I am still getting the same error with today's build of
freesurfer-linux-centos7_x86_64-dev.tar.gz
SHA256 9ea8be61f2f4132770f52459a3e1c746f633727123f9f354953e93466dee165c
build-stamp.txt freesurfer-linux-centos7_x86_64-dev-20181113-8ab
.txt freesurfer-linux-centos7_x86_64-dev-20181113-8abd50c
Thanks,
Baxter
Greve, Douglas N.,Ph.D. wrote:
I just fixed it
On 11/12/2018 09:35 PM, Bruce Fischl wrote:
Hi Baxter
we are seeing this locally as well. Probably a bug introduced into
the last day or two. We will post a fix soon
cheers
v.tar.gz
> SHA256 9ea8be61f2f4132770f52459a3e1c746f633727123f9f354953e93466dee165c
> build-stamp.txt freesurfer-linux-centos7_x86_64-dev-20181113-8abd50c
>
> Thanks,
> Baxter
>
>
> Greve, Douglas N.,Ph.D. wrote:
>> I just fixed it
>>
>> On 11/12/2018 09:35 PM, Bruce Fischl wrote:
>>> Hi Baxter
>&g
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I am still getting the same error with today's build of
freesurfer-linux-centos7_x86_64-dev.tar.gz
SHA256 9ea8be61f2f4132770f52459a3e1c746f633727123f9f354953e93466dee165c
build-stamp.txt freesurfer-linux-centos7_x86_64-dev-20181113-8abd50c
T
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Ah, all the ones with v.mgz used the bigventricles option… Must be something to
do with that.
Simon
From: Simon Jones
Sent: 13 November 2018 21:35
To: freesurfer@nmr.mgh.harvard.edu
Subject: QA_tools do not find v.mgz
I have run some Freesurfer
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I have run some Freesurfer 6 recon-all processed data through the Freesurfer QA
analysis QA_tools_v1.2. The output looks mostly good but I repeatedly see these
errors.
ERROR: Subject a1 missing output file ../mri/v.mgz
ERROR: Subject a1 missing outp
Hi Rosalia
you can use mri_convert for this:
mri_convert file.nii.gz file.mgz
should do the trick
cheers
Bruce
On Tue, 13 Nov 2018, Rosalia Dacosta
Aguayo wrote:
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Dear Free Surfer team,
I wonder how I could pass from .nii.gz format to .mgz form
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Hi all,
I am trying to find out which regions in Destrieux atlas would correspond
to mPFC?
Any ideas ?
Also for lateral parietal cortex ..
Than you,
Daiana
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Yes, use the SAVE REG button. You should be able to see that it has
changed.
On 11/13/2018 12:22 PM, Gamaliz wrote:
>
> External Email - Use Caution
>
> Once I manually fix the registration how do I save it? I know there is
> SAVE REG. Will this overwrite the previous file automatically?
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Great, that worked. I tried it and everything else stayed the same except
for the ICV. Thanks
:)
On Tue, Nov 13, 2018 at 12:22 PM Gamaliz wrote:
> Once I manually fix the registration how do I save it? I know there is
> SAVE REG. Will this overwrite
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Once I manually fix the registration how do I save it? I know there is SAVE
REG. Will this overwrite the previous file automatically?
On Tue, Nov 13, 2018 at 12:13 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Just run
> recon-all -s s
Just run
recon-all -s subject -segstats
and the new ICV should appear in the aseg.stats file
On 11/13/2018 12:08 PM, Gamaliz wrote:
>
> External Email - Use Caution
>
>
> I have a fewT1 scans that have obvious incorrect registration
> to mni_average_305. I opened tkregister2 --s subjid --
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I have a few T1 scans that have obvious incorrect registration
to mni_average_305. I opened tkregister2 --s subjid --fstal --surfs and I
am able to fix the registration, but I wonder how to use the ew
registration to recalculate the new ICV. I am intere
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Dear Free Surfer team,
I wonder how I could pass from .nii.gz format to .mgz format in order to
change the brainmask.mgz generated by FreeSurfer for my bet image from FSL.
I have noticed that lot of brainmask images have optic radiations and part
of th
I just fixed it
On 11/12/2018 09:35 PM, Bruce Fischl wrote:
> Hi Baxter
>
> we are seeing this locally as well. Probably a bug introduced into
> the last day or two. We will post a fix soon
>
> cheers
> Bruce
>
>
> On Mon, 12 Nov 2018, Baxter P. Rogers wrote:
>
>> External Email - Use Caut
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Dear Free Surfer team,
I am visually checking for errors in every step of the recon-all process.
In the skull stripping stage, some participants have left skull behind, but
the grey matter (gm) and white matter (wm) separation is right.
Should I edit
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