Freesurfer

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30132 discussions

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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RA position at Ohio State
by Scott Hayes 21 Jun '18

21 Jun '18

External Email - Use Caution Research Assistant Position The Buckeye Brain Aging Lab (B-BAL) Department of Psychology Ohio State University Applications are being sought for a full-time research assistant position, in the Buckeye Brain Aging Lab (B-BAL) directed by Dr. Scott Hayes. The B-BAL studies the relationship among aging, physical activity, cognition and the brain [using Magnetic Resonance Imaging (MRI) metrics]. We also examine the neural correlates of memory in healthy and clinical populations. The Research Assistant 1 assists in the general coordination and conduct of research in the B-BAL, including administration of neuropsychological tests and/or questionnaires to young and older adults; recruits, screens, and schedules human subjects, including coordination of subject appointments (cognitive, MRI, and physical fitness assessments), subject payments, and submission of IRB amendments; assists with participant recruitment efforts between the laboratory and community partners; assists with research lab purchases and maintains lab supplies; assists with cognitive, MRI, and physical fitness data collection, including obtaining informed consent, cognitive testing (computer and paper and pencil based testing), MRI data acquisition, and record keeping; assists with cognitive and MRI data processing and analyses, supervises undergraduate research assistants. Desired qualifications include: Bachelor's degree in psychology, neuroscience, computer science, engineering, or physics; programming experience in either UNIX or MATLAB, as well as experience in neuroimaging data analyses; knowledge of software packages, such as FreeSurfer, FSL, AFNI, or SPM. The position is available for one year with the possibility of extension for additional years based on satisfactory performance and availability of funds. If you are interested in being considered for the position, please apply online at https://www.jobsatosu.com, under job listing #439956 and submit a current CV and the names of three references. If you have questions about the position or the lab, please contact Dr. Scott Hayes at hayes.1074(a)osu.edu *The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status.*

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Linear mixed modeling advice
by Mark Wagshul 20 Jun '18

20 Jun '18

External Email - Use Caution Hi. I am hoping someone out there can give me some advice on an analysis I'd like to try with our Freesurfer data. We have data (1 mm isotropic MPRAGE at 3T) on healthy older individuals, and have run them through the Freesurfer pipeline, generating cortical volume and thickness measurements. We are interested in studying the moderating effects of cortical atrophy on functional measures taken outside of the MRI. Our hypothesis is that the difference between two different functional measures is moderated by cortical volume/thickness. Thus it is really the interaction term = GM volume/thickness * task (binary 0/1) which we are after. So, we have fixed effects = GM volume/thickness, task, GM*task, age, .... Other covariates Random effects = subject. Repeated measure = task We have already run these analyses using mean cortical volume and thickness, as well as regional cortical volume and thickness in the PFC, and found very significant interaction effects. We would now like to refine these analyses with VBM/SBA analysis. I am hoping that someone can provide some guidance for us in terms of setting up such a model? (This is different from the standard LME analyses in which the imaging measure is the dependent variable. Here our dependent variable is our functional measure taken outside of the scanner, while the imaging measure - e.g. cortical thickness - is a moderating effect on the RHS of the equation. I'm not sure why this couldn't be done on a voxel-wise or vertex-wise basis, but hopefully someone can enlighten me if I'm being overly naive). Thanks in advance for the advice! Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einstein.yu.edu<mailto:mark.wagshul@einstein.yu.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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Error with Hippocampal Subfields and Amygdala Nuclei
by Andrea, Nicolas 20 Jun '18

20 Jun '18

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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problem with mri_convert --conform?
by Weisholtz, Daniel S.,M.D. 20 Jun '18

20 Jun '18

Hello all, I am having a problem running recon-all with a particular subject due to a very large topological defect. I traced the problem to the white matter segmentation it it seems to be due to an inhomogeneity such that the WM is darker in the superior/anterior part of the brain and lighter in the inferior/posterior part of the brain. I was going to try to correct this problem with control points, but I discovered that starting with orig.mgz, all the brain volumes have a very reduced voxel intensity range (~166-168). rawavg.mgz has a much more typical-appearing voxel intensity range. So I think something is going wrong with the mri_convert --conform step that converts rawavg.mgz to orig.mgz. Since the control points seems to be incorporated at the autorecon2 stage, I’m not sure it would help here. I am attaching rawavg.mgz and orig.mgz. I am very grateful for your thoughts. Sincerely, Dan Weisholtz

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