Hi Doug,
I have a gamma.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ and I
also have a contrasts.sig.mgh file in the gmldir.
Could either of these be used instead of csdbase.sig.ocn.mgh? Or how could I
retrieve this file?
Thanks for your help!
Clara
- Ursprüngliche Mail -
V
Dear Experts,
I load the T1 and aseg file in freeveiw and select the lookup table ,and
show as isosurface in 3D view for a label .Is it possible to change the
color(for example label 13 is blue but I want to show it as
yellow!).another question is that if I want to show multiple labels which
are n
Hi,
I’m doing volumetric analyses on MR structural data. The problem is that the
scanning has been done on different MR machines, as well as with different
sequences in some cases. This leads to different absolute values between
subjects for volumes and thicknesses when being run through the Fr
The Nipype development team will be holding a workshop and hackweek at MIT,
Cambridge, MA, USA, from March 27 - 31.
For details and registration see: http://nipy.org/workshops/
2017-03-boston/index.html
cheers,
satra
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Dear All,
When I run mri_normalize on the same image using two freesurfer versions I
get distorted results only on the V6. Can someone let me know how I can get
the same results with V6?
command:
mri_normalize
V5 output: voxel value range: 0 - 182
[image: Inline image 1]
v6 output: voxel valu
Hello,
As I understand, adding the -no-isrunning flag will cause recon-all to ignore
the 'isrunning.pial' file.
I previously interrupted recon-all (while it was in the middle of a process)
and I have now begun to re-run my subjects using this flag.
I just wanted to check that any data which
At the moment, unfortunately, not as the high resolution morphs are very
large.
Lilla
On Mon, 20 Feb 2017, Bhavana Ganesh wrote:
Hi Lilla,
Is there a work around for this because I would at max be able to allocate 8GB
for the tool but I dont have the resource for 35GB.
Regards,
Bhavana
Hi Darko
what you are asking for is an unsolved problem in brain morphometry. We
try very hard to be insensitive/adaptive to MR sequence, but depending on
how big your acquisition differences are it is a very, very difficult
problem. Do you have the sam esubject(s) scanned on the different
pr
Hi Nazanin,
To change color you will need to modify the look up table, i.e., load your own
look up table. There is no way to only display a few selected labels. As a
workaround, you may try applying a look up table with only a few labels in it.
Best,
Ruopeng
> On Feb 21, 2017, at 5:20 AM, N S
Hi Arman
have you tried changing the windowing levels in whatever software you used
to create that image? You can't get the exact same results in V6 as in V5.3
as the algorithm has changed a bit.
cheers
Bruce
On Tue, 21 Feb 2017, Arman Eshaghi wrote:
> Dear All,
>
> When I run mri_normalize
Hi Joe,
you just want to make sure that no other process really is running
otherwise they may conflict with each other e.g. by trying to write the
same file at the same time.
cheers
Bruce
On Tue, 21 Feb 2017, Joe Necus (PGR) wrote:
Hello,
As I understand, adding the -no-isrunning flag
Dear Ruopeng,
Thank you for the fast response ,where can I learn how to create my custom
lookup table step by step ? and what the format of this file is?any help
will be very appreciated.
Best Regards,
Nazanin
On Tue, Feb 21, 2017 at 6:45 PM, Ruopeng Wang
wrote:
> Hi Nazanin,
>
> To change col
Just open FreeSurferColorLUT.txt file in your freesurfer installation
directory, you should be able to figure the format.
> On Feb 21, 2017, at 10:59 AM, N Saf wrote:
>
> Dear Ruopeng,
>
> Thank you for the fast response ,where can I learn how to create my custom
> lookup table step by step
You will have to run mri_glmfit-sim
On 02/21/2017 04:07 AM, Clara Kühn wrote:
> Hi Doug,
>
> I have a gamma.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ and I
> also have a contrasts.sig.mgh file in the gmldir.
