Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

FreeSurfer / Tracula segmentation between seed points?
by Christian Owen 05 Apr '23

05 Apr '23

External Email - Use Caution Hi, Does Freesurfer / Tracula provide any way to automatically segment a tract between two arbitrarily selected points? Christian

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Re: [Freesurfer] Freeview segmentation fault
by fsbuild 04 Apr '23

04 Apr '23

External Email - Use Caution You can set the environment variable FS_LICENSE to point to your license file.  Some people set that in their shell init file, e.g., .bashrc, and keep the file license.txt in their home directory.  For example, $ cd $HOME$ head -1 license.txtme(a)somedomain.com        <—— email you used to register $ export FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEme(a)somedomain.com        <—— email you used to registerStarting with the Freesurfer 7.3.2 release, the Mac build used Xquartz 2.8.2.   If you are not already running 2.8.2 or newer then I would download and install the latest version of Xquartz from https://secure-web.cisco.com/1SXQ4X5w-vvi7X1Bgt8BsNVoSPV15hx0E9DH… - R.

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Freeview segmentation fault
by OSE KADIRI 04 Apr '23

04 Apr '23

External Email - Use Caution Hello, I am having some trouble using Freeview on my university cluster with my MacBook (macOS Monterey version 12.4). Freeview works fine from a Windows machine, but when I try to view images (using XQuartz on my Mac), I get "segmentation fault." It does not seem to be a memory issue and I'm not using multiple screens. I can successfully run MATLAB and gnuplot using XQuartz. Any help is greatly appreciated! Thank you, Ose -- Ose Kadiri Staff Research Associate, Deters Lab Department of Integrative Biology & Physiology, UCLA Pronouns: she/her

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FLAIRpial bug
by Silvia De Francesco 04 Apr '23

04 Apr '23

External Email - Use Caution Dear developers, We encountered the bug related to the analysis with FLAIR in recon-all (recon-all -s ${subj} -i T1.nii.gz -FLAIR FLAIR.nii.gz -FLAIRpial -all). We obtain a worse segmentation with FLAIR than only with T1. We use FreeSurfer v. 7.3.2 We also tried to run the analysis placing the line PlaceMMPialSurf --mm_min_inside 50 --mm_max_inside 200 --mm_min_outside 10 --mm_max_outside 50 in the global-expert-options.txt file in the $SUBJECTS_DIR and run recon-all -s ${subj} -FLAIRpial -autorecon3, the output seems better but the pial is ever worst than with only T1. What does the values of mm_min_inside mm_max_inside mm_min_outside mm_max_outside mean? Some suggestions to solve this problem? Thank you Silvia

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FreeSurfer VM pass code
by Toni Gurguí 04 Apr '23

04 Apr '23

External Email - Use Caution Hello, I would like to request the pass code for the FreeSurfer Virtual VM image. Best, T.

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Volume extraction of thalamus subfields in v7.3.2
by Melissa Thalhammer 04 Apr '23

04 Apr '23

External Email - Use Caution Dear Freesurfers, as already mentioned in a mailing list post (https://secure-web.cisco.com/1SAqhNan43pmaxS84P-6UvHZVgMO0LlOO5VahC9RJjjs3L…) subfield_segmentation in FS v7.3.2 does not create a statsfile including the output volumes. Instead, some txt file is created in /mri (i.e., ThalamusNuclei.volumes.txt). For summarizing the volumes across subjects, neither asegstats2table (because it looks for *.stats files) nor the quantifyThalamicNuclei.sh is applicable to the new function subfield_segmentation output directly. I've just adapted quantifyThalamicNuclei.sh and changed line 55 to the new version txt file names (see attached). Best, Melissa

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Issue with running recon-all on Synthsr output
by hmarzban＠student.ubc.ca 04 Apr '23

