Freesurfer

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Open Position: Postdoc or PhD Student for Deep Learning based Lesion Recognition in human MRI
by Dr. rer. nat. Johannes Jungilligens 11 Jun '21

11 Jun '21

External Email - Use Caution *Postdoc or PhD Student for Deep Learning based Lesion Recognition in human MRI* available from July 1st, 2021, or later. The position will be embedded in a three-year project within the Human Centered AI Network (HUMAINE) at Ruhr-University Bochum (RUB), Germany. The highly interdisciplinary project deals with the identification and characterization of epilepsy-causing lesions in MRI images of the brain and their discrimination from non-epileptogenic lesions. The project is conducted at the epilepsy center of the university medical center Knappschaftskrankenhaus (Ruhr-Epileptology, Jörg Wellmer) in close collaboration with the Bioinformatics group at the Center for Protein Diagnostics RUB (Axel Mosig). The applicant should hold a degree in computer science, physics, or comparable studies and have experience along with profound theoretical and practical knowledge of deep learning in the context of three-dimensional medical imaging, in particular using state-of-the-art frameworks such as tensorflow of pyTorch. We offer an inspiring working environment in well-established interdisciplinary structures, providing state-of-the-art IT infrastructure in a highly dynamic interdisciplinary setting with project partners covering the whole range between medicine, machine learning, sociology, and business. The salary is that of a full-position scientist according to German payment standards. For further information and application, feel free to contact Jörg Wellmer ( Joerg.Wellmer(a)kk-bochum.de) and Axel Mosig (axel.mosig(a)rub.de)

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T1 hippocampal subfields exited with ERRORS
by 林鈺庭 11 Jun '21

11 Jun '21

External Email - Use Caution Dear Developer and Eugenio, We encounter the error at the end of the analysis,it looks like this: *Smoothing mesh collection with kernel size 0.750000 .../usr/local/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 40: 499 Killed /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML S013 /data 0.333333333333333333333333333333333333 /usr/local/freesurfer/average/HippoSF/atlas/AtlasMesh.gz /usr/local/freesurfer/average/HippoSF/atlas/AtlasDump.mgz /usr/local/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt 0.05 right L-BFGS v21 '/usr/local/freesurfer/bin/fs_run_from_mcr /usr/local/freesurfer/bin/' 0* *Linux f8e6a6f8a44a 5.10.25-linuxkit #1 SMP Tue Mar 23 09:27:39 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux* *T1 hippocampal subfields exited with ERRORS at Thu Jun 10 10:22:54 UTC 2021* I've attached the log file here, could you help us with this error? Thank you so much! Best regards, Josephine

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Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"
by Chester Kang 11 Jun '21

