Good Morning,
I have now been able to get the testing command: tksurfer bert rh pial to
run, but it stops midway and issues a bus error. Please see the following
script:
DBM-Users-MacBook-Pro-4:~ dbmuser$ tksurfer bert rh pial
subject is bert
hemiis rh
surface is pial
surfer: current subjects
Daer Claire
The bus error might be related to Xquartz. Installing Xquartz again solved
the issue on most Intel-based Macs.
Cheers
Jürgen
Jürgen Hänggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University o
Hi Claire
what version are you using? And what is your hardware and software
environment? RAM, OS version, etc?
Bruce
On Mon, 20 Oct 2014, Claire Morley
wrote:
Good Morning,
I have now been able to get the testing command: tksurfer bert rh pial to
run, but it stops midway and issues a b
Dear mailing list,
I am really stuck here.. Please can someone tell me why I cannot find the recon
edit button on freeview!
I am not sure if the version of Freesurfer I have downloaded is old, or I have
done something wrong, or I am just blind.. But I cannot find the 'recon edit'
button in freev
Hi Areti
what version of freeview are you using?
Bruce
On Mon, 20 Oct 2014, Smaragdi A.
wrote:
> Dear mailing list,
>
> I am really stuck here.. Please can someone tell me why I cannot find the
> recon edit button on freeview!
>
> I am not sure if the version of Freesurfer I have downloaded is
Hi Bruce,
Thank you for getting back to me! Its the 1.0 version, downloaded from the
website.
Thanks,
Areti
On 20/10/2014 14:24, "Bruce Fischl" wrote:
>Hi Areti
>
>what version of freeview are you using?
>Bruce
>On Mon, 20 Oct 2014, Smaragdi A.
>wrote:
>
>> Dear mailing list,
>>
>> I am
Hi ,
The command is only used to unpack Siemens DICOM files, How can
I unpack the non Siemens DICOMs?
Thanks,
Moahmad
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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The informat
Hi Mohamad
You could convert the Dicoms in other s/w to .nii and then read them.
Maybe Bruce and Doug have more elegant solutions
Hth
Shantanu
On Mon, October 20, 2014 10:41 am, Alshikho, Mohamad J. wrote:
> Hi ,
> The command is only used to unpack Siemens DICOM files,
> How can I unpack the
I think this is the contrast you need
00000000 0.50.50.50.5 - 0.5
-0.5-0.5-0.5
On 10/19/2014 06:33 PM, Bronwyn Overs wrote:
> Dear Freesurfer Mailing List,
>
> I am running a GLM in freesurfer 2 categorical variables (2 levels),
> and three c
dcmunpack will unpack any dicoms
On 10/20/2014 11:21 AM, Shantanu Ghosh wrote:
> Hi Mohamad
>
> You could convert the Dicoms in other s/w to .nii and then read them.
> Maybe Bruce and Doug have more elegant solutions
>
> Hth
> Shantanu
>
>
> On Mon, October 20, 2014 10:41 am, Alshikho, Mohamad J.
Hi Koushik,
no, I cc the list, maybe someone has done tests or seen papers. I read
somewhere on atlas construction, that 10 images are fine, but that is
cross subject. Here we only have small changes within subject, so from
my experience less are fine , BUT
- 2 of course are not enough: in 2 t
Thanks for your response Martin.
From: Martin Reuter [mailto:mreu...@nmr.mgh.harvard.edu]
Sent: Monday, October 20, 2014 12:56 PM
To: Govindarajan, Koushik Athreya
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] adding time points to longitudinal base template
Hi Koushik,
no, I cc t
Dear FreeSurfer Experts,
How could the longitudinal analysis be performed in order to show
whether a parameter at time 1 is predictive of changes in cortical
thickness over time ? and can thecorresponding regions be shown in
FreeSurfer ?
In a statistical analysis, as we see it, we must perfo
Hi Doug,
But in freeSurfer wiki
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData they mentioned the
following "The program that does this is unpacksdcmdir (this is only used to
unpack Siemens DICOM files)." when I used this command on a my data set it
gives me an error for certain su
did you try dcmunpack?
On 10/20/2014 03:30 PM, Alshikho, Mohamad J. wrote:
> Hi Doug,
> But in freeSurfer wiki
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastUnpackData they mentioned the
> following "The program that does this is unpacksdcmdir (this is only used to
> unpack Siemens DICOM fi
Sorry I did not notice that this is a different command. I will try it now. and
I will let you now
Thanks a lot
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu
Dear Freesurfer Experts,
I have a label file of a number of ROI's I've made based on a mask. I'm
trying to get an idea of what cluster are significant within a focused
region of the label file.
To make the correction a little less sever, I pre-computed some monte-carlo
values using mri_mcsim
mri
what do you mean it has trouble understanding? What is your command line
and terminal output. Also, are you following these instructions?
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
On 10/20/2014 03:50 PM, Thomas DeRamus wrote:
> Dear Freesurfer Experts,
>
> I have a label
I guess the better term would be to say that I'm not sure if the cluster
correction is using the monte-carlo I made from the label file correctly.
I see on the wiki and in the mailing list you can use a different directory
and then spec that folder using mri_glmfit-sim with the --cache-dir flag.
W
You should not spec --sim. If you do not, does it work?
doug
On 10/20/2014 04:10 PM, Thomas DeRamus wrote:
> I guess the better term would be to say that I'm not sure if the
> cluster correction is using the monte-carlo I made from the label file
> correctly.
>
> I see on the wiki and in the ma
It does not I'm afraid. The error I get says the following:
mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir
/media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/
--sim-sign abs --2spaces
ERROR: must spec --sim
Does the same if I remove the --sim-sign abs
Dear all,
I used the the 3 steps of longitudinal analysis explained in freesurfer
longitudinal tutorial and need to compute the ratio Parenchyma/CSF for each
of time points. Is this equivalent to compute the (total gray matter
volume + total cortical matter volume)/CSF from aseg.stats file ?
Tha
Dear all,
I used the the 3 steps of longitudinal analysis explained in freesurfer
longitudinal tutorial and need to compute the ratio Parenchyma/CSF for each
of time points. Is this equivalent to compute the (total gray matter
volume + total cortical matter volume)/CSF from aseg.stats file ?
Tha
you need to add --cache threshold sign (and don't use --sim-sign or --sim)
On 10/20/2014 05:42 PM, Thomas DeRamus wrote:
> It does not I'm afraid. The error I get says the following:
>
> mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir
> /media/rkbatch/gyrification/fsaverage/mul
Thanks Douglas. That is exactly what I wanted.
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
That one gives the following error:
mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir
/media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverage/rh/Socialbrain/
--cache 2 abs
cmdline mri_glmfit --y rh.diagnosisxageICVslopetest.volume.10.mgh --fsgd
SBM_glmVolumeNOGENDER.fsgd dod
Hi Mia, sorry for the delay. I think the problem is that the geometry
info in the CT header is incorrect. The directions are not orgthogonal,
and, when made orthogonal, the pixel sizes look wrong. How did you
create ct.mgz?
doug
On 10/12/2014 08:52 PM, Borzello, Mia wrote:
> Hi,
>
> Any insig
Hi Doug,
I ran the following command line dcmunpack -scr in my script
and it gives me a list of the run/series. How can I save this list as a log
file. I tried to add the flag -targ and the flag -log but it gives me an error
and asked me to specify the series run numbe?
Any suggestions please?.
In this case if I don't have T1 MPRAGE can I use any other available T1 like
sag_T1 or Ax_T1 (the name of run/series after using unpacksdcmdir)? or it is
imperative to use T1 MPRAGE for the segmentation.
Bests,
From: freesurfer-boun...@nmr.mgh.harvard.edu
Hi
I have a few questions regarding the use of “mri_volcluster” for
clusterwise thresholding. Essentially, we have a volume of pvalues
obtained from a two tailed t-test comparing beta values from condition A vs
condition B.
When I ran this command:
mri_volcluster --in transformedP.nii --sum
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