Hello, experts,
I am trying to obtain a V1 mask and use it as a seed of my fiber
tracking. But I do not know how to get the BA.nii.gz file, and I've
obtained BA.ctab and lh.BA.annot files by using flag recon_all. Would
someone give me some suggestions about this?
Thanks so much for your help!
Y
Dear FS experts,
I'm studying the most common artifacts on MRI scanning. I started with the
SNR calculation (which is included in recent FS versions), but I'm afraid
that these artifact is filtered/processed with the scanner control program,
and I'm wasting time trying to calculate this ratio.
My
Dear FS-experts,
I've been using optseq for many years without problems, however, I run into a
couple now.
My code is the following:
optseq2 --ntp 255 --tr 2.0 --tprescan 4.0 --psdwin 0.0 16.0 1 --ev Gain2 5.0
8.0 --ev Gain4 5.0 8.0 --ev Gain6 5.0 8.0 --ev Gain8 5.0 8.0 --ev Loss2 5.0 8.0
--ev
Hello Nick,
just installed and tested the BETA version. Up to now no problem encountered.
Recon-all is just running as a test (using -use-gpu). OS is Lubuntu 13.04. I
report on the segmentation as soon as it is finished.
So long Joerg
On Sun, 12 May 2013 22:41:25 -0400 (EDT)
"Nick Schmansky"
Just for completeness, I refer to my first contribution:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html
On Mon, 13 May 2013 13:58:30 +0200
Joerg Pfannmoeller wrote:
> Hello Nick,
>
> just installed and tested the BETA version. Up to now no problem enco
Hi Lulu
what version are you running? If it's a newer one you should have label
files in the label subdir named [lr]h.V1.label and [lr]h.V1.thresh.label (a
thresholded version of the first one).
cheers
Bruce
On Mon, 13 May 2013, lujiao luo
wrote:
Hello, experts,
I am trying to obtain a
Hi Jordi
this is definitely vendor specific. In Siemens you can for example turn
on "prescan normalization" which will correct for intensity bias. You can
have it generate two series - one with and one withour the correction. What
other artifacts do you mean? There are lots of possibilities...
Hi Bruce,
Thank you for your fast answer. I'm focusing on SNR, Motion Correction and
Intensity Inhomogeneities.
Regards,
2013/5/13 Bruce Fischl
> Hi Jordi
>
> this is definitely vendor specific. In Siemens you can for example turn on
> "prescan normalization" which will correct for intensity
Hello Bruce,
Thanks so much for your reply.
Yes, you are right, I've obtained the lh.V1.label. But I couldn't figure
out how to create a roi.nii.gz mask by using the lhV1.lable file or
lhBA.annot, and then I can use it as a seed for my fiber tracking.
Yours Lulu.
2013/5/13 Bruce Fischl
>
try mri_label2vol
cheers
Bruce
On Mon, 13 May 2013, lujiao luo wrote:
Hello Bruce,
Thanks so much for your reply.
Yes, you are right, I've obtained the lh.V1.label. But I couldn't figure out
how to create a roi.nii.gz mask by using the
lhV1.lable file or lhBA.annot, and then I can use it as
Thanks so much for your suggestion, Bruce. I will have a try.
Yours Lulu
2013/5/13 Bruce Fischl
> try mri_label2vol
>
>
> cheers
> Bruce
> On Mon, 13 May 2013, lujiao luo wrote:
>
> Hello Bruce,
>> Thanks so much for your reply.
>>
>> Yes, you are right, I've obtained the lh.V1.label. But I
Question from the MR Physics peanut gallery:
How are you defining/measuring SNR for the anatomical sequences?
(Sticking to Siemens.) The way I think about this, if what you have are the
dicoms from an mprage which was collected with a receiver array, acceleration
and pre-scan normalization, the
Hi Bruce,
Thanks for your help yesterday. I was able to create the .mgh file using
the -output_type mgh option, but I am still unable to load it in tksurfer
as label or anything else. If you or Doug have any other suggestions, I
would really appreciate it. Thanks!
Jonathan
On Sun, May 12, 2013
Hi again
I am sorry I found out that I needed to delete this file IsRunning.trac
and then it works again.
Sorry for the inconvenience
Best
Celine
> Hi Freesurfer team
> I am very new with tracula so my problem might be very obvious.
>
> I previously run trac-all -prep on a patient and it worked fi
you should be able to load it into tksurfer as an overlay.
cheers
Bruce
On Mon, 13 May
2013, Jonathan DuBois wrote:
Hi Bruce,
Thanks for your help yesterday. I was able to create the .mgh file using the
-output_type mgh option, but I am still unable to
load it in tksurfer as label or anythi
Thanks for the clarifications, Doug!