>
> Could either of these be used instead of csdbase.sig.ocn.mgh? Or how c
Hi FS gurus,
I am remote logging in to nmr nexlin machines from my work iMAC and I am trying
to view some freesurfer results with Freeview, but I am getting the following
error:
llebois@nexlin9:/eris/ressler/DD_FS_160222/150305_NTD015_FS/mri/assembly$
freeview -v nu.mgz left_discreteLabels.mg
Sorry for the delay. I could not replicate this error on my end. It
looks like the $FREESURFER_HOME/subjects/fsaverage/label/lh.aparc.annot
might be bad on your system. Try this
tksurfer fsaverage lh inflated -aparc
does that generate the same errors?
On 02/16/2017 02:35 PM, Uquillas, Federi
Hm. I already did that. In none of my glmdirs are files like the
csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran:
mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir
$SUBJECTS_DIR/average/multi-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces
Cheers Clara
- U
Can you send the terminal output?
On 02/21/2017 11:44 AM, Clara Kühn wrote:
> Hm. I already did that. In none of my glmdirs are files like the
> csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran:
>
> mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir
> $SUBJECTS_
Hi Doug, thanks so much for looking into this. I just ran that comman and I get
the same errors indeed.
Would you be able to recommend a way for us to fix this so we can look at the
left hemi significant clusters after mri_glmfit-sim?
Best,
Fred
On 2/21/17, 11:33 AM, "freesurfer-boun...@nmr
I've attached it for you as a .txt file
- Ursprüngliche Mail -
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 21. Februar 2017 17:47:23
Betreff: Re: [Freesurfer] cluster as ROI
Can you send the terminal output?
On 02/21/2017 11:44 AM, Clara Kühn wrote:
>
Does this file exist?
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
On 02/21/2017 11:54 AM, Clara Kühn wrote:
> I've attached it for you as a .txt file
>
> - Ursprüngliche Mail -
> Vo
I think your installation of FS got corrupted. Try downloading and
reinstalling FS (same version of what you have). If you want, you can
just copy over fsaverage from the new download.
On 02/21/2017 11:50 AM, Uquillas, Federico D'Oleire wrote:
> Hi Doug, thanks so much for looking into this. I
No, they are not
On 02/17/2017 05:09 PM, Reza Rajimehr wrote:
> During the functional analysis in FS-FAST, are the external regressors
> convolved with the hemodynamic response function?
>
> Thanks,
> Reza
>
>
> ___
> Freesurfer mailing list
> Freesurf
Hi Lilla,
It’ s a Mac Pro with 64Gb Ram.
Best,
Cristian
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The information in this e-mail is intended only for the person to wh
yes!
- Ursprüngliche Mail -
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 21. Februar 2017 17:58:37
Betreff: Re: [Freesurfer] cluster as ROI
Does this file exist?
/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-D
then that is the "ocn" file to use with mri_segstats
On 02/21/2017 12:18 PM, Clara Kühn wrote:
> yes!
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve"
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Dienstag, 21. Februar 2017 17:58:37
> Betreff: Re: [Freesurfer] cluster as ROI
>
> Do
ah! Perfect, thank you! I'll give that a try.
- Ursprüngliche Mail -
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 21. Februar 2017 18:23:48
Betreff: Re: [Freesurfer] cluster as ROI
then that is the "ocn" file to use with mri_segstats
On 02/21/2017 12:18
I have one last question about the whole thing.
What is the measurement in the output file? My subjects have values between 0.6
and 1.5. As the measure is surface area I was expecting different numbers. Do I
have to multiply by some constant to get to mm²?
Thank you
Clara
- Ursprüngliche M
That will be the average value over the vertices in the ROI, which is
not what you want for surface area. Add --accumulate to the mri_segstats
command line to get the total area
On 02/21/2017 12:43 PM, Clara Kühn wrote:
> I have one last question about the whole thing.
>
> What is the measureme
that doesn't change the values. I've attached the file for you.
- Ursprüngliche Mail -
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 21. Februar 2017 18:56:17
Betreff: Re: [Freesurfer] cluster as ROI
That will be the average value over the vertices in the
sorry, gave you the wrong flag. Use --sumwf instead of --accumulate
On 02/21/2017 01:08 PM, Clara Kühn wrote:
> that doesn't change the values. I've attached the file for you.
