Hi list,
there is a way to convert niifty or .par/.rec in DICOM?
Thank you very much,
Stefano ___
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Hi Colin,
On Oct 24, 2013, at 00:24 , Colin Reveley wrote:
> Hi -
>
> I wonder if anyone has experience in dealing with T1 images where there is
> hyperintenisty of blood vessels?
This looks like receive & transmit surface coil data to me. For
MPRAGEs, in my experience, switching t
Dear freesurfer community,
we have encountered some problems with setting control points to improve
segmentation quality. Mainly, white matter was classified as grey matter
after completion of the first run that incorporated control points. Now we
have several questions, we would be very thankful
Hi Sven,
Whats most likely happening is that you are defining SUBJECTS_DIR prior
to sourcing SetUpFreeSurfer.csh. Freesurfer will not overwrite the
SUBJECTS_DIR environment variable if it already exists at the time of
sourcing the SetUpFreeSurfer.csh. This is most likely occuring in your
.cshr
Dear all,
Excuse if these are simple questions but I am a bit confused on the
significance of the volume measures.
1. Are the volumes of ROIs calculated after normalization?
2. If volumes are calculated post-normalization, why is correction for eTIV
needed?
3. What is the quickest way to correc
No, the last 3 columns (Min Max Range) are the minimum, maximum, and range
(maximum - minimum) or the values in path.pd.nii.gz.
But it does look like mri_segstats can get you what you want, if you use a
binarized version of path.pd.nii.gz. Use mri_binarize (possibly with a
threshold, if you
Hi Zeke,
that seems to have worked (strangely because I didn't really do anything
different before other than a fresh reinstall).
However, now I have problems with the license file when trying to test the
installation as suggested on the "Testing your freesurfer installation"
webpage.
I did
If there really is a .license in the FREESURFER_HOME directory then
everything should be working fine. What is the output when you type:
'ls -l /Applications/freesurfer/.license'
at the command line? And what is the output when you type:
'ls -l $FREESURFER_HOME/.license'
On 10/24/2013 11:25 A
Hi Sue, that looks correct. I think it is an open question as to whether
you should use the corrected maps or use the uncorrected and then
correct the final map. Maybe someone else can chime in.
doug
On 10/23/2013 09:49 AM, Susan Ruiz wrote:
> Hi Doug,
>
> This is /very/ helpful.
>
> Procedur
Hi Carina, I still don't understand what you are trying to do. It looks
like you have run the individual analysis (recon-all). Have you looked
at the results for the individual? Do they look ok? QDEC is for group
analysis, but you should make sure that the individuals look ok first
doug
On 10/
Hi Ronny, you added 5 new conditions, so it should have increased by at
least 5. However, if you are using a derivative with the HRF, then you
will have 2 regressors for each condition and it will increase by 10.
I don't know why it does not like the 2nd one. Can you send me the
Xtmp.mat file?
Hello FS experts,
In QDEC when I click on a vertex a scatter plot is generated with each
individuals data for that vertex. Is there a simple way to extract that data
(for each subject) into spreadsheet form for a specific vertex?
-Andrew
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Hi Caspar, there are a couple of things you can do:
1. Go into the mri_glmfit folder used to create the input contrasts to
the conjunction. Create a subfolder. Save the conjunction as sig.mgz and
create a file called "C.dat" (it can be empty) in this folder. Then run
mri_glmfit-sim specifying
Hi Freesurfer users,
I need to design a ROI map for my project. It has to be based on certain
coordinates. The ideal is to draw a circle based on the coordinates in the
Talairach space in Freesurfer, which I do not know how to achieve. The
alternative is to draw a spherical cluster in fsl and conv
no we don't, sorry
On 10/24/2013 07:26 AM, std...@virgilio.it wrote:
> Hi list,
>
> there is a way to convert niifty or .par/.rec in DICOM?
>
> Thank you very much,
>
>
> Stefano
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https
How far outside are they? Can you send a pic?
doug
On 10/23/2013 01:16 PM, Subhabrata Chaudhury wrote:
> Even the Supratentorial volume ? Supratentorial volume includes some
> structures outside the surfaces ?
