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30064 discussions

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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Is it possible to add additional T1 scans to improve surfaces/segmentation
by Michael Mc Laughlin 01 Apr '23

01 Apr '23

External Email - Use Caution I am working with standard neuro radiological MRI scans. These typically have something like this:: a) T1 headscout volume: 1.6mmx1.6mmx1.625mm 160x160x128 b) T1 se tra 0.72x0.72x5.2 320x320x30 c) T2 tse tra scan 0.72x0.72x5.2 320x320x30 d) T2 FLAIR (dark fluid) scan 0.58x0.58x5.2 460x460x30 c) T1 tse sag 0.72x0.72x5.2 320x320x30 c) T2 tse sag 0.72x0.72x5.2 320x320x30 I have found that the best results are obtained if I do the following: i) Start with the T1 headscout volume: 1.6mmx1.6mmx1.625mm This produces poor pial results but much better than using the T1s with a small number of slices. ii) Add in the flair data: Use -FLAIR and -autorecon3 with a FLAIR MRI scan This dramatically improves the pial surfaces and they look almost normal iii) Add some T2 data. This give more improvement of the pial surfaces See attached image for how the cortex looks after these stages My questions are: *1) How can I add in the data from the higher resolution T1 scans? (with only 30 slices)* *2) If I add a second T2 scan with -T2 -T2pial -autorecon3 will the results improve even more?* Regards, Michael

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White matter exclusions occurring in v7.3.2 but not v5.3
by Keefe, Sarah 31 Mar '23

31 Mar '23

External Email - Use Caution Hi FreeSurfer Team, Our group is working on reprocessing scans that we originally processed (performed quality control and edited where necessary) with FreeSurfer 5.3 with the HCP patch. We are aiming to reprocess everything with FreeSurfer version 7.3.2. So far when checking and editing FreeSurfer 7 outputs we're regularly seeing areas of brain that should be included within the white matter surface but are not, particularly in the accumbens and orbitofrontal areas. The areas are of lower intensity within the scans, but FreeSurfer 5.3 is able to handle these areas accurately - we don't see these issues in our runs on the same scan files done in FreeSurfer 5.3. I've attached a screenshot of the Freesurfer output of each version side by side on one of the slices where the exclusion is happening. We're seeing this on maybe 1 in 10 Freesurfer 7 scans. All did fine in 5.3. We're finding that the problem is not limited to certain scanners - one of these examples is from a Biograph PETMR scan and the other is from a Prisma. Is there a recommended flag or flags we could use with Freesurfer 7 recon-all that might get us closer to the way 5.3 handles this? The Freesurfer 5.3 parameters we originally used were: -all -qcache -hippo-subfields -nocubic -mprage The Freesurfer 7.3.2 parameters we are using now are: -all -qcache I have the recon-all outputs of both versions and the original scan available and can send them via FTP if that would be helpful. Other notes: Running with the -mprage flag added to the Freesurfer 7.3.2 recon-all launch was not different from the FS 7.3.2 recon-all launch without the flag but I can send that output along as well if it would be useful. Also, these examples are done in 7.3.2 but we've also run into this issue with 7.1.1. Really appreciate any assistance you can provide, as trying to figure this out has been delaying our processing a bit. Thanks so much, Sarah ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Synthseg segmentation of skull etc
by Fraser Aitken 31 Mar '23

31 Mar '23

External Email - Use Caution Dear Freesurfer community I have some low field T1 and T2 MRI images that I would like to use to create a head model for EEG source localization. I have been using SynthSR to improve the images and Synthseg for the basic segmentation etc and wondered if anyone had used synthseg to extract skull and scalp as well as WM/GM/CSF etc and how this might be done ? (or if this was possible) best wishes Fraser

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automatic screenshots to all axial slices
by Gonzalo Rojas Costa 31 Mar '23

31 Mar '23

External Email - Use Caution Hi: I need to take screenshots of all axial slices of a volumetric image that I am viewing using freeview (flair with a segmentation). How can I do it automatically? Sincerely, Gonzalo Rojas Costa

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multiple axial slice screenshots
by Gonzalo Rojas Costa 31 Mar '23

31 Mar '23

External Email - Use Caution Hi: I need to take screenshots to all axial slices of a volumetric image that I am viewing using freeview (flair with a segmentation). Sincerely, Gonzalo Rojas Costa

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moving results from fsaverage space to subject space
by Jennifer Kilmer 31 Mar '23

31 Mar '23

External Email - Use Caution Hello— I am having difficulties figuring out how to move PET images from the fsaverage space back to the subject space. Using the PETSurfer wiki instructions for surface-based analysis, we have sampled each subject’s surface onto the surface of fsaverage using mri_vol2surf, which was then smoothed using mris_fwhm, and finally the results were brought back from surface space to volume (using mri_surf2vol), still in the fsaverage space. We are doing an analysis in SPM comparing each individual subject to controls and would like to move these results to the subject space, because remaining in the fsaverage space has given us results that do not match up very well and make the analysis difficult. We have attempted using mri_vol2vol but the resulting gray matter ribbon did not align with our subject T1. Is it necessary to combine the talairach lta/m3z register files and/or inverse them to achieve this? and if so, how? or if there is a simpler way to move the results from fsaverage space back into subject space, please let me know. Thank you in advance for your help! Jennifer

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Re: [Freesurfer] HPC Usage - Moving On from CentOS7
by fsbuild 31 Mar '23

31 Mar '23

External Email - Use Caution We don’t use Alma OS which I believe is somewhere downstream from the official RedHat CentOS8 Stream distribution, i.e., the libs may not be the same.  I also don’t see that RedHat CentOS8* releases include CentOS7 versions of libraries. - R. On Mar 30, 2023, at 12:12, Horn, Mitchell Jacob <MJHORN(a)mgh.harvard.edu> wrote:As an update I’ve tested another run (bert, 7.2.0, no flags, recon-all) on an OS-8 system but set LD_PRELOAD to the 7 system’s libm.so: export LD_PRELOAD=/alma/cos7lib/libm.sorecon-all …. And that produced the equivalent results of all my CentOS7 runs: <image002.png> I believe this is very important information to the general community for stability with the imminent and inevitable switch to OS-8 HPC platforms. Best,Mitch_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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