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve"
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Dienstag, 2
Hi,
I have 3 beginner questions about the use of mri_glmfit-sim
1. Under what type of circumstances should I run mri_glmfit-sim with
permutation simulations?
2. The voxel threshold of 0.01 (cache 2) is used a lot. Is this too lenient in
cortical thickness comparisons?
3. About the sign of the
Hi,
I am trying to run a cortical thickness analysis comparing four groups – my
goal is to conduct an omnibus F-test testing for any group differences. I have
0 covariates/nuisance regressors.
This would be equivalent to the “Contrast 4 group.effect.mtx” in this page, for
3 groups: https://sur
That four group test will yield the same exact result as
1 -1 0 0
1 0 -1 0
1 0 0 -1
so I think you are ok
On 02/21/2017 03:09 PM, Gold, Andrea (NIH/NIMH) [F] wrote:
>
> Hi,
>
> I am trying to run a cortical thickness analysis comparing four groups
> – my goal is to conduct an omnibus F-test
Hi Doug,
Since our external regressors are stimulus-related (e.g. mean luminance of
stimuli), we need to convolve them with a hemodynamic response function. In
mkanalysis-sess, we have used -spmhrf 0 to model conditions. Is there a
code or Matlab script for HRF convolution, so that we apply exactl
You can use the following matlab code. You can ignore the warning
printed after the toepliz operation. The OriginalRegressor should be a
vector of length Ntp, then write out the NewRegressor to a new external
regressor file.
TR=2; % seconds
Ntp=100;
t = TR*[0:Ntp-1]';
h = fast_spmhrf(t);
a =
On 02/21/2017 02:26 PM, Shane Schofield wrote:
> Hi,
>
> I have 3 beginner questions about the use of mri_glmfit-sim
>
> 1. Under what type of circumstances should I run mri_glmfit-sim with
> permutation simulations?
This is a little bit of an open question as there is a big debate going
on now
Dear experts,
I am recently not able to pull from freeSurfer git repository.
The error message is following:
error: The requested URL returned error: 403 Forbidden (curl_result = 22,
http_code = 403, sha1 = b3b71d49c42db73a6f1dad0229111dc3f900a1d3)
error: Unable to find b3b71d49c42db73a6f1dad02
-- Forwarded message --
From: Kaiming Yin
Date: 1 July 2016 at 11:15
Subject: Cerebral (without ventricles) Volume = aseg.stats /
SupraTentorialNotVent ?
To: FreeSurfer Mailing List
Dear guys,
Could I ask which value in the stats/aseg.stats represents the volume of
the cerebrum
After downloading CentOS 6 x86_64 (64b) stable v6.0.0 unzipping on Ubunt
16.04 (64b) machine with
tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
Returns an error:
gzip: stdin: unexpected end of file
tar: Child returned status 1
tar: Error is not recoverable: exit
Hi - So I went ahead an uninstalled and then reinstalled the update to see if
that fixed the problem, and it seems to be working fine now. Thank you for your
help!
Best
Abby
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on
p;q=from:%22Douglas+N+Greve%22>
Tue, 21 Feb 2017 12:53:08
-0800<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170221>
That four group test will yield the same exact result as
1 -1 0 0
1 0 -1 0
1 0 0 -1
so I think you are ok
From: "Gold, Andrea (
Hi there,
We are attempting edits on base images and a couple of questions came up
when re-running through the pipeline:
1. After cp, wm, or pial edits on the base image, is it okay to
simply start at ‘-autorecon2’ or must the specific starting points be used?
(ie. “-autorecon2-cp”, “-autor
Glad to hear!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Abigail Waters
[awate...@suffolk.edu]
Sent: Tuesday, February 21, 2017 7:31 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] -trac-all -prep F
Thank you very much ,it was a great help .
Best Regards,
Nazanin
On Tue, Feb 21, 2017 at 7:34 PM, Ruopeng Wang
wrote:
> Just open FreeSurferColorLUT.txt file in your freesurfer installation
> directory, you should be able to figure the format.
>
> On Feb 21, 2017, at 10:59 AM, N Saf wrote:
>
>
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