> Thanks
> Subha
>
>> - Original Message -
>>
>> From: Bruce Fischl
>>
>> Sent:
On 10/24/2013 10:37 AM, Dorian P. wrote:
> Dear all,
>
> Excuse if these are simple questions but I am a bit confused on the
> significance of the volume measures.
>
> 1. Are the volumes of ROIs calculated after normalization?
No, everything is done in native space.
>
> 2. If volumes are calculat
You can do this, eg, to extract vertex 529
mri_segstats --i /path/to/qdec/Untitled/y.mgh --seg
$SUBJECTS_DIR/fsaverage/surf/lh.curv --sum junk.sum --id 1 --avgwf
vertex.529.dat --vox 529 0 0
doug
On 10/24/2013 11:47 AM, O'Shea,Andrew wrote:
> Hello FS experts,
> In QDEC when I click on a v
I think the problem is that the order of the conditions is always the
same combined with an absence of fixation points. I don't think you can
do this analysiswith this design.
doug
On 10/24/2013 12:08 PM, preci...@nmr.mgh.harvard.edu wrote:
> Xtmp.mat Attached
>
>
>> Hi Ronny, you added 5 new
Can you load it properly in tksurfer?
On 10/23/2013 12:44 AM, Marcos Martins da Silva wrote:
>
> Hi, Doug
> Sorry for this late feedback.
> Just so you can understand what is binLeftHippoBody.mgz I will explain
> its origin.
> 1) recon-all --hippo-subfields
> 2) mri_concat the posterior*.mgz to
Thank you Douglas.
The eTIV has values like 1543825. Dividing ROIs by this value would create
very small values.
Is there a standard TIV (i.e. from the talairach brain) to use as
denominator for creating a ratio value? Or what is the best way to create a
reasonable factor (i.e. 0.7-1.3) to correc
Why is a small # a problem? It simply represents the fraction of the
total intracranial volume occupied by that structure.
cheers
Bruce
On Thu, 24 Oct 2013,
Dorian P. wrote:
> Thank you Douglas.
> The eTIV has values like 1543825. Dividing ROIs by this value would create
> very small values.
>
Dear all,
I've been using Freesurfer v4.5.0 for some time and have reconned about 100
participants. I am wondering if there is an automatic way to obtain the
total gray matter volume for all the subjects I have run so far under this
version, or would it be necessary to update to v5.2?
Any help wo
Hi FS Community,
Does the "Total cortical white matter volume" parameter in the aseg.stats file
represent the total wm volume in the brain?
Thank you in advance,
Panos
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Sven,
Well that certainly is odd that. My guess is that there is some sort of
extension that Mac is hiding in the finder window (along the lines of
what you were talking about with the text editor).
Im also a little concerned about the double '//' that is part of your
FREESURFER_HOME environme
Hi Elissa,
The invalid drawable terminal output you can ignore when running Freeview.
Presumably bert is not located in /Applications/freesurfer/elissa_thesis/,
so that's why the bert commands are failing. Not the same subjects
directory that ABU is in.
To fix the tkmedit library error it lo
Hi Freesurfer users,
For the longitudinal stream in FS5.1, there are only 4 options of measures
(do-avg, do-rate, do-pc1 and do-spc). However, if I need other measures,
such as the difference between two time points (thick2-thick1), how should
I do to get the values and still be able to do the vox
Hi,
I am working on a dataset using free surfer.
I have NIFTII files which I am converting using mri_convert. Upon completion of
mri_convert, the orientations of the files are wrong. This likely leads to an
incorrect talairach (I was getting errors but used -notal-check) and leads to
an incorr
How do you know the nifti files are correctly oriented to begin with?
doug
On 10/24/2013 07:07 PM, Chiu, Bryan (PHTH) wrote:
> Hi,
>
> I am working on a dataset using free surfer.
>
> I have NIFTII files which I am converting using mri_convert. Upon
> completion of mri_convert, the orientations of
areyou loading the label (output of mri_cor2label) or did you create an
annotation? Try loading the label. Then try loading
LeftHippoBody_surf.mgh. If that does not look ok, check the registration
between binLeftHippoBody.mgz and subj1 with --regheader
doug
On 10/24/2013 06:40 PM, Marcos Mart
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