Freesurfer June 2018

freesurfer@nmr.mgh.harvard.edu

105 participants
154 discussions

Question about GLM results in Freesurfer
by jahanvi patel 25 Jun '18

25 Jun '18

External Email - Use Caution Hello, We have a question about using glm_fit in freesurfer. When we model several covariates (behavioral scores) in glm, and we wanted to know the correlation between cortical thickness changes with the changes of behavioral scores. We obtained the correlation results nicely after using freesurfer's monte carlo correction (eg. increase of behavioral scores is correlated with the increase of cortical thickness changes). Should we still perform the bonefferi corrections on the results we got ? (because we have entered 5 covariates into the glm model, so we are wondering if it is still needed to divide the alpha-value by 5 to determine the final significant findings)? Thank you so much for helping us, Jahanvi

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Re: [Freesurfer] Group Analysis Covariates
by Hua, Jessica 25 Jun '18

25 Jun '18

External Email - Use Caution Hi FreeSurfer experts, Just bringing this question back up to the top: I analyzed my data following the guidelines on the FreeSurfer Tutorial/Group Analysis page . I am trying to plot the adjusted values (covariates: age, sex, and ICV) for the significant clusters for each of my participants. Is there a way to extract or calculate the adjusted values for each participant in each cluster after accounting for covariates (age, sex, and ICV)? Best, Jessica ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Saturday, June 23, 2018 11:00 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 172, Issue 36 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. FreeSurfer Manual Edit Sequence (David S Lee) 2. Using grad_unwarp (James Gullickson) ---------------------------------------------------------------------- Message: 1 Date: Fri, 22 Jun 2018 11:37:44 -0500 From: David S Lee <david.s.lee(a)wisc.edu> Subject: [Freesurfer] FreeSurfer Manual Edit Sequence To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAGcZjx8px96eS=O64q5nivBObJP9cqDha3_R87G3GHdjkVQnqA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Experts, When performing manual edits on brain masks, white matter, and gray matter, do I have to strictly follow the sequences(process stages) listed here <https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all>? For instance, the link suggests that "autorecon2-pial is used after editing brain volume *after running -autorecon2". In other words, is it okay to perform "autorecon2-pial" before "autorecon2-wm"? Thank you for your time, -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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Amygdala nuclei - stable version -SOLVED
by Liza van Eijk 24 Jun '18

24 Jun '18

External Email - Use Caution Hi Lisa Thanks a lot for the interest! The tool itself is pretty Steele and unlikely to change any time soon. But the rest of FreeSurfer... who knows when 6.1 will come out. If you're worried about reproducibility of results, you can always process your subjects with FreeSurfer 6.0 and then run the subfields/amygdala on top. Cheers Eugenio PS would you mind posting this question on the list? It's be great to share (ill just copy-paste the answer) From: Liza van Eijk Sent: Wednesday, June 20, 02:39 Subject: Amygdala nuclei - stable version Dear Dr Iglesias, I am interested in using your amygdala nuclei segmentation tool. Would you happen to know when a stable release is coming out? Thanks again, Liza van Eijk PhD Candidate University of Queensland Brisbane, Australia

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differing display colors for 2+ labels in tksurfer
by Yagmur Ozdemir 19 23 Jun '18

23 Jun '18

External Email - Use Caution Hello freesurfer experts, I am aiming to view 3 to 8 different labels on one flattened surface patch created&viewed in tksurfer. Even if I can manually select the color of first label, the next ones end up sharing the same color and I cannot seem to change this from the interface and I didn't come across any command line options for this. Any advice on how to set these different colors? I see that freeview can handle this, but to my knowledge it cannot open flattened patches? Any help would be deeply appreciated. Best Idil

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Using grad_unwarp
by James Gullickson 22 Jun '18

22 Jun '18

External Email - Use Caution All, I am interested in using grad_unwarp. I have been reading up on the documentation a bit and from what I understand not all the necessary files are distributed with the public version of Freesurfer, due to proprietary information in the tables. However, there is a script called grad_unwarp in my $FREESURFER_HOME/bin directory. I have access to the .grad files necessary for my project, so I was planning to just piece together the environment manually. Based on: https://surfer.nmr.mgh. harvard.edu/fswiki/GradUnwarp there are a few pieces I'm missing: - create_displacement_tables script - grad_unwarp_converter.pl script - matlab files Is there somewhere I can locate these missing scripts/files? Thanks, James

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FreeSurfer Manual Edit Sequence
by David S Lee 22 Jun '18

22 Jun '18

External Email - Use Caution Hello Experts, When performing manual edits on brain masks, white matter, and gray matter, do I have to strictly follow the sequences(process stages) listed here <https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all>? For instance, the link suggests that "autorecon2-pial is used after editing brain volume *after running -autorecon2". In other words, is it okay to perform "autorecon2-pial" before "autorecon2-wm"? Thank you for your time, -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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Merging aparc+aseg.mgz and brainstemSsLabels.v10.FSvoxelSpace.mgz
by Mehul Sampat 21 Jun '18