11 Jun '21

External Email - Use Caution Hi Eugenio, The command that was run is segmentHA_T1.sh. I've rerun and copy-n-pasted the entire session below. "... chesterk@selma:~$ source SetUpFreeSurfer_mac.sh -------- freesurfer-darwin-macOS-7.1.0-20200511-813297b -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer_v7.1.0 FSFAST_HOME /Applications/freesurfer_v7.1.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Users/chesterk/subjects MNI_DIR /Applications/freesurfer_v7.1.0/mni FSL_DIR /usr/local/fsl_v6.0.4 chesterk@selma:~$ cd subjects chesterk@selma:~/subjects$ segmentHA_T1.sh 1001126copy #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri 11 Jun 2021 11:25:12 AEST ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/free surfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sy s/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib:/Applications/frees urfer_v7.1.0/lib/gcc/lib:/Applications/freesurfer_v7.1.0/lib/gcc/lib /Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlveus ML.sh: line 33: /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML.a pp/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64 T1 hippocampal subfields exited with ERRORS at Fri 11 Jun 2021 11:25:12 AEST For more details, see the log file /Users/chesterk/subjects/1001126copy/scripts/hippocampal-subfields-T1.log chesterk@selma:~/subjects$ more 1001126copy/scripts/hippocampal-subfields-T1.log ------------------------------ USER chesterk HOST selma.nnf.unimelb.edu.au PROCESSID 37954 PROCESSOR x86_64 OS Darwin ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64 ------------------------------ freesurfer-darwin-macOS-7.1.0-20200511-813297b setenv SUBJECTS_DIR /Users/chesterk/subjects cd /Users/chesterk/subjects /Applications/freesurfer_v7.1.0/bin/segmentHA_T1.sh 1001126copy #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri 11 Jun 2021 11:25:12 AEST ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/free surfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sy s/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib:/Applications/frees urfer_v7.1.0/lib/gcc/lib:/Applications/freesurfer_v7.1.0/lib/gcc/lib /Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlveus ML.sh: line 33: /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML.a pp/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64 T1 hippocampal subfields exited with ERRORS at Fri 11 Jun 2021 11:25:12 AEST ..." Please let me know if I can provide any other details. Thanks! Regards, Chester On 10/6/21, 12:51 am, "freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-bounces(a)nmr.mgh.harvard.edu on behalf of freesurfer-request(a)nmr.mgh.harvard.edu> wrote: >External email: Please exercise caution > >Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > >To subscribe or unsubscribe via the World Wide Web, visit > https://secure-web.cisco.com/11QCqR7prxSgfCTvoUKKRK8tL2ls0hM_Sfukn_muBU55xc… >.mgh.harvard.edu >or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > >You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Freesurfer digest..." > > >Today's Topics: > > 1. Re: Hippocampal Subfields error "no such file or > directory"/"dyld library not loaded" (Iglesias Gonzalez, Juan E.) > 2. Ill-Conditioned/Badly Scaled Matrix Error (Lurie, Lucy) > 3. LGI FS 7.1 (Del Re, Elisabetta) > 4. mri_glmfit with pvr (stdp82(a)virgilio.it) > 5. Re: FW: WM or Pial edits to correct surfaces (Fischl, Bruce) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 9 Jun 2021 12:24:19 +0000 >From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> >Subject: Re: [Freesurfer] Hippocampal Subfields error "no such file or > directory"/"dyld library not loaded" >To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >Message-ID: <8419D11C-C916-4249-9983-557A252291EC(a)mgh.harvard.edu> >Content-Type: text/plain; charset="us-ascii" > >Dear Chester, >What command did you exactly run? There seems to be a mix of T1 and >T1+additionalMRI segmentation commands in there. >Cheers, >/Eugenio > >Juan Eugenio Iglesias >Senior research fellow >CMIC (UCL), MGH (HMS) and CSAIL (MIT) >http://secure-web.cisco.com/1qi_706jGqyyM3M3yDYUokzl_m0IkJHWaqcVYgXiltKvmf2… >s.com > >> On Jun 9, 2021, at 00:23, Chester Kang <ckkang(a)unimelb.edu.au> wrote: >> >> External Email - Use Caution >> >> Hello FreeSurfer Developers, >> >> I am trying to run subfield segmentation of the hippocampus using >>Freesurfer v7.1.0. Recon-all has been previously run on all subjects, >>however with a different version of Freesurfer (v5.3.0). >> >> Getting the error(s): "No such file or directory" and on further >>investigation "dyld: Library not loaded: @rpath/libmwlaunchermain.dylib" >> >> I've searched the archive but could not find a solution. >> >> Could someone please help? >> >> Below are details of the system and unsuccessful troubleshooting >>attempts. >> >> Regards, >> Chester >> >> >> FreeSurfer version: 7.1.0 >> Platform: Mac OS 10.13.3 >> hippocampal-subfields-T1.log is below: >> >> Things that have been checked/tried or troubleshooting attempted: >> - SIP protection is disabled (csrutil status shows "disabled") >> - Checked that there are files and correct permissions in the >>"lib/gcc/lib" and the "MCRv84" folders >> - tried to unset DYLD_LIBRARY_PATH (in the SetUpFreeSurfer.sh) >> - checked the DYLD_LIBRARY_PATH value and run a step directly (both >>with "" empty value and the values below) >> >> $ echo $DYLD_LIBRARY_PATH >> >> >>.:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/fr >>eesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib >>/gcc/lib >> >> $ >>/Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus >>ML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML >> >> >>/Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus >>ML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML >> dyld: Library not loaded: @rpath/libmwlaunchermain.dylib >> Referenced from: >>/Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveus >>ML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML >> Reason: image not found >> Abort trap: 6 >> >> >> >> === hippocampal-subfields-T1.log === >> >> >> "... >> ------------------------------ >> USER chester >> HOST selma.nnf.unimelb.edu.au >> PROCESSID 17656 >> PROCESSOR x86_64 >> OS Darwin >> ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 >> Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: >>Tue Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64 >> ------------------------------ >> >> freesurfer-darwin-macOS-7.1.0-20200511-813297b >> >> setenv SUBJECTS_DIR /data/netapp02/work/chester/global_pass_all >> cd /data/netapp02/work/chester/global_pass_all >> /Applications/freesurfer_v7.1.0/bin/segmentHA_T1.sh 1002310 >> >> #-------------------------------------------- >> #@# Hippocampal Subfields processing (T1) left Tue 8 Jun 2021 15:25:15 >>AEST >> ------------------------------------------ >> Setting up environment variables >> --- >> DYLD_LIBRARY_PATH is >>.:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/fr >>eesurfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84 >>//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib >> >>/Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlve >>usML.sh: line 33: >>/Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML >>.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file >>or directory >> Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: >>Tue Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64 >> >> T1 hippocampal subfields exited with ERRORS at Tue 8 Jun 2021 15:25:16 >>AEST >> >> ..." >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> >>https://secure-web.cisco.com/11QCqR7prxSgfCTvoUKKRK8tL2ls0hM_Sfukn_muBU55xc… >>.mgh.harvard.edu > > > > >------------------------------ > >Message: 2 >Date: Wed, 9 Jun 2021 13:09:17 +0000 >From: "Lurie, Lucy" <llurie(a)email.unc.edu> >Subject: [Freesurfer] Ill-Conditioned/Badly Scaled Matrix Error >To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >Message-ID: <3BCD8EA8-8DA7-4A8A-BA82-8B7A4F2D2588(a)ad.unc.edu> >Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > >Hello > >I am trying to a whole brain analysis with one group and five covariates. >I am getting an error that the design matrix may be ill-conditioned or >badly scaled. I checked over the fsgd file in TextEdit and it seems to be >formatted correctly. I am using Freesurfer version 5.3.0 and my platform >is macOS Big Sur version 11.4. I would appreciate any help further >troubleshooting this error. Thank you! > >ERROR: matrix is ill-conditioned or badly scaled, condno = 13