Hi everyone,
I am a new user of freesurfer. As a first step, I wrote a script (see
below between ---) to run recon-all on the anatomical data. Since I found
it very slow, and our server has multi-cores, I run this script manually
several times, thus it appeared to be parallel.Then I have severa
Hi everyone,
I just re-checked the folder [fsaverage], their modified date was quite
old, probably they are just copies from freesurfer installation folder
rather than results of my scripts. Then my question 2 become void...
best!
Peng
-- Forwarded message --
From: peng
Date
at 2:39 PM, Bruce Fischl wrote:
> Hi Peng
>
> the recon-all instances should be able to be run in parallel. The first
> time you run one it will see that fsaverage does not exist, and will
> symlink it to $FREESURFER_HOME/subjects/fsaverage (which is our existing
> coordinate syst
if N is relative large
(say, 200). Can anyone give me a hint which function shall I use?
best
Peng
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The information in this e-ma
t/surf/lh.thickness --pdf uniform --o junk.mgh
>
> mri_binarize --i junk.mgh --min .9 --o mask.mgh
>
> The first command synthesizes a surface overlay with uniformly distributed
> random numbers between 0 and 1. The second command thresholds at .9, so
> you'd get about 10% of th
3-D array of
the individual MRI data. Is it possible to do it in freesurfer? I guess the
surface-based procedure shall work well for this. It might be a very junior
question, if it was documented somewhere before, please let me know the
link. Thank you very much for help.
best
Peng
ots in individual) ->
Bn(volume representation of dots in individual). If this assumption is
correct, I would like to use Bn for my computation and ASn for display
later.
I hope I have made myself clearer.
best
Peng
On Mon, Mar 10, 2014 at 4:21 PM, Douglas N Greve
wrote:
>
> Do you mean you
Thanks for your reply. I am using *ICBM 2009a Nonlinear Asymmetric 1×1x1mm
template. *I did not expect that it will make much difference in the
algorithm. Does freesurfer favor certain template than others?
btw: the individual mri is also 1 mm resolution.
On Tue, Mar 11, 2014 at 8:46 PM, peng
==
Thanks a lot.
On Tue, Mar 11, 2014 at 5:06 PM, Douglas N Greve
wrote:
>
> Hi Peng, there's a lot going on there, and it is not specific enough for
> me to make recommendations. Take a look at the docs we have on our
> coordinate systems
>
>
> http://surfer.nm
ds mris_flatten took 2-3
hours.
btw: the inflated surface is OK either checked by freeview or matlab.
best
Peng
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The information in
More information, error from tksurfer is as following:
MRISalloc(16711682, 480): could not allocate vertices
Cannot allocate memory
-- Forwarded message --
From: peng
Date: Fri, May 9, 2014 at 1:01 PM
Subject: a question on flat surface
To
again! Also thanks to anyone who would like to comment!
best
Peng
On Fri, May 9, 2014 at 5:12 PM, Bruce Fischl wrote:
> Hi Peng
>
> the flat maps are stored in a different format than the surfaces, called a
> "patch" format (since they are only a piece of the whole surface -
Great, Thank you Bruce!
On Sat, May 10, 2014 at 3:09 PM, Bruce Fischl wrote:
> Hi Peng
>
> we provide matlab code (read_patch.m) for reading patches and for reading
> patches converted to ascii format (read_patch_asc.m). You can use
> mri_convert to generate the ascii format
>
this is
not possible, is there a matlab tool similar to 'write_file.m' so I can
output my data in matlab to the newer format (substitution of w-file)?
Thanks in advance.
best
Peng
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Thank you Bruce!
On Wed, Jan 6, 2016 at 8:03 PM, Bruce Fischl
wrote:
> Hi Peng
>
> you can use read_wfile to read it into matlab, then save_mgh or MRIwrite
> to save them in .mgz format. Note that you will need to make sure that the
> vector you are writing is the correct leng
Thank you Douglas!
On Wed, Jan 6, 2016 at 8:10 PM, Douglas N Greve
wrote:
> You can also use mri_surf2surf to convert it to mgh or curv format
>
> On 01/06/2016 02:03 PM, Bruce Fischl wrote:
> > Hi Peng
> >
> > you can use read_wfile to read it into matlab, then save_
and line of freeview? e.g.
when I want to generate a lot of screenshots by the -ss option.
