Re: [Freesurfer] Volume Version of ?h.sphere.reg and method to read it

Dear FreeSurfer Team, I want to morph a subject's VolumeSourceEstimate to an average subject. Is there a method to create a volume/voxel-based warp map and read/use it in mne-python ? If that is possible it would solve all my problems. Since there is a surface-based registration file (?h.sphere

[Freesurfer] Postdoc and PhD student positions, TU Dresden, Germany

We are seeking a postdoc and two PhD students to work in the Neural Mechanisms of Human Communication Research Group led by Katharina von Kriegstein at the TU Dresden, Germany. Postdoc Position The main research goal of the position is to investigate behavioural and neuroscience principles of p

[Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance

Thank you very much. Where I should put 0 0 0 0 .25 .25 .25 .25? Which are the contrast reported below that I should modify? C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 C5) gr1-gr4_intercept 1

[Freesurfer] Problem with mris_anatomical_stats on .label which is threshold under negative value on FS-FAST, using tksurfer

Hi list, aftermri_label2label --srcsubject Subj01 --srclabel ROI.label --trgsubject Subj01 --trglabel Subj01/label/ROI.label --hemi lh --regmethod surfaceandmris_anatomical_stats -l Subj01/label/ROI.label -b Subj01 I have run mris_anatomical_stats -l Subj01/ROI_neg.label -b Subj01 lh the follow

[Freesurfer] occiptal flattening

Hello, I have been trying to flatten patches (the occipital cortex) in order to create retinotopic maps. However, when I run mris_flatten, the command window says it cannot read the patch file I have created. I have followed the tutorial page and have included -1 in my command, and still nothing ap

Re: [Freesurfer] recon-all exits with errors

Hi Ali can you send us your full command line, the full screen output and the recon-all.log file that should have been generated in the subject's scripts dir? cheers Bruce On Fri, 6 Oct 2017, Ali Radaideh wrote: Dear FreeSurfer Experts, I have just launched a new project and collected new

[Freesurfer] License files with FreeSurfer 5.2.0

I am re-running some old scans on current hardware to do comparisons with 5.2.0 output from old hardware, 5.2.0 output from current hardware, and current 6.0.0 output, all of the same input image. I am aware that FreeSurfer 5.2.0 is deprecated and don't intend to use its output, per se. My problem

Re: [Freesurfer] TRACULA qc: forceps minor and major

Hi Linnea Marie – You’re right in your assessment. Are you using 6.0? You can reinitialize those bad cases, by adding “set reinit = 1” in your config file and changing the path list and subject list to specify only the tract and subjects that you want. Then rerun trac-all --prior and trac-all —p

Re: [Freesurfer] preproc-sess

Thanks Bruce and Doug! Follow-up questions: which anatomical volume does bbregister register the functional to? Also, is there any need to reorient the functional image before preprocessing? On Tue, Sep 5, 2017 at 11:34 AM, Douglas N Greve wrote: > > > On 08/31/2017 11:47 AM, Jiahe Zhang wrote:

Re: [Freesurfer] TRACULA trac-all prep error

Hi Fred – Because of your language setting, unix is using commas instead of decimal points and this is messing something up. Try changing your environment with "setenv LANG en_US.UTF-8” . Best, a.y From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Fred Sampedro mailto:freds

Re: [Freesurfer] Error with TRACULA using dcm and nii

Hi Christopher – If you have not resolved this, please send along the bvals and gradient table files. It seems to expect a 35th volume in your nifti file, which has 34 volumes. Best, a.y From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Ferrier, Christopher Q." mailto:cfe.

Re: [Freesurfer] TMI(total motion index) of diffusion MRI

Hi - Yes, it sounds like there is no drop-out in your data, so there is no reason to use drop-out measures to compare across subjects. Best, a.y On 8/30/17, 1:34 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 이 정환" wrote: >Hello > >I’m attempting to analysis diffusion MRI using TRACU

Re: [Freesurfer] Tracula - QA for Forceps Minor

Hi Abby - You can try first reinitializing without increasing the number of control points, and if that doesn’t work then increase them. Increasing the number of control points increases the degrees of freedom in the shape of the path, which can be good, e.g., for the corpus callosum of subject

Re: [Freesurfer] Descriptions of regions in Yeo 2011 Network atlases

Hi Adam, Language activations definitely hit Default B, but Default B is also activated by tasks such as theory of mind (see Figure 4 here: https://www.biorxiv.org/content/biorxiv/early/2017/06/19/149567.full.pdf), so I am not sure we can consider it to be a pure language network. Although there

[Freesurfer] Fw: Re: 1 mistake in FreeSurfer

-- ?? Tian Amin 13071892606 amint...@zju.edu.cn, 237416...@qq.com Master Degree Candidate, Zhejiang University Interdisciplinary Institute of Neuroscience and Technology, ZIINT. Huajiachi Campus, No. 268 Kaixuan Road, Jianggan District, Hangzhou, Zhejiang Province, China, 31

Re: [Freesurfer] recon-all exits with errors

Dear Bruce, many thanks for your email. I have noticed that the FreeSurfer I am still using is 5.3.0 and this version seems not to work with my Ubuntu 16.10 due to issues related to the current version of "Perl" (version 22). I have just downloaded the latest version of FreeSurfer (version 6) and