Re: [Freesurfer] recon-all -localGI with longitudinal pipeline output

Thank you, Martin! Mihaela On Thu, Feb 9, 2017 at 8:29 AM, Martin Reuter wrote: > Hi Mihaela, > > probably you are trying to run the localGI on a longitudinal directory. As > the help text output says, you need to make sure you tell that to recon-al > by passing the original command again (incl

[Freesurfer] orientation in freeview

Hi all, I have a problem maybe relevant to the orientation of images in freeview. I have two images, one is fMRI and one is MRI. They are produced from the same machine at the same time. I loaded both of them in freeview and it showed they are matched very well, even they have different resolution

Re: [Freesurfer] Topup before trac-all

Hi - Running topup is not a problem. Just make sure that there's as many entries in the gradient table and b-value table as there are frames in the DWI file. So if with topup you're combining 2 sets of DWIs (collected with opposite phase-encode directions), you also have to combine the correspon

[Freesurfer] Control points and WM edits

Hello Freesurfer, I played around with mri_normalize for control point section by changing the parameters using -b 20 or 23 and writing it in an expert file. However, when I ran recon-all -autorecon2-cp -autorecon3 -expert expert.opts, the command showed "mri_normalize - mprage -noconform ) se

[Freesurfer] Topup before trac-all

Hi, I would like to preprocess my dti data with topup (from FSL) before running trac-all. Is this a sensible approach? When I tried running trac-all -prep with the output file from topup (*_hifi_nodif.nii.gz) I got an error message: mv -f /usit/abel/<>/topuop/146/dmri/bvecs /usit/abel/<.

Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0

The same thing happened to me on my mac when I changed the FREESURFER_HOME variable in the terminal, but not in the .bashrc file that I source when the terminal opens. Hope this helps! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center On Feb 9, 2017, at 1:4

Re: [Freesurfer] mrisComputeCorrelationTerm: delta is not finite at vno 0

Hello Juhyoung, If its complaining about "RB_all_2008-03-26.gca" then something must have happened where you still have portions of the old freesurfer installed, or your mixing versions because Freesurfer v6 has no mention of RB_all_2008-03-26.gca. Please try completely removing the /Applications/

Re: [Freesurfer] Error in recon-all (Skull Stripping)

Thank you, we did that, and it was indeed an issue with the way we ran it. Diana > El 9 feb 2017, a las 18:19, Douglas Greve > escribió: > > It says that it was "Killed" which sounds like the job exceeded some resource > on the supercomputer. You should contact the administrators to see what

Re: [Freesurfer] Expert file for recon-all -hires

hello antonin, Thanks for the correction. Best, Paul On Thu, Feb 9, 2017 at 12:21 PM, Antonin Skoch wrote: > Dear Paul, > > for the most recent version 6.0 the default is 10. > > Looking at the help of mris_inflate binary and also to the source code. > > Antonin > > > Hello Falk Chris and Antoni

Re: [Freesurfer] Expert file for recon-all -hires

Dear Paul, for the most recent version 6.0 the default is 10. Looking at the help of mris_inflate binary and also to the source code. Antonin Hello Falk Chris and Antonin, The default is 55 https://surfer.nmr.mgh.harvard.edu/fswiki/mris_inflate. Best, PaulOn Thu, Feb 9, 2017 at 10:42 AM, Falk

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Re: [Freesurfer] Error in recon-all (Skull Stripping)

It says that it was "Killed" which sounds like the job exceeded some resource on the supercomputer. You should contact the administrators to see what the limits are and whether you exceeded them. You can also run the same subject on a regular computer and see if it dies in the same place. On

[Freesurfer] Fwd: LGI using Yeo Atlas

Hi, I used following command to extract LGI values from a set of subjects: recon-all -s -localGI Output stats is saved in lh.aparc_lgi.stats file. By default, its calculating LGI values of 35 areas using *Desikan-Killiany Atlas *but I am interested in calculating LGI values using Yeo atlas of 7

Re: [Freesurfer] Expert file for recon-all -hires

Hello Falk Chris and Antonin, The default is 55 https://surfer.nmr.mgh.harvard.edu/fswiki/mris_inflate. Best, Paul On Thu, Feb 9, 2017 at 10:42 AM, Falk Lüsebrink wrote: > Dear Chris and Antonin, > > I found in some archived message or in the wiki that the default used to > be 50 iterations at s

Re: [Freesurfer] Expert file for recon-all -hires

Hi Chris the smaller the voxels the more you will need to inflate. I'm hoping to find some time to make this adaptive as in principal it's all computable, but haven't gotten to it yet. cheers Bruce On Thu, 9 Feb 2017, Christopher Markiewicz wrote: > Hi all, > > If I'm reading this >

Re: [Freesurfer] Expert file for recon-all -hires

Dear Chris and Antonin, I found in some archived message or in the wiki that the default used to be 50 iterations at some time in previous releases of FreeSurfer for standard recon-all. Therefore, I changed it to 50 as default for every resolution in the recent release. This works fine for exam

Re: [Freesurfer] Expert file for recon-all -hires

Dear Chris, I have found that -n 15 is for our 0.7x0.7x0.7mm3 data not enough. I determined optimal value -n 30, empirically, by looking at the shape of inflated surface with various number of iterations. Over -n 30 there was almost no further progression in inflation. I suppose that better m

[Freesurfer] Expert file for recon-all -hires

Hi all, If I'm reading this < https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon> correctly, the current best practice for `-hires` is to include an expert file containing "mris_inflate -n 15", and that this should work for all voxel sizes (0.75mm)^3 - (1mm)^3? Or do we need to empirical

Re: [Freesurfer] recon-all -localGI with longitudinal pipeline output

Hi Mihaela, probably you are trying to run the localGI on a longitudinal directory. As the help text output says, you need to make sure you tell that to recon-al by passing the original command again (including the -long ….) and instead of -all you specify -localGI. Renaming hides from recon

Re: [Freesurfer] Edits to Aseg in the Longitudinal Stream

Hi Tamara, that depends on where you edit. Cross or base or long. Generally when editing in the longitudinal stream you always use the same recon-all command that you used initially, and only replace the -all with the new flag to tell it to start later in the process (here -autorecon2-noaseg )

Re: [Freesurfer] Longitudinal stream with v6 but cross with v5.3

Hi Matthieu, sorry for the late reply. Yes you should be able to do that (as long as it is consistent for all subjects). Test it for one subject and then run the rest. Best, Martin > On 30 Jan 2017, at 16:51, Matthieu Vanhoutte > wrote: > > Dear experts, > > Does anybody could answer my la

[Freesurfer] Parallelization implementation in Freesurfer 6.0

Hello Freesurfer team! Having gone through the instructions for making use of the parallelization in Freesurfer v6, I'm confused as to how exactly the calls for fine grained and coarse grained paralleization differ. As per the release notes, following is stated - *Parallelization: a new flag was

[Freesurfer] Error in recon-all (Skull Stripping)

Dear FreeSurfer developers, I am a new FreeSurfer user and I am trying to run it in a supercomputer for the first time. Recon-all finished with errors (see log attached) during skull stripping. I have searched the archives and only found that it could be a memory problem, but I am unsure ab