Thank you in advance!
best
Peng
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The inform
Dear Ruopeng,
Thank you for the information.
best
Peng
On Fri, Jan 27, 2017 at 4:10 PM, Ruopeng Wang
wrote:
> Hi Peng,
>
> No, there is no command-line option for that. I will add it in future update.
>
> Best,
> Ruopeng
>
>> On Jan 27, 2017, at 9:49 AM, peng w
Thanks for the advice, bruce.
On Fri, Jan 27, 2017 at 4:17 PM, Bruce Fischl
wrote:
> probably you should just smooth the volume and save it as a new volume
> before running freeview
>
> cheers
> Bruce
> On Fri, 27 Jan 2017, Ruopeng Wang wrote:
>
>> Hi Peng,
>>
Dear Ruopeng,
I have the same problem even before the current version 6 release, and
it was "solved" by invoke freeview from the command line (term). I guess,
to start from the icon, it might use different setup files.
best
Peng
On Fri, Feb 17, 2017 at 4:41 PM, Ruopeng Wang
wr
nt
of the overlay. I have the index of this location in the surface
vertices.
Thank you in advance.
best
Peng
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The information in
data from the same subject, processed by freesurfer.
4. Softwares, matlab2014b, freesurfer v5.3, MNE2.7.4
Thank you very much!
best
Peng
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Hi Bruce,
Thank you for your help, I will also post this in the MNE group.
best
Peng
On Fri, Dec 12, 2014 at 3:20 PM, Bruce Fischl
wrote:
> Hi Peng
>
> yes, for sure. This is what Matti Hamalainen's excellent MNE package is
> designed for. I'll cc Matti so he can chime
1
Obviously, the first one would need more test runs, which in fact was
nearly 2 hours for the subjects . And the second one need only 1/4
time, but is risky. I am afraid it would induce difference between
stimuli within condition.
Do you have any suggestions on it?
Thanks a lot.
piece of
advice. But I can't change the ratio because I have to combine the
fMRI data with a finished EEG experiment with the same paradigm.
On 6/29/07, Daniel G. Wakeman <[EMAIL PROTECTED]> wrote:
Hi Peng,
I'm sure Doug and others will have very valuable advice, but why not j
-autorecon-all -subjid
R2261_S0283'. I tried several subjects and got the same error. I am
wondering whether you can look at the 'recon-all.log' file and
'recon-all.error' file and help me figure out what the problem is and how
to solve it?
Thank you very much! Looking
Thank you! Hopefully, I can either figure it out myself or be helped by
someone.
Thanks!
Best,
Peng
On Wednesday, December 9, 2015, Bruce Fischl
wrote:
> Hi Peng
>
> nifti should be fine as input, but definitely don't use analyze. It
> doesn't preserve the directi
r the home
folder and copied the license info into it, but it still did not work. May
you give any suggestions to fix this problem?
Thank you! Looking forward to your reply!
Sincerely,
Peng
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Hi!
I am a relative beginner with freesurfer and was going through the steps listed
on freesurfer wiki about detailed description of each steps autorecon2 covers.
During "Automatic Topology Fixer (-fix)", the description stated that "user
should check the orig surface in the volume to make sure
already sent it twice and got the same
result.
Thanks!
Cheng Peng
On Wednesday, July 23, 2014 9:39 AM, Cheng Peng wrote:
Hi, Bruce,
I attached the nu.mgz file with this email, i'm at home right now and would
upload T1.mgz later if need to. As far as i know individual recon-all runs wer
External Email - Use Caution
Whatever I filled the form I got "Spammer. Go away!" message. Please help!
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The freesurfer license.
https://surfer.nmr.mgh.harvard.edu/registration.html
On Wed, Feb 13, 2019 at 1:38 PM Hoopes, Andrew
wrote:
> Hi, what are you trying to register for? A wiki account?
>
> Andrew
>
>
>
>
>
> *Fro
External Email - Use Caution
Please help!
Repost with a better title.
