Dear Sahil,
to assure that there is no other issue with your setup, I would recommend to
obtain cluster-wise p-pvalue of that big cluster to see if it is reasonable,
i.e. if it is somewhat close to the significance.
Therefore, I would load *_clustere_tstat_fwep and click to the area of big
ok, I've figured out that this is indeed the case:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23348.html
Also, following these instructions I was able to get RAS from the tkreg RAS in
FreeView:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024293.html
Hello FreeSurfer Developers,
I’m attempting to convert a dlabel file from the Human Connectome Project to a
volumetric ROI that I can use for fiber tractography on other platforms. I
followed the tutorial provided by HCP (hcp-users FAQ #9: How do I map data
between FreeSurfer ... - HCP
Hello FreeSurfer community,
I am trying to extract the cortical thickness from a specific ROI.
I followed the pipeline: cortical thickness of a volume-defined ROI. But for
the last step:
mri_segstats \
--seg $SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh \
--in
Dear Antonin,
Setting minimum to 1.3 for *_clustere_tstat_fwep doesn't show any
significant cluster and similarly thresholded map *dpv_tstat.mgz also
doesn't show anything at -log10(0.05) = 1.3. As you said, it seems like
even though there is big cluster but after FWER correction, the
Dear Doug,
My PET data is 3 x 5 minute acquisitions. Each subject has
subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am supposed
to align and average them.
Please advise.
Thanks!
--
Shane Schofield
On 8 March 2017 at 22:31:06, Douglas Greve (gr...@nmr.mgh.harvard.edu)
No, the template is a within subject template used for registration. If
your pet data only has one frame (eg, FDG SUV), then you don't need to
run mri_convert or mri_concat, just use your pet image as the template
On 3/8/17 11:11 AM, Shane S wrote:
Hello Freesurfer,
I have 3 PET images per
Dear Sahil,
If you used -logp as Anderson suggested, you should set your min to 1.3 to
threshold your *_clustere_tstat_fwep map and see the clusters.
What is the value of *_clustere_tstat_fwep in the region of the big cluster
seen at thresholded map *dpv_tstat.mgz ? This should correspond to
Dear Sahil,
could you send the full command-line and unthresholded view of
*_clustere_tstat_fwep ?
How the data showed in screenshot 1 were produced?
How are the actual p-values of your clusters in *_clustere_tstat_fwep?
You can also use -saveglm and inspect the files containing values of GLM
Hi Bruce and all,
Thanks for the suggestion on scaling -- it would be nice if it were
consistent, but it varies quite a lot from scan to scan. At the most,
about 30 of the top slices are affected, but often the number of affected
slices is fewer, and sometimes the spatial extent of the artifact
Dear FreeSurfer community,
The Open Science Grid (http://www.opensciencegrid.org) is a federation of
university and laboratory HPC facilities which share computing capacity to
support science.
We have developed a command line tool "fsurf" you can use from your laptop
or
desktop computer to
Hello Freesurfer,
I have 3 PET images per individual. I am learning PetSurfer based on the Greve
et al., 2014 paper.
On the PetSurfer link, there are 2 methods.
mri_convert pet.nii.gz —frame frameno template.nii.gz
or
mri_concat pet.nii.gz --mean —0 template.nii.gz
What are the differences?
Dear Joelle,
regarding the conversion to .bvecs, could you please show the example of
difference between bvecs converted by mri_convert of FreeSurfer and mrconvert
of mrtrix3?
Do you have most recent version of mrtrix3? There have been a quite extensive
discussion on implementation of FSL
Hi
I have processed my data with freesurfer. And an expert have made manual
segmentations and sendt it to me as masks (analyze format = img & hdr).
I now want to view these masks with the data I have run through
freesurfer, but I am not sure how to proceed. Any advices?
Thanks a lot.
Best
Hi Lionel
we usually try to avoid analyze as a format as it frequently doesn't
contain enough information to e.g. disambiguate left from right. That
said, just bring the mask and the data up in freeview and see if they
align
cheers
Bruce
On Wed, 8 Mar 2017, Lionel Giriteka wrote:
> Hi
>
> I
Hey all,
When loading two T1 in freeview, one for a subject and one for fsaverage, and
switching between them, only the tkreg RAS coordinates changes while moving the
mouse, not the RAS.
Does it mean that the RAS in freeview is always in MNI305?
Thanks,
Noam
Hi all,
That's exactly as Antonin says -- I have very little to add :-)
Only a few suggestions:
- With surfaces, both cluster and TFCE statistics tend to be slow. Consider
using the tail approximation ("-approx tail -n 500 -nouncorrected")
- Include -logp, so that the p-values are in log-10
??Dear Tracula experts,
I am applying Tracula on a longitudinal data set, and have some questions I am
hoping you could help me with:
Firstly, upon visual inspection, several tracts appear to be quite messy, or
small (on the default freeview threshold) for most subjects. However, the -stat
Dear Reetta-Liina,
Thanks for pointing out this inconsistency.
The mapping is:
GC-ML-DG = GC-DG
CA3 = CA2/3
molecular_layer_HP = molecular layer
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
Hello,
I am trying to test for the effect of different variables on cortical
thickness. The variables (with type) are: index (continuous). Gender(factor),
Age(continuous), Years of education (continuous), Depression (factor),
Vascular comorbidity (factor), and MMSE (continuous). Later, I
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