Hi Renata,

 

Is there a problem with the “-s” argument, i.e. the “/” in  - s 20110815/

 

HTH - Don

 

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Vaz pandolfo, Renata
Sent: Thursday, July 07, 2016 8:05 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label

 

Dear FreeSurfer developers,

I am running recon-all on a healthy subject and I am also trying to get the hippocampal subfields segmentation.
On the mri directory there is no hippocampus output, and the recon-all exited with errors.
>From my understanding, the error is with the lh.BA1_exvivo.label:

SUBJECTS_DIR    /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815
FREESURFER_HOME /usr/local/freesurfer
Loading source label.
Invalid argument
ERROR reading /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label

The command I used was:
recon-all -all \
-i ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz -s 20110815/ \
-sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
-T2 o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \
-T2pial -hippocampal-subfields-T1

When trying to solve the problem, I noticed that I could have run a separate command for the hippocampal subfields and I ran this one:

recon-all \
-s 20110815/ \
-sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/  \
-hippocampal-subfields-T1T2 ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz  20110815_T2

Since the previous data had errors, I didn't really expect this to work, but I tried it anyways.

It exited "without errors", but on the log there was the following error twice:

Error:Cannot find CTF archive /usr/local/freesurfer/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf

Extra info:

Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611 

uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux 

logs: recon-all and hippocampal-subfields-T1T2 attached

If anyone has had the same problem, could you please tell me how to solve it?
And if I am doing something wrong, please tell me the correct way so I can continue with the analysis.

 

Thank you!

Renata

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