Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30134 discussions

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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TRACULA - RH ILF Issue
by Douglas Merkitch 08 Dec '16

08 Dec '16

Hello Freesurfer experts, I've finished processing a subject through the TRACULA pipeline (freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae), and I'm getting a weird result for the right inferior longitudinal fasciculus (see screenshots). I don't think this is just a display issue? I do know that you would most likely need more information from me, but I'm not sure what you will need. Any help would be appreciated! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu> [cid:8039F12F-7097-4088-89FE-37A8150D514A][cid:07350CB0-F3CF-40A8-9301-04D35C77B560]

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HC Subfields LongHippo
by Sebastian Huhn 08 Dec '16

08 Dec '16

Dear Freesurfer Community, I ran the Freesurfer longitudinal pipeline for my subjects (7T, T1_data, 2 timepoints each). Now I want to continue with the longitudinal segmentation of hippocampal subfields: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields However, when I want to run the command: longHippoSubfieldsT1.sh <baseID> I get the error message "bash: longHippoSubfieldsT1.sh: command not found" First thing I did, was checking the Freesurfer folder for the longHippo..sh file. I am using FS 6.0 but the file is not available. So my questions: where can I get the file longHippoSubfieldsT1.sh or what else can I do to proceed with the HC subfield segmentation? Thanks a lot for your support Best Sebastian

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