data_type, signed_flag, min, max, Can you tell me where STRING comes from? I could not find this datatype in either the sources or the dependencies.

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mri_nu_correct error: Ubuntu 16.04
by William George Henry Collishaw 08 Dec '16

08 Dec '16

Hello Freesurfer Developers, I'm attempting to run recon-all on Ubuntu 16.04, on failure I am getting the following log: mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig .mgz --o orig_nu.mgz Linux jupiter 4.4.0-43-generic #63-Ubuntu SMP Wed Oct 12 13:48:03 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s M87100718 exited with ERRORS at Thu Dec 8 13:48:35 MST 2016 I googled the issue and found recommendations to use the development version of freesurfer OR downgrade Perl from 5.22 to 5.18. I tried both of these separately and neither worked. I am still getting the same error. The recon-all.log is attached? freesurfer version used with perl 5.18 - freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 freesurfer version used with perl 5.22 - ?freesurfer-Linux-centos6_x86_64-dev-20161205-aab1c9c Thanks, William Collishaw?

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FreeSurfer v6.0 release
by KALEY E ELLIS 08 Dec '16

08 Dec '16

Hello, We are currently setting up our study's structural analyses using FreeSurfer. When will the next version of FreeSurfer (6.0) be released? Thank you! Kaley Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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FreeSurfer v6.0 release date
by KALEY E ELLIS 08 Dec '16

08 Dec '16

Hi FreeSurfer, We are currently setting up our study's structural analyses using FreeSurfer. When will the next version of FreeSurfer (6.0) be released? Thank you! Kaley Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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