Freesurfer December 2016

freesurfer@nmr.mgh.harvard.edu

95 participants
146 discussions

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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Problem running recon-all in newly installed Ubuntu 16.04LTS
by Nasos Petridis 08 Dec '16

08 Dec '16

Hello freesurfer experts, I've recently set up a PC running Ubuntu 16.04LTS and tried to run a freesurfer version which was running well on another PC (also running Ubuntu 16.04LTS)...the nightly build for centos6 of 2016-09-03. I'm running the recon-all script. While running mri_ca_register, I get >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> label assignment complete, 7 changed (0.00%) det(m_affine) = 1.19 (predicted orig area = 6.7) label assignment complete, 8 changed (0.00%) Segmentation fault (core dumped) ERROR: mri_ca_register with non-zero status 139 but continuing despite the error >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and a little bit later the program exits. Comparing the recon-all.log files from the runs in the two PCs, they appear identical until the above error appears, with the exception of the "main basin size", where the problematic PC gives a value which is 3.5% of that in the "good" PC. Any idea what may be going wrong with the new PC? Many thanks, Nasos

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mri_convert dcm 'Mosaic' 2 mgz
by Marianna Riello 07 Dec '16

07 Dec '16

Dear all, I am wondering whether mri_convert can compute .mgz files for the reconstructions with the 'Mosaic Format SIEMENS DICOM files'. I have been computing .mgz with the enhanced format .dcm so far, and it always worked. I have used mri_convert to compute .mgz from .nii (I previously transformed the mosaic .dcm format in nifti with mricron but the reconstruction failed) Thanks in advance, Marianna

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Optseq: psdwinMAX value for events of 8s?
by Xavier Guell Paradis 07 Dec '16

07 Dec '16

Dear FS team, I have one short question regarding Optseq: What is the recommended psdwinMAX value for events of 8s? I have read in this forum that events of 3s should have a psdwinMAX of 21s or even 24s; does this mean that events of 8s should have a psdwinMAX of 26-29s? Thank you very much, Xavier. Xavier Guell Paradis, M.D. Visiting Scientist Massachusetts Institute of Technology McGovern Institute for Brain Research Office: 46-4033A Phone: (617) 324-4355 Email: xaviergp(a)mit.edu

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Treating multiple subjects as a single subject in TRACULA
by Vivek Subramanian 07 Dec '16

07 Dec '16

Hi, I have DWI data from two subjects acquired using b-values of 0 for the B0's and 700 for the DWI's. There are 10 B0's and 60 DWI's in each dataset. I was successfully able to follow the instructions to use TRACULA on data from a single subject (recon-all; then trac-all -prep, -bedp, and -path), but I now want to infer a "group tractography" by running TRACULA on data from both subjects in the group as if they were from the same subject. This should yield one tractography for the entire group. I have registered all T1's to a common MNI template so they have the same dimensions. Cortical reconstruction was performed on the average of the subjects' T1s. When I run TRACULA, however, rather than pulling the bvecs from the DWI's, it takes them from a file called gradient_mgh_dti60.gdt, which is located under the Freesurfer installation. This file only contains 60 diffusion gradient directions. These closely match those of the 60 DWI files from one subject (but are not exactly the same), but because the contents of gradient_mgh_dti60.gdt are only being copied over once to the bvecs file in the subject directory, the bvecs file has only 60 sets of entries (+10 sets of 0's for the set of B0's). In other words, the file contains three rows of data (one for each spatial dimension), each with 10 zeros followed by 60 bvec entries. I expect there to be three rows of data, with 10 0's, followed by 60 bvec entries, followed by 10 0's, followed by 60 bvec entries. The bvals file, however, is fine; i.e. there are 10 0's, followed by 60 700's, followed by 100 0's, followed by 60 700's. This causes the -prep phase of trac-all to exit with errors when dtifit fails because the bvals and bvecs files don't have the same number of entries. I'm wondering what I need to do to get around this issue so the data can all be treated as if it came from the same subject and the bvecs are taken from the DWI's rather than from the gradient_mgh_dti60.gdt file. If you'd like, I can upload the bvecs and bvals files that trac-all -prep generates and also the output stream to the terminal. Thank you, Vivek

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Freesurfer December 2016