[Freesurfer] Job posting: 2-year postdoctoral position

External Email - Use Caution Enquires and applications to Dr. Martine Migaud (martine.mig...@inra.fr) Job title: Multi-modal MRI analysis of a large mammalian brain model Structure: A 2-year postdoctoral position is available in the group of Dr. Martine Migaud, at the laboratory

Re: [Freesurfer] 6.0.1 automatic download

External Email - Use Caution Thanks! Best, Chris PS Apologies for brevity and potential typos. This message was composed on a phone. On Wed, Sep 12, 2018, 5:06 PM Hoopes, Andrew wrote: > Hi Chris, that is the same version as before. Sorry, our pubftp disk went > down a few day

[Freesurfer] segmentation fault with mri_vol2vol or lta_convert

External Email - Use Caution Hello I notice a systematic segmentation fault with several function that use a .lta file (lta_convert or mri_vol2vol) This is due to a too long filename path in the .lta file : If I manually edit the .lta file and change the file_path associate to t

Re: [Freesurfer] Midline errors

Hi Maxime if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate. cheers Bruce On Thu, 13 Sep 2018, Maxime Perron wrote: External Email - Use Caution Hi Freesurfer Experts

Re: [Freesurfer] /mri/orig/001.mgz vs T1.mgz

External Email - Use Caution These images were both opened in freeview. Should they be aligned differently? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Wednesday, Septe

Re: [Freesurfer] 回复： questions about trac-all -stat

Hi Qianwen, (1) & (2): The native space coordinates along the path of all subjects (which are in their path stats files) are mapped to MNI space simply to identify a common midpoint for all subjects. This midpoint is mapped back to native space, and the FA/MD/etc. values for each subject are sa

[Freesurfer] Interpretation of pcc.mgh for negative contrasts

External Email - Use Caution Hi List, a dimple question about using partial correlation (pcc.mgh) as effect size measure. I am running multivariate regression and setting positive and negative contrasts one variable at a time, e.g. a design matrix with columns like Intercept

Re: [Freesurfer] QAtools tkmedit snapshots are black

External Email - Use Caution Hi, I'm also having a problem with the snapshots coming out black on CentOS 7 (but not CentOS 6). I'm using a slightly modified version of the first tcl script located on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/QaImageScripts, and the fol

[Freesurfer] Identifying labels overlapping with overlay volume

External Email - Use Caution I’ve got a custom .annot file covering the entire cortical surface in fsaverage space, and I wish to see which labels overlap with an overlay statistical contrast volume generated by mri_glmfit. I extracted the vertex indices from my custom .annot fil

Re: [Freesurfer] Identifying labels overlapping with overlay volume

When you run mri_glmfit-sim, you can pass it your own annotation (--annnot). Would that do what you want? On 09/13/2018 01:02 PM, Mcnorgan, Christopher wrote: > > External Email - Use Caution > > I’ve got a custom .annot file covering the entire cortical surface in > fsaverage space, and

Re: [Freesurfer] Interpretation of pcc.mgh for negative contrasts

not sure what your question is. The pcc should have the same sign as the contrast. On 09/13/2018 12:20 PM, Nicola Toschi wrote: > External Email - Use Caution > > Hi List, > > a dimple question about using partial correlation (pcc.mgh) as effect > size measure. I am running multivariate

Re: [Freesurfer] Interpretation of pcc.mgh for negative contrasts

External Email - Use Caution Thank you Doug, that was exactly the question... it may be a trivial one but I have been messing aroung with several effects size calculation for a while and just wanted to make sure. So negative contrast (-1), negative beta.mgh, positive (?) gamma.

Re: [Freesurfer] Interpretation of pcc.mgh for negative contrasts

gamma and pcc should be the same sign. The relationship to the sign of beta depends on your contrast. If beta is negative and your contrast element is negative, then you will get a positive gamma and pcc. On 09/13/2018 02:15 PM, Nicola Toschi wrote: > External Email - Use Caution > Thank you Dou

[Freesurfer] Hippocampal-Amygdala subfields error

External Email - Use Caution Hello Freesurfer devs, I ran the hippocampal and amygdala subfields command in my sample and I get the following error in several subjects: *Constructing image-to-world transform from header information (asmr1.mgz)Constructing image-to-w

Re: [Freesurfer] Hippocampal-Amygdala subfields error

External Email - Use Caution Hi Miguel Angel, This bug was recently fixed in the dev version. If you download the most recent one, you won’t have this problem. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) Universit

[Freesurfer] Are these regions orbitofrontal cortex

External Email - Use Caution Hi Freesurfer experts I got the meancurve, and I want to check the orbitofrontal cortex (OFC). I know 'lh_S_orbital_lateral_meancurv' 'lh_S_orbital_med-olfact_meancurv' are OFC. But which brain regions are these belonged to 'lh_S_orbital-H_Shaped_mea

[Freesurfer] AAL template OFCant_L 2811 is lateral or medial in FS

External Email - Use Caution Hi FS experts, I want to know whether OFCant_L2811 is 'lh_S_orbital_lateral_meancurv'or 'lh_S_orbital_med-olfact_meancurv'? Thanks. Rujing 2018-09-14 charujing123 ___ Freesurfer mailing list Freesurfer@nmr

Re: [Freesurfer] Midline errors

External Email - Use Caution Hi Bruce, I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification. The pr