External Email - Use Caution

Hi,

Yes, otherwise there is no way to debug the lines in your script.

Best, Rosalia

El jue., 10 oct. 2019 14:41, Olamide Abiose oabiose@stanford.edu escribió:

    External Email - Use Caution

Hi Rosalia,

I'm running this as a command line argument, because I'm only testing one subject. Are you asking for the segmentHA_T1.sh script?

---

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta Aguayo rdacostaa@gmail.com *Sent:* Thursday, October 10, 2019 2:34 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Issues with segmentHA_T1.sh command

    External Email - Use Caution

Hi Olamide,

How to check your line errors without the bash script you are using? Could you at least send the .sh script?

Best regards, Rosalia

On Thu, Oct 10, 2019 at 8:29 PM Olamide Abiose oabiose@stanford.edu wrote:

    External Email - Use Caution

Hello,

I'm having great difficulty running the segmentHA_T1.sh command. I'm using the latest development version of Freesurfer and have downloaded Matlab R2014b. I get the following message when I try to run the command. Any advice/suggestions you can offer would be greatly appreciated!

Thank you very much.

#-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Wed Oct 9 17:49:49 PDT 2019 /usr/bin/time -o /dev/stdout @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01 run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004 /mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice 0.333333333333333333333333333333333333 /opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz /opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz /opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 /opt/freesurfer-dev/bin/ 0

---

Setting up environment variables

LD_LIBRARY_PATH is .:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client:: Error using checkRequiredMCRProducts (line 25) Java exception occurred: java.lang.NullPointerException at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56) at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108) at com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)

Error in deployrc (line 9)

Error in matlabrc (line 238)

Command exited with non-zero status 255 @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 84096 L 41.67 41.74 45.01 @#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 41.42 41.68 44.90 Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Wed Oct 9 17:50:15 PDT 2019

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

I see, in that case, you should ask directly to Dr Eugenio Iglesias as he is the one who created this script.

His last known email is: e.iglesias@ucl.ac.uk

I am sure he will answer you as soon as possible, but if you see that there is no answer. Then send it to the list cc to him as well. And mention his name in your email so he will take your email quickly.

Best Wishes, Rosalia

On Thu, Oct 10, 2019 at 8:49 PM Olamide Abiose oabiose@stanford.edu wrote:

    External Email - Use Caution

Okay, here it is. I just want to stress that it's not my script, but the amygdala subfield module released by Freesurfer ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmy...). I don't have permission to directly edit it, but please let me know if I'm misunderstanding your request, or if you'd like further clarification.

Thanks again.

---

#! /bin/tcsh -f

set tcsh61706 = (`tcsh --version | grep "6.17.06"`) if ("$tcsh61706" != "") then echo "" echo "WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!" echo "" # workaround to force expected behavior: set anyerror endif

# check MCR installation checkMCR.sh if ($status) then exit 1 endif

# If no arguments given if( $#argv == 0 || $#argv > 2) then echo " " echo "Usage: " echo " " echo " segmentHA_T1.sh SUBJECT_ID [SUBJECT_DIR]" echo " " echo "Or, for help" echo " " echo " segmentHA_T1.sh --help" echo " " exit 1 endif

