Dear FreeSurfer Experts,
I am trying to visualize fMRI activation (generated from fsl) on the fsaverage
inflated surface, using mni152.register.dat.
It's odd that I find the results to be slightly different between tksurfer and
freeview. However, I made sure that I am using the same threshold..
Direct link:
http://rfmh.iapplicants.com/ViewJob-499585.html
Please email me with any questions.
Best, Andrew
Andrew J. Gerber, M.D., Ph.D.
Interim Director, MRI Unit
Assistant Professor of Clinical Psychiatry
New York State Psychiatric Insitute / Columbia University
Division of Child and Adolesc
Hi list,
I have 2 questions, please.
1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX (FSL)?
2-I'd like to export cortical masks from FS to FSL.
An option is mri_binarize but this way failed in probtrackx (fsl).FSL list have
advised me that I should use label2surf command to
1 - Yes.
2 - You can use mri_aparc2aseg to grow the cortical labels into the white
matter (say, by 2mm). The file that it will produce will be a volume file,
so then you just run mri_binarize to extract specific labels. Make sure
you save them in nifti format for FSL.
On Wed, 25 Sep 2013, std.
Hi all,
A few questions.
1. Is there a way to run scans of post-surgical brains that takes resections
into account and gives more accurate results than "recon-all -all"?
2. Is it possible to obtain resection volumes with FreeSurfer? I tried to do
this indirectly by finding the difference betwee
Thanks Anastasia. I have some problem when I use mri_binarize.FSL list and
guide advise me to use label2surf. There are a way to obtain specific labels in
.label instead of .nii.gz?
Stefano
Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 25-set-2013 17.49
A:
Cc:
Ogg: Re:
Hi FS Community,
I am using the mri_volcluster command but for some reason the --sumfile
shows up as an unknown flag. Is there another way to get a summary text
file?
(I am using FS 5.3 stable.)
Thank you for your time!
Best,
Panos
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Cédric,
Does the first column of your Base_File_FreeSurfer.dat contain the
freesurfer subject id? the first column must contain that. from the
email below, where you show one line of the file, it looks like Subj# is
the first column and SubjID is the second.
Nick
On Thu, 2013-09-19 at 14:07
I'm curious whether or not freesurfer, when calculating surface values, takes
the original surface into account? If not, which surfaces are included in this
calculation?
jon
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mg
Hi Nick,
The first column is fsid, the reason why you see a number before fsid, is
because it's a line-number copied from g/n-edit.
Cheers
Cédric
-Original Message-
From: Nick Schmansky
Date: Wednesday, September 25, 2013 6:44 PM
To: Cédric Koolschijn
Cc: "freesurfer@nmr.mgh.harvard
Cédric,
can you send me the .dat file?
N.
On Wed, 2013-09-25 at 16:58 +, Koolschijn, Cédric wrote:
> Hi Nick,
>
> The first column is fsid, the reason why you see a number before fsid, is
> because it's a line-number copied from g/n-edit.
>
> Cheers
> Cédric
>
>
>
>
> -Original Mes
I've read in the mailing list archives people have had issues with tkmedit and
free view displaying control points differently. For me the first brain I've
loaded up has a single control point in free view that does not show in
tkmedit. Others have complained of free view showing points seemingl
Would it be possible to send us the volume and control point files?
Thanks,
Ruopeng
On 09/25/2013 02:09 PM, Jonathan Holt wrote:
> I've read in the mailing list archives people have had issues with tkmedit
> and free view displaying control points differently. For me the first brain
> I've load
Hi FS Community,
I have been using control points and adding wm voxels in the wm.mgz volume
of a subject, in order to fix the reconstruction, and after doing so for a
number of times, when I tried to run the command:
tkmedit brainmask.mgz -aux wm.mgz -surfs
the following message popped up:
Rea
Yep, I'll upload to the ftp server.
On Sep 25, 2013, at 2:28 PM, Ruopeng Wang wrote:
> Would it be possible to send us the volume and control point files?
>
> Thanks,
> Ruopeng
>
> On 09/25/2013 02:09 PM, Jonathan Holt wrote:
>> I've read in the mailing list archives people have had issues wit
For FSL guide:
Normal
0
false
false
false
IT
JA
X-NONE
Hi Jon
no, I don't think we use the orig surface for anything we report.
cheers
Bruce
On Wed, 25
Sep 2013, Jonathan Holt wrote:
> I'm curious whether or not freesurfer, when calculating surface values, takes
> the original surface into account? If not, which surfaces are included in
> this ca
Hi Panos
that means that you reran one of the surfaces but not the other. Try
running recon-all -make all, which should check to see if the
surfaces/volumes are up-to-date and rebuild them if needed. Note that
having an euler number of 2 doesn't mean the surfaces match, they also need
to have
Thanks Bruce!
Panos
> Hi Panos
>
> that means that you reran one of the surfaces but not the other. Try
> running recon-all -make all, which should check to see if the
> surfaces/volumes are up-to-date and rebuild them if needed. Note that
> having an euler number of 2 doesn't mean the surfaces m
Hi Anastasia,
I am setting up the dmrirc file to run Tracula. I am using Siemens Dicoms,
so I did not specify any setting for bval and bvec, but when trac-all -prep
starts running it gives the following error: mv: cannot stat
'paths.../SubjectID/dmri/dwi_orig_flip.mghdti.bvecs': No such file or
dir
Hi Jon,
You can do this with using the -c flag followed by the path to the
control.dat file, presumably in the tmp folder of the subject's recon
folder.
FYI: under the help menu in Freeview is a quick reference guide for
shortcut keys and common actions.
Also, type 'freeview -help' in a termin
Uploaded look for CPsDon'tMatch. It's the subject directory so surfaces,
volumes, tmp folder with control.dat
jon
On Sep 25, 2013, at 2:34 PM, Jonathan Holt wrote:
> Yep, I'll upload to the ftp server.
> On Sep 25, 2013, at 2:28 PM, Ruopeng Wang wrote:
>
>> Would it be possible to send us th
Try mri_annotation2label.
On Wed, 25 Sep 2013, std...@virgilio.it wrote:
For FSL guide:
I should transforms a group of labels into a surface
Usage:
label2surf -s -o -l
Compulsory arguments (You MUST set one or more of):
-s,--surf input surface
-o,--out out
Hi Gari - Sorry, right now the assumption is that the gradient vectors are
the same for all subjects. How different are they?
a.y
On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Anastasia,I am setting up the dmrirc file to run Tracula. I am using
Siemens Dicoms, so I did not specify
Hi all,
I am trying to convert a surface file to nifti using mri_surf2surf. The problem
is that my surface has a prime number of vertices, so I can't use —reshape. Is
there a way around this issue?
Thank you in advance,
Connor Lane
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Hi! Thanks for the fast answer.
If I do: diff id1.bvec id2.bvec
I can see some clear differences.
I was told that in FSL I should use the bvecs and bvals created in dcm2nii
per subject, so I understand I should do the same now?
Do you think an option would be to script the creation of a dmrirc fil
Hi Gari - Yes, that's your best option right now. Sorry for the
inconvenience. I'll make sure to add the option to have one gradient file
per subject in the next version.
a.y
On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote:
Hi! Thanks for the fast answer. If I do: diff id1.bvec id2.bve
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