21 Jun '18

External Email - Use Caution Hi Eugenio and Bruce, We used freesurfer-6.0.0 to segment the brain-stem into different different structures. I see we get two mgz files after this process: aparc+aseg.mgz and brainstemSsLabels.v10.FSvoxelSpace.mgz Do you have any recommendations to combine these two masks into a single mask ? I see pons in brainstemSsLabels.v10.FSvoxelSpace.mgz overlaps with the brain-stem in aparc+aseg.mgz but the midbrain in brainstemSsLabels.v10.FSvoxelSpace.mgz overlaps with brain-stem and the ventral-dc in aparc+aseg.mgz. Any recommendations are appreciated. Thanks Mehul

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are *h.pial and bem watershed surfaces in same co-ordinate system?
by Levin Kuhlmann 21 Jun '18

21 Jun '18

External Email - Use Caution Hi everyone, Can someone tell me if the 'surfs/*h.pial' surfaces generated in freesurfer and the surfaces generated by mne_watershed_bem/mri_watershed (i.e. 'bem/watershed/*brain_surface, 'bem/watershed/*inner_skull_surface', etc) are in the same co-ordinate systems? And if they are not in the exact same co-ordinate system, what transform is required to co-register the surfaces in the 'surfs' folder with the surfaces in the 'bem/watershed' folder? For a given subject, when I plot the *h.pial and *inner_skull_surface in freesurfer's freeview the brain sits nicely in the inner skull. When I plot the brain and inner skull in fieldtrip the brain surface crosses the inner skull. Therefore I am not sure if freesurfer's freeview has to do something to co-register *h.pial and *inner_skull_surface , or if something is going wrong in fieldtrip when loading in these two surfaces even though I use the exact same function to load them in (ft_read_headshape). I am using default scripting for running freesurfer and mne_watershed_bem (an mne script that runs mri_watershed) as can be seen in the file at this link: https://www.dropbox.com/s/znivq8cbc8c1959/sge_launch_freesurfer_mne_ants_al… Cheers, Levin Kuhlmann, PhD Centre for Human Psychopharmacology Swinburne University of Technology & Departments of Medicine and Biomedical Engineering The University of Melbourne. lkuhlmann(a)swin.edu.au<mailto:lkuhlmann@swin.edu.au> levink(a)unimelb.edu.au<mailto:levink@unimelb.edu.au> Ph: +61412 552283

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Re: [Freesurfer] Error with Hippocampal Subfields and Amygdala Nuclei
by Iglesias Gonzalez, Eugenio 21 Jun '18

21 Jun '18

External Email - Use Caution Hi Nick, I believe Doug had a similar problem (atlas not flipping for right hippocampus) because he mixed versions of FreeSurfer. Your call is definitely a bit weird… First, you’re running the hippocampal subfields with FS6. And then, you’re calling a script (segmentSubject.sh) which is supposedly segmenting the amygdala. Questions: 1. What’s inside that script (segmentSubject.sh)? 2. The amygdala module also segments the subfields. Why would you need to segment the subfields alone with FS6 in first place? Either way, the most likely solution is the following. Since the subjects have been run through recon-all (from what I can see), you can source the development version, and simply run: segmentHA_T1.sh bert (replace bert by your subject name). Further instructions, including commands to visualize the output, can be found here: http://freesurfer.net/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Andrea, Nicolas" <NANDREA(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, 20 June 2018 at 21:09 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Cc: "Jacobs, Heidi Irma Louisa" <HJACOBS(a)mgh.harvard.edu> Subject: [Freesurfer] Error with Hippocampal Subfields and Amygdala Nuclei Hello, I am attempting to run two FS commands to provide data on the hippocampal subfields and the amygdala nuclei. I have run this on ~700 cases, but a few seem to have an error with the segmentation (see attached images for examples). Here is the script that I’ve run that shows where the data is and is run on the specific subject whose images are attached. This was written as a csh script. #Hippocampal subfields setenv SUBJECTS_DIR /autofs/space/rincewind_003/users/Amygdala/subjects source /usr/local/freesurfer/nmr-stable6-env recon-all -s HAB_133_FOK_2.1 -hippocampal-subfields-T1 -no-isrunning #Amygdala nuclei cd /autofs/space/rincewind_003/users/Amygdala/hippoAmyg ./segmentSubject.sh HAB_133_FOK_2.1 $SUBJECTS_DIR left ./segmentSubject.sh HAB_133_FOK_2.1 $SUBJECTS_DIR right If you have any insight on what might be going wrong with the segmentation, that would be most helpful. The recon-all.log is included. Thanks! Nick

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How to quickly edit aparc+aseg and recalculate volume tables.
by Jeff Crawford 21 Jun '18

21 Jun '18

External Email - Use Caution Dear Freesurfer Experts, I have some experience editing the pial surface with tkmedit. (As in this wiki page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_tktools ) As I recall, this process can be time consuming, because the regeneration of the peel needs to be sent back through the processing stream. Similarly, editing subcortical structures through tkmedit or freeview also requires you to send it back through recon-all ( https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithDa… ) If I am only interested in the volumetric values created through stats2table, is there a quicker way to recalculate the values I have just manually edited? As I understand it, stats2table just adds up the voxels from the specific labels in the aparc+aseg segmentation, so if I manually edit the voxels of that segmentation and save it, wouldn't I just need some command to recount all those voxels to update the table? I just see no reason for having to spend more time with recon-all if I only need such a simple adjustment. Am I wrong? If I am, then I would also like to know which method, freeview or tkmedit, would allow me to edit more quickly, as I have only used tkmedit in the past. Hope your week has been good to you, Jeff

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Freesurfer June 2018