# If requesting help if( $1 == "--help") then echo " " echo "SEGMENTATION OF HIPPOCAMPAL SUBFIELDS AND NUCLEI OF THE AMYGDALA (T1)" echo " " echo "Use this script to segment the hippocampal subfields and nuclei of the amygdala" echo "from the main T1 scan used in the recon-all stream. It supports standard (1mm)" echo "and high resolution T1 scans." echo " " echo "To use this module, you first need to process the input scan with the main " echo "FreeSurfer pipeline (recon-all). If you want to analyze high-resolution scans" echo "(i.e., voxel size smaller than 1mm) at their native resolution, they must be" echo "processed with the recon-all flag -cm. Then, you can run the following command" echo "to obtain the segmentation: " echo " " echo " segmentHA_T1.sh SUBJECT_ID [SUBJECT_DIR]" echo " " echo " (the argument [SUBJECT_DIR] is only necessary if the" echo " environment variable SUBJECTS_DIR has not been set" echo " or if you want to override it)" echo " " echo "The segmentation method is described in [1], and the atlases are described in [1]" echo "(hippocampus) and [2] (amygdala):" echo " " echo "See further information, including how to visualize the results, at:" echo " " echo " https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmy... " echo " " echo "[1] Iglesias, J.E., Augustinack, J.C., Nguyen, K., Player, C.M., Player, A., Wright," echo "M., Roy, N., Frosch, M.P., McKee, A.C., Wald, L.L., Fischl, B., and Van Leemput, K.," echo "A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution" echo "MRI: Application to adaptive segmentation of in vivo MRI. Neuroimage 115, 2015, 117-137." echo "http://dx.doi.org/10.1016/j.neuroimage.2015.04.042" echo " " echo "[2] Saygin, Z.M. & Kliemann, D. (joint 1st authors), Iglesias, J.E., van der Kouwe, A.J.W.," echo "Boyd, E., Reuter, M., Stevens, A., Van Leemput, K., McKee, A., Frosch, M.P., Fischl, B.," echo "and Augustinack, J.C., High-resolution magnetic resonance imaging reveals nuclei of the" echo "human amygdala: manual segmentation to automatic atlas. Neuroimage 155, 2017, 370-382." echo "http://doi.org/10.1016/j.neuroimage.2017.04.046" echo " " exit 0 endif

# Error if SUBJECTS_DIR (the environment variable) does not exist if ($#argv == 1) then if (! $?SUBJECTS_DIR) then echo " " echo "SUBJECTS_DIR variable does not exist" echo "Please define it or provide subjects directory as second input" echo " " exit 1 endif endif

# Error if SUBJECTS_DIR (the environemnt variable) is empty if ($#argv == 1) then if ( $SUBJECTS_DIR == "" ) then echo " " echo "SUBJECTS_DIR variable is empty" echo "Please redefine it or provide subjects directory as second input" echo " " exit 1 endif endif

# If SUBJECTS_DIR is provided, just set it if ($#argv == 2) then set SUBJECTS_DIR = $2 endif

# Set name of subject set SUBJECTNAME = $1

# Error if subject directory does not exist if (! -d $SUBJECTS_DIR ) then echo " " echo "Subjects directory:" echo " $SUBJECTS_DIR" echo "does not exist" echo " " exit 1 endif

# Error if directory of specific subject does not exist if (! -d $SUBJECTS_DIR/$SUBJECTNAME ) then echo " " echo "Directory of subject to process:" echo " $SUBJECTS_DIR/$SUBJECTNAME" echo "does not exist" echo " " exit 1 endif

# Error if subject not processed (far enough) if (! -e ${SUBJECTS_DIR}/${SUBJECTNAME}/mri/wmparc.mgz || \ ! -e ${SUBJECTS_DIR}/${SUBJECTNAME}/mri/norm.mgz || \ ! -e ${SUBJECTS_DIR}/${SUBJECTNAME}/mri/transforms/talairach.xfm ) then echo " " echo "Cannot find wmparc.mgz or norm.mgz or talairach.xfm for the subject." echo "Has the subject been procesed with recon-all?" echo " " exit 1; endif

# Make sure that the (T1) hippocampal subfields are not running already for this subject set IsRunningFile = ${SUBJECTS_DIR}/${SUBJECTNAME}/scripts/IsRunningHPsubT1.lh+rh if(-e $IsRunningFile) then echo "" echo "It appears that T1 Hippocampal Subfields is already running" echo "for this subject based on the presence of IsRunningHPsub.lh+rh" echo "It could also be that T1 Hippocampal Subfields was running at one" echo "point but died in an unexpected way. If it is the case that there" echo "is a process running, you can kill it and start over or" echo "just let it run. If the process has died, you should type:" echo "" echo "rm $IsRunningFile" echo "" echo "and re-run." echo "----------------------------------------------------------" cat $IsRunningFile echo "----------------------------------------------------------" exit 1; endif

