Freesurfer March 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
229 discussions

Problem Installing FS
by Millan, Carlos 01 Mar '16

01 Mar '16

Hi Zeke, I do have a file named license.txt in my FREESURFER_HOME directory as well as another one named LICENSE that comes with the FS installation. When I type: $> cd /Applications/freesurfer $> ls -l license.txt What happens is this: -rw-r--r--@ 1 carlosmillan staff 55 Feb 26 12:25 license.txt Does it mean I already have the license installed but I do not have administrator privileges and that’s why I’m not able to run FS? At this point I’m calling IT here at UM to see if that’s the problem, which is possible because it is not allowing me to use “sudo” either and the system says “sorry” after typing my password. Thanks, Carlos

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Corrupted head surface with mkheadsurf?
by Maheen Siddiqui 01 Mar '16

01 Mar '16

Hi FreeSurfer users, I have used the "mkheadsurf" command to create a head surface for my subject. However when I try to use "read_surf" to read the "lh.seghead" file that is created, the magic number is not one that is recognised. Having read some previous posts/questions with similar problem/error, I think the problem is probably within the "lh.seghead" file. I think someone wrote that incompatibility of the magic number means that the surface is corrupted. Is there a way to check errors of mkheadsurf? Or whether something is wrong? It looked fine in freeview. Does anybody have any advice? Thanks, Maheen

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Problem Installing Freesurfer
by Millan, Carlos 01 Mar '16

01 Mar '16

Dear Freesurfer Team, I am a researcher here at University of Miami and recently downloaded Freesurfer to do Cortical Thickness analysis. Unfortunately, I have followed the installation steps very carefully as indicated on your web page but I do not know if there is a security issue on this Mac or what is it? But when I am trying to test freesurfer I get a message that says "license not found". I have tried to install the license by copying and pasting the license text I received (license.txt) into the $FREESURFER_HOME directory but it did not work; so I tried to write the commands “cd /Applications/freesurfer” and then “pico license.txt”. In the next window I also pasted the license and then I saved the changes in pico, but that did not work either. Is there anything else I should do? I am attaching some screenshots from the terminal. Maybe those help you assessing the problem. Thank you, Carlos Millan Research Assistant Epilepsy Division – Neurology Department University of Miami [cid:D9BCD62E-EF2A-49DD-BC1F-A770010B9731]

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Seeking postdoctoral candidates for datascience positions
by Satrajit Ghosh 01 Mar '16

01 Mar '16

We are seeking two postdoctoral computational/data scientists with a PhD in computer science, electrical or biomedical engineering, neuroscience, statistics, or related fields to apply for positions in the McGovern Institute for Brain Research at Massachusetts Institute of Technology. The projects cover a broad array of neuroinformatics. - Datamining of gene-behavior-anatomy relationships - Architecting next generation dataflow systems - Reproducible research platforms and applications - Nonlinear image and other high-dimensional registration - Predictive analytics in mental health - Linked data platforms Working on these projects will involve collaboration partners within and across regional and international institutions. Candidates are expected to develop algorithms and prototype ideas, contribute to opensource tools, and perform software engineering, testing, and validation. Candidates will have the opportunity to mentor undergraduate and graduate students, and contribute to datascience at MIT. The ideal candidates will have strong computational skills, enjoy collaborating, and be able to adapt to and adopt a diverse set of technologies. A documented PhD in computer science, electrical or biomedical engineering, neuroscience, statistics, or related field is required before starting this position. Positions are available for one year, with a possibility of yearly extension depending on performance and funding. For inquiries please contact Satrajit Ghosh (satra(a)mit.edu)

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Re: [Freesurfer] Ex-Vivo Surface Misoriented in tkmedit, but not Freeview
by John Plass 01 Mar '16

01 Mar '16

Hi Bruce, Thanks for your help. In freeview, the surface outline overlays on the volume correctly, and both the volume and the surface are oriented correctly in terms of R-L, A-P, and S-I axes. In tkmedit, the volume is oriented correctly, but the surface appears to be oriented with some of the axes swapped. E.g., from the coronal view in tkmedit, I see a coronal slice of the volume, but the outline of an axial slice of the surface, with the anterior part pointing down. John

