Hello FreeSurfer users,
Currently I'm trying to analyze DWI data using the new TRACULA package. The
packages looks promising and I managed to process a few tracts (the ILF and UNC)
But now I would like to process more tracts at once. So I ran the trac-all
subroutines to check every step. All goe
Hi Jeff,
in most cases that won't run anything. -make all will check the
timestamps on the various volumes/surface and only rerun things in cases
where something further back in the stream has a newer timestamp than
something newer. You need to run it with -all
cheers
Bruce
On Thu, 16 Jun 201
Just as an FYI, we also recently encountered the same problem, also
using mri_convert as our DICOM to NIFTI converter. Our work-around was
to just switch to dcm2nii.
Jolinda: I don't know why mri_convert is populating a "slice_code" entry
for a Siemens MPRAGE acquisition, since an MPRAGE is a
Hi Stijn - It's hard to tell where it fails without seeing all the output
of the command. Can you please send the log file from scripts/trac-all.log
that shows the error, and also your dmrirc file? Thanks!
a.y
On Fri, 17 Jun 2011, Michielse Stijn (SP) wrote:
> Hello FreeSurfer users,
>
> Curr
Thank you for the help!
On Tue, Jun 14, 2011 at 9:10 PM, Douglas Greve wrote:
> **
> You should be able to use the reg and mni305.2mm.nii.gz in 4.5
> doug
>
>
> On 6/14/11 12:25 PM, Balaji Goparaju wrote:
>
> Thanks for the response! I seem to be getting better results.
>
> I was wondering if the
Hello.
We are in the process of trying to develop a QC pipeline for our Freesurfer
processed images. I was wondering if anyone has developed any type of
automated QC they would be willing to share with us or have any suggestions on
how to proceed.
Any help would be most appreciated.
Thanks.
Hello,
I just received my confirmation for posting on the mailing list.
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Subject: Welcome to the "Freesurfer" mailing list (Digest mode)
From:freesurfer-requ...@nmr.mgh.harvard.edu
Date:Fri, June 17, 2011 4:25 pm
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Hi John,
We do have a set of QA scripts which were created to check the version of
FS used, the order of the output files, the order of all the steps in FS,
take several snapshots, and then create a summary log file and an html
file to view the snapshots. The scripts have been neglected for some
you can also use wm-anat-snr. Run it with --help to get more info.
Louis Nicholas Vinke wrote:
> Hi John,
> We do have a set of QA scripts which were created to check the version of
> FS used, the order of the output files, the order of all the steps in FS,
> take several snapshots, and then crea
Hi,
Can somebody please help me figure out how to correct this issue?
1 subject - 2 functional scans
1) run recon-all on subject anatomical.
2) process functional series (using AFNI/FSL) - each individually.
3) use (http://afni.nimh.nih.gov/pub/dist/doc/program_help/@ROI_Corr_Mat.html)
@ROI_Co
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