Hello,
is there an atlas for the cerebellum using freesurfer ?
Many thanks for the information.
Best
Giovanni
2018-01-11 9:15 GMT+01:00 de Marco :
> Many thanks Bruce for your rapid and clear response.
> Have a nice day
> Best
> Giovanni
>
> Envoyé de mon iPhone
>
> > Le 11 janv. 2018 à 02:27,
Hi All,
I tried to run a subject through FreeSurfer 6.0 for hippocampal Subfield
segmentation but exited with errors.
The content of the recon-all.error file is below.
SUBJECT CHRM2001
DATE Sun Feb 25 00:34:13 GMT 2018
USER 15233963
HOST psych-sl03
PROCESSOR x86_64
OS Linux
Linux psych-sl03
Dear Experts,
I was wondering if someone might be able to help me understand what the
difference is between the two commands below. It seems that they can be used
interchangeably, because I can forsee a situation in which one might not
remember which command to run and also have done several typ
Hi Arkadiy
-make all uses the makefile utility to only rerun the processing steps
that are needed based on the timestamp of the various files in the
subject's dir and a table of dependencies.
cheers
Bruce
On Mon, 26 Feb 2018,
Maksimovskiy, Arkadiy wrote:
Dear Experts,
I was wondering if
Hi Giovanni
do you mean a cerebellar parcellation? We have several prototypes but
haven't distributed anything yet.
cheers
Bruce
On Mon, 26 Feb 2018, Giovanni de Marco
wrote:
Hello,
is there an atlas for the cerebellum using freesurfer ?
Many thanks for the information.
Best
Giovanni
2
Hi FreeSurfer experts,
I would like to use the asegstats2table and the aparcstats2table commands
on my longitudinal data, that have been processing following the
longitudinal pipeline (recon-all -cross, - base and finally -long). And I
have two questions :
1) Am I obliged to do the long_stats_sl
Hi Emily, I looked over these subjects. While a few of the flagged spots
are not really problems, most of them are true inaccuracies. I think the
underlying problem is that your data is pretty noisy and have some
ringing. What kind of acq was it? Scanner, field strength, pulse seq?
Was it acqui
Dear Theo,
Can you please provide us with the command you executed, and the complete
output logs?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: on behalf of
Does anybody else have a comment on the experienced artefact?
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Does anybody else have a comment on the experienced artefact
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Hi FreeSurfer Expert,
I followed the Anatomical ROI analysis tutorial and make a aseg.vol.table for
the 40 subjects. However, the segment volume can various a lot in different
subjects, such as Left-Lateral-Ventricle, Left-Inf-Lat-Vent. I attached a
screenshot. Thanks for your response.
Best
sorry Gabor, can you repost the rest of the thread? What was the artefact?
On Mon, 26 Feb 2018, Gabor Perlaki wrote:
> Does anybody else have a comment on the experienced artefact?
>
>
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Hi Doug,
They were initially reoriented for VBM analysis, but nothing else was changed
(comparing original versus reoriented, there does not seem to be differences).
The subjects are elderly (mean age = 74.08). We are investigating a new
pre-dementia syndrome so there may be greater atrophy in
On 02/21/2018 11:47 AM, C.P.E. Rollins wrote:
> Dear Freesurfer Developers,
>
> I'm following the very well-documented steps proposed by Marie Schaer
> for measuring local gyrification index in the paper "How to Measure
> Cortical Folding from MR Images: a Step-by-Step Tutorial to Compute
> Local
Can you be more specific about which step is failing and how you are
verifying the failure?
On 02/21/2018 05:21 PM, Albrecht, Daniel S. wrote:
>
> Hello,
>
>
> We are attempting to extract cortical thickness values from a
> pre-defined ROI in MNI space.
>
>
> Originally, we had followed the ins
I'm not sure I understand what you are asking about. Do you mean in the
aseg.mgz or the aparc+aseg.mgz? Unknown is usually just stuff outside of
the head, but sometimes can be in the head (eg, with aparc+aseg.mgz).
On 02/22/2018 08:51 AM, Daniel van de Velden wrote:
> Dear fellow colleagues,
>
I think it should work; We are not using tksurfer any more (freeview
instead), but I think it should still work
On 02/23/2018 05:16 PM, Sarah Cole wrote:
> Hi,
>
> I was wondering if this method is still applicable in version 6
> https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs
>
>
> I ca
On 02/24/2018 12:00 AM, Martin Juneja wrote:
> Hi experts,
>
> I am not sure if this has already been addressed in FS discussion.
>
> If my fsgd file looks like following:
>
> Class Male
> Class Female
> Variables Performance Age
> Input S1 Male 181 25
> Input S2 Female 167 23
>
>
>
> I
Thanks much Dough for your reply.
So if I add another column Performance*Age (after removing the mean of
each) in my fsgd file (and remove individual columns for Performance and
age), could you please tell what will be the contrast matrix (after only
Gender as a covariate) in that case i.e. for fo
You would keep both Perform and Age in addition to adding Perform*Age. I
would first use DODS to test for a difference between groups in the
Perform*Age variable [0 0 0 0 0 0 1 -1]. If there are no differences,
then use DOSS to test for an effect of Perform*Age [0 0 0 0 1].
On 02/26/2018 04:40
You should check the accuracy of the segmentations in a few of the
outlier subjects
On 02/26/2018 03:18 PM, Ting Li wrote:
> Hi FreeSurfer Expert,
>
> I followed the Anatomical ROI analysis tutorial and make a
> aseg.vol.table for the 40 subjects. However, the segment volume can
> various a lo
I don't know about #1 (I think not). For #2 you shold use the subject
names from the longitudinal analysis
On 02/26/2018 11:39 AM, Lisa Delalande wrote:
> Hi FreeSurfer experts,
>
> I would like to use the asegstats2table and the aparcstats2table
> commands on my longitudinal data, that have be
It doesn't work on tksurfer. But it's ok.
So Doug, is this the latest tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview
for FS-FAST and creating functional ROI?
More specifically, do I need to use "mri_vol2surf" to get the activation on
the surface?
A FreeSurfer build from source requires KWWidgets, but it has been deprecated
for 10 years. What does Freesurfer use this code for?
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