Dear FS experts,
I have created some seed files and wanted to ask you if everything is fine with
this procedure.
After using recon-all -subject xy -i xy.nii.gz -all, I labelled my files with
mri_binarize --match ID --i aparc.a2009s+aseg.mgz --o label.nii.gz
Then I used bbregister and
Dear FS experts,I am trying to generate my stats data tables with QDEC -after
successfully loading my data table- and come across the following error.Any
recommendations would be greatly appreciated.Thank you in advancePabloData
table loading completed successfully.
SUBJECTS_DIR is
How are you generating the stats? The aseg.stats file uses partial
volume correction...
On 08/03/2015 04:48 PM, Jonathan Plasencia wrote:
That is partly correct. The nii is not matching the stats file (which
it is my understanding the stats file is based off the mgz file. If
this is the
yes, I think that was the issue and it is now sorted out
Bruce
On Tue, 4 Aug 2015,
Douglas N Greve wrote:
How are you generating the stats? The aseg.stats file uses partial
volume correction...
On 08/03/2015 04:48 PM, Jonathan Plasencia wrote:
That is partly correct. The nii is not matching
Have you looked in /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats to
see if there might be a problem?
On 08/04/2015 05:43 AM, pablo najt wrote:
Dear FS experts,
I am trying to generate my stats data tables with QDEC -after
successfully loading my data table- and come across the following
Hello,
I am very new to freesurfer who have been using SPM and FSL, and just started
doing individual subject analysis. I already had an error message on recon-all
step.
I am using:
Vertualbox, OS is RedHat 64-bit
I am using bash (I prefer to do so) so I am not in tsch shell.
The recon-all
I'm not sure, but it may be that there are some files that are nii and
others that are nii.gz. Eg,
ls -tl /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/015/masks/
total 1248
-rw-rw 1 arodthom roffmagp 3579 Aug 3 18:06 brain.e3.nii.gz
-rw-rw 1 arodthom roffmagp 5383 Aug
I cannot replicate the problem, but I'm inside the surfer domain. Have
you tried from another computer? We had these kinds of problems before
and the problem was a firewall on the side of the person trying to do
the download.
doug
On 08/03/2015 06:36 PM, Perugini, Alessandra wrote:
Hi,
I am
Dear suffers
Now, I’m running the group analysis using qdec as a beginner.
2 groups, 4patients per each group..
after successful data table loading, I choosed 'Generate Stats Data Tables
button’
I found the error message like below,, could you help me ?
thanks
Hyon-Ah
Data table
Hi,
If I am only interested in the gm thickness (ThickAvg) of a specific
structure/s (e.g. precentral) is it sufficient to only QC these specific
structures/s or does the wm and pial surface need to be accurate across the
entire hemisphere for the accurate determination of gm thickness of
Just doing those structures should be fine
Bruce
On Aug 4, 2015, at 10:46 PM, prasser pras...@zoho.com wrote:
Hi,
If I am only interested in the gm thickness (ThickAvg) of a specific
structure/s (e.g. precentral) is it sufficient to only QC these specific
structures/s or does
thanks!
Date: Tue, 4 Aug 2015 15:01:43 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec - Generate stats data table
You can just run recon-all with the -wmparc flag. It should be pretty
quick, less than 30 min or soo
On 08/04/2015
Hi Brent
are you saying you just multiplied the gray matter intensities by some
scale factor (1)?
Bruce
On Tue, 4 Aug 2015, Brent Womble wrote:
Hi everyone,
I've been making synthetic brains to test how Freesurfer handles various
structural changes.
One of the changes I'm testing is
Yes. Here is the MATLAB script:
for i = [1:20]%Load the original image and gray matter
maskraw=load_nii([pwd,'/',
num2str(i), '/pre.nii'])a=single(squeeze(raw.img));
c1_raw=load_nii([pwd,'/', num2str(i),
'/c1pre.nii']);c1=squeeze(c1_raw.img);%Mask
is gray around edges. Threshold to make it
Yes, it is for 12dof. It is not hidden for any particular purpose
(except maybe that I'm lazy). In general, I don't think it is a good
idea to use 12 or 9 dof unless you have an explicit reason to.
On 08/04/2015 01:54 PM, Perea Camargo, Rodrigo Dennis wrote:
Hi all,
I am using a previous
What you really want to simulate is an underlying geometric deformation
(like atrophy) that gets propagated through an image formation model to
create an atrophic image. I don't think multiplying the image intensities
is a good model for what you want. Atrophy doesn't look like a uniform
Hi Doug,
Thanks for getting back to me. I tried deleting those files, and got the same
error, although the terminal output looked slightly different towards the end
(in terms of the compensation values).
