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Dear Freesurfer experts,
I intended to extract centroid of the atlas
"Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz"
According to the post:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-May/057046.html
I used the c
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I found whether procedure 1 or 3 produced the misaligned result. Did I miss
some steps? [image: bbregister_misalign.png]
Best,
Foucault
On Tue, Jun 5, 2018 at 3:52 PM zuxfoucault Wong
wrote:
> Thanks Douglas!
>
> I also got replies from t
Douglas N. Greve
wrote:
>
>
> On 06/04/2018 04:01 AM, zuxfoucault Wong wrote:
> >
> >
> > Hi Freesurfer experts,
> >
> > I am trying to resample the cerebellum atlas
> > Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
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Hi Freesurfer experts,
I am trying to resample the cerebellum atlas
Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz to
fmriprep output volume
${sub}_task-rest_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz. I was
wondering if the
-annot option. If you want time courses as the
> output, use the --avgwf. Also, you'll probably want to add --exclude 0 to
> not report data from unknown regions.
>
> On 3/16/18 7:23 AM, zuxfoucault Wong wrote:
>
> Dear FreeSurfer experts:
>
> When I registered the m
Dear FreeSurfer experts:
When I registered the map of functional activation on each hemisphere, how
can I extract mean activation value based on each parcellation region on
the surface?
According to FreeSurfer tutorial
https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0/IndividualFMR
you want to exclude the 0s and only look at the individual regions.
>
> I changed --thmin 0 to --thmin 0.1 and the results looked good.
>
> Kx
>
> On 21 February 2018 at 09:28, zuxfoucault Wong
> wrote:
>
>> Attach name file and result file.
>>
>> Thank y
Attach name file and result file.
Thank you for your time!
Best,
Foucault
On Wed, Feb 21, 2018 at 5:24 PM, zuxfoucault Wong
wrote:
> Hi Kirstie,
>
> Thank you very much for the suggestions!
> I modified my snippet to prevent it from looping the same value and still
> got t
hat to get all the values
> in an array you need ${labels[@]}.
>
> I don’t think you need greater precision than you have. The regions are
> pretty far apart in mm terms :)
>
> Kirstie
>
> Sent from my iPhone, please excuse any typos or excessive brevity
>
> On 21 Feb
Dear Freesurfer experts,
Based on this
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/07.html
, I
wrote a short script to extract the centroids from Desikan-Killiany atlas.
##
for hemi in lh rh; do
mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./l
="sm_50" and
CUDA_DIR="/usr/local/cuda" in configure.in
Any suggestions would be appreciated!
Best,
Foucault
On Sat, Jan 13, 2018 at 9:39 AM zuxfoucault Wong
wrote:
> Hi Freesurfers,
>
> I tried different ways to compile freesurfer for support cuda 9.1.
> Unfo
Hi Freesurfers,
I tried different ways to compile freesurfer for support cuda 9.1.
Unfortunately, I still cannot get it work.
While I tried to compile a specific module freesurfer/utils where the
errors generated, I got the error message. Any suggestions would be
appreciated!
gcc -DHAVE_CONFIG_H
Hi Freesurfers,
Referring to
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-October/054329.html,
I still got errors as following after compiling
tcltktixblt via build_tcltktixblt.csh as the instruction in
https://archive.fo/sNCX#selection-971.5-971.26 on ubuntu 16.04.
/usr/bin/ld: Ic
Hi Freesurfers,
Referring to
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-October/054329.html,
I still got errors as following after compiling
tcltktixblt via build_tcltktixblt.csh as the instruction in
https://archive.fo/sNCX#selection-971.5-971.26 on ubuntu 16.04.
/usr/bin/ld: Ic
zuxfoucault Wong
wrote:
> Hi FreeSurfers,
>
> I am trying to build freesurfer from source on ubuntu 16.04 in order to
> run `recon-all -use-gpu` that is compatible with the latest cuda 9.1.
>
> I followed the instruction here to build freesurfer
> http://surfer.nmr.m
Hi FreeSurfers,
I am trying to build freesurfer from source on ubuntu 16.04 in order to run
`recon-all -use-gpu` that is compatible with the latest cuda 9.1.
I followed the instruction here to build freesurfer
http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page.
However, in
$FREESURFER_HOME/FreeSurferEnv.sh`
should not introduce any unexpected events for the analysis?
Best,
Foucault
On Wed, Jan 3, 2018 at 11:09 AM zuxfoucault Wong
wrote:
> Dear list,
>
> If I changed the location of subjects_dir (via
> `export SUBJECTS_DIRS=/new_location/) a
Dear list,
If I changed the location of subjects_dir (via
`export SUBJECTS_DIRS=/new_location/) after `source
$FREESURFER_HOME/FreeSurferEnv.sh`, could I still completely run the
`recon-all -all`? I mean some folders in the default location of
subjects_dir, such as fsaverage, would not be included
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