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Actually Im not really sure why Matlab pops up here.. this is ran there is
nothing that is Matlab dependent in the PreFreesurfer Pipeline...
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Freesurfer@nmr.mgh.harvard.edu
https:/
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you can ignore the nifti errors in the beginning of the error message,
because it was just a small glitch that I solved. the rest of the errors
still stand, and are unclear to me..
On Thu, 14 Feb 2019 at 11:09, Shachar Gal wrote:
> Hey,
>
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Hey,
So I disabled SIP, and tried to run the subject from the beginning, and sadly I
encountered an error while running the PreFreesurfer Pipeline, which worked
fine until disabling SIP.
This is the error message:
** ERROR (nifti_image_read): short
u/pub/dist/freesurfer/patches/
any ideas where this patch needs to come from?
thanks,
Shachar
On Wed, 13 Feb 2019 at 16:09, Shachar Gal wrote:
> Hey Tim,
>
> I tried to run the “-E fs_update”, and got this message:
>
> rsync -zbrlv --progress --suffix=.1550066275_bak
> rsync:
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Hey Tim,
I tried to run the “-E fs_update”, and got this message:
rsync -zbrlv --progress --suffix=.1550066275_bak
rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/*
/Applications/freesur
Wed, 13 Feb 2019 at 10:21, Shachar Gal wrote:
> Hey Douglas,
> A couple of question about the patch
> In order to use it, I need to download the regular Freesurfer version-6,
> and replace only the scripts that are in the patch? (i.e
> Make_average_surface, recon_all, conf2hires,
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Hey Douglas,
A couple of question about the patch
In order to use it, I need to download the regular Freesurfer version-6, and
replace only the scripts that are in the patch? (i.e Make_average_surface,
recon_all, conf2hires, longmc)
Which recon-all to
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hey,
is there any update regarding the release of the FreeSurfer 6
HCP-compatible version?
cheers,
Shachar
On Mon, 14 Jan 2019 at 14:58 Shachar Gal wrote:
> thanks,
> hope it'll work
> anyway, looking forward for the version 6 rele
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thanks,
hope it'll work
anyway, looking forward for the version 6 release
cheers,
Shachar
On Mon, 14 Jan 2019 at 14:08 Glasser, Matthew wrote:
> Ubuntu 14.04 should still work.
>
> Matt.
>
> From: Shachar Gal
> Date: Monday
Shachar Gal wrote:
> hello,
> I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version) on
> ubuntu, and I encounter this error (copying from the recon-all.log)
> ___
> #@# Talairach Sun Jan 13 17:35:07 IST 2019
> /home/shachar/pia
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hello,
I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version) on
ubuntu, and I encounter this error (copying from the recon-all.log)
___
#@# Talairach Sun Jan 13 17:35:07 IST 2019
/home/shachar/piano_h
f the HCP pipelines and
> FreeSurfer that is almost ready.
>
> Matt.
>
> From: on behalf of Shachar Gal <
> gal.shac...@gmail.com>
> Reply-To: Freesurfer support list
> Date: Monday, December 24, 2018 at 3:12 AM
> To: Freesurfer support list
> Cc: Ido Tavor , Ni
, Shachar Gal wrote:
> Sorry, out of the office for the day. I'll get back to you about it
> tomorrow
>
> Shachar
>
> On Sun, Dec 23, 2018, 16:56 Glasser, Matthew wrote:
>
>> External Email - Use Caution
>>
>> Is that FreeSurfer 5.3?
>&
gt; On Sun, 23 Dec 2018 at 16:28, Glasser, Matthew wrote:
>
>> External Email - Use Caution
>>
>> Which version of FreeSurfer is this and did you do some OS upgrade in
>> between?
>>
>> Matt.
>>
>> From: on behalf of Shach
Sun, 23 Dec 2018 at 16:28, Glasser, Matthew wrote:
> External Email - Use Caution
>
> Which version of FreeSurfer is this and did you do some OS upgrade in
> between?
>
> Matt.
>
> From: on behalf of Shachar Gal <
> gal.shac...@gmail.com>
> Reply
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hello,
I'm running the hcp's FreeSurfer pipeline, and for some reason, after
working successfully several times, on different subjects, im getting this
error:
***
/Users/georgieboy/Research/Piano/test/222/222/mri
\n mri_nu_correct.mni --n 1 --proto-iter
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