Okay, I changed some other things and now the recon-all is running. I will see how it looks tomorrow.

I used: recon-all -all \

-i

~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz -s new_trial_20110815 \

-sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/ \ -T2

~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \

-T2pial -hippocampal-subfields-T1

Thanks!

On Thu, Jul 7, 2016 at 2:15 PM, Vaz pandolfo, Renata rvp8@njit.edu wrote:

Thank you!

But now the error is:

ERROR: cannot find o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz 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

recon-all -s 20110815 exited with ERRORS at Do 7. Jul 14:14:09 CEST 2016

Maybe I have to put the whole path?

On Thu, Jul 7, 2016 at 2:10 PM, Krieger, Donald N. kriegerd@upmc.edu wrote:

...

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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