Re: [Freesurfer] Recon-all Longitudinal Talairach issue

[Douglas N. Greve]

Can you send the recon-all.log file that contains the error?

On 1/24/2024 4:01 AM, Kapteijns, Kirsten wrote:


External Email - Use Caution

Dear all,

I have run recon-all successfully on multiple subjects on multiple 
timepoints. If I open the mri folder, it shows the correct talairach 
files and no issues arose during processing.


However, when I then run the longitudinal pipeline (first base, which 
also shows correct files) on the subjects (recon-all -long SUBJXXtp1 
SUBJXXbase -all) the talairach shows an failure detection and the 
subsequent file is talairach.invalid.mgz.


The actual segmentation etc. seems fine when inspecting, but when I 
then want to run segmentBS.sh on these processed folders, it gives an 
error.


I have run this a few month back without issue, and had just a few 
subjects left, but now all of them show this same error. Any idea how 
this could be caused?


Kind regards,

Kirsten

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[Freesurfer] Recon-all Longitudinal Talairach issue

[Kapteijns, Kirsten]

External Email - Use Caution

Dear all,


I have run recon-all successfully on multiple subjects on multiple timepoints. 
If I open the mri folder, it shows the correct talairach files and no issues 
arose during processing.
However, when I then run the longitudinal pipeline (first base, which also 
shows correct files) on the subjects (recon-all -long SUBJXXtp1 SUBJXXbase 
-all) the talairach shows an failure detection and the subsequent file is 
talairach.invalid.mgz.
The actual segmentation etc. seems fine when inspecting, but when I then want 
to run segmentBS.sh on these processed folders, it gives an error.

I have run this a few month back without issue, and had just a few subjects 
left, but now all of them show this same error. Any idea how this could be 
caused?


Kind regards,

Kirsten

De informatie in dit bericht is uitsluitend bestemd voor de geadresseerde. Aan 
dit bericht en de bijlagen kunnen geen rechten worden ontleend. Heeft u deze 
e-mail onbedoeld ontvangen? Dan verzoeken wij u het te vernietigen en de 
afzender te informeren. Openbaar maken, kopi?ren en verspreiden van deze e-mail 
of informatie uit deze e-mail is alleen toegestaan met voorafgaande 
schriftelijke toestemming van de afzender. Het Radboudumc staat geregistreerd 
bij de Kamer van Koophandel in het handelsregister onder nummer 80262783.

The content of this message is intended solely for the addressee. No rights can 
be derived from this message or its attachments. If you are not the intended 
recipient, we kindly request you to delete the message and inform the sender. 
It is strictly prohibited to disclose, copy or distribute this email or the 
information inside it, without a written consent from the sender. Radboud 
university medical center is registered with the Dutch Chamber of Commerce 
trade register with number 80262783.
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