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.igles...@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 <oabi...@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/HippocampalSubfieldsAndNucleiOfAmygdala). > 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/HippocampalSubfieldsAndNucleiOfAmygdala > " > 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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta > Aguayo <rdacos...@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 <oabi...@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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta > Aguayo <rdacos...@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 <oabi...@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
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