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Thank you!
So the answer to the first question is that yes I can convert it back to a
curvature file and that curvature file can be loaded as an overlay. So this
must mean that the problem is with reading the .asc file rather than the file
being co
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Hi Doug,
Thank you for your response.
I tried the link which you sent yesterday. But got stuck while creating
qdec.fsgd file.
Below i have pasted the terminal output after loading the data.
1 Left-Lateral-Ventricle continuous 0
2 Left-Inf-Lat-Vent
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Hi Martin,
It's been a long time since this discussion but I return on this from
now... The problem is that I followed longitudinal images of two groups
where I had mainly missing time points at the end. Than you suggested:
*If you have mainly missing
can you send the command-line output as text?
On 10/16/2018 11:12 AM, Sparsh Jain wrote:
>
> External Email - Use Caution
>
> Hey!
> I sent two responses on Friday. The second response was bigger than 1
> MB so it awaited moderator approval. I don't know if you received it
> eventually.
Hi Maxime,
I'm having trouble finding your data - can you please use the filedrop instead?
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks,
Bram
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Maxime Perron
Sent: Friday, October 12, 2018 11:17:0
Hi Amanda
can you try it in freeview? tksurfer has been deprecated for a while now
cheers
Bruce
On
Tue, 16 Oct 2018, Worker, Amanda wrote:
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Thank you!
So the answer to the first question is that yes I can convert it back to a
curvature file and
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Hello Freesurfer experts,
We have a large longitudinal dataset (n=~200) of up to 4 time points per
participant. All images were processed using Freesurfer v6.0 and have already
undergone QA, and editing the cross, Base or long where needed.
We are
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I tried updating freesurfer 6.0 using the command fs_update. I get the
following output.
> Build is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>
>Running this will update some of your freesurfer binaries.
>
> Shall I proceed? [y/
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Hi Bram,
No worries.
Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h
Thanks,
Maxime
On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder wrote:
Hi Maxime,
I'
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Sorry. Here are the good links :
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t
Maxime
On Oct 16, 2018, at 2:22 PM, Maxime Perron wrote:
Hi Maxime,
What did you edit in the aseg? It looks like the CC_* have been mislabeled.
Bram
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Maxime Perron
Sent: Tuesday, October 16, 2018 2:23:22 PM
To: Freesurfer support list
Subject: Re: [Freesurf
When you look at the vertex in matlab, are you correctly accounting for
the fact that FreeView uses 0-based indexing and matlab uses 1-based?
Eg, vertex 234741 in Freeview would be 234742 in matlab. You seem to be
using 234740 in matlab below
On 10/15/2018 05:11 PM, Bruss, Joel E wrote:
>
>
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Hi Bram,
I modified the label of the lateral ventricules because they were mislabeled too (Freesurfer_S043_test). I didn't change the label of the CC_*. Do you think that can fix the middle line?
Thanks,
Maxime
De : freesurfer-bo
Hmm, not sure what to tell you. The label is derived directly from the
annot. If you click on a vertex in the branch, does it appear to be in
the label based on what displays in the control panel? If you load it on
the inflated surface, do you still see the branch?
On 10/15/2018 08:42 PM, Ting
That looks like the terminal output for qdec. You cannot use qdec with
your design. If you have questions about the FSGD, I'll be happy to
answer them.
On 10/16/2018 11:00 AM, vittal korann wrote:
>
> External Email - Use Caution
>
> Hi Doug,
>
> Thank you for your response.
> I tried th
Possibly - I would definitely start there. The surfaces are following the
corpus callosum into the right hemisphere because the aseg labeling is off.
Best,
Bram
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Maxime Perron
Sent: Tuesday, October 1
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Hi FS Team,
We are running our first fsfast pipeline, and starting with a single
subject to test everything. We successfully ran preproc-sess with the
following command:
preproc-sess -s 11987_20180731 -surface fsaverage lhrh -mni305 -fwhm 5
-per-run -
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There surely seems to be a link indeed; I'll look at where to correct the labeling and will give you feedback on the result. In the meantime, should you have any advice on such an optimal way, I'll be glad to hear it.
I'll keep you posted soon
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I couldn't remember if it's 1+ or 1-. Either way, either direction give
similar coordinates that don't match up to what I can see in FreeView.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas
which coords are you looking at? They should be the "surface RAS" coords.
On 10/16/2018 04:05 PM, Bruss, Joel E wrote:
>
> External Email - Use Caution
>
> I couldn't remember if it's 1+ or 1-. Either way, either direction
> give similar coordinates that don't match up to what I can see
You can load them in freeview through tksurferfv, something like
tksurferfv fsaverage lh inflated -aparc -ov
fmcpr.odd.sm5.fsaverage.lh.nii.gz
There's not much to see:)
On 10/16/2018 03:00 PM, Jacob Matthews wrote:
>
> External Email - Use Caution
>
> Hi FS Team,
>
> We are running our
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I attached that to the previous email, but it got rejected by the moderator
for some reason!
Sparsh
On Tue, Oct 16, 2018 at 1:03 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> can you send the command-line output as text?
>
> On 10/16/
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If I loaded the label to the inflated surface, it also gives me the cluster
with branches. As you can see in the below.
If I loaded the annot file to the inflated surface, it works well. Thanks for
your help.
Ting
> On Oct 16, 2018, at 1:51 PM
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Dear FreeSurfer Experts,
I am running Qdec 1.4 and I want to extract raw data (in this case, volume)
from the significant clusters after Monte-Carlo simulation. In this
particular case, the summary file shows 5 significant clusters after
correction:
#
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