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ineffective skull strip
by Lars M. Rimol 01 Mar '16

01 Mar '16

Hi, We have run recon-all on 33 healthy subjects in their 20ies with FreeSurfer version 5.3.0, on a Linux CentOS 6.7. The original T1's look good (example image attached). We used the braindeer tool(http://brainder.org/2011/09/10/quickly-inspect-freesurfer-cortical-sur… to check the quality of the cortical reconstruction, and we find that in 10-15 subjects the cortical surface reconstruction was unsuccessful. We think it may have to do with an incomplete skull strip (please see attached images). In order to get rid of residual dura (and some skull) we changed watershed first to 20 then to 5, using these commands: 1) recon-all -skullstrip -wsthresh 20 -clean-bm -subjid <subject name> 2) recon-all -autorecon-pial -subjid <subject name> ( We also tried: recon-all -skullstrip -clean-bm -multistrip -subjid <subject name> ) None of this changed the outcome much. Neither did -gcut ..... An alternative is of course manual editing, but we are wondering whether using BEaST to do the skull strip, and then replacing the brainmask.mgz with the brainmasking resulting from BEaST (and then recon-all -autorecon-pial -subjid <subject name> ), could be a workable solution. Would you recommend to do that/ not to do that? Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Regarding: skull strip
by Dr Sampada Sinha 01 Mar '16

01 Mar '16

Dear freesurfer experts, I am trying to do analysis of T1w images. However, with one participant, try as I might I am not able to get rid of a portion of skull. I tried all the three methods explained very well on freesurfer skullstrip wiki page. But, the portion of skull still remains. I also tried to run the recon-all after fsl bet process, but then I am getting a large topological error and the process get stuck there for days on end, until I don't close the terminal. I am attaching all the processed images using ws threshold, multistrip, gc strip and finally of talairach_with_skull_2.lta. I will greatly appreciate if this can be sorted by you all. Also, I would like to bring to your notice of the command error while doing skullstrip with talairach_with_skull_2.lta. The third command IMHO should be (as it works with this one!): cp talairach_with_skull.lta talairach_with_skull_2.lta and not, cp talairach_with_skull_2.lta talairach_with_skull.lta Thanks and regards, Sampada Sinha Pre-doctoral student KGMU, Lucknow India

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Problem with brainstem substructures segmentation
by Riccardo Gubellini 01 Mar '16

01 Mar '16

Dear Freesurfer users, Sorry for reposting this message again, but I really need your help. We have downloaded the Freesurfer 6.0 version since we are really interested in the brainstem segmentation. We are working with a pc equipped with a 3.6 GHz CPU and 16 GB RAM. We installed freesurfer6.0 on a virtual machine Linux (CentOs 6.7) enabling 4vcpu 11Gb of RAM. Disk space was 50 GB and after installation we have 15 GB free for data. We have launched recon-all –all for some cases and everything went right. Then we have tried to launch recon-all –all –s nameofsunbject –brainstem-structures and the process, after about 6 hours, stacks, during the SegmentSubject process and after having computing hyperparameters for estimation of Gaussian parameters. Do you have any ideas of what is happening? We tried to launch the brainstem segmentation also for the test data ( ftp://surfer.nmr.mgh.harvard.edu/pub/data/hipposubfields-testdata.tgz) but we still have the same problem. Could it be a problem the use of a virtual machine Linux instead of real Linux machine? Thank you for your help. Riccardo Gubellini

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question about white matter segmentation
by Jasmin Alves 29 Feb '16

29 Feb '16

Hello freesurfer support, I have been quality checking after the recon-all command according to the trouble shooting tutorials and have noticed quite a few participants that have white matter segmentation occurring on parts of the skull (see screen shot) but these regions are not outlined as white matter, is it necessary to use the voxel edit to remove where the skull is considered part of the white matter mask? Thank you, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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Freesurfer March 2016