Dear all,
Using FreeSurfer 7.1.1, I made my analysis file with the following (I assume
-nksip should be in the number of TRs and not in seconds):
mkanalysis-sess -analysis retino_surf_pr_lh_sm0 -surface self lh -fwhm 0 -fsd
bold -per-run -retinotopy 32 -spmhrf 0 -paradigm retino.par -TR .800 -ns
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Many thanks!
Alejandro
On Wed, Jul 21, 2021 at 3:36 PM Douglas N. Greve wrote:
>
> No, not for thickness.
>
> On 7/21/2021 3:54 PM, Alejandro Meruelo wrote:
> > External Email - Use Caution
> >
> > Hello,
> >
> > Hope all is well! For cortic
No, not for thickness.
On 7/21/2021 3:54 PM, Alejandro Meruelo wrote:
> External Email - Use Caution
>
> Hello,
>
> Hope all is well! For cortical thickness statistical calculations in
> FreeSurfer using Qdec, is there any adjustment needed for brain size?
>
> Many thanks for your assista
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Hello,
Hope all is well! For cortical thickness statistical calculations in
FreeSurfer using Qdec, is there any adjustment needed for brain size?
Many thanks for your assistance,
Alejandro
___
Freesurfer ma
Can you try resetting freeview’s preferences. You can do it in a terminal with
the following command:
rm ~/Library/Preferences/edu.harvard.mgh.nmr.FreeView.plist
Wait for a few seconds and try starting freeview again.
Ruopeng
On Jul 21, 2021, at 1:49 PM, Sahil Bajaj
mailto:sahil.br...@gmail.c
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Hello Kiyotaka,
Please try refreshing your copy/install of the Ubuntu 7.2.0
distribution as the packages have been updated to fix the warning below.
I think you were using the installer, so you could try the commands
below to download and re-ins
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Hi,
I reinstalled FreeSurfer and now the latest version i.e., 7.2.0, but
somehow I am still getting the same error message, please see below. I am
still unsure how can I fix this issue?
Last login: Wed Jul 21 12:43:52 on ttys003
freesurfer-d
Yes, just run recon-all with the -fill option to regenerated the
filled.mgz (it will be the same filled.mgz but it will have a colortable
embedded; it will also create filled.auto.mgz to help keep track of the
edits). The just edit filled.mgz and proceed as normal. When you edit,
make sure you
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Great. Many thanks for your suggestions.
My best
Aj
On Wed, Jul 21, 2021, 12:31 Fischl, Bruce wrote:
> There isn’t really anything available for the latter approach. I would
> suggest the former and potentially including site as a nuisance variable.
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Dear Freesurfer Experts,
Is there any way to remove pial edits selectively after you go through the
first round of edits and save the brain mask?
Details: I've pial edited for a few brains and saved their brain masks. But
when I was going through a seco
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Read the release notes. Can I with the new version run a recon-all over
processed 7.1.1. I am interested in the ability to edit filled.mgz and
applying this to 7.1.1 recons.
On Mon, Jul 19, 2021 at 5:46 PM Douglas N. Greve
wrote:
> We are please t
There isn’t really anything available for the latter approach. I would suggest
the former and potentially including site as a nuisance variable. You very much
want to balance across site in terms of whatever effect you are looking for
(e.g. don’t scan all your patients on one and all your contro
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Thank you so much for your reply.
I have subjects who got MRIs on either GE or PH. There are mild image
intensity differences between the two scanners. To combine volumetric data
from both scanners, an easier way would be to express volumes as percen
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HI Xiaofang,
I'm not sure there is an out-of-the box method to do this, but you should
be able to modify FreeSurfer's qatools to generate relevant metrics and
screenshots for your application.
See
https://secure-web.cisco.com/1qSsYKc06MzXRP-vLirz5AAd
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Hi,
I have tried to segment the thalamic nuclei and amygdala, using
segmentThalamicNuclei.sh and segmentHA_T1.sh.
But is there any method to quickly check whether the segmentation is accurate?
Because I have so many scans that using freeview to
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Don,
I have found the following library to be useful for this purpose
https://secure-web.cisco.com/1U3Y67JfA4BlNJYX4ut9RehuCYpVbRmTunPkJWXOMufx-L2LYyccGN07nwOp17bs4N9M2lOSMLzk7W7ZkJQjbT2SooMuk-PVSRpQj_nEtWq4F_JStrLxRmY2CYnkOjkCCWCySLA3VsXYMsjiZzP8HTnx
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Thanks, Bruce, and thanks for getting back so quickly.
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fischl, Bruce
Sent: Wednesday, July 21, 2021 11:08 AM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] shortest distance b
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Hello,
Can you please clarify the following:
Do we use subcortical QC rating for all subcortical measures such as
accumbens as well measures such as total white matter volume. We do not use
it for estimated total intracranial volume as this is accurat
Hi Don
By far the easiest way to do this is to find the locations of the points on the
sphere then compute the length of the great circle arc connecting them, then
correct by the ratio of the sqrt of the areas of the two surfaces.
Alternatively I think Rudolph may have had some tools for comput
Hi Rosie
The order in recon-all is fixed. In general control points can change a region
of an image, while the wm segs are pointwise, so I guess it makes sense to do
the cps first, particularly since they are a lot easier and may fix some of the
seg errors
Cheers
Bruce
From: freesurfer-boun..
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Dear experts,
I would like to compute the shortest distance along the gray/white boundary
between two points on the boundary, i.e. between points with "white"
parcellation regions. The distance need not be guaranteed to be minimized and
the path nee
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Hi Bruce,
Thank you for answering my question.
But the order matter, right? That is, first do control points and once
corrected, then do wm_segmentation edits, right?
Sorry for insisting, but this is very important to me.
Kind regards,
Rosie
On
Hi Rosie
Recon-all won’t delete edits unless you explicitly tell it to. That said,
control points my affect the region you are working on (and possibly correct
some defects!)
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Rosalia Dacosta Aguayo
Sent: Wednesday, July 2
Hi Robin
If you run-recon-all you will get a map that we call “sulc” for each subject.
When we generated our original manual parcellations we used it to guide where
to place the boundary between a sulcus and a gyrus. Essentially we used the
zero-crossing of sulc. Load it on an white surface and
Hi AJ
No, not easily. Maybe you can tell us your overall goal to see if we can help?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of AJ
Sent: Wednesday, July 21, 2021 1:27 AM
To: Freesurfer support list
Subject: [Freesurfer] Intensity equalization
External Ema
Hi Amir - I should make it clearer in the documentation that, unless you have a
specific need to change one of the configuration variables, you should just
leave it out of your configuration file entirely. This is the best way to make
sure that the defaults are being used. Only have in your conf
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Dear Freesurfer team,
Sorry for this basic question.
I wonder if once I have edited the white matter (topological defects), I
can run control points without deleting what I have done to white matter
segmentation.
Kind regards,
Rosie
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