Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

Correcting for dura/pia mater
by Leavitt, Mackenzie 04 Jan '18

04 Jan '18

Hello Freesurfer Developers, I am brand new to Freesurfer, so I'm just getting acquainted with how to use the program. Our clinic is attempting to run quality control on our imaging data for the last five years. One issue that I've noticed many times in our sample is that the Freesurfer program includes portions of the dura and pia mater in the brain mask volume after running reconstruction. On particularly bad images, it looks like a small part of the skull is included too. I've browsed through the tutorial datasets on Freesurfer, but it seems like there isn't an obvious way to make edits to images to correct for this. Please let me know what edits I should make if I want to correct for this. In addition, let me know if there is a way to correct for this error that can be quickly applied to a large number of subjects at once. There are at least 150 brains that have this issue, so it would be helpful if there was a way to correct this error quickly. Best, Mackenzie =================================== Please consider the environment before printing this e-mail Cleveland Clinic is currently ranked as the No. 2 hospital in the country by U.S. News & World Report (2017-2018). 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.

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Change the location of SUBJECTS_DIR
by zuxfoucault Wong 04 Jan '18

04 Jan '18

Dear list, If I changed the location of subjects_dir (via `export SUBJECTS_DIRS=/new_location/) after `source $FREESURFER_HOME/FreeSurferEnv.sh`, could I still completely run the `recon-all -all`? I mean some folders in the default location of subjects_dir, such as fsaverage, would not be included in the new subjects_dir. Would this cause trouble to the subsequent freesurfer routine? Thanks for your time! Best, Foucault

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Postdoctoral position available in the Poldrack Lab
by Chris Gorgolewski 04 Jan '18

04 Jan '18

Apologies for cross-posting. The Poldracklab at Stanford is looking to hire a postdoc with expertise in fMRI data analysis, starting as soon as possible. Our lab is a dynamic and collaborative group that includes basic cognitive neuroscience researchers focused on the study of decision making and executive function alongside methodological researchers focused on reproducible data analysis and data sharing. Stanford University is located in sunny northern California, deep in the heart of Silicon Valley and a short train ride to San Francisco. The postdoc will be able to contribute to a number of ongoing research projects in our lab and collaborating labs by analyzing fMRI data from those studies. In addition, the postdoc will have the opportunity to develop their own research program with the domain of scientific or methodological problems currently being investigated within the lab ( https://poldracklab.stanford.edu/projects) The successful candidate should: - Have a PhD in a relevant field of study and demonstrated experience with the processing and statistical analysis of fMRI data. - Have strong and demonstrated computer programming skills, including Python. Experience with Nipype is strongly preferred. Candidates will be asked to submit a link to their open source code repository for review. - Have strong skills in statistics and machine learning. - Have solid experience with computational data analysis, including strong UNIX/Linux skills and experience using high performance computing clusters. Experience with cloud computing platforms is also preferred. - Be dedicated to open source software development and data sharing. The Poldracklab is strongly committed to diversity in science, and we particularly welcome applications from members of traditionally underrepresented groups. Eligible candidates will be asked to complete a data analysis problem using a specified dataset and present a report of their results as well as sharing their analysis code, in order to demonstrate their expertise with data analysis. Interested candidates should email the following to russpold(a)stanford.edu: - A cover letter describing your background and research interests - CV (including a link to code repository, e.g. Github, Bitbucket) - Names and email addresses of two references

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Substituting standard freesurfer spatial normalization with enantiomorphic approach
by King, Daniel (Research Student) 04 Jan '18

04 Jan '18

Hello Freesurfer List, I am looking to use freesurfer to analyse MRI images from some patients which have diverse traumatic pathology, with gross lesions occurring in WM and GM as well as some occurring across the boundary. I have run these through recon-all with freesurfer v6 but am concerned about the ability of the Taliarch transform step to spatially normalize the images due to the distortions introduced by the lesion. I would therefore like to use an enantiomorphic approach such as Nachev et al (2008) Neuroimage using a replacement approach which mirrors volumes from the undamaged hemisphere to 'Fill' the lesion. If I was to do this, what would I need to generate to feed into the freesurfer pipeline and what would I replace? I assume I would need to rerun recon -all without the Taliarch step and use the new output instead? Will these lesions effect any other downstream functions such as the registration step or do these use the taliarch transform? Any help would be greatly appreciated! Best wishes, Dan King

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GC-DG
by 郑凤莲 03 Jan '18

03 Jan '18

Hi professor, I am using FS 6.0 for hippocampal subfield. I have a doubt what is the full name of GC-DG? I didn't find it in the wiki. Sincerely, Zheng

2 1

Scan sequences and parameters in hippocampus segmentation.
by Qin weiting 03 Jan '18

03 Jan '18

Dear FreeSurfer experts, I'm sorry that English is not my mother language. I have met some trouble in choosing the scan sequences and parameters of data collecting in hippocampus segmentation, I have read the MORPHOMETRY PROTOCOLS on FreeSurfer Wiki, but our lab only has GE Discovery MR 750W instead of Siemens MRI. How should the T1 and T2 scan sequences and parameters be designed on a GE MR 750W? Thank you very much！ Best, Qin weiting

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Thresholding of Monte-Carlo simulation
by yoichiro takayanagi 03 Jan '18

03 Jan '18

Dear FS experts, I’m wondering whether the Monte-Carlo simulation accountｓ for spatial or intensity thresholds (or both). Thanks, Yoichiro Takayanagi

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AnatomiCuts in tracula
by Knut J Bjuland 03 Jan '18

03 Jan '18

Dear Freesurfer expert I have used Tracula and I read that AnatomiCuts could improve Tracula performance. Can I use AnatomiCuts with Tracula in Freesurfer 6.0 or developer version. If this is not the case, will it be released in Freesurfer 6.1 Best regards Knut Jørgen Bjuland PhD

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Does this analysis work for new born baby
by Ting Li 03 Jan '18

03 Jan '18

Dear Stuff, Happy new year. Does Freesurfer work for new born baby MRI or not? If I want to use it for baby MRI, what should I pay attention to? Thanks a lot! Best wishes, Ting

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FSAVERAGE - RECON-All
by Savaş Aker 03 Jan '18

03 Jan '18

Dear all, I would like to learn the following: I ran recon-all -all command, and now want to use only parcellation results of Desikan-Killiany Atlas or Destrieux (mean curvature, cortical thickness, etc.). So I will use values under STATS folder (e.g. lh.aparc or Lh.aparc.2009 for mean curvature and thickness) and do my own statistical analysis with these values. To make it clear, I will NOT continue on qdec for statistical analysis. So I did NOT run -qchache command for preparing my data for qdec (so my data was not sampled to fsaverage). Considering these, do I still use fsaverage in any stage of my analysis (running recon-all without qchace option)? I want to use only results of e.g. Desikan-Killiany Atlas, and do not want my data to be resampled to fsaverage. Thanks, Savas

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