Hi,
Running the mri_glmfit-sim with a threshold set to 20, we get,
among other files, cache.th20.pos.sig.cluster.mgh and
cache.th20.pos.sig.masked.mgh. Could you explain how to interpret the
"masked" file? Thanks
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Hi everyone,
I am running FreeSurfer on Ubuntu virtual machine and have hit the
same error during my recon-all.
ERROR: cannot find or read transforms/talairach.m3z
ERROR: mri_ca_register with non-zero status 0
All previous responses point to a RAM issue. However, I've only hit
the error with som
Hello Bruce and Nick,I'm writing with the same topic from the last time, for which I haven't get aswered and I'm a stocked with it. Is about the FS inter-hemispheric registration. I'm sending you the threat so i don't make this mail too long...http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
Dear Freesurfers,
Do the anatomical input images to recon-all have to be in the same
orientation (neurological/radiological) or is it ok as long as the
orientation labels are correct?
All the best,
Anders
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Gabriel,
Where did you get the mri_convert? Did it come with the installation?
The GLIBC_2.4 error indicates that mri_convert was built on a newer OS,
like Centos6, than the one you are running on. I'd recommend using our
centos4 build of freesurfer.
Nick
>
>
> Hello Bruce and Nick,
>
> I'm w
Tudor,
the log indicates that you need to run this:
rm /media/Dell/_FS/buckner_data/tutorial_subjs/bert/scripts/IsRunning.lh+rh
to get recon-all to run again.
Nick
> Hi Nick,
>
> Thanks for your reply! I increased the memory available to FS in the
> virtualbox to the maximum allowed value (80
Hi Doug,
I'm not sure why that does not make sense, shouldn't the input of
mri_concat be several to-be-concatenated files rather than a single file?
Anyway, after trying out the command with only one of the files from the
tutorial,
*mri_concat --debug
/media/Dell/_FS/buckner_data/subjects/140/su
Hi Bruce-
The teams at UCSF and the SFVAMC would be more than willing to provide letters
of support.
Regards,
Wil
───
William Irwin | Imaging Core Supervisor
University of California | Mission Bay
Sandler Neurosciences Building
Memory and Aging Center | MC: 1207
675 Nel
Dear Bruce,
Thank you very much for your reply.
I can convert my labels to Freesurfer labels and try the mri_ca_label
now. May I ask some more questions?
1) What subjects were used to train the atlas in the current version?
Were they healthy or diseased subjects?
2) How the current implementati
Hello,
This worked perfectly 2 years ago :), but now I am having some trouble.
I run reg-feat2anat & aseg2feat with no problem.
I now need a correlation matrix of every ROI (created by freesurfer) against
every other ROI. For this I used @ROI_Corr_Mat
(http://afni.nimh.nih.gov/pub/dist/doc/pr
as long as the direction cosines are correct (which they will be if you
start with the dicoms from the scanner) you should be fine
Bruce
On Thu, 31 Jan 2013, Anders Hougaard
wrote:
> Dear Freesurfers,
>
> Do the anatomical input images to recon-all have to be in the same
> orientation (neurol
thanks Wil
Bruce
On Thu, 31 Jan 2013, Irwin, William wrote:
Hi Bruce-
The teams at UCSF and the SFVAMC would be more than willing to provide letters
of support.
Regards,
Wil
???
William Irwin | Imaging Core Supervisor
University of California | Mission Bay
Sandler Neu
Tudor,
I'm a bit at a loss as to why it wont work. It appears you have plenty of
available memory. Also, another person on the list confirmed that bert
will run to completion in the fsv5.1 WindowsVM.
I noticed though that it appears you have the buckner tutorial data. I
dont have my virtual mac
1. 40 subjects, 10 young, 10 middle ages, 10 elderly (healthy) and 10 with
AD.
2. Many small things, the big one (described in our 2004 paper) is that we
now use a nonlinear warp
3. Yes, hydrocephalus for example is hard, although we have made recent
improvements in the warping that handle enl
Hi Ed, that sounds strange. What were the condition numbers for the two
analyses? This should be printed out into the terminal. It is also
possible that it is a scaling issue. This should not be an issue in 5.1,
but it is possible that it could have an effect if two columns are very
similar.
d
Hi Paul, this mostly looks right. I think the problem may be that you
are including the unknown label on the command line. I think that
mris_label2annot will ignore the 0 inthe ctab file, which means that it
assign the first label passed (lh.unknown.label) to the the first
non-zero ROI in the c
Catherine, I've created new scripts (attached)that will allow you to do
this. Put them into $FREESURFER_HOME/bin (but make backups of the ones
there:).
doug
On 01/30/2013 05:43 PM, Nucleos P wrote:
The options for these 3: GausCurv FoldInd CurvInd do not exist when I use the -h
Thanks,
Cath
From mri_glmfit-sim --help
csdbase.sig.masked.mgh - the original sig volume masked to showonly
clusters.
doug
ps. I hope you ran it with a threshold of 2 and not 20!
