[Freesurfer] Thalamic Nuclei {Disarmed}

External Email - Use Caution Hi Experts, I am using Freesurfer dev version for the segmentation of thalamic nulei. Previously, I have used this version for amygdala and hippocampus segmentation. However, the segmentThalamicNuclei.sh file can't be found in this version. Is there

[Freesurfer] recon-all to fsaverage

External Email - Use Caution Dear Freesurfers, I would like to apply recon-all to the fsaverage subject of my sample to get all the labels that are obtained in each individual subject. However, it is not possible because my average subject doesn't contain the file /orig/001.mgz re

[Freesurfer] Parcelation in gadolinium image

External Email - Use Caution Good morning, When I am using T1 with gadolinium, some errors appear in the later 3D mapping obtained. In particular, the boundaries of some of the structures which have gadolinium in the original image are not well defined in the parcelation. Do you kn

[Freesurfer] LGI in QDEC

External Email - Use Caution Hi experts, I am using qdec software for the statistic of LGI. I have created the .Qdecrc file. However, when I set Monte Carlo Null-Z Simulation (fwhm=10), there is an error: "Error running mri_surfcluster, Error: fwhm out-of-range(<1 or >30)". Then

Re: [Freesurfer] recon-all to fsaverage

Hi Jose can you clarify what you mean by "...to get all the labels that are obtained in each individual subject." You almost certainly don't need to recon fsaverage to do this, but I'm not sure exactly what you mean cheers Bruce On Tue, 12 Mar 2019, Laboratorio de Neurociencia Funcional wro

Re: [Freesurfer] Parcelation in gadolinium image

Hi Maria can you send us an image to show us what you mean? Usually contrast-enhancement lights up the dura and can cause bits of non-brain tissue to be left around, which you might need to deal with. cheers Bruce On Tue, 12 Mar 2019, María Martínez Rodrigo wrote: External Email

[Freesurfer] Error with mri_label2label(Segmentation fault(core dumped))

External Email - Use Caution Hi Bruce, I drawed a 3D ROI on the original image using freeview,and saved it as an label file. Then I wanted to sample it to my subject and to found the closest surface vertices so that I can extract the cortical thickness of ROI. I used the co

Re: [Freesurfer] Thalamic Nuclei {Disarmed}

External Email - Use Caution Dear Zheng, You’ll need a more recent dev version to use the thalamic nucle segmentation. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London Research staff Martinos

Re: [Freesurfer] recon-all to fsaverage

External Email - Use Caution Hi Bruce, what I really need is to obtain several labels that are only included in the aparc+aseg, not for each subject but for the entire sample. My goal is to use these labels (ROIs) in VBM analysis after they are trasformed to volume and further reg

Re: [Freesurfer] Error with mri_label2label(Segmentation fault(core dumped))

Can you send the full terminal output? On 3/12/19 10:36 AM, 310913949 wrote: External Email - Use Caution Hi Bruce, I drawed a 3D ROI on the original image using freeview,and saved it as an label file. Then I wanted to sample it to my subject and to found the closest surface verti

Re: [Freesurfer] Parcelation in gadolinium image

External Email - Use Caution Thank you for your answer! That is exactly what happens. The contrast makes that region lighter because of the presence of an hemorragy but I don't what could I use to obtain the parcels well defined in that area. El mar., 12 mar. 2019 14:56, Bruce Fis

Re: [Freesurfer] recon-all to fsaverage

I'm still not sure what you are trying to do. If you are running vbm, you can usually get the T1 sampled in the MNI space for all subjects. You can average them together and run the average through recon-all On 3/12/19 11:44 AM, Laboratorio de Neurociencia Funcional wrote: > > External E

Re: [Freesurfer] recon-all to fsaverage

External Email - Use Caution I just want to use some labels contained in the aparc+aseg.mgz and the aparc.a2009s+aseg.mgz files to build an anatomical template that can be used in VBM analysis. To my understanding, these labels should be obtained from the entire sample since they w

Re: [Freesurfer] recon-all: making sure that brain.mgz will be in RAS orientation.

Hey Bruce. Originally this is what I did. I used mri_convert on the relevant nii files, but I was wondering what to do with the surfaces files. I thought it'll be easier to create all of these files directly in RAS orientation. Thanks, Noam -Original Message- From: freesurfer-boun...@nm

[Freesurfer] Postdoctoral fellowship in Neuroimaging, genetics, and addiction at UVM

External Email - Use Caution Hello all, Please see the below postdoctoral advertisement sent on behalf of Hugh Garavan and Scott Mackey. We are seeking a postdoctoral fellow who will join a consortium of leading addiction researchers to work on an exceptionally large neuroim

Re: [Freesurfer] Trouble updating free surfer

External Email - Use Caution This fixed the issue: sudo rm -f /Applications/freesurfer/lib/gcc/lib/libgomp.1.dylib sudo ln -s /usr/local/Cellar/gcc/8.2.0/lib/gcc/8/libgomp.1.dylib /Applications/freesurfer/lib/gcc/lib/libgomp.1.dylib On Mar 11, 2019, at 6:14 PM, Shana Adise