# If not explicitly specfied, set to 1 if($?ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS == 0) then setenv ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 endif

# If everything is in place, let's do it! First, we create the IsRunning file echo "------------------------------" > $IsRunningFile echo "SUBJECT $SUBJECTNAME" >> $IsRunningFile echo "DATE `date`" >> $IsRunningFile echo "USER $user" >> $IsRunningFile echo "HOST `hostname`" >> $IsRunningFile echo "PROCESSID $$ " >> $IsRunningFile echo "PROCESSOR `uname -m`" >> $IsRunningFile echo "OS `uname -s`" >> $IsRunningFile uname -a >> $IsRunningFile if($?PBS_JOBID) then echo "pbsjob $PBS_JOBID" >> $IsRunningFile endif

# Parameters set RUNTIME="$FREESURFER_HOME/MCRv84/"; set RESOLUTION="0.333333333333333333333333333333333333"; set ATLASMESH="$FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz"; set ATLASDUMP="$FREESURFER_HOME/average/HippoSF/atlas/AtlasDump.mgz"; set LUT="$FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt"; set K="0.05"; set OPTIMIZER="L-BFGS"; set MRFCONSTANT="0"; set SUFFIX="v21";

# Now the real job set hippohemilist=(left right) set HSFLOG = (${SUBJECTS_DIR}/${SUBJECTNAME}/scripts/hippocampal-subfields-T1.log) rm -f $HSFLOG

echo "------------------------------" > $HSFLOG echo "USER $user" >> $HSFLOG echo "HOST `hostname`" >> $HSFLOG echo "PROCESSID $$ " >> $HSFLOG echo "PROCESSOR `uname -m`" >> $HSFLOG echo "OS `uname -s`" >> $HSFLOG echo "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS $ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS " >> $HSFLOG uname -a >> $HSFLOG if($?PBS_JOBID) then echo "pbsjob $PBS_JOBID" >> $HSFLOG endif echo "------------------------------" >> $HSFLOG echo " " >> $HSFLOG cat $FREESURFER_HOME/build-stamp.txt >> $HSFLOG echo " " >> $HSFLOG echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" >> $HSFLOG echo "cd `pwd`" >> $HSFLOG echo $0 $argv >> $HSFLOG echo "" >> $HSFLOG

foreach hemi ($hippohemilist) echo "#--------------------------------------------" \ |& tee -a $HSFLOG echo "#@# Hippocampal Subfields processing (T1) $hemi `date`" \ |& tee -a $HSFLOG

# command set cmd="run_segmentSubjectT1_autoEstimateAlveusML.sh $RUNTIME $SUBJECTNAME $SUBJECTS_DIR $RESOLUTION $ATLASMESH $ATLASDUMP $LUT $K $hemi $OPTIMIZER $SUFFIX ${FREESURFER_HOME}/bin/ $MRFCONSTANT"

fs_time ls >& /dev/null if ($status) then $cmd |& tee -a $HSFLOG set returnVal=$status else fs_time $cmd |& tee -a $HSFLOG set returnVal=$status endif

if ($returnVal) then

uname -a | tee -a $HSFLOG
echo "" |& tee -a $HSFLOG
echo "T1 hippocampal subfields exited with ERRORS at `date`" \
|& tee -a $HSFLOG
echo "" |& tee -a $HSFLOG
echo "For more details, see the log file $HSFLOG"
echo ""
rm -f $IsRunningFile
exit 1;

