Dear FS team,
I would like to correct for multiple comparisons after I run command-line GLM
analysis on aparc.stats tables (my ROI's are few regions from DK-atlas). I
tried to do the Monte Carlo simulation but get an error that a masking-file is
missing. In general, how could I correct for mult
Dear FS team,
I tried to run GLM-analysis using aparc stats files. At first I created these
files for a few subjects of interest (e.g. aparc_rh_thickness_stats.txt) and
checked whether they looked ok, which they did (values were pretty similar).
Then I used the following command (for example):
Dear FS team,
I tried to run GLM-analysis using aparc stats files. At first I created these
files for a few subjects of interest (e.g. aparc_rh_thickness_stats.txt) and
checked whether they looked ok, which they did (values were pretty similar).
Then I used the following command (for example):
Dear FS team,
Apologies in advance for perhaps again a rather basic question. I attempted to
load the aparc overlay in freeview by using the written command from the group
analysis page, however it failed to load correctly.
I used the following command:
freeview -f
fsaverage/surf/lh.inflated:a
ge is based on the upcoming
6.0, I believe. So some of the command line options are not available in 5.3.
Best,
Ruopeng
> On Jul 29, 2016, at 9:11 AM, Caroline Beelen
> wrote:
>
> Dear FS team,
>
> Apologies in advance for perhaps again a rather basic question. I attempted
>
? The command on the webpage is based on the upcoming
6.0, I believe. So some of the command line options are not available in 5.3.
Best,
Ruopeng
> On Jul 29, 2016, at 9:11 AM, Caroline Beelen
> mailto:caroline.bee...@kuleuven.be>> wrote:
>
> Dear FS team,
>
> Apologies i
Dear FS,
Sorry to bother again, but I'm currently in need for some quick help.
Today, I also ran into another problem. I tried to display only few ROI's in
Freeview instead of the whole brain. Therefore, I tried to create a new
annotation file consisting of only few labels (from regions of DK-at
Greve
Subject: Re: [Freesurfer] mapping error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
Content-Type: text/plain; charset="windows-1252"
what is your command line?
On 8/3/16 6:00 AM, Caroline Beelen wrote:
>
> Dear FS,
>
> An aparc.annot ctab file was created but I g
rvard.edu>
Message-ID:
mailto:f3f77469-16ad-6fdf-f647-80aee162d...@nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset="windows-1252"
what is your command line?
On 8/3/16 6:00 AM, Caroline Beelen wrote:
>
>
>
>
aparc.
; manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever
> format, but should be binary
>
> ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol != 0);
>
> newaseg = aseg;
>
> newaseg.vol(ind) = 77;
>
> MRIwrite(newaseg,'aseg.mgz')
Dear FS,
I have a question on visualizing results from GLM analysis... How can I
visualize corrected results in Freeview after having applied bonferroni/FDR
correction (somewhere else)?
I saw it is not possible (error: masking file missing) -and was told it is not
necessary- to apply monte carl
Dear Freesurfer experts,
I just started using Freesurfer for performing MRI (T1)- group-based ROI
analysis and managed to go through the first recon-all processing stream and
making few manual edits. Then I followed first steps of the Qdec -procedure.
However, there is a separate section on ROI
Dag Jolijn,
Heb jij je al aangemeld voor onderstaande Freesurfer course? Er is volgens mij
nog steeds niets van die andere beschikbaar, dus ik twijfel ook om te gaan (zou
wel nuttig zijn!). Al is het een beetje achter de feiten aan…
Vriendelijke groet,
Caroline
Van: freesurfer-boun...@nmr.mgh
http://www.u930.tours.inserm.fr/
Service de Neurochirurgie
et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours
- France
tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07
Le 12 févr. 2016 à 09:53, Caroline Beelen
mailto:caroline.bee...@ppw.kuleuven.be>> a
é
Dear Freesurfer team,
Forgive me if this is a foolish question...
I wanted to overlook cortical thickness, area and volume measures in Gnumeric
file after recon-all (checking edits made). However, for several subjects I
noticed that the values of mean thickness (final column) were calculated wr
: [Freesurfer] gnumeric file
Hi Caroline
the data are in native space. Summary statistics means e.g. the volume of the
left hippocampus. You don't need any registration algorithm for this type of
thing - you just tabulate it across subjects
cheers
Bruce
On Thu, 17 Mar 2016, Caroline Beelen
ens Douglas Greve
Verzonden: woensdag 16 maart 2016 15:38
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] gnumeric file
On 3/16/16 6:52 AM, Caroline Beelen wrote:
Hi FS team,
Sorry for these rather basic questions...
I'm not sure whether the gnumeric file is an ascii
u looked at the lh.aparc.thickness.table? If it is correct then it is
something strange with gnumeric and I'm not sure we are qualified to help you.
As for 3, the tables contain summary stats and so don't need to be mapped into
any common space.
cheers
Bruce
On Thu, 17 Mar 20
Dear FS team,
We want to create a ROI based on the wm parcellation in the 2009s atlas. We ran
the following command:
mri_aparc2aseg --s --labelwm --hypo-as-wm --rip-unknown --ribbon --o
mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz ( was replaced by
our subject)
We get the following er
Dear FS team,
Thank you for your answers before (email: WmParc). We now realize that we've
formulated our question wrong, since our problem is mainly in creating the
wmparc.a2009s.mgz file. We ran the following command:
mri_aparc2aseg --s --labelwm --hypo-as-wm --rip-unknown --ribbon --o
mri/wm
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-72
r decision only based on wm intensity values?
Thank you for your reply.
Kind regards,
Caroline Beelen
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The information in this e-mail i
gards, Caroline Beelen
-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens
freesurfer-requ...@nmr.mgh.harvard.edu
Verzonden: donderdag 18 mei 2017 18:00
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Freesurfer Digest, Vo
External Email - Use Caution
Dear FS,
I followed the group analysis page for glm analysis and it worked fine until
the final step. I'm using version 5.3. After performing glm-fit-sim it says
"glm-fit done" (for all files), but when trying to open these it says:
"Reading colorta
D:
<504d6069-399f-163d-39a9-dcc6c02d3...@mgh.harvard.edu<mailto:504d6069-399f-163d-39a9-dcc6c02d3...@mgh.harvard.edu>>
Content-Type: text/plain; charset="Windows-1252"
What says that? What command are you running? What is the other terminal
output?
On 10/01/2018 04:54
s of Freesurfer digest..."
Today's Topics:
1. FW: RE: error glm-fit-sim (Caroline Beelen)
2. Re: output values of vertices on surface into a textfile
(Sims, Sara A)
3. Re: output values of vertices on surface into a textfile
(Bruce Fischl)
4. Re: output values of
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