1) I am using FS stable version 5.0.0, so I'm assuming that the --2spaces flag
has probably been implemented for the more recent FS versions.
2) Thanks, that makes a lot more sense now.
In addition, since clusters are formed based on the number of neighbori
Hi all,
last question promise. Successfully completed mris_make_surfaces for both
hemispheres. in my day-to-day editing I open tkmedit thusly:
tkmedit brainmask.mgz -aux $SUBJECTS_DIR/subjid/mri/wm.mgz -surface
$SUBJECTS_DIR/subjid/surf/lh.white -aux-surface
$SUBJECTS_DIR/subjid/surf/rh.white
Hi Jon
there shouldn't be more surfaces I don't think - the ?h.white and
?h.pial should still be the ones you look at
Bruce
On Mon, 13 May 2013, Jonathan Holt wrote:
> Hi all,
>
> last question promise. Successfully completed mris_make_surfaces for both
> hemispheres. in my day-to-day editing
it there a way to mask the data before running the Qdec analysis on it?
- Original Message -
From: "Douglas Greve"
To: freesurfer@nmr.mgh.harvard.edu
Sent: Sunday, May 12, 2013 11:24:12 PM
Subject: Re: [Freesurfer] Restricting ROI Analysis
Hi Skyler, I don't think we have the ability to
Bruce,
how is it that I might load multiple surfaces, loading lh after having loaded
rh makes the other disappear. this is loading manually, not from the command
line
On May 13, 2013, at 11:14 AM, Jonathan Holt wrote:
> Hi all,
>
> last question promise. Successfully completed mris_make_surfa
you can use file->aux-surfaces->load aux main surface (or something like
that). Or use freeview.
cheers
Bruce
On Mon, 13 May 2013, Jonathan Holt wrote:
> Bruce,
>
> how is it that I might load multiple surfaces, loading lh after having loaded
> rh makes the other disappear. this is loading manu
Hi Glen, if it is just a slab, you are probably smoothing in a bunch of
0s. Try smoothing only the areas within a mask of the slab. You can do
this by passing a label to mri_surf2surf ( you can also create a mask
and pass it to mris_fwhm).
doug
On 05/13/2013 10:12 AM, Glen Lee wrote:
> Inline im
On 05/13/2013 11:11 AM, Fotiadis, Panagiotis wrote:
> Thanks for the clarifications, Doug!
>
> 1) I am using FS stable version 5.0.0, so I'm assuming that the --2spaces
> flag has probably been implemented for the more recent FS versions.
>
> 2) Thanks, that makes a lot more sense now.
>
> In add
no
doug
On 05/13/2013 11:16 AM, Jon Wieser wrote:
> it there a way to mask the data before running the Qdec analysis on it?
>
> - Original Message -
> From: "Douglas Greve"
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Sunday, May 12, 2013 11:24:12 PM
> Subject: Re: [Freesurfer] Restricting
I think you are at the limit of what is possible. You have TR=2 and
Ntp=255 for a total scan time of 510sec. You have 9 event types, each
5stim+2null=7sec long, each repeated 8 times. This calls for 504 for
stimulation and so only 6 sec total left for jitter.
doug
On 05/13/2013 05:28 AM, Koo
Sorry, I wasn't adjusting the overlay values so I couldn't see it. Thanks
for your help!
Best,
Jonathan
On Mon, May 13, 2013 at 11:09 AM, Bruce Fischl
wrote:
> you should be able to load it into tksurfer as an overlay.
>
> cheers
> Bruce
>
> On Mon, 13 May 2013, Jonathan DuBois wrote:
>
> Hi B
sure, glad it's working
Bruce
On Mon, 13 May 2013, Jonathan DuBois wrote:
Sorry, I wasn't adjusting the overlay values so I couldn't see it. Thanks for
your help!
Best,
Jonathan
On Mon, May 13, 2013 at 11:09 AM, Bruce Fischl
wrote:
you should be able to load it into tksurfer as an ov
Hello
Is it fine to process the anatomical data in v4.5 and analyze the results in
v5.1?
Thanks,
Hiroyuki
Notice: This UI Health Care e-mail (including attachments) is covered by the
Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential an
yes, that is fine.
doug
On 05/13/2013 12:25 PM, Oya, Hiroyuki (UI Health Care) wrote:
>
> Hello
>
> Is it fine to process the anatomical data in v4.5 and analyze the
> results in v5.1?
>
> Thanks,
>
> Hiroyuki
>
>
>
>
> Noti
Great, thank you for your time!