Here it is below:
--
oops, sorry for the delay, thanks for the reminder. The problem is that
you have a blank line at the end of your long.qdec.table.dat file.
Remove the line and see if it works.
doug
On 08/04/2015 12:42 PM, Clara Kühn wrote:
Hi Doug,
did the fordoug.log file give any information about why
Dear Anastasia and Tracula experts,
I would like to run between-group statistics using the pathstats.byvoxel.txt
outputs. It is clear from the website how to manage the NANs. However, what
would you suggest to use for between-group or correlational analyses? Is there
a
Hi Doug,
did the fordoug.log file give any information about why FreeSurfer can't find
my qdec file?
Cheers and thanks for working on this!
Clara
- Ursprüngliche Mail -
Von: Douglas Greve gr...@nmr.mgh.harvard.edu
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Montag, 3. August 2015
Hi Brent
a quick look and it seems that your answer is yes? You are multiplying
the image intensities by some scale factor?
Bruce
On Tue, 4 Aug 2015, Brent Womble wrote:
Yes. Here is the MATLAB script:
for i = [1:20]
%Load the original image and gray matter mask
Yes, I'm multiplying the image intensities by a scaling factor. Sorry if
that wasn't clear.
-Brent
On Aug 4, 2015 12:09, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Brent
a quick look and it seems that your answer is yes? You are multiplying
the image intensities by some scale factor?
Hi all,
I am using a previous script to update a pipeline for pre-processing diffusion
data. My objective related to this question is the (what I think is a hidden)
argument “- -12” when using bbregister (v. 1.49.2.3 FreeSurfer 5.3). Will this
denote 12 degrees of freedom for my registration?
You can just run recon-all with the -wmparc flag. It should be pretty
quick, less than 30 min or soo
On 08/04/2015 12:04 PM, pablo najt wrote:
Thank you this subject had a zip copy of the wmparc.stats
Now I am missing this file from another subject. Do I need to run
recon-all from start or
You don't need to cite mri_label2vol, it is just a spatial transformation
On 08/02/2015 09:21 PM, jinyi wrote:
Hello freesurfers
I am working on a paper based on freesurfer and other images
process tools.
I am wondering the citation problems, In the freesurfer wiki, a
help page
We ran freesurfer on a participant with randomness flag enabled on a
separate OS (centOS vs. unbuntu) and we still get the exact same aseg.stats
values. Our question is does the randomness flag vary the results in
aseg.stats like it does with aparc.stats
Prashanth Nyalakanti
pnyalaka...@mrn.org
The F would be
1 -1 0 0
0 0 -1 0
Your t-contrasts are correct (you don't need to do both directions)
On 08/03/2015 03:40 PM, Lim, Lena wrote:
Hi experts,
I have 3 groups: (A, PC and HC) and 1 covariate: IQ. For a DOSS file,
how should I define the F contrast? Would it still be: I -1 0
There is still a warning about multiple formats. This means you have
not deleted all the offending files.
On 08/04/2015 12:19 PM, Rodriguez-Thompson, Anais wrote:
Hi Doug,
Thanks for getting back to me. I tried deleting those files, and got the same
error, although the terminal output
Great, thank you for your help!
On 8/4/15, 2:36 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu wrote:
Yes, it is for 12dof. It is not hidden for any particular purpose
(except maybe that I'm
Thank you, Zeke for your help!
Best wishes,
Hisako
-Original Message-
From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu]
Sent: Tuesday, August 04, 2015 4:08 PM
To: Freesurfer support list; Fujiwara, Hisako
Subject: Re: [Freesurfer] recon-all exited with errors
Hello Hisako,
This is a
Hello,
Sorry if this isn’t the right forum for the question, but not sure where to
direct it.
I’m trying to incorporate some FSL commands into a Matlab script. I’m using a
Linux machine and running Matlab 7.11.0 (2010b). I tried to access the FSL
toolbox through Matlab using:
Ah, that's probably correct. I think it worked on my system because I source
the FSL conf file in my .bashrc
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Not sure. I guess you could say the duration is 0 for the controls, but
it has to make sense for your data, which I cannot tell you
On 08/04/2015 04:29 PM, Matthieu Vanhoutte wrote:
Thanks for quick answer ! How could I regress out the effect of
epilepsy duration on patients, knowing that
The statistics will work properly, but they do assume that the variances
are the same in different groups. This assumption is generally ok if you
have a balanced design, which you don't. Also, your p-values are going
to be driven by the lowest number of subjects. With only 5 you might not
see
sorry, I don't remember what that thread is. Can you repost with the
thread in the email?
