Freesurfer

freesurfer@nmr.mgh.harvard.edu

8 participants
30078 discussions

adding volume to aparc aseg
by Benjamin Deck 09 Aug '22

09 Aug '22

External Email - Use Caution Hi there, I have extracted an ROI mask for the subthalamic nucleus from MNI space and registered this with the subject's native space orig.mgz I would like to append this to the subject's automated segmentation from aparc+aseg.mgz. So I can use this segmentation as an atlas file for some later analyses. How should I go about doing this? Thanks, Ben -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1hWYRq8yK6uEx7JNWsNm2fv3yOgY5qceoUGFXdE_STPbBo…> Virus-free. http://secure-web.cisco.com/1t_mdtThOttLpGrWZn30jNxRm-K40bf-DIUL12waXusxlOD… <https://secure-web.cisco.com/1aBIr17KsDr5cY41N84azRobzbZ41tuCue3naVrEgSPP5S…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Using averaged T1-images to calculate cortical thickness
by Trolle, Carl 09 Aug '22

09 Aug '22

Hello dear FreeSurfer team, We are undertaking a multicenter study analyzing cortical thickness of controls and persons with a neurological condition. Unfortunately, there are issues with motion artifacts and image quality. To counter this, we’ve created averaged T1-images by combining one axial and one sagittal image in SPM for one of the study sites. Also, we are using recon-all with the optional T2- and T2-pial flags. Our impression is that the image quality has improved with the averaged images as compared to the non-averaged ones. Do you have any thoughts on this method or if combining images this way might cause issues when trying to calculate and compare cortical thicknesses? The averaged T1-images are only created for one of the study-sites and we plan on using study site as a covariate in our model. Will be happy to post images or logs if those may be helpful Kind regards, Carl FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Platform: CentOS Stream 8

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MP2RAGE sequence recon-all
by Renew Andrade 09 Aug '22

09 Aug '22

External Email - Use Caution Dear community: I need to run recon-all on some subjects with a MP2RAGE sequence. Can I do with any flag or directly -i “mp2rage”. Best, Rene Andrade.

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Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution
by Trolle, Carl 09 Aug '22

09 Aug '22

Thank you for the help and for getting back to me, After using the custom-fill option and labelling the central sulcus (yellow), I've been running the following code: "mris_register -L subject/label/?h.central_sulcus.label $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs S_central subject/surf/?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif subject/surf/?h.sphere.reg". Which is followed by "mris_ca_label subject ?h subject/surf/?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs subject/label/?h.aparc.a2009s.annot" or "recon-all -make all -subject". For some reason, I don't see any difference in the subject Destrieux-labelling (the incorrect shift is still there) and I suspect that I'm not doing this correctly. Would it be possible for you to check if I'm using the wrong syntax or if I might have missed out on some parts necessary for this solution to work? Kind regards, Carl

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Thalamus Parcellation - HCP data
by Asa Borzabadi Farahani 09 Aug '22

09 Aug '22

External Email - Use Caution Hi, I hope this email finds you all well. I have a basic question about the right way of using ThalamicSegmentation method ( implemented by Iglesias et al. 2018). I plan to use this subject-specific atlas on the data processed via the HCP pipeline. In this regard, after doing the PreFreeSurfer and Freesurfer bash files introduced by the HCP team, I use the subject-specific folder created by FreeSurfer and run the SegmentThalamicNuclei on the data of the subject. The point is that, HCP pipeline ultimately converts all timeseries into CIFTI format ( subcortical areas in 2mm template), hence the mgz file created by the SegmentThalamicNuclei bash file, should be converted into the CIFTI to be useful when defining ROIs. So, I am using the following commands to get the subject-specific thalamic labels in the CIFTI space. Could anyone having more experience confirm if it is a reasonable way or help if there exists a more accurate option? Regards, Asa Farahani mri_convert -rt nearest -rl /029/T1w/T1w_acpc_dc_restore.nii.gz /029/mri/ThalamicNuclei.v13.T1.mgz ThalamicNuclei029.v13.T1.nii.gz applywarp --rel --interp=nn -i ThalamicNuclei029.v13.T1.nii.gz -r /029/MNINonLinear/T1w_restore.nii.gz -w /029/MNINonLinear/xfms/acpc_dc2standard -o ThalamicNuclei029.v13.T1.native.nii.gz applywarp --interp=nn -i ThalamicNuclei029.v13.T1.native.nii.gz -r /029/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o ThalamicNuclei029.v13.T1.Atlas_2mm.nii.gz wb_command -volume-label-import ThalamicNuclei029.v13.T1.Atlas_2mm.nii.gz FreeSurferColorLUT.txt ThalamicNuclei029.v13.T1.Atlas_2mm.nii -drop-unused-labels wb_command -cifti-create-dense-from-template template..dlable.nii T029.dlabel.nii -volume-all ThalamicNuclei029.v13.T1.Atlas_2mm.nii.gz

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preproc-sess doesn't support python3
by Peled, Noam 09 Aug '22

09 Aug '22

Dear group, I'm trying to help a colleague use FsFast, a wrapper I wrote in python. When calling preproc-sess, there is an inner call to slicedelay, which calls to a python command: [cid:image001.png@01D8AB29.B7C046B0] The syntax is in python2, and my colleague has only python3. If it's only in the print statements, could you please add parenthesis to support python3 syntax? Thanks! Noam

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Help for pass code to open Freesurfer Virtual Machine image (.7z)
by Yuuichi Oosawa 09 Aug '22

09 Aug '22

External Email - Use Caution Hello, I'm a student researching Magnetoencephalography estimation and have been trying to install Freesurfer on a Windows OS using a Virtual Machine, following the instructions below: "You will be prompted for a pass code when the archive is successfully opened. If you do not have the pass code to open the image, then *send an email to the Freesurfer help list* to receive it." I do not have the pass code to open it and therefore I'm emailing the freesurfer help list, please advise. Thank you for your help in advance! Yuuichi Oosawa -- E-Mail: oosawa-yuuichi659(a)g.ecc.u-tokyo.ac.jp

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FreeSurfer 7.3.2 officially released
by Douglas N. Greve 08 Aug '22

08 Aug '22

Hi, at long last we have an official release of 7.3. See the release notes can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes and also copied below. Thanks to all who tested the beta version. best doug * Bug fix when converting diffusion tensor data with a negative determinant from DICOM. There was a bug in the old code that made the bvecs incorrect in this case. The bvecs will now be correct regardless of whether you use the old code or the new -dcm2niix option (see below) * Bug fix: ability to fill in underlabeled ventricles. This is not done by default yet. To implement, add "-vent-fix -1 7000 1" to the mri_ca_label command line. This can be incorporated into recon-all by an expert options file with the line "mri_ca_label -vent-fix -1 7000 1". * Bug fix: ability to force white matter (WM) between putamen and cortex. This is not done by default yet. To implement, add "-insert-wm-bet-putctx 1" to the mri_ca_label command line. This can be incorporated into recon-all by an expert options file with the line "mri_ca_label -insert-wm-bet-putctx 1". If you want to use both the ventricle fix and the WM insertion, then create a line "mri_ca_label -vent-fix -1 7000 1 -insert-wm-bet-putctx 1" to the expert options files * Bug fix: improve surface placement in inferior frontal area near putamen. There are some cases where the white surface is not placed well in these areas because of the close proximity of putamen to cortex; it is probably the case that the surface is not well-defined in this region anyway, but the placement can be improved by creating an expert options file with the line "WhitePreAparc --rip-bg-no-annot" * Bug fix/New: ability to automatically edit the filled.mgz to remove voxels from amygdala and parts of hippocampus. These voxels can often cause topological defects that are not fixed properly. This is not done by default yet. To implement, create an expert options file with the line "mri_edit_wm_with_aseg -fix-scm-ha 1". * Bug fix: cross hemisphere analysis (xhemi <https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>). In previous versions, the surface registration (surfreg) would use the annotation during the registration procedure which caused some misalignment. Now surfreg will require that you specify either --annot (old behavior) or --no-annot (new recommended). The errors are small, so, if you have an ongoing analysis, you can stick with the old behavior. * Global Expert options file. If you have a file called global-expert-options.txt in your $SUBJECTS_DIR, recon-all will automatically read in this file as an expert options file * Defect labels will now only encompass actual cortical areas. Before, they would also include vertices on the medial wall, which was not very useful * New: Conversion from DICOM can now be done with dcm2niix as a backend using -dcm2niix with either dcmunpack or mri_convert. This should give the same result as when using the old code except it will be much faster and can now handle all cases that dcm2niix can handle, including enhanced dicom. At some point, this will become the default method. Thanks to Chris Rorden and Yujing Huang for getting this working. * New: Gradient unwarping. There is a new program called mri_gradunwarp; you still have to supply the gradient unwarping spherical harmonics tables. * New: Minimally Invasive Defacing tool (MiDeFace <https://surfer.nmr.mgh.harvard.edu/fswiki/MiDeFace>). * New: segment_subfields <https://surfer.nmr.mgh.harvard.edu/fswiki/SubregionSegmentation> beta version new software to run subfield segmentation (hippocampus, amygdala, thalamic). The old software required matlab. The new tool is written in python but will not give exactly the same result but will be extremely close. Does not work with T2 yet. * New: SynthStrip <https://surfer.nmr.mgh.harvard.edu/docs/synthstrip> deep learning tool to strip skulls * New: ScLimbic <https://surfer.nmr.mgh.harvard.edu/fswiki/ScLimbic> subcortical limbic deep learning segmentation tool * New: HypothalamicSubunits <https://surfer.nmr.mgh.harvard.edu/fswiki/HypothalamicSubunits> deep learning segmentation of hypothalamic subunits * New: SynthSeg <https://surfer.nmr.mgh.harvard.edu/fswiki/SynthSeg> deep learning contrast-independent whole brain segmentation (including cortical parcellation) * New: Segmentation-based (SB) cost function <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5690540/pdf/nihms916015.pdf> for multimodal registration in mri_robust_register * New: better version control. You can create a file called fs-allowed-versions.txt in $SUBJECTS_DIR with a list of allowable versions for your analysis. If this file exists, then both the current version of FS and the version listed in $subject/scripts/build-stamp.txt must be in the list for recon-all to proceed. This helps to prevent using different/incompatible versions of FS within the same analysis while allowing the mixture of compatible versions. * New: interface for X11 virtual frame buffer (fsxvfb). When you run freeview from fsxvfb, no X server is needed. This is good for taking a bunch of pictures when you don't want freeview popping up all the time. Eg, fsxvfb freeview orig.mgz -ss mypic.png --quit

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accumbens nucleus volumes
by Alexopoulos, Dimitrios 08 Aug '22

08 Aug '22

External Email - Use Caution The accumbens nucleus is very difficult to delineate in some younger (3yo) subjects and in infants run through the infant pipeline. The pipelines segment the region but I'm not sure how reliable the volume measures are. Can the accumbens volume be included with another structure (i.e caudate)? Jim ________________________________ 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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segmentation of thalamic nuclei: possibility of generating connectome
by Lauren Taylor 08 Aug '22

08 Aug '22

External Email - Use Caution Hello FreeSurfer Developers, I am trying to generate a connectome in MRtrix3 using FreeSurfer parcellations and segmentations. I am specifically interested in the subregions of the thalamus and noticed that the newest version of FreeSurfer (7.3.1) has added segment_subregions. This command runs on my M1 mac without error and successfully outputs ThalamicNuclei.FSvoxelSpace.mgz, ThalamicNuclei.mgz, and ThalamicNuclei.volumes.txt. I am wondering if it is possible to generate a file similar to aparc+aseg.mgz that is generated in recon-all, but with thalamic subregion segmentations included. I was thinking that the following steps could possibly work: * Run recon-all * Run segment_subregions thalamus * mri_surf2volseg: * mri_surf2volseg --i ThalamicNuclei.FSvoxelSpace.mgz --fix-presurf-with-ribbon ribbon.mgz --o aseg_new.mgz \ --lh-cortex-mask ../label/lh.cortex.label \ --rh-cortex-mask ../label/rh.cortex.label \ --lh-white ../surf/lh.white --lh-pial ../surf/lh.pial \ --rh-white ../surf/rh.white --rh-pial ../surf/rh.pial * merge seg --src aseg.mgz --merge aseg_new.mgz --o aseg_all.mgz * mri_surf2volseg --i aseg_all.mgz --label-cortex --o aparc+aseg_thalamus.mgz --lh-annot ../label/lh.aparc.annot 1000 --rh-annot ../label/rh.aparc.annot 2000 --lh-cortex-mask ../label/lh.cortex.label --rh-cortex-mask ../label/rh.cortex.label --lh-white ../surf/lh.white --lh-pial ../surf/lh.pial --rh-white ../surf/rh.white --rh-pial ../surf/rh.pial I appreciate your time, and I look forward to hearing from you. Thanks, Lauren Taylor

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