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I was attempting to view some of our images and kept receiving this error
message (shown below). I tried looking online and saw some comments about not
having a compatible version of XQuartz and the MacOS but they both seem be
compatible versions an
Try using freeview (or tkmeditfv, a tkmedit command-line-style frontend
for freeview). tkmedit is depricated.
On 7/11/19 10:55 AM, Valerio, Kate wrote:
>
> External Email - Use Caution
>
> I was attempting to view some of our images and kept receiving this
> error message (shown below).
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Dear Freesurfer experts,
Now I am using both FSFAST and SPM to preprocessed my functional image
data. In FSFAST, I replaced the subcortical template with the whole brain
in the folder "mri.2mm", to get the whole brain volumetric data. I have
also dilut
is this an individual or group? what version of FS are you running.
On 7/11/19 11:10 AM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> Now I am using both FSFAST and SPM to preprocessed my functional image
> data. In FSFAST, I replaced the subcortical tem
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It is group level, result of 2nd-level analysis. I preprocessed data of 50
subjects with FSFAST and SPM respectively, then I used SPM to do the 1st-
and 2nd-level modelling. The version of FS now I use is 6.0 I think:
freesurfer-Linux-centos6_x86_64-sta
You can check the masks of each subject. There might be one whose mask is too
small, and that will affect the final mask. If you run isxconcat-sess, it will
create a file called masks.nii.gz with all the masks in them. You can load it
up in freeview (or spm) and scroll through them.
On 7/11/201
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From: "Maedeh Khalilian"
To: "freesurfer@nmr.mgh.harvard.edu"
Date: Thu, 11 Jul 2019 07:37:05 +0430
Subject: A Question Regarding Topology Correction
Dear FreeSurfer experts,
I know that FreeSurfer does segmentation, surface reconstruction
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Yes, you are right. Many thanks.
On Thu, 11 Jul 2019 at 12:49, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> You can check the masks of each subject. There might be one whose mask is
> too small, and that will affect the final mask. If yo
Hi Maedeh
in principle you can, although it would be a lot easier if you just had a
reasonable quality T1. If not, you will need to create all the files that
recon-all expects to exist prior to the topology correction step (wm.mgz,
norm.mgz, orig.mgz, ). Maybe the easiest thing to do would
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Hi all,
I have my data organized in this way:
study/sub/T1/data.nii.gz
infantFS wants the input as study/sub/mprage.nii.gz.
Is there a way to feed my data to infantFS without reorganizing/renaming?
-i switch seems to not be recognized by infantFS.
Th
Hi Mahmoud
Currently the -i flag is not activated. I can add that in a bit.
Can you create soft links to your input images?
Lilla
On Thu, 11 Jul 2019, Mahmoud wrote:
>
> Hi all,
> I have my data organized in this way:
> study/sub/T1/data.nii.gz
>
> infantFS wants the input as study/sub/mpr
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Thanks for your response, Lilla.
Soft links would be an alternative. Thanks for pointing to it.
When would you think you can add the -i flag? if it's reasonably soon, I
may wait to use the updated code. (BTW, how can I get the updated code?)
Also, it w
oops, sorry for the delay. You are probably right that it has to do with the
big vents. There must be some obscure label that gets created for which the
tissue type is unknown to the gtm. But there should have been more info in the
terminal output. Can you send me everything it prints out?
On 7
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