On 08/04/2015 03:20 PM, Rodriguez-Thompson, Anais wrote:
Hi Doug,
I deleted all of the template.nii files, and now the command works. Thank you
for your advice!
In regards to my other thread
Hello,
This is a recently discovered bug either mni related or virtual box
related. The issue is that the mri_nu_correct.mni command will fail
when executed in the VirtualBox environment on a subject whose data
exists on a shared folder between the host and the virtual machine.
Currently the
Thanks for quick answer ! How could I regress out the effect of epilepsy
duration on patients, knowing that this factor is null for controls ?
Cheers,
Matthieu
Le 4 août 2015 22:22, Douglas N Greve gr...@nmr.mgh.harvard.edu a
écrit :
The Epilepsy_Duration is the same for all MaleControl
I don't think that will work because the shell where FSLDIR gets set is
not the same shell as that of the system command. Try putting those two
in the same string and then running system on that
On 08/04/2015 04:36 PM, Albrecht, Daniel S. wrote:
Hello,
Sorry if this isn’t the right forum
Sorry, disregard my previous email! I just realized that I should have created
a new message thread.
Below is the previous email thread. Given this issue, could I rename the
preproc-sess output volume (fmcpr.nii.gz) to fmcpr.sm5.nii.gz in order to run
the command? Given preproc-sess at -fwhm
Hello Hisako,
This is a recently discovered bug either mni related or VirtualBox
related. The issue is that the mri_nu_correct.mni command will fail
when executed in the VirtualBox environment on a subject whose data
exists on a shared folder between the host and the virtual machine.
Just use either system or the exclamation mark and type the FSL commands
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Albrecht, Daniel S.
[dsalbre...@mgh.harvard.edu]
Sent: Tuesday, August 04, 2015 4:36 PM
Hello,
What is the contents of the $FREESURFER_HOME/build-stamp.txt file?
-Zele
On 08/03/2015 11:54 PM, Li, Zhihao wrote:
Hi FS experts,
I was trying to run recon-all within the VirtualBox of NeuroDebian 8.0
on a WIN8 host. The program stopped immaturely at the step of
Hi Doug,
Below this email is the email thread. I was wondering whether I could rename
the preproc-sess output volume (fmcpr.nii.gz) to fmcpr.sm5.nii.gz in order to
run the command. Given preproc-sess at -fwhm 5, this volume should be smoothed
at 5 and should be the input for analysis, correct?
Hello experts,
Could anyone provide me an advice or answer to this problem ?
Thanks in advance !
Best regards,
Matthieu
Le 28 juil. 2015 14:12, Matthieu Vanhoutte matthieuvanhou...@gmail.com
a écrit :
Dear Freesurfer's Experts,
Please find below an error occuring when I use mri_glmfit :
The Epilepsy_Duration is the same for all MaleControl subjects. You
can't use that as a covariate if it does not have any variation
On 08/04/2015 04:10 PM, Matthieu Vanhoutte wrote:
Douglas,
Please fond attached the fsgd file.
Cheers,
Matthieu
Le 4 août 2015 21:45, Douglas N Greve
You should just run it through with the other hemisphere even if the
values are bogus. The aseg.stats file will not be produced until both
hemis are done, but you can ignore anything that relates to the bad hemi.
doug
On 08/03/2015 11:36 AM, Andrea Horváth wrote:
Dear Freesurfers,
I tried to
Hi Doug,
I deleted all of the template.nii files, and now the command works. Thank you
for your advice!
In regards to my other thread (selxavg3-sess error), where selxavg3 looks for a
file that doesn't exist (fmcpr.sm5.nii.gz), could I rename the preproc-sess
output volume (fmcpr.nii.gz) to
can you send the fsgd file?
On 08/04/2015 03:42 PM, Matthieu Vanhoutte wrote:
Hello experts,
Could anyone provide me an advice or answer to this problem ?
Thanks in advance !
Best regards,
Matthieu
Le 28 juil. 2015 14:12, Matthieu Vanhoutte
matthieuvanhou...@gmail.com
Douglas,
Please fond attached the fsgd file.
Cheers,
Matthieu
Le 4 août 2015 21:45, Douglas N Greve gr...@nmr.mgh.harvard.edu a
écrit :
can you send the fsgd file?
On 08/04/2015 03:42 PM, Matthieu Vanhoutte wrote:
Hello experts,
Could anyone provide me an advice or answer to this
Thank you this subject had a zip copy of the wmparc.statsNow I am missing this
file from another subject. Do I need to run recon-all from start or is there a
shortcut for getting this file?Thanks Doug.Pablo
Date: Tue, 4 Aug 2015 11:42:43 -0400
From: gr...@nmr.mgh.harvard.edu
To:
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