Freesurfer

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30088 discussions

Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors
by David S Lee 20 Jun '19

20 Jun '19

External Email - Use Caution Hello FreeSurfer Experts, I wanted to re-post this question (posted June 4th), yet did not receive your guidance: I have visually checked 116 subjects that have been processed using Freesurfer's latest hippocampal/amygdala subfield segmentation algorithm (Development version 20180518 <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…>) and came across 5 cases that failed the QC. My T1s had been processed using FS 5.3, and I used the command "segmentHA_T1.sh" from the latest Dev version. - 3 subjects are missing a mask of the anterior amygdaloid area (AAA), but in the volumetric output, there are values for the regions. - 2 subjects' medical nuclei masks are located in the Putamen region (more superior/detached from the rest of the amygdala). I found the exact same inquiry RE: AAA region posted on April 30, 2019, but I did not see any response. What would be your recommended course of action to resolve these issues? Is there a way to see volumetric measures in the freeview GUI (when clicking a region) to possibly manually trace the missing regions? Thank you for your time, -- David S. Lee Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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neuroimaging pre-registration template
by Remi gau 20 Jun '19

20 Jun '19

External Email - Use Caution Dear neuroimagers, We are organizing a hackathon<https://docs.google.com/document/d/1fckBKZEv_Jh0hJ6oVdYuK21krhZtnH0uhwcHp0j…> to develop a tool to help researchers creating a pre-registration / registered-report for neuroimaging experiments. The hackathon is embedded in the upcoming meeting of the Society for Improving Psychological Science<https://www.improvingpsych.org/SIPS2019/> in Rotterdam, NL, July 7-9. We are thus interested in the challenges that people face when preregistering their studies. If you have pre-registered (or currently are pre-registering) one of your neuroimaging study, please take 5 minutes to fill in this survey<https://docs.google.com/forms/d/e/1FAIpQLSe9IAMFThhpPday_tHvkh1dTGCqjcdKpeb…> and give us any feedback you can. Thank you for your time! Johannes Algermissen, David Mehler, Remi Gau, Stephan Heunis

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Change colorbar font color in Freeview
by Saskia Helbling 20 Jun '19

20 Jun '19

External Email - Use Caution Hi all, I changed the background color in Freeview to white and now want to change the font color of the colorbar to black for better visibility. Any ideas on how to do this? Many thanks in advance, Saskia

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problem with reconstruction
by Barletta, Valeria 20 Jun '19

20 Jun '19

Dear Freesurfers, I am having issues with a reconstruction which is giving me giant defects that I cannot correct (see screenshots). I tried to work on the wm and also to use the command recon-all -subject NIMMS02_2year_recon -T2 T2SPACE.nii.gz -T2pial -autorecon3 ... to correct using T2 images. Nothing worked. This never happened to me except this time. Any suggestions? Thank you a lot, Vale

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Parcellation to FS surface annotation
by Williamson, Brady 19 Jun '19

19 Jun '19

External Email - Use Caution Hello, I am trying to convert parcellations in MNI space (BrainNetome and Craddock 200) to a surface annotation file in fsaverage space. I have seen several posts that seem to talk about steps that may be applicable but none of them are very efficient. Is there an easy/direct way to do this conversion? It seems like I am missing something really obvious, like a one line command, that would do the trick. Thank you for any assistance, Brady

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Problem with installation test
by Shrabani Ghosh 19 Jun '19

19 Jun '19

External Email - Use Caution Hi freesurfer, I am following the installation test as suggested ( https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall and am currently stuck at example 2. When I ran recon-all, I got the output: "bash: /home/sghos003/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory" Any suggestions? Thank you. Shrabani Ghosh

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Re: [Freesurfer] Longitudinal Masking and FDR
by Hua, Jessica 19 Jun '19

19 Jun '19

External Email - Use Caution Dear Kersten, Thank you so much for your help! 1. As recommended, I masked my analyses using the label. 2. And that would be great if you could take a look at it when you have time. In the mean time, I will continue to try to figure out how to modify the FDR2 script. Best, Jessica Hua

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picture edit
by Abby tang 18 Jun '19

18 Jun '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to get some pictures about my results , so QDEC was used. However I can't adjust those pictures which QDEC produced, such as picture1. When I read other's paper, they provided different pictures just like picture2. I want to compare the relationship between age and thickness, which is controlled the effect about sex,education and eTIV. I want to get more beautiful pictures, but the ability of QDEC is limited. I have tried freeview, but I don't know what file should be loaded in freeview. After qdec processing, what file format should be selected to load freeview? Or if there are other method to use freeview direct to regressive age and thickness? Could you give me some advices? Thank you! Hope your reply. Thank you for your help. Best regards Abby

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DesikanKilliany ROI for mri_glmfit
by Tammi Kral 18 Jun '19

18 Jun '19

External Email - Use Caution Hello, I would like to use the insula label/ROI from the DesikanKilliany atlas with mri_glmfit. How do I reference this label, as I don't see a LUT for this atlas. I appreciate any suggestions. Thanks, Tammi R.A. Kral, M.S. -- Doctoral Candidate, Psychology University of Wisconsin-Madison Center for Healthy Minds Waisman Brain Imaging Laboratory

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Smoothing the pill surface
by Nillo, Ryan Michael R 17 Jun '19

17 Jun '19

Hello FreeSurfer users/developers, I want to generate a smooth pial surface similar to the one displayed on the LGI page (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI) without having to run the entire recon-all process. Additionally, I want to map this surface to the white surface. Is there an easy way to do this? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging External Email - Use Caution

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