Hi Anastasia,
Just to be clear, is this what you mean by a more diffuse volumetric
distribution. Here is a snapshot of the right inferior longitudinal fasiculous.
I am just getting a better sense of what to look for in terms of bad vs. good
tracts.
Emily
- Original Message -
From: "An
Dear all,
It seems that there is a serious error in the Parcellation stats files
(i.e. ?h.aparc.stats) when using the FLAIR / T2 processing pipeline of FS
5.3.
starting a particular recon-all with
recon-all -s ${SUBJID} -i ${DIR} -FLAIR ${DIR/t1/flair} -FLAIRpial -all
and looking through the
Hi Dear Fs Experts,
I am looking for an atlas segmented all white matter without to leave any
unsegmented white matter like in WMPARC
I highly appreciate your help and support
Thanks
Mohamad
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Stupid me!
I just found what I need: mri_cor2label. It does exactly what I want:
"A utility to sample a volume onto the surface, then create a label of
all super-threshold points
regardless of whether they are connected or not"
I failed to recognize that I would have to binarize my fMRI
activati
p.s. if that is what you want, it would be pretty easy to do in matlab:
v = load_mgh('file_created_by_vol_2_surf.mgz');
ind = find(v > threshold);
write_label(ind-1, [], v(ind), 'label_file_want_to_create');
On
Thu, 24 Jul 2014, Bastian Cheng wrote:
> Dear Freesurfer-Experts,
>
> Is there an a
Dear Freesurfer-Experts,
Is there an automated way to convert an overlay volume to a label file?
I guess I would look for a command called "vol2label".
I am currently projecting volume files (fMRI activiation hotspots) to
surfaces (mri_vol2surf): this works nicely.
However I then would have to d
Hi Bastian
can you explain further what you would like? A utility to sample a volume
onto the surface, then create a label of all super-threshold points
regardless of whether they are connected or not?
cheers
Bruce
On Thu, 24 Jul 2014,
Bastian Cheng wrote:
> Dear Freesurfer-Experts,
>
> Is t
Hi Pablo
I would guess this just a display problem - that freeview is incorrectly
setting the initial window levels. Try changing them. One nice feature of
freeview is that if you highlight the intensity volume in the "volumes"
list in the pane on the left, you can do shift-middle-mouse and sel
Hi Katharina
they are pretty similar but you can imagine some things affecting one and
not the other (e.g. white matter atrophy might shrink the white surface
area more than the pial). Or conditions like polymicrogyria might affect
the pial more than the white
cheers
Bruce
On Thu, 24 Jul 2014
Dear Dr. Fischl,
Thank you for offering to look at our data.
I have used the FTP server to upload a zip archive, based on the website
instructions (http://freesurfer.net/fswiki/FtpFileExchange)
The file is in:
transfer/incoming/1353.zip (using anonymous and my email address for the
user/passwor
FreeSurfer experts,I have a question about one of my scans after running
recon-all -all. When I open the image with freeview for inspecting brain mask
volume.To give you a better idea of the problem I have attached a screenshot of
the T1 volume. All my other images did not show the coloured b
Dear administrators,
I've got the problem that I cannot make out the difference between "area"
and "area.pial". As far as I understand "area" refers to white matter
surface area while "area.pial" includes everything up to pia mater
(including CSF). Unfortunately I don't know what I am exactly look
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