On 01/31/2013 06:24 AM, Fernando Valle-Inclán wrote:
> Hi,
> Running the mri_glmfit-sim with a threshold set to 20, we ge
The threshold must be in the form of -log10(pthreshold). So, if you want
pthreshold=.05, then use 1.3
doug
On 01/31/2013 07:37 AM, Richter, Julia wrote:
> Dear Doug,
>
> thanks for your reply. I tried the command you suggested, but I always get an
> error message that there is something wrong
Hi Doug,
Two questions:
1) In fsfast preprocessing is STC done first or MC? is there a way to
control the order?
2) Also if STC is not mentioned in the analysis line and only done in the
preprocessing would the analysis be run on the STC data automatically? or
should I specify STC in the analysi
On 01/31/2013 03:09 PM, Maryam Vaziri Pashkam wrote:
> Hi Doug,
>
> Two questions:
> 1) In fsfast preprocessing is STC done first or MC? is there a way to
> control the order?
MC is done first, then STC. There is not an easy way to control the
order, though it may be possible.
>
>
> 2) Also if S
Hi Shani, what is fs_read_dat.m? I've never seen it before. Why do you
need to transform the surface? What are you using to create the display
below (ie, command line)?
doug
On 01/31/2013 10:53 AM, Shani Ben Amitay wrote:
> Dear freesurfers
> I used bbregister to coregister diffusion images with
On 01/31/2013 12:30 PM, Tudor Popescu wrote:
> Hi Doug,
>
> I'm not sure why that does not make sense, shouldn't the input of
> mri_concat be several to-be-concatenated files rather than a single file?
Sorry, I did not mean to imply that the command line was wrong, rather
that the behavior did n
Hi list,
I'm running trac-all -prep -c
but I have this error
dtifit -k
/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m
/Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz
-r /Applications/freesurfer/subjects/subject_prova/Diff01/dmr
Sorry, I don't think we have such a program. You could do it in matlab
fairly easily, eg,
f = MRIread('filtered_func_data');
fmat = fast_vol2mat(f);
a = MRIread('aparc+aseg');
seglist = unique(a.vol(:));
seglist = seglist(2:end); % remove segid=0 (unkown)
clear roimean
for nthseg = 1:length(segl
Hi Stefano - Are the original bvecs (that you specify in your
configuration file) arranged in 3 rows or 3 columns?
a.y
On Thu, 31 Jan 2013, std...@virgilio.it wrote:
Hi list,
I'm running trac-all -prep -c
but I have this error
dtifit -k
/Applications/freesurfer/subjects/subject_prova/Dif
Hi Anastasia,
I attach the bvecs that I'm using. The second is produced in the dmri.You are
noting that the first is in 3 rows, the second contains only 3 row with a 0
This is the last errorfslroi
/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz
/Applications/freesurfer/sub
Hi Stefano - See "Specifying Diffusion Gradient Table" in the tracula
tutorial for the correct format:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
a.y
On Thu, 31 Jan 2013, std...@virgilio.it wrote:
Hi Anastasia,
I attach the bvecs that I'm using. The second is produced in th
Hi Anastasia,
I'm frustrated because I'm checking to resolve this problem anywhere but the
error is the same. Can it depend from interaction between fs and new iMAC
version (Mountain Lion)?
Thanks,
Stefano
Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 31-gen-2013 22.53
A:
Hi Stefano - I'm sorry that you're frustrated. Do you mean that you
arranged the bvecs as 3 columns (not 3 rows) and are still getting the
same error?
a.y
On Fri, 1 Feb 2013, std...@virgilio.it wrote:
Hi Anastasia,
I'm frustrated because I'm checking to resolve this problem anywhere but t
Yes Anastasia. To check it, I'm attaching the last bvals,bvecs files (original)
and bvals.norot (in my dmri).Thank you very much for your kindness.
Stefano
Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 1-feb-2013 0.42
A:
Cc:
Ogg: Re: [Freesurfer] R: Re: R: Re: bvecs tr
You're very welcome. You can send me your data.nii.gz and I'll try to see
if I can replicate the error. You can send it through here:
http://gate.nmr.mgh.harvard.edu/filedrop2/
On Fri, 1 Feb 2013, std...@virgilio.it wrote:
Yes Anastasia. To check it, I'm attaching the last bvals,bvec
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