04 Apr '23

External Email - Use Caution Dear developers, I recently ran Synthsr on one of my images and now I am attempting to run recon-all. The output states that it finished without any errors in just 0.006 hours, but I am unable to proceed with the processing. Have any of you encountered this issue before? I would greatly appreciate your recommendations on how to proceed. (I am confident that there are no issues with the Freesurfer version and recon-all, as I have successfully run a 3T MP-RAGE image) Thank you Hengameh

2 1

Which motion correction parameters are used in FSFAST?
by Andy Kim 03 Apr '23

03 Apr '23

External Email - Use Caution Dear FreeSurfer Developer, Hi. Thanks to FreeSurfer, I could perform surface-based activation analysis with FSFAST. Now I want to do surface-based functional connectivity analysis. For the sake of consistency, I want to use the same nuisance regressors as used in FSFAST. Unfortunately I'm stuck in motion correction parameters. According to https://secure-web.cisco.com/10LyHLSQ2Psfux7V-2TqU0TpTUpRE9gROQ8dm_KryluL_Q…, motion correction parameters are stored in mcprextreg. Since there are 6 columns, I guess they are 3 translations and 3 rotations. On the other hand, none of them are in mcAll, X.mat. What are the 18 motion correction parameters in X.mat? and which motion correction parameters are used as nuisance regressors in FSFAST? Thanks in advance. Kind regards, Andy (Junghyun) Kim

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Finding non-contiguous labels within an annotation
by Colleen Hughes 03 Apr '23

03 Apr '23

External Email - Use Caution Hello, I have an fsaverage5 parcellation/annotation based on Schaefer 200 (attached). The parcel boundaries are supposed to be adjusted iteratively resulting in 200 contiguous parcels with new boundaries. In this person, it is clear from plotting in freeview that 1 vertex from a visual parcel migrated to be surrounded by the SOM (blue) and VAN (violet) network on the lateral side (same hemisphere). This doesn’t happen in all subjects, so I’d like to write a function to find this and similar parcels that are not contiguous in a more automated fashion. So far, I’ve used the matlab read_annotation.m function to count vertices per parcel but that’s not quite right because it treats all vertices with the same label as the same thing. Not sure if there is a way to identify neighboring vertices so I can see if any have the same label (contiguous) or not. I investigated mri_surfcluster but I’m not sure how to make it treat the annotation as the input. Perhaps there is a way to project the values (1-200) associated with each label to their vertices. And then mri_surfcluster requires contiguity so it may identify if there is a mismatch between the expected # of parcels and observed # of clusters. I am using freesurfer 7.3.2, Matlab 2020a, M1 iMac. Any thoughts on how to identify non-contiguous vertices within a parcellation? Thank you, Colleen -- Colleen Hughes, PhD Postdoctoral Researcher Laboratory of Brain and Cognition Montreal Neurological Institute-Hospital McGill University

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Re: [Freesurfer] moving results from fsaverage space to subject space
by Douglas N. Greve 03 Apr '23

03 Apr '23

Hi Jennifer, remember to send questions to the freesurfer list, thanks! Answers below On 4/3/2023 4:01 AM, Jennifer Kilmer wrote: > > External Email - Use Caution > > Hi Douglas, > > Thank you for your response. I have a few more questions; > > We can do the analysis in the surface space, but how could we move the > results from the surface space (FS average) to the original subject > volumetric space? Do you need to go to fsaverage space? If all you want to do is the surface-based smoothing, then you can do it in the native space, then use mri_surf2vol to map it back into the volume. Run it with --help. Use method2 with --fillribbon and --surfval as your surface pet data. > > "Why not map the individual to fsaverage space and do the comparison > there?" > We already do that in MNI space using volume smoothing and go back to > the individual subject space. We want to use the surface smoothing as > it's "... constrained to be only within cortical GM" (PMC4008670). As > we have to compare also with volumetric maps from electrophysiology > data, we need to go back to the individual volumetric space. > > > I hope this clears things up, please let me know if there is anything > we can try to achieve this. > > Jennifer

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