lp in advance!
Kind regards,
Diana
PS: I am also enclosing the test dmrirc file that I was using.
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR /Volumes/Diana/Preprocessed/DTI/Test_script/ADDI_013
# Output directory where trac
ULA?
Thank you in advance for your time!
Warm regards,
Diana
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Dear FreeSurfer team,
Could you please provide me with the developer password (version 7.2.0)
to open the image?
Thank you!,
Diana
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Will try, thanks for the advice!
Diana.
El vie, 29 oct 2021 a las 18:00, Wang, Ruopeng ()
escribió:
> From the screenshot it looks like a remote display issue. Maybe you can
> try a different X client, such as MobaXterm
> (https
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Hi Douglas, thank for you reply. I have a windows 10 pc and I'm using the
ubuntu app (version 18.04.5) to run FreeSurfer 7.1.1. I am using Xming
6.9.0.31 as a visual platform to open freeview. Maybe it could be a
windows-specific problem?
Best,
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Dear Douglas and Bruce,
my name is Diana, I am encountering the same issue as Ellen with
Fix-topology taking too long. Once we make sense of the origin of the issue
(for example, I confirmed that my smoothwm.nofix has a lot of holes), do
you know if
anything in the original file
or the recon-all configuration to fix this issue?
Thanks a lot for your help!!! Best,
Diana
#@# Fix Topology rh Tue May 18 04:37:48 UTC 2021
mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix
-orig orig.nofix -out orig.premesh -ga -seed 1234 NoUMA0233 rh
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Dear FreeSurfer team,
My name is Diana Ortega, I am a Neuroscience PhD student at Universidad
Politécnica of Madrid. I run a job to compute recon-all in parallel for 30
subjects remotely on a supercomputer at my research institution. This job
finished
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Thank you Tim, the explanation and screenshot helped indeed.
Diana
El mar., 9 jun. 2020 a las 10:07, Tim Schäfer () escribió:
> External Email - Use Caution
>
> These are different versions of the fsaverage template, but with reduced
to me what fsaverage 3, 4, 5 and 6 are?
Thank you!
Diana
p.d. I copied below the contents of $FREESURFER_HOME/subjects/
localhost:/usr/local/freesurfer/subjects> ls fs
fsaverage/ fsaverage3/fsaverage4/fsaverage5/fsaverage6/
fsaverage_sym/
localhost:/usr/local/freesurfer/subje
one? If I have to
create it, which are the steps to do so?
Best wishes, Diana
El lun., 8 jun. 2020 a las 19:36, Tim Schäfer () escribió:
> External Email - Use Caution
>
> I think all you need to do is copy (or symlink) fsaverage to your data
> directory, the label file is in
/lh.cortex.label
How can I create this label file?
Thank you very much in advance for your help, please find below the whole
output.
Best, Diana
nsubjects = 25
INFO: turning on jacobican correction
tmpdir is output/tmp.mris_preproc.21054
/home/neuroimagen/AnalisisLongitudinalLMM
Log file is output
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Thank you Doug,
I'll do that!
Best, Diana
On 20/5/19 20:54, Greve, Douglas N.,Ph.D. wrote:
> You will not need to run the entire stream again. Did you run it in
> high-res mode? If the volumes are conformed (eg, orig.mgz is 1mm,
> 25
have
to rerun the whole analysis in case they have.
Thank you!
Diana
--
Diana Tordesillas Gutiérrez, PhD
Neuroimaging Unit IDIVAL
IDIVAL Building
Avda. Cardenal Herrera Oria s/n
39011 Santander
Spain
Tel. +34 942202677
diana.tordesil
it, this doesn't seem to be a real issue; however, I
would love to better understand why this doesn't matter in the long run,
i.e. why the brainmask does not later affect parcellation of subcortical
regions(?).
Thank you for your time!
Diana
_
Thank you, we did that, and it was indeed an issue with the way we ran it.
Diana
> El 9 feb 2017, a las 18:19, Douglas Greve
> escribió:
>
> It says that it was "Killed" which sounds like the job exceeded some resource
> on the supercomputer. You should contact
about this.
The version of freesurfer is:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2
Thank you for your help,
Diana
Diana Tordesillas Gutiérrez, PhD
Neuroimaging Unit IDIVAL
IDIVAL Building
Avda. Cardenal Herrera Oria s/n
39011
degree) to
Dr. Diana Tordesillas-Gutiérrez, e-mail: diana.tordesil...@humv.es
--
Diana Tordesillas Gutiérrez, PhD
Neuroimaging Unit IDIVAL
IDIVAL Building
Avda. Cardenal He
rcome this issue?
Thank you in advance!
Kind regards,
Diana
P.S. The Matlab code consists of just 2 lines of reading and saving the same
file under a different name.
%read the surface file
[verticesWhite, facesWhite] = read_surf(['.../surf/lh.white']);
%save the same
ignorance.
Many thanks,
Diana Omigie
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addressed. If you
parcellation
are listed.
Do you have any suggestion or idea how to match the vertex number for
both
parcellations in order to get the anatomical labels for the finer
parcellation?
Kind regards
Diana
Am 14.04.2010 um 15:01 schrieb Bruce Fischl:
> yes, you can use the talairach.xfm file to get MNI coo
Coordinates of these vertices and the label corresponding
to them?
Thanks very much for your help!
Kind regards
Diana
Am 12.04.2010 um 00:31 schrieb Bruce Fischl:
> Hi Diana,
>
> the parcels from mris_make_face_parcellation are uniform, not
> localized
> to gyral/sulcal lab
appreciated.
Thanks in advance
Best regards
Diana
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Dear Nick
Is it possible to refer the "faces" I got with the command below to the
labels from an annotation file?
[Macintosh-10:subjects/fsaverage_fineparc_uniformareas/surf] diana%
mris_make_face_parcellation rh.inflated
/Applications/freesurfer/lib/bem/ic4.tri rh.ic4.annot
I
getting the following error message:
"Segmentation fault" (after 1374 entries are read)
The same command works just fine with a parcellated .annot file I generated
with a lower threshold (p.e. 150mm2).
Any help would be appreciated
Reg
?h_aparc.a2005s_300_stat.txt
Thanks for your help
Diana
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former version):
aparcstats2table: error: option --parc: invalid choice: 'aparc.a2005s_300'
(choose from 'aparc', 'aparc.a2005s')
How can I force the -parc option to read my own parcellations?
Diana
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Diana
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into each
subjects label folder ensuing mris_anatomical_stats?
Any help would be appreciated
Regards
Diana
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rh_annot_100
Now I would like to spatially register these labels onto each subject's
brain, in order to bring these parcellations into a common standard space so
that we can compare the parcellations across subjects.
I there a manual or a tool for such a procedure?
Thanks in advance
Regards
methodology was applied by Hagmann et al., PLoS Biol 6: 14791493, 2008.)
Does a finer parcellation scheme become part of future Freesurfer releases?
Or have someone some experience in such a procedure?
Any information would be much appreciated.
Kind regards
Diana Wotruba
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