External Email - Use Caution
That did the trick, thank you!
On Mon, Dec 21, 2020 at 12:43 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Thanks, Zach. May I ask you to try running the command with an absolute path for the subjects directory, please?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1bRUKxXjytzl-yJaVkXunh__6KCeqv2CjEiNZh17y5cE47Nw...
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zachary Miller mill5076@umn.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, December 21, 2020 at 13:17 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] segmentHA_T1.sh Error {Disarmed}
External Email - Use Caution *My directory structure is:
FStests/CDN0001_MSB/CDN0001_10_7.1.1
The command echo Hello > FStests/CDN0001_MSB/CDN0001_10_7.1.1/tmp/test.txt
does create test.txt in the tmp directory.
On Mon, Dec 21, 2020 at 11:43 AM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
Hi Zach,
Just to double check: your directory structure is:
FStests/CDN0001_MSB/CDN0001
So the following directory:
FStests/CDN0001_MSB/CDN0001/tmp
exists and is writable? For example, this command:
echo Hello > FStests/CDN0001_MSB/CDN0001/tmp/test.txt
will create the file:
FStests/CDN0001_MSB/CDN0001/tmp/test.txt
Cheers,
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zachary Miller mill5076@umn.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, December 21, 2020 at 12:14 *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] segmentHA_T1.sh Error
External Email - Use Caution *Hello,
I am having trouble running segmentHA_T1.sh and I hope that someone will know the solution. Per a similar thread on this mail archive, I have verified that I have writing permissions in the subject directory. My command line and FS output are below.
Thank you,
Zach
Command:
segmentHA_T1.sh CDN0001_MSB_10_7.1.1 FStests/CDN0001_MSB
Output:
#@# Hippocampal Subfields processing (T1) left Fri Dec 18 14:14:40 CST 2020
Setting up environment variables
LD_LIBRARY_PATH is .:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//runtime/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//bin/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/os/glnxa64:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/panfs/roc/msisoft/freesurfer/7.1.1/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/panfs/roc/msisoft/netcdf/4.6.2-gcc8.2.0-serial/lib:/panfs/roc/msisoft/hdf5/hdf5-1.10.4-gcc8.2.0-ompi-4.0.0/lib:/panfs/roc/msisoft/openmpi/el6/4.0.0/gnu-8.2.0.CentOS7/lib:/panfs/roc/msisoft/java/openjdk-11.0.2/lib:/panfs/roc/msisoft/java/openjdk-11.0.2/lib/jli:/panfs/roc/msisoft/java/openjdk-11.0.2/lib/server:/panfs/roc/msisoft/gcc/8.2.0/lib64:/panfs/roc/msisoft/isl/0.19_gcc8.1.0/lib:/panfs/roc/msisoft/mpc/1.1.0_gcc8.1.0/lib:/panfs/roc/msisoft/mpfr/4.0.1_gcc8.1.0/lib:/panfs/roc/msisoft/gmp/6.1.2_gcc8.1.0/lib:/panfs/roc/msisoft/fsl/6.0.1/lib:/panfs/roc/msisoft/matlab/R2014b/runtime/glnxa64:/panfs/roc/msisoft/gcc/8.1.0/lib64
Registering imageDump.mgz to hippocampal mask from ASEG
Error using myMRIread (line 16)
Error in myMRIread: temporary directory does not exist
Error in segmentSubjectT1_autoEstimateAlveusML (line 157)
@#@FSTIME 2020:12:18:14:14:40 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 e 26.52 S 1.16 U 7.38 P 32% M 268532 F 598 R 75671 W 0 c 1553 w 10745 I 492960 O 0 L 2.09 8.46 13.64
@#@FSLOADPOST 2020:12:18:14:15:06 run_segmentSubjectT1_autoEstimateAlveusML.sh N 14 2.32 8.00 13.35
Linux cn0224 3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
T1 hippocampal subfields exited with ERRORS at Fri Dec 18 14:15:06 CST 2020
--
Zachary Miller
Researcher | Institute of Child Development | College of Education and Human Development | cehd.umn.edu http://secure-web.cisco.com/1sz1OjDmLqXbn7QdcfQPSyVRpMWzjVeK8cvH2a4MYh2hG2Y3iLeIhIEkgnzntI3yZYCagi1FFxnF4exfBfm4jCfM0HiHS99i9uMcYaoQt1641hmLuwdjjYNAJZYm-WO1RbLKUNg_w1hvGXYxGcLZn1TnkdsmO3N9rDo7yNPgLhKgXE5udATYH_r5OqPMp4pY9KXelAaP7_IJcyDr7gJRXqLNMwPA5W8IRJYoShY-4XZL5yML3DwBN-SAtqVEWzw7NceUQQWYcqRyFCHb00QOTgg/http%3A%2F%2Fcehd.umn.edu
mill5076@umn.edu
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Zachary Miller
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