[Freesurfer] Postdoctoral Position, University of Oslo

External Email - Use Caution I am delighted to advertise the following postdoctoral research fellowship on behalf of Prof Anders M Fjell: At the Center for Lifespan Changes in Brain and Cognition, University of Oslo, Norway, we have an available postdoc position for an excellent c

[Freesurfer] Undefined function or variable called 'fspecial'

External Email - Use Caution Hello FS experts, I am trying to run the gyrification index and not able to move in the right direction. When execute this command "recon-all -s CSRI005 -localGI" and here is the output copied from the terminal "#@# Local Gyrification Index lh Wed Jul

Re: [Freesurfer] Undefined function or variable called 'fspecial'

External Email - Use Caution Hello, Vittal, do you have image processing toolbox of MATLAB installed? The function fspecial is part of this toolbox. Antonin Hello FS experts,I am trying to run the gyrification index and not able to move in the right direction. When execute th

[Freesurfer] nii to gii conversion

External Email - Use Caution Dear Freesurfer experts, I would like to run tractography using probtrackx2 tool from one seed ROI (cortex) through another waypoint ROI. I need both these masks (ROIs) in gii format. Seed ROI I extracted using Freesurfer (recon-all, mri_convert and

[Freesurfer] Post-doc position at Neuroplasticity & Development Lab Johns Hopkins University

External Email - Use Caution Post-doc position at Neuroplasticity & Development Lab Johns Hopkins University, PI: Marina Bedny The Neuroplasticity & Development Lab invites applicants for a post-doctoral fellowship position. The postdoctoral fellow will develop a research program

Re: [Freesurfer] nii to gii conversion

External Email - Use Caution Hi Jan, mri_vol2surf is not the correct command to achieve this. Use mri_mc or mri_tesselate. See also https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61335.html Antonin Skoch Dear Freesurfer experts, I would like to run tractograp

[Freesurfer] Postdoc position at MGH/Harvard Medical School

External Email - Use Caution << I will attend the AAIC2019 conference in Los Angeles. Send me an email if you like to meet and discuss this position >> Postdoctoral Opportunity at Mass General Hospital – Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the

[Freesurfer] Freesurfer versions & Amygdala Subnuclei.

External Email - Use Caution Dear Freesurfer List- I had a (hopefully) quick question about amygdala subnuclei segmentation. I know that the subnuclei routine is only available in the dev versions of Freesurfer, but can data already processed with stable v6.0.0 be used (with said

Re: [Freesurfer] Petsurfer: PET -> MNI305 problem

Did yyou check the tal registration of the subjects as created by recon-all? tkregister2 --mgz --s subject --fstal --surf orig On 7/10/19 2:32 PM, Eckbo, Ryan wrote: > > Hi Doug and experts, > > We're interested in running a voxel wise test-retest reliability > analysis on a set of PBR28 PET i

Re: [Freesurfer] Error in analyze (Qdec)

External Email - Use Caution Hi Greve Can you download those files? I have uploaded it in ftp, the file name is QDEC.tar.gz. Hope you can help me. Thank you very much. Abby Abby tang 于2019年7月10日周三 上午9:46写道： > Hi > I have uploaded it in ftp, the file name is /home/abby/QDEC.tar.g

[Freesurfer] mri_glmfit residualized data after motion correction

Hello FreeSurfers, I have an existing pipeline that computes the residualized time series after removing any linear trends using mri_glmfit: mri_glmfit --y ${source_dir}/${r}/${filepat}.${surf}.${hemi}.nii.gz \ --glmdir ${source_dir}/${r}/${hemi}.detrend \

[Freesurfer] A Question Regarding Topology Correction

External Email - Use Caution Dear FreeSurfer experts, I know that FreeSurfer does segmentation, surface reconstruction and topology correction through its routine pipeline using "recon-all" . However, I have some T2w brain MR images and I have done the segmentation and extracte