Dear freesurfer group,
I have two questions:
Can I compare one patient with a created control group in Freesurfer on the
following outcome measures: cortical thickness, brain volume and gyrification?
If so, how can you visualise that?
When you do the cortical analysis with freesurfer can you
I've two questions regarding hippocampal subfield segmentation:
1, Is there any article or other document which containes an optimal T2
protocol with detailed sequence parameters for hippocampal subfield
segmentation? (eg. BW, echo time, repetition time, FOV, echo train,
paralell imaging on/off, .
Hi Gabor,
A good place to start is ADNI’s high-res hippocampal T2 protocol. You can find
the details on their website. It’s a coronal, anisotropic acquisition of a slab
covering the hippocampus (0.4mm in plane, 2mm thickness, 25-30 slices). I’ve
been playing a bit with more isotropic acquisition
Dear Freesurfer Experts.
Is there a way to create a freesurfer surface label from entering a
MNI152 coordinate?
I am aware that I can use tcl with tksurfer:
mar_vertex X 1
labl_new_from_marked_vertices
labl_dilate
However as far as I know I can only input vertex numbers, not coordinates.
Any
Dear FS experts,
I want to create mask from the atlas "aparc.DKTatlas+aseg.mgz". I need the mask
to be free of any CSF or ventricles components. Is there any way to subtract
these labels (CSF and ventricles) from the atlas "aparc.DKTatlas+aseg.mgz".
Thank you for your help
John__
Dear Eugenio,
The ADNI protocol is quite similar to the default Siemens highres
hippocampus protocol, however I haven't find a more detailed version of
this one: http://adni.loni.usc.edu/wp-content/uploads/2017/07/ADNI3-
MRI-protocols.pdf
Do you know a more detailed version of the ADNI protocol?
Hi again,
You can find the detailed protocols here:
http://adni.loni.usc.edu/methods/documents/mri-protocols/
Click on your scanner model (or similar) and search for the sequence
“HighResHippcampus”.
Regarding the distortion correction: I’ll leave this one for Andre ;-)
Cheers,
/Eugenio
--
Juan E
you can do it in two steps. First, use mri_binarize to create a mask of
the structutures you want. Then use mri_mask to apply the mask to the
aparc.DKT file
On 12/03/2017 07:44 AM, John Anderson wrote:
> Dear FS experts,
> I want to use mri_binarize to create (binarized and free of CSF and
> v
On 12/03/2017 06:35 PM, Taylor, Johnmark wrote:
> Hello,
>
> A few quick questions about the "Per-Run" option in preproc-sess. I
> understand that in this option, each run's images are registered to
> the middle timepoint of that run, rather than the first timepoint of
> the first run. I was w
In theory, this is just a two "group" analysis. Search the wiki for FSGD
to get examples. You can include covariates, but you must use a DOSS
model when running mri_glmfit
On 12/04/2017 04:41 AM, Dijkshoorn, A.B.C. (Aicha) wrote:
>
> Dear freesurfer group,
>
> I have two questions:
>
> Can I co
Yes, you should take those into account. Not sure what you mean by
"which stat analysis".
On 12/01/2017 07:50 PM, 郑凤莲 wrote:
> Hi professor,
>
> I am using Freesurfer 6.0 and get the volume of subcortical
> structures. I want to get the relationship between age and volume. I
> only have one
How do you know what is right and left in the volume?
On 12/01/2017 01:59 PM, Defenderfer, Matthew K wrote:
>
> Hi,
>
> I have a strange issue I can't figure out. I am currently trying to
> use the parcellation from Gordon et al. 2014
> (http://www.nil.wustl.edu/labs/petersen/Resources.html) to
mri_concat file1 file2 ... --o concatfile.mgh
On 11/30/2017 01:28 PM, Abisan - wrote:
> Hi Freesurfer experts,
>
> I want to concatenate multiple preprocessed fMRI runs in the form of
> .mgh freesurfer surface space files (2-D matrices vertexes *
> time_frames). Is there a tool that can do this
If you want to do a conjunction, you can run mri_concat with the
--conjunct option (see --help for more details). If you want to look at
simple overlap, you can threshold each sig map (mri_binarize), then
combine them together something like
fscalc map2.bin.nii.gz mul 2 add map1.bin.nii.gz -o o
You can break the annotation into separate labels
(mri_annotation2label), then merge the ones you want into a single label
(mri_mergelabels), then recombine them into an annotation (mris_label2annot)
On 11/29/2017 10:03 PM, Michiko H. wrote:
> Hi Freesurfer Experts,
>
> I was wondering what the
I think you would need to figure out what such a combination would look
like. Eg, you could have a separate label for each possible combination
contrasts above threshold, though this would create a combinatorial
explosion.
On 11/29/2017 02:48 PM, Nguyen, Tin wrote:
>
> Hello,
>
> I have been
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Hi Greve,
Thanks for your help. I have 28 females and 26 males in one group. If it is
necessary to take gender and eTIV as a covariate, I don't know how to take
them as covariate in SPSS. Subcortical volume can be divided by eTIV, but for
gender, I don't know how to do. And the mean age of
Hi Bruce,
For subcortical volume, gender is not as a covariate(28 femaless and 26 males).
Then, is it necessary to take gender as a covariate for cortical thickness,
volume and surface area in qdec?
Sincerely,
Zheng
At 2017-12-02 11:45:10, "Bruce Fischl" wrote:
>Hi Zheng
>
>For vol
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