Re: [Freesurfer] Help for smoothing the pial surface

External Email - Use Caution Hello Ryan, > On June 26, 2019 at 9:26 PM "Nillo, Ryan Michael R" > wrote: > [...] > I want to generate a smooth pial surface similar to the one displayed on the > LGI page (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI >

[Freesurfer] recon-all multiple subjects 'for' loop?

External Email - Use Caution Hello, I would like to run recon-all on multiple subjects. I have 650 subjects, so running them in separate terminals isn't an option. Each subject has their own folder (e.g. sub-CC121428) containing a single T1w.nii.gz file. Unfortunately, I have v

Re: [Freesurfer] Labelling SurfStat p-value surface map

External Email - Use Caution Hi Tim, Thanks a lot for the effort! Indeed, I self-created an mgh file from a matrix of 10242x1x1 elements. After a few adjustments, it perfectly works in order to view the data on Freeview. I overlayed the individuals' data on lh.pial of fsaverage5 (

[Freesurfer] BA label questions

?Hi All, I'm revisiting an old dataset that was previously run using FS 5.1, and now we upgraded it to FS 6.0. I seem to notice there are different set of BA.labels, ones that are called ?h.BA.label, and ones (generated from 6.0) called ?h.BA_exvivo.label. Is ?h.BA.label deprecated by ?h.BA_ex

Re: [Freesurfer] recon-all multiple subjects 'for' loop?

Hi Benjamin you can run them all in the same terminal by backgrounding them (adding the & character at the end of the command line) cheers Bruce On Thu, 27 Jun 2019, Benjamin Stott wrote: External Email - Use Caution Hello,  I would like to run recon-all on multiple subj

Re: [Freesurfer] Labelling SurfStat p-value surface map

glad to hear it worked out Bruce On Thu, 27 Jun 2019, Loïc Daumail wrote: External Email - Use Caution Hi Tim, Thanks a lot for the effort! Indeed, I self-created an mgh file from a matrix of 10242x1x1 elements. After a few adjustments, it perfectly works in order to view the

Re: [Freesurfer] BA label questions

Hi Victor yes, the old names are deprecated - the _exvivo ones are the newest ones to use cheers Bruce On Thu, 27 Jun 2019, Zeng,Victor (BIDMC - Psychiatry) wrote: ​Hi All, I'm revisiting an old dataset that was previously run using FS 5.1, and now we upgraded it to FS 6.0. I seem to not

Re: [Freesurfer] mri_glmfit will not use mask or label

External Email - Use Caution Thank you, that worked perfectly! Best, Jen On Wed, Jun 26, 2019 at 5:27 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Try running it without --cortex > > On 6/26/19 4:57 PM, Jennifer Legault wrote: > > > > External Email - U

Re: [Freesurfer] recon-all multiple subjects 'for' loop?

External Email - Use Caution Hi Bruce, Thanks for getting back to me. I wanted to write a bash script that would allow me run recon-all, I'm just not sure how to set it up. Is it possible to use a .txt file to do this? I know others have used a .txt file containing the subject

Re: [Freesurfer] recon-all multiple subjects 'for' loop?

I think so, if you add an & at the end of -qcache On Thu, 27 Jun 2019, Benjamin Stott wrote: External Email - Use Caution Hi Bruce,  Thanks for getting back to me. I wanted to write a bash script that would allow me run recon-all, I'm just not sure how to set it up. Is it

[Freesurfer] converting correlation coefficient file into a table

External Email - Use Caution Dear List, I finished first level analysis of functional connectivity of all subjects with respect to Left hippocampus, and have several files (ces.nii.gz, pcc.nii.gz). Is there any command that I can convert this particle correlation coefficient (

Re: [Freesurfer] converting correlation coefficient file into a table

If you want to compute FC between ROIs, then try fcseedcor. Run with -help to get more info On 6/27/19 11:42 AM, Wenzhen Zhao wrote: > External Email - Use Caution > > Dear List, > > I finished first level analysis of functional connectivity of all subjects > with respect to Left hippoc

[Freesurfer] Area information on certain views

Dear freesurfer team, I searched the archives, but couldn't find this kind of question. I've used the brainstem segmentation tool to get the volume of each brainstem structures, but now I am trying to get the area (mm^2) of midbrian and pons on mid-sagittal view. Do you know of an easy way to