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esurfer-boun...@nmr.mgh.harvard.edu on behalf
> of Greve, Douglas N.,Ph.D." behalf of dgr...@mgh.harvard.edu> wrote:
>
> it would be helpful if you were to tell us exactly what you were doing
> (eg, URL, which text box, etc)
>
> On 2/13/19 3:
help. Appreciate it!
X. Peng
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n existing subject, then
omit all -i flags.
I have tried all the suggestions listed in the error information, but none
worked.
Does anyone have any suggestion? I would really appreciated it.
Many Thanks
Peng
----
Peng Liu, PhD Candidate
Institut für
responds with the same error.
I have also tried the same data in another laptop. Also showed up the
error. Would you say it might be something wrong with the data itself?
(Although I am quite certain this is the raw T1 data which has never been
performed any analysis).
Many Thanks
Peng
External Email - Use Caution
Hello Douglas,
If I do ls $SUBJECTS_DIR/ben, the T1 image will show up as predicted.
However if I tried to recon-all, the error will pop up.
Many Thanks
Peng Liu, PhD Candidate
Institut für Kognitive
the .lut file (attached below), when loading it
into freeview, the colour scale is from 0 to 6.
[image: image.png]
Does this mean I should also include scale information in the .lut file?
Any help would be much appreciated.
Peng Liu
Map.lut
Description: Binary data
the .lut file (attached below), when loading it
into freeview, the colour scale is from 0 to 6.
[image: image.png]
Does this mean I should also include scale information in the .lut file?
Any help would be much appreciated.
Peng Liu
Map.lut
Description: Binary data
colours and five colours only...
Is there any specific reason to not display negative scales with look up
table? Will it cause any error or jeopardize the results displayed?
Many Thanks
Peng
On Mon, 6 Apr 2020 at 16:13, Ruopeng Wang
wrote:
> Hi Peng,
>
> Your lookup table only contain
External Email - Use Caution
Thank you so much. I shall modify my other scripts then.
Peng
On Mon, 6 Apr 2020 at 16:59, Ruopeng Wang
wrote:
> I don’t think look up table works with negative indices. It was mainly
> designed for label volumes.
>
> Ruopeng
>
&
'mni305.cor.mgz' be okay as
reference image?
Any help would be much appreciated.
Kindly Regards
Peng Liu
[image: Otto-von-Guericke University Magdeburg]
Peng Liu, PhD Candidate
Institut für Kognitive Neurologie und Demenzforschung (IKND)
[image: Otto-von-Guericke University Magdeburg]
Peng Liu, PhD Candidate
Institut für Kognitive Neurologie und Demenzforschung (IKND)
Otto-von-Guericke Universität Magdeburg
Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)
Leipziger Str. 44| Haus 64| Raum 217
39120 Magde
, I wonder how would I get
other labels, which command should I run?
Many Thanks
PL
On Wed, 24 Jun 2020 at 16:09, Douglas N. Greve
wrote:
> I'm not sure what you mean by "like lh.BA3b.label". Are you just talking
> about the file name or the actual label?
>
> On 6/24/2
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Hi Bruce,
I have tried this label, but it seems not working as it should be. That is
why I wanted to create labels like before.
Thank you so much!
PL
On Wed, 24 Jun 2020 at 16:58, Fischl, Bruce wrote:
> Hi Peng
>
>
>
> I think &
not working as it should be?
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Peng Liu
> *Sent:* Thursday, June 25, 2020 7:23 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Brodmann area
at do you mean with 'not working'? Is an incorrect area highlighted on
> the brain? Does some command you are using respond with an error message?
>
> Tim
>
> > On June 25, 2020 at 5:33 PM Peng Liu wrote:
> >
> >
> > External Email - Use Cauti
External Email - Use Caution
Could you please send me the pass code to unzip the file?
Thanks,
Shichun
The information contained in this electronic e-mail transmission and any
attachments are intended only for the use of the individual or entity to whom
or to which it is addres
External Email - Use Caution
For some reasons I haven’t received the email yet.
Could you please send the pass code to me again?
Thanks,
Shichun
From: fsbuild [mailto:fsbu...@contbay.com]
Sent: Tuesday, April 26, 2022 8:39 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Peng, Shichun
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