[Freesurfer] FS_7_2_0_Ubuntu_18_04_06.ova.7z password

[Marcel Heers]

External Email - Use Caution

Can you please share the password for the above mentioned VirtualBox with
me?

Thanks in advance!
Marcel
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[Freesurfer] hippocampal subfields as masks for mri_segstats

[Marcel Heers]

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Dear all, (dear Eugenio),

I would like to use hippocampal subfields as masks for mri_segstats to
retrieve intensity values. I am having problems loading the subfields file
although it works fine with aseg.mgz.

Does  anyone know the cause?

Thank you in advance!

Best regards
Marcel

mri_segstats --seg $SUBJECTS_DIR/test/mri/aseg.mgz --ctab-default --sum
output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz

mri_segstats --seg $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz
--sum output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz

ERROR: loading $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz
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[Freesurfer] Scripts to prepare MP2RAGE sequence for recon-all pipeline

[Marcel Heers]

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Dear all,

does anyone share scripts to prepare MP2RAGE sequences for freesurfer's
standard processing pipeline, e.g. the method used by Fuijmoto et al.
NeuroImage 2014?
Thanks for your help!

Marcel
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[Freesurfer] hippocampal subfields

[Marcel Heers]

External Email - Use Caution

Dear Eugenio,

there is one error in the error.log: 'Could not set locale'.

Best regards

Marcel
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[Freesurfer] hippocampal subfields error

[Marcel Heers]

External Email - Use Caution

Dear Eugenio,

I am currently testing the newest version of your hippocampal subfield
analysis script. If I process the data on my macbook the files
hipposubfields.lh.T2.v21.file_ID contain the volumes of the different
nuclei, but on the linux server these files remain empty. On the server I
installed freesurfer as local user. Do you have any suggestions how to
check what might go wrong?

Thanks for your help!

Marcel
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Re: [Freesurfer] scalp mesh

[Marcel Heers]

Dear Don, dear Bruce,

thank you for your imediate helpful comments! I tried out mri_watershed
within freesurfer and mne_watershed_bem within mne and both of them do what
I was looking for.

Marcel

2010/5/28 Bruce Fischl 

> Hi Marcel,
>
> we build one internally but don't usually write it out. You can check out
> the options to mri_watershed if you want to save it. I think the MNE MEG/EEG
> analysis stream does this routinely
>
> cheers,
> Bruce
>
> On Thu, 27 May 2010, Marcel Heers wrote:
>
>  Dear all,
>>
>> while I am doing my first steps using freesurfer, I am searching for a
>> scalp
>> mesh, which I could use for the brainstorm toolbox. Is there a scalp mesh
>> produced during recon-all, which I can use for this purpose? Thanks for
>> every hint!
>>
>> Marcel
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Marcel Heers, M.D.
Stubenlohstr. 22
D-91052 Erlangen
phone: +499131-8889500
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] scalp mesh

[Marcel Heers]

Dear all,

while I am doing my first steps using freesurfer, I am searching for a scalp
mesh, which I could use for the brainstorm toolbox. Is there a scalp mesh
produced during recon-all, which I can use for this purpose? Thanks for
every hint!

Marcel
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.