I ran the following command to generate surfaces and hippo subfields on 6.0 (Jan. 2017 version) using both a T1 mprage and T2 space (both 1mm isotropic). recon-all –s subject –i dicom.dcm –hippocampal-subfields-T1T2 T2.nii.gz T1T2 –all.
The command appears to have run successfully but I get a note at the end of the processing stream that there is no file ‘volumesAmygdla.txt’ (see screen message below). Is this expected even though I’m not using the later developmental release? Jim
----------------------------------------------------------------------- Not resampling, only changing vox2ras matrix To check registration, run:
tkregister2 --mov T2inT1space.mgz --targ /data/nil-bluearc/shimony/neonatal/wunder_9_10yo/freesurfer6_0/processed_data/neo321e_fs/mri/norm.mgz --regheader --reg /tmp/reg
mri_vol2vol done mv: cannot stat 'volumesAmygdala.txt': No such file or directory Everything done! It took 1921.1425 seconds
Started at Wed Mar 14 17:04:06 CDT 2018 Ended at Thu Mar 15 05:35:24 CDT 2018 #@#%# recon-all-run-time-hours 12.522 recon-all -s neo321e_fs finished without error at Thu Mar 15 05:35:24 CDT 2018 done jimalex@linux1%
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Yes! It's all fine. It was just a placeholder for the segmentation of the nuclei of the amygdala, which is available in there development version. Cheers Eugenio
Sent from my phone, please excuse brevity and typos
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios dimitriosalexopoulos@wustl.edu Sent: Monday, March 19, 2018 4:22:06 PM To: Freesurfer support list Subject: [Freesurfer] no file ‘volumesAmygdla.txt’ from FS6.0 - Jan. 2017 release
I ran the following command to generate surfaces and hippo subfields on 6.0 (Jan. 2017 version) using both a T1 mprage and T2 space (both 1mm isotropic). recon-all –s subject –i dicom.dcm –hippocampal-subfields-T1T2 T2.nii.gz T1T2 –all.
The command appears to have run successfully but I get a note at the end of the processing stream that there is no file ‘volumesAmygdla.txt’ (see screen message below). Is this expected even though I’m not using the later developmental release? Jim
----------------------------------------------------------------------- Not resampling, only changing vox2ras matrix To check registration, run:
tkregister2 --mov T2inT1space.mgz --targ /data/nil-bluearc/shimony/neonatal/wunder_9_10yo/freesurfer6_0/processed_data/neo321e_fs/mri/norm.mgz --regheader --reg /tmp/reg
mri_vol2vol done mv: cannot stat 'volumesAmygdala.txt': No such file or directory Everything done! It took 1921.1425 seconds
Started at Wed Mar 14 17:04:06 CDT 2018 Ended at Thu Mar 15 05:35:24 CDT 2018 #@#%# recon-all-run-time-hours 12.522 recon-all -s neo321e_fs finished without error at Thu Mar 15 05:35:24 CDT 2018 done jimalex@linux1%
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Thank for the confirmation.
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Monday, March 19, 2018 11:26 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] no file ‘volumesAmygdla.txt’ from FS6.0 - Jan. 2017 release
Yes! It's all fine. It was just a placeholder for the segmentation of the nuclei of the amygdala, which is available in there development version. Cheers Eugenio Sent from my phone, please excuse brevity and typos
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl.edumailto:dimitriosalexopoulos@wustl.edu> Sent: Monday, March 19, 2018 4:22:06 PM To: Freesurfer support list Subject: [Freesurfer] no file ‘volumesAmygdla.txt’ from FS6.0 - Jan. 2017 release
I ran the following command to generate surfaces and hippo subfields on 6.0 (Jan. 2017 version) using both a T1 mprage and T2 space (both 1mm isotropic). recon-all –s subject –i dicom.dcm –hippocampal-subfields-T1T2 T2.nii.gz T1T2 –all.
The command appears to have run successfully but I get a note at the end of the processing stream that there is no file ‘volumesAmygdla.txt’ (see screen message below). Is this expected even though I’m not using the later developmental release? Jim
----------------------------------------------------------------------- Not resampling, only changing vox2ras matrix To check registration, run:
tkregister2 --mov T2inT1space.mgz --targ /data/nil-bluearc/shimony/neonatal/wunder_9_10yo/freesurfer6_0/processed_data/neo321e_fs/mri/norm.mgz --regheader --reg /tmp/reg
mri_vol2vol done mv: cannot stat 'volumesAmygdala.txt': No such file or directory Everything done! It took 1921.1425 seconds
Started at Wed Mar 14 17:04:06 CDT 2018 Ended at Thu Mar 15 05:35:24 CDT 2018 #@#%# recon-all-run-time-hours 12.522 recon-all -s neo321e_fs finished without error at Thu Mar 15 05:35:24 CDT 2018 done jimalex@linux1%
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
freesurfer@nmr.mgh.harvard.edu
-
Alexopoulos, Dimitrios -
Iglesias Gonzalez, Eugenio