[Freesurfer] postdoc at UCSF

The Neuroradiology Section and Memory and Aging Center (MAC) at the University of California, San Francisco (UCSF) are seeking an exceptional postdoctoral candidate in imaging genetics of neurodegenerative disorders. Using a variety of techniques, ranging from human structural and functional MRI

[Freesurfer] R: Re: mri_surf2vol

Thanks. I'm reading the surf2surf help but I do not understand the --trgsurfreg options. I'using mri_surf2surf --hemi rh --srcsubject fsaverage --srcsurfval thickness -- src_type curv --trgsubject Control21 --trgsurfval file?? Which is the file? Thanks Stefano >Messaggio originale

[Freesurfer] V1 Atlas ( brodman maps)

Dear Experts, I want to calculate PET signal within each Brodman map! I will give an example: If I want to caclulate PET singal for every parcellate and segment in the brain I do the following:   bbregister  --t1 --mov T1_MPRAGE.nii.gz --init-fsl --reg t1.reg.dat --s SUBJID   

Re: [Freesurfer] WmParc

you can also use mri_binarize --i wmparc.nii --match 1006 --o lh_entorhinal.nii On 05/13/2016 06:12 PM, Pradeep wrote: > Hi, > > This task will be a bit easy using fslmaths > > - convert mgz file to nii using mri_convert > -then use fslmaths -thr -uthr > > > example: > fslmaths wmparc.nii

Re: [Freesurfer] mri_surf2vol

The overlay Control21/rest/fc.ramgseed.surf.rh/R_Amygdala/sig.nii.gz is in fsaverage space, so either change the subject to fsaverage, or use mri_surf2surf to map the overlay into Control21's space, then run mri_surf2vol On 05/13/2016 06:03 PM, std...@virgilio.it wrote: > Hi list, > > I'm

[Freesurfer] mri_surf2vol

Hi list, I'm using FS-FAST for seed based functional connectivity.For a subject, I would like to report the sig.nii.gz from the inflate to volume space. I'm using mri_surf2vol --surfval Control21/rest/fc.ramgseed.surf.rh/R_Amygdala/sig.nii.gz --hemi rh --fillribbon --subject Control21 --identity

Re: [Freesurfer] Split a lablemap in the .annot format into parts

you can try mris_divide_parcellation On 05/13/2016 01:56 PM, Boris Rauchmann wrote: > Dear FS Community, > > is there an easy way to split a lablemap in the .annot format into parts? > In detail I would like to split network 6 (frontoparietal) of the yeo > atlas

Re: [Freesurfer] T2pial and [LONG]

Hi Kasper, It should work (I tried it a while ago with the dev version and it did not crash :-). Could not really tell if it helped much either. I don't remember if functionality is available in FS5.3 to include that in a long run. In dev, you would include the T2 for both the cross and long

[Freesurfer] Split a lablemap in the .annot format into parts

Dear FS Community, is there an easy way to split a lablemap in the .annot format into parts? In detail I would like to split network 6 (frontoparietal) of the yeo atlas (fsaverage/label/rh.Yeo2011_7Networks_N1000.annot) into the frontal, parietal and temporal part on each side. Is there an

Re: [Freesurfer] Connectivity from external seeds

a. You can map your seeds to the cortical surface of your subject (mri_vol2surf), then to fsaverage (mris_surf2surf), then view them on fsaverage. b. Not sure what you mean by this. The FC analysis just computes maps and those maps are compared at the second level. At that point it does not

[Freesurfer] Connectivity from external seeds

Hello FS experts, I am sorry for reposting this question in the forum: I calculated subject-wise resting-state FC maps after defining seeds into subject-wise anatomical space as mentioned in the manual. Now, location of seed regions across subjects differ a little. According to manual, FS maps

Re: [Freesurfer] segfault using brainstem module from dev version

Hi Martin, Thanks for the help. From the brainstem-structures.log, mri_robust_register is called by the brainstem module as follow: /data1/vbeliveau/software/freesurfer-Linux-centos4_x86_64-dev-110516/bin//mri_robust_register --mov imageDump.mgz --dst

Re: [Freesurfer] segfault using brainstem module from dev version

Hi Eugenio and Vincent, I cannot remember when I say robust_register crash the last time. It should never happen. So it could also be that the inputs are already corrupted. Can you send the inputs to that command so that I can try to replicate and see if this is still a bug or what is going

Re: [Freesurfer] segfault using brainstem module from dev version

It seems that mri_robust_register crashed. Martin, any ideas? The algorithm worked because the rough registration from the previous step was apparently enough to yield a decent segmentation. Maybe we should consider stopping the whole process if mri_robust_register dies... Juan Eugenio

Re: [Freesurfer] 2 unrelated questions regarding structural data

Hi Josh, The WU-UMN HCP outputs provide the thickness values already aligned to a common mesh in the *thickness.{32,164}k_fs_LR.dscalar.nii files (both 32k and 164k mesh version available).  You  should be able to run a nice, permutation-based group analysis on those using the FSL

[Freesurfer] 2 unrelated questions regarding structural data

Hello, 1) I am working with the recent release of human connectome data and am trying to run group analysis ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). I want to correlate brain volume with an behavioral variable. It is difficult to tell which files I need in order for

Re: [Freesurfer] Manual correction for brainstem module

Just a short note for other people who may use the matlab script to get volumes from the corrected hard segmentations. The volume in cubic mm should be total voxels divided by 8 instead of multiplying by 8. Cheers, Jacky 2016-05-12 17:44 GMT+02:00 Eugenio Iglesias : > Yes!

Re: [Freesurfer] T2pial and [LONG]

Hi Kasper, I don't see why not, but we haven't done this yet I don't think, so there may be undiscovered bugs. Bruce On Fri, 13 May 2016, Kasper Jessen wrote: Dear FreeSurfer, Currently, we have only manual edited the BASE (the CROSS was left unedited) in an longitudinal data. However, some

[Freesurfer] T2pial and [LONG]

Dear FreeSurfer, Currently, we have only manual edited the BASE (the CROSS was left unedited) in an longitudinal data. However, some cortical areas (f.eks. such as the inferior temporal area) are difficult to edit accurately due to image quality. I then read through the release notes (stable