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Hi everyone,
I am currently working on cortical thickness analyses using freesurfer
v. 6.0.1. (on Debian /Linux 7). All of my data sets show a segmentation
error in the anterior protions of the temporal lobe (mostly STG and
almost always bilateral).
Hi Freesurfer Team,
I have a couple cases with large hemispheric ICH that have caused my recon to
hit the default wall-time of 96 hours. It seems to get hung up on the
correcting topology defects step for the affected hemisphere. My goal is to
have the recon at least finish so I can analyze the
Hi Meike
can you send us some images? And what volume are the intensity values
around 73 for white matter? That is way to low for the norm.mgz or the
brain*.mgz
cheers
Bruce
On Fri, 10 Jan 2020, Meike Hettwer wrote:
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>
> Hi everyone,
>
> I am currently work
No, sorry
On 1/6/2020 6:54 PM, Emilie Reas wrote:
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I am running mri_glmfit using the --pvr option and do not get a pcc.mgh file
with the output. I found an old thread from 2017 in which Douglas Greve
explained that "mri_glmfit will not generate a pcc file wi
I think the problem is that you apply the registration twice instead of
once. the first time is on the volume output of bbregister, but then you
do it again when you run mri_vol2surf. I would just use SWI-bet.nii.gz
(input to bbregister) as input to mri_vol2surf. Also, it is unnecessary
to do
I also usually use spm intensity noramlization, but I think you could
also use fsl.
On 1/6/2020 11:45 PM, falk.luesebr...@med.ovgu.de wrote:
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>
> Dear Manoj,
>
>
> in case you want to rely on tools provided with FreeSurfer only, N3 can
> produce good result
If you don't care about the affect hemisphere, I think you can just specify to
analyze only the unaffected with --hemi lh or --hemi rh
On 1/10/2020 8:19 AM, Horn, Mitchell Jacob wrote:
Hi Freesurfer Team,
I have a couple cases with large hemispheric ICH that have caused my recon to
hit the defa
Your FSGD and command look correct. As for whether it is a good idea or not,
I'm not sure (you're probably the best person to decide that). One thing to
keep in mind is that if there are true thickness differences you might see some
differences due to partial voluming. I would also remove the m
On 1/9/2020 10:23 AM, Steve Petersen wrote:
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Dear Freesurfer experts,
I would like to perform external analysis with the hippocampus, parahipocampus
and entorhinal volume. As I understand its the hipocampo volume should be
corrected using the subject´s int
when you make the average subject, just use --ico 5
On 1/9/2020 11:15 AM, Marina Fernández wrote:
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Dear Freesurfer experts,
Now, I would like to downsample the average subject of a dataset (that is a 7th
order icosahedron tesselation) to have surfaces with
Did you check the registration to see if it is ok? If it is ok (or if you fix
it), you can then turn off the talairach check with -no-tal-check
On 1/9/2020 4:32 PM, Isabella Leung wrote:
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Hello Freesurfer Community,
I have been processing my T1 data through
sorry, I'm not sure I'm following. It looks like you did two analyses, one with
10mm smoothing and CFT=.05, the other with 12mm and CFT=.001. You get a cluster
for each in the same area, but they are not overlapping. Is that right?
On 1/6/2020 2:58 PM, Martin Juneja wrote:
External Emai
Yes, that is a valid solution. Thanks for giving us a heads up.
doug
On 1/8/2020 2:43 PM, Lewis, Lydia R. wrote:
Hello Freesurfer Team,
I am running the fsfast analysis stream for resting state data and recently
came across an issue with the funcroi-sess command. I originally used
funcroi-confi
I think you can just give each trial a different condition number in
the paradigm file
On 1/8/2020 3:04 PM, Katsumi, Yuta wrote:
> Dear Doug,
>
> I would like to perform GLM on a trial-by-trial basis in FSFAST. That is, I'm
> interested in obtaining beta estimates per trial and using them as in
That in and of itself is probably not problematic as it is in the medial wall.
But I'm a little worried that the subcortical segmentation is not accurate. Can
I take a look at the subject? You can get it to me with:
>From the linux command line,
Create the file you want to upload, eg,
cd $SUBJEC
I think this was answered yesterday. Check the previous posts
On 1/9/2020 7:58 AM, Kirill Elin wrote:
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Dear FreeSurfer Developers,
I am trying to run the script and the recon-all command and getting
Exited with errors output.
1. FreeSurfer Version freesurfer-L
On 1/8/2020 10:17 AM, Boris Rauchmann wrote:
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Ok. i figured it out. The problem was just that you can not specify the file
type - so .mgz in BN_Atlas_subcotex.mgz was actually the problem.
Ah, ok. This is actually fixed in our development version.
Now I ru
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Hello FreeSurfer Developers,
I'm attempting to compare longitudinal cortical thinning rates (pc1) between 3
groups using mri_glmfit using FreeSurfer 6.0. The tutorial suggests that you
could use the multiple comparisons corrections that come with it
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Dear Dough,
Thanks for your reply. Below, I am summarizing my concerns from previous
emails:
*Q1. *I was wondering which of the following two options is better than the
other (or neither may be !):
(i) CFT < 0.001 and CWT < 0.1 (i.e., CWT = 0.07) (smo
Uuummm could it be possible that you’re using the quantification script from a
dev version that is more recent than the one you used to analyze the data? In
that case, the script would expect v21 instead of v20, which would explain the
problem.
Cheers,
/E
Juan Eugenio Iglesias
Senior research f
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Hello all,
I want to apply the denoising and eddy current reduction on input images 3DT1
and 3D Flair. Are there any algorithms in Freesurfer to perform the noise and
eddy current reduction? Does recon-all involve denoising and eddy current
reductio
We don't have anything to denoise. You can try using ANTS DenoiseImage, but
using on the input might change where the surface is placed. We are
experimenting with using it inside the stream in a place where it is less
likely to bias the surface placement.
I don't understand the eddy current que
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