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Hello FreeSurfer Developers,I'm attempting to using DK atlas as label to mask
my global brain index. I found the lh/rh.DKTatlas40.gcs in /freesurfer/average
folder. But I don't know how to read this gcs files. Can I convert this file
from gcs to
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Dear FreeSurfer developers
*For my MRI data, I have cortical parcellations and segmentations for the
Destrieux and Desikan-Killiany atlases. Now, **I am attempting to use
Schaefer 2018 atlas
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Could it be a solution to reinstall freesurfer? I tried to install a newer
gcc version and now Matlab gave to me this error
--
ERROR: FreeSurfer environment FREESURFER_HOME is
x-uw-ex-currentlocation-365-recipient: Outside
x-microsoft-exchange-diagnostics: =?iso-8859-1?Q?1; BN6PR08MB3457;
23:h3jFLjrIuHkcPFvrLhHBU9z+V3cOOa91ZNYCDsY?=
=?iso-8859-1?Q?AIBTV4WgIhBwN2rjSjmqtjq3GXwY3fh6agtDeYX5AKtqs0b8BAv3KdjoFj?=
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Hello Freesurfer experts,
May I know if it is possible to transform the FS-FAST pre-processed data
(left surface + right surface + subcortical region) to SPM-readable format?
How could I combine the three pre-processed data together and transform
them
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Hello Douglas,
Yes it works
El jue., 14 mar. 2019 a las 18:51, Greve, Douglas N.,Ph.D. (<
dgr...@mgh.harvard.edu>) escribió:
> It looks like the library is not set up properly. Does freesurfer work
> outside of matlab?
>
> On 3/14/19 1:46 PM, Miguel
It looks like the library is not set up properly. Does freesurfer work
outside of matlab?
On 3/14/19 1:46 PM, Miguel Ángel Rivas Fernández wrote:
>
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>
>
> Dear Freesurfer devs,
>
>
> Have you had occasion to review this error?. Could it be due to the
> gcc
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Dear Freesurfer devs,
Have you had occasion to review this error?. Could it be due to the gcc
version?
Thank you very much for your help.
Best regards,
El mié., 13 mar. 2019 a las 16:09, Miguel Ángel Rivas Fernández (<
miguelrivasf...@gmail.com>)
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We just found the mistake. I created the SUVR images already in T1 space so I
remade the lta files using the SUVR images and now it works.
Kind regards
Donatienne
Van: freesurfer-boun...@nmr.mgh.harvard.edu
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Dear Experts,
Having launched recon-all process on one subject with supplemental FLAIR
data in order to better define pial surface, I still need to follow some
recon editing during the QC of this patient.
However, when re-launching recon-all to
Hi Zheng, qdec is not longer being supported. Use the "command line"
stream, see here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
On 3/12/19 7:47 AM, 郑凤莲 wrote:
>
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>
> Hi experts,
> I am using qdec software for the statistic of LGI. I
Can you send the command line with out variables and the full terminal
output?
On 3/14/19 8:48 AM, Donatienne Van Weehaeghe wrote:
>
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>
> Dear,
>
>
> Apologies, this is a copy and paste error the full command was:
>
>
> #mri_gtmpvc --i
>
We don't really have a good way to do this. In theory, you could
concatenate them together and then let the motion correction fix the
misalignment, but I could imagine it would create some problems.
On 3/14/19 8:00 AM, Daniel Callow wrote:
>
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>
> Hello
Can you tar or zip the subject's folder and upload here.
ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming
When the upload is complete, send an email to us and indicate the name
of the file.
On 3/14/19 7:27 AM, Maria-Eleni Dounavi wrote:
>
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>
> Dear
As I said before, I would average the T1weighed images that vbm puts in
mni152 space, then run recon-all on that
On 3/14/19 6:06 AM, Laboratorio de Neurociencia Funcional wrote:
>
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>
> Dear Doug,
>
> please let me know if it is possible to run the recon-all
The size of the cluster is not going to be affected by the number of
iterations (only by the threshold). Why would you think that the cluster
size is affected by the number of iterations?
On 3/14/19 5:45 AM, Giuliana Klencklen wrote:
>
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>
> Hi Douglas,
>
>
Look here, example #9
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 3/14/19 5:01 AM, Tim Hahn wrote:
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>
> Dear Freesurfer experts,
>
> as far as I understand, Freesurfer employs the Desikan-Killiany Atlas
> (by default) to compute the various
You can use this version of mris_apply_reg
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg
Something like
mris_apply_reg --src-xyz lh.white --lta rawavg.lta lh.white.rawavg
Where rawavg.lta is created with
tkregister2_cmdl --mov orig.mgz --targ rawavg.mgz --regheader --reg
You can use mri_segstats to get whole-cortex means (use --slabel and
specify the lh.cortex.label and add --id 1). You can do the same thing
with the variances. The problem with doing it after mri_glmfit is that
the variances will not reflect the spatial averaging over cortex. If you
really
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Hi Dr. Greve,
Sorry about that - I had followed the "Reply via email" link on the
archive page instead of posting to the forum directly.
Thank you for this response. Can extracting the means be done at the
whole-brain level? If we get the means and
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Hello Doug,
If I collected 3 dti scans at each time point and I wanted to know how
would I go about incorporating them all into dt_recon to improve my SNR?
Could I just pull all the DICOMS into 1 folder? Or process each one
separately?
Thanks,
Daniel
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Dear,
Apologies, this is a copy and paste error the full command was:
#mri_gtmpvc --i
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUVR_cerebellum.nii.gz
--reg
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Dear Freesurfer developers and users,
I am running the freesurfer recon-all pipeline for a big dataset and I am
particularly interested in the hippocampus. For 20% of my subjects the
hippocampus along with other subcortical structures are misplaced
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Dear Doug,
please let me know if it is possible to run the recon-all to the fsaverage
subject of my sample to obtain specific labels (from the aparc+aseg.mgz and
the aparc.a2009s+aseg.mgz files) derived from my analysis sample.
Many thanks in
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Hi Douglas,
According to your suggestion, I used the permutation simulation approach. I
chose a cluster forming threshold set at 0.05 and explored how the number
of iterations effects the data. For example, I used this command for 1,000
iterations:
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Dear Freesurfer experts,
as far as I understand, Freesurfer employs the Desikan-Killiany Atlas
(by default) to compute the various parameters based on the aseg and
aparc files. For my analysis, I now need the Desikan-Killiany Atlas ROI
mask(s)
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