endif end

# Convert the txt files into a stats file so that asegstats2table can # be run Note: the number of voxels is set to 0 and there is no info # about intensity. The only useful info is the volume in mm and the # structure name. The segmentation IDs also do not mean anything. # Could run mri_segstats instead, but the volumes would not include # partial volume correction. foreach hemi (lh rh) set txt=$SUBJECTS_DIR/$SUBJECTNAME/mri/$hemi.hippoSfVolumes-T1.$SUFFIX.txt set stats=$SUBJECTS_DIR/$SUBJECTNAME/stats/hipposubfields.$hemi.T1.$SUFFIX.stats echo "# Hippocampal subfield volumes as created by segmentHA_T1.sh" > $stats cat $txt | awk '{print NR" "NR" 0 "$2" "$1}' >> $stats set txt=$SUBJECTS_DIR/$SUBJECTNAME/mri/$hemi.amygNucVolumes-T1.$SUFFIX.txt set stats=$SUBJECTS_DIR/$SUBJECTNAME/stats/amygdalar-nuclei.$hemi.T1.$SUFFIX.stats echo "# Amygdala nuclei volumes as created by segmentHA_T1.sh" > $stats cat $txt | awk '{print NR" "NR" 0 "$2" "$1}' >> $stats end

# All done! rm -f $IsRunningFile

echo " " echo "All done!" echo " " echo "If you have used results from this software for a publication, please cite:" echo " " echo "Iglesias, J.E., Augustinack, J.C., Nguyen, K., Player, C.M., Player, A., Wright," echo "M., Roy, N., Frosch, M.P., McKee, A.C., Wald, L.L., Fischl, B., and Van Leemput, K.," echo "A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution" echo "MRI: Application to adaptive segmentation of in vivo MRI. Neuroimage 115, 2015, 117-137." echo "http://dx.doi.org/10.1016/j.neuroimage.2015.04.042" echo " " echo "In addition, if you have used the segmentation of the nuclei of the amygdala, please also cite:" echo "" echo "Saygin, Z.M. & Kliemann, D. (joint 1st authors), Iglesias, J.E., van der Kouwe, A.J.W.," echo "Boyd, E., Reuter, M., Stevens, A., Van Leemput, K., McKee, A., Frosch, M.P., Fischl, B.," echo "and Augustinack, J.C., High-resolution magnetic resonance imaging reveals nuclei of the" echo "human amygdala: manual segmentation to automatic atlas. Neuroimage 155, 2017, 370-382." echo "http://doi.org/10.1016/j.neuroimage.2017.04.046" echo " "

exit 0

---

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta Aguayo rdacostaa@gmail.com *Sent:* Thursday, October 10, 2019 2:44 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Issues with segmentHA_T1.sh command

    External Email - Use Caution

Hi,

Yes, otherwise there is no way to debug the lines in your script.

Best, Rosalia

El jue., 10 oct. 2019 14:41, Olamide Abiose oabiose@stanford.edu escribió:

    External Email - Use Caution

Hi Rosalia,

I'm running this as a command line argument, because I'm only testing one subject. Are you asking for the segmentHA_T1.sh script?

---

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta Aguayo rdacostaa@gmail.com *Sent:* Thursday, October 10, 2019 2:34 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Issues with segmentHA_T1.sh command

    External Email - Use Caution

Hi Olamide,

How to check your line errors without the bash script you are using? Could you at least send the .sh script?

Best regards, Rosalia

On Thu, Oct 10, 2019 at 8:29 PM Olamide Abiose oabiose@stanford.edu wrote:

    External Email - Use Caution

Hello,

I'm having great difficulty running the segmentHA_T1.sh command. I'm using the latest development version of Freesurfer and have downloaded Matlab R2014b. I get the following message when I try to run the command. Any advice/suggestions you can offer would be greatly appreciated!

Thank you very much.

#-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Wed Oct 9 17:49:49 PDT 2019 /usr/bin/time -o /dev/stdout @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01 run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004 /mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice 0.333333333333333333333333333333333333 /opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz /opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz /opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 /opt/freesurfer-dev/bin/ 0

---

Setting up environment variables

LD_LIBRARY_PATH is .:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client:: Error using checkRequiredMCRProducts (line 25) Java exception occurred: java.lang.NullPointerException at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56) at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108) at com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)

Error in deployrc (line 9)

Error in matlabrc (line 238)

Command exited with non-zero status 255 @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 84096 L 41.67 41.74 45.01 @#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 41.42 41.68 44.90 Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

T1 hippocampal subfields exited with ERRORS at Wed Oct 9 17:50:15 PDT 2019

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer