Freesurfer

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18 participants
30131 discussions

PET-segmentattion
by Bouchra Guelib 10 Aug '22

10 Aug '22

External Email - Use Caution I want to segment registered PET to T1 MRI to 45 subcortical regions as the regions in aseg.stats of MRI. I used mri_segstats --seg MRI-floder/mri/aparc+aseg.mgz --reg Pet2T1.register.dof12.lta --sum petsuv.segstats.dat --i PET-SPM.mgh --ctab-default into petsuv.segstats.dat, I found only 40 regions, not as aseg.stats what should I change in my commend? -- *GUELIB Bouchra: *Ph.D. student *Lire *Laboratory University: Constantine 2-Abdelhamid Mehri- *Algeria * Alternative email: Guelibbouchra(a)gmail.com

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incorrect aseg/aparc but good surfaces
by Alexopoulos, Dimitrios 09 Aug '22

09 Aug '22

External Email - Use Caution Any ideas what would be causing this issue with a 3yo subject run through 7.2. - see screenshots below. The white/pial surfaces look fine, but the left hem aseg/aparc have mostly labelled GM and little WM. The output from the aseg.stats are included below. Note the GM volumes looks reasonable but the left hem WM is low as indicated in the aseg. Thanks. Jim [cid:image005.jpg@01D8A724.5EB32690] [cid:image006.jpg@01D8A724.5EB32690] [cid:image007.jpg@01D8A724.5EB32690] # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 305367.653313, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 308463.210941, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume, 613830.864253, mm^3 # Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume, 29082.113381, mm^3 # Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume, 164061.703793, mm^3 # Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume, 193143.817174, mm^3 ________________________________ 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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Sclimbic segmentation fault error?
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 09 Aug '22

09 Aug '22

External Email - Use Caution Hi all, I am receiving this error when trying to run sclimbic module. It's not being very descriptive about what the error is so I was wondering if you all can help debug. My SUBJECTS_DIR is correct mri_sclimbic_seg --s GP0050 /usr/local/freesurfer/dev7/python/scripts/mri_sclimbic_seg --s GP0050 Excluding seg [853] Using CPU Using 1 thread(s) Loaded lookup table /usr/local/freesurfer/dev7/models/sclimbic.ctab Loaded population stats /usr/local/freesurfer/dev7/models/sclimbic.volstats.csv nb_labels 14 Segmentation fault i am using freesurfer-linux-centos7_x86_64-dev-20220802-56c77e1 Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --

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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

2 1

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

2 3

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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