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Same here. Any help with this issue? SIP is off!
Thanks
Joe
-- Forwarded message -
From: Aaron Tanenbaum
Date: Tue, Oct 16, 2018 at 11:16 AM
Subject: [Freesurfer] updateing freesurfer.
To: Freesurfer
External Email - Use C
External Email - Use Caution
Hello FSL and Freesurfer Experts,
We are trying to find the paths between 5 fMRI ROIs (seeds).
We are using the --network option.
How do we go about thresholding the fdt_path.nii.gz?
Thanks so much,
Joe
probtrackx2 --network -x ${dtidir}/seeds.txt -
Hello,
I chose comment out the set bvecfile, bvallist, bvalfile fromt the design
script.
>From my understanding those variable above are not needed if we have a
proper DICOM.
All my subjects ran without error, but,
How can I confirm that my DICOM version is compatible wtih tracula,
How do I kn
thanks guys!
On Fri, Apr 28, 2017 at 4:16 PM, Douglas N Greve
wrote:
> No, you can do it with
>
> mri_binarize --i aparc+aseg.mgz --match ID --o roi.ID.nii.gz
>
> where ID is the parc id from the FreeSurferColorLUT.txt
>
>
> On 04/28/2017 06:58 PM, VA Research wrote:
&g
Does freesurfer output individual roi volume masks for each of the
cortical parcellations in aparc+aseg?
thanks
Joseph Veliz
VA Hospital West LA
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installation which should bypass the issue. But I guess your all set
> anyway.
>
>
> On 03/28/2017 05:32 PM, VA Research wrote:
> > disabled SIP got it working
> >
> > briefly why would SIP (files system not accessible) halt the trac-all?
> >
> >
> >
>
3/28/2017 03:46 PM, VA Research wrote:
> > I will try to disable SIP
> >
> > (although i dont want to restart the system because i am curious if this
> > XL defect will ever be corrected running 80 plus hours now... lol)
> >
> > attached is the trac -all.log
> >
gt; integrity-protection-mac-os-x/
>
> However, I am still curious how/why you are getting this error. Is there
> a trac-all .log file somewhere you can send me so I can see at what
> point exactly this error occurs?
>
> -Zeke
>
>
>
> On 03/28/2017 03:29 PM, VA Research
Hello,
i am on el capitan 10.11.6 , XQuartz 2.7.8
I named the old Applictions/freesurfer directory something else and
installed freesurfer 6.0 and sourced through the script, i also changed the
subject directory
but otherwise i think this is a clean install of FS 6.0
I am running trac-all -p
> Search for items with “b0” in the example config file:
> https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
>
> Best,
> a.y
>
> From: on behalf of VA Research <
> n.n.di.methyl.tryptami...@gmail.com>
> Reply-To: Freesurfer support list
> Date: Tuesday, March
Hello FSL and FS pros,
I am trying to pre process DW images but am not sure how to unwarp images.
We are using Siemens Skyra 3T and output fieldmaps;
2 files output from the scanner;
the first file contains two magnitude files in one
the second file contains the single phase difference image
--
Did you receive a reply/
Any news update for 6.0 release?
On Mon, Jul 25, 2016 at 1:01 PM, Trisanna Sprung-Much <
trisanna.sprung-m...@mail.mcgill.ca> wrote:
>
> Hi there
>
> Do we have a potential date for the Freesurfer 6.0 release? I was told I
> would want to re-run all my subjects to create
a wmparc that does not have the unsegmented wm with
> something like
>
> cd $SUBJECTS_DIR/subject
> mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown
> --volmask --ctxseg aparc+aseg.mgz --wmparc-dmax 100 --o mri/wmparc2.mgz
>
> Then create your lobes from that
>
Hello FS experts,
Does anyone have some form of step-by-step instructions on how to do this ?
Thanks so much
Joseph
Brainiac . wrote:
>* Hi All,
*>>* I need to classify WM into different lobes (temporal, parietal,
*>* frontal, occipital). I tried to do the lobe mapping using
*>* parcellations f
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