Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]Using a Different Atlas for Anatomical ROI Analysis

External Email - Use Caution Dear Shawn, I can't fully answer your question, but maybe as a start: I think the idea behind the suggestion to run recon-all on the template is that this would allow you to map the results of the FreeSurfer thickness analysis (which are in by defau

[Freesurfer] Full-time postbac position

External Email - Use Caution The Connectomics of Anxiety and Depression (CAD) Lab at the University of Delaware is hiring a full time postbac research assistant. The individual will contribute to an ongoing NIMH-funded R01 grant examining longitudinal change in brain networks that

Re: [Freesurfer] Requesting to clarify doubts on data analysis

Hi KC 1. Volumes are typically correlated with TIV and so if you don’t care about TIV itself you probably want to include it as a nuisance variable (both cortical and subcortical) 2. Thickness does not show this correlation and typically does not need to be correlated. Surface area does,

[Freesurfer] Postdoctoral position in Developmental/Affective/Clinical Neuroscience

External Email - Use Caution Dr. Jeffrey Spielberg is accepting applications for a *Postdoctoral Researcher position* in the *Connectomics of Anxiety and Depression* Lab at the University of Delaware. The researcher will contribute to an ongoing NIMH-funded R01 grant examining long

[Freesurfer] PhD Position Available @ University of Delaware: Movement Disorders/Parkinson's Disease Research

External Email - Use Caution The Motor Neuroscience and Neuroimaging Laboratory in the Department of Kinesiology and Applied Physiology at the University of Delaware ( https://secure-web.cisco.com/1FGUBbOfcKBczlqb5RsAtMzP59F-DjBkVa-NfDgzN_TBY1B6pmehlEYdgemvsbr9Pn2pTXAnKJue2LVdp4HTh

[Freesurfer] Postdoctoral Positions in Clinical and Contemplative Neuroscience at McLean Hospital/Harvard Medical School

[cid:ffcafe71-529c-423a-8564-7c00e4b3ff4d] Postdoctoral Positions in Clinical and Contemplative Neuroscience at McLean Hospital/Harvard Medical School Postdoctoral positions are available under the mentorship of Dr. Matthew D. Sacchet within the Meditation Research Group of the Center for

[Freesurfer] fsaverage_sym lobes parcellation mri_annotation2label

External Email - Use Caution Dear freesurfer community, when trying to obtain lobe labels for fsaverage_sym, mri_annotation2label segfaults - see terminal output below. It works smoothly for fsaverage and any other subjects. Is there any workaround? >mri_annotation2label --subj

Re: [Freesurfer] Pipeline errors - matlab

Thanks! But can you please share the full log, please? I’d like to see what happens before the error ;-) Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On Nov 22, 2021, at 00:15, Lab of Autism and Developmental Neuros

[Freesurfer] register.dat

External Email - Use Caution Hi Experts, My tracula completed with no error. So I was trying to view the fa.nii with the following command: freeview -v mri/brain.mgz mri/orig.mgz mri/wmparc.mgz:colormap=lut:opacity=0.2 dmri/dtifit_FA.nii:reg=touch/rusage.mri_ca_register.dat:color

Re: [Freesurfer] register.dat

External Email - Use Caution Sorry for the trouble, I seemed to find the registration matrix located in xfms/anatorig2diff.bbr.dat. Is that one correct? Best, Jackie On Mon, Nov 22, 2021 at 12:36 PM Zeng, Qi wrote: > Hi Experts, > > My tracula completed with no error. So I wa

[Freesurfer] Freeview grey matter, white matter and Tracula outputs

External Email - Use Caution Hi, If I want to freeview fully segmented grey matter, white matter, and Tracula outputs, are the following commands correct to the request? # to visualize the segmented cortical outputs freeview -v mri/aparc+aseg.mgz Question: why is one hemisphere b

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

Ah yes, I did say that this would be feasible in 7.2, before 7.2 came out ?? One more bug fix, in the same place (and then in the dev version): https://raw.githubusercontent.com/ayendiki/freesurfer/trcdev/scripts/trac-preproc >From now on the dTE from the config file will supersede the one from t

Re: [Freesurfer] Freeview grey matter, white matter and Tracula outputs

See "viewing volumes with freeview" in the tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview When you view the aseg, aparc+aseg, or any other FreeSurfer segmentation volume, make sure that the colormap is not grayscale but "look-up table". You can get the AD and

[Freesurfer] Converting .trk files in mini space to nifti using dorm_trk2trk

Hi, I'd like to convert *trk files that are in mni space to nifti files using dmri_trk2trk. The *trk files are here: /autofs/vast/freesurfer/centos7_x86_64/7.2.0-beta/trctrain/hcp/mni Attempts so far (that have failed) are: dmri_trk2trk --in TRACK_FILE.display.trk --outvol TRACK_FILE.display.

Re: [Freesurfer] Freeview grey matter, white matter and Tracula outputs

External Email - Use Caution Hi Anastasia, I tried to visualize the RD.nii with the following steps, however, it doesn't represent well as fa.nii does. (attached below). 1) RD = (L2+L3)/2: fslmaths dtifit_L2.nii -add dtifit_L3 -div 2 dtifit_RD.nii 2) mri_vol2vol --mov dmri/lowb.