Panos
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, May 13, 2013 11:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Sub
Hi Nick,
I installed it on Ubuntu 13.04 and all tools seem to work. I didn't test
recon-all yet.
Cheers,
Daniel
On Sun, May 12, 2013 at 10:41 PM, Nick Schmansky
wrote:
> Fedora 18, Ubuntu 13 and Gentoo 64 users,
>
> another beta of the upcoming v5.3 is available here:
>
>
> ftp://surfer.nmr.mg
Hi Xi-Nian,
As Doug said, they don't do the same thing. The method in the paper uses a
different kind of interpolation to allows the preservation of the amount of
area, whereas mris_preproc achieves the same globally using a Jacobian
correction. The results aren't expected to be identical at the v
Dear freesurfer mailing list, I have got a question with regard to the
freesurfer parcellation. I'm using the atlas with 68 cortical areas. I would
like to determine where to locate anatomical and functional areas in this
atlas. In this way I would like to locate the areas that are involved in
Hi Jasper
you can look in:
https://surfer.nmr.mgh.harvard.edu/pub/articles/HBM09-Destrieux-Sulcal.pdf
or if you have specific questions ask Christophe (ccd). The Brodmann area
and functional boundaries generally don't simply follow the anatomy (except
for V1). We also explictly label some of th
Hi Matt,
Thanks for the link.
Reading on pages 29-31, I am struck by the complexity of the procedure. Not to
say that it doesn't work, or that the single T1w image free-surfer stuff is
simple :-), on the contrary, it's just that I was expecting to see something
about an optimization that used
Dear freeSurfer expert,
I am trying to perform whole brain functional connectivity analysis
Is there a wiki for resting state analysis? I have only found this wiki page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc
So far I have run the following commands:
preproc-s
Hello
Im preparing an LGI(local gyrification index) manuscript and seems i don't
know the default radius that is used for the circular region defined on the
outer surface
that the boundary of is then projected onto the pial surface to get the
corresponding pial region ?
hope im clear, not the
Hello Gregory,
The radius of the circular region is 25 mm by default. If you want you can
change it, but I will not advise radii below 20 mm or above 30 mm.
Best,
Marie
On May 13, 2013, at 11:44 AM, Gregory Kirk
wrote:
>
> Hello
>
> Im preparing an LGI(local gyrification index) manuscrip
Hi Efrat, you've done the preproc-sess correctly, but you'll need to
modify the mkanalysis-sess. See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
dpug
On 05/13/2013 02:26 PM, Efrat Kliper wrote:
>
> Dear freeSurfer expert,
>
> I am trying to perform whole b
p.s. make sure that the echoes are in float format, not uchar/int/short
(you need to use -odt float in the mri_convert command line)
On Mon, 13 May
2013, Bruce Fischl wrote:
> you can use file->aux-surfaces->load aux main surface (or something like
> that). Or use freeview.
>
> cheers
> Bruce
>
I'll definitely do that next time...
although it didn't seem to pose any noticeable issues this time around?
jon
On May 13, 2013, at 3:52 PM, Bruce Fischl wrote:
> p.s. make sure that the echoes are in float format, not uchar/int/short (you
> need to use -odt float in the mri_convert command
I'm surprised it would work well if they are not float. You'll lose a lot
of precision
On Mon, 13 May 2013, Jonathan Holt wrote:
> I'll definitely do that next time...
>
> although it didn't seem to pose any noticeable issues this time around?
>
> jon
> On May 13, 2013, at 3:52 PM, Bruce Fischl w
I wont question it, but this is my first multi echo brain and it's the most
beautiful i've ever seen. so crisp.
On May 13, 2013, at 3:55 PM, Bruce Fischl wrote:
> I'm surprised it would work well if they are not float. You'll lose a lot of
> precision
> On Mon, 13 May 2013, Jonathan Holt wrot
Hi Jamie, did you look at the help for mri_glmfit? Run it with --help.
doug
ps. Please post questions to the list so that others can benefit. thanks!
On 05/13/2013 04:12 PM, Jaime Ide wrote:
> Dear Douglas,
>
> Thanks for your helpful page at
> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnal
Gordon Xu who helped us set up the protocol reminded me of the following:
"The main benefit of the readout PF is to reduce echo spacing, hence less
blurring in the slice direction. The side benefit is that it also reduces
the minimum TE, hence less dropout. However, you do give up some SNR at
the
Tested recon-all tonight on lubuntu 13.04. I did not encounter any problems.
Also freeview runs without an error for the subject bert.
On Mon, 13 May 2013 14:40:10 +0200
Jörg Pfannmöller wrote:
> Just for completeness, I refer to my first contribution:
>
> http://www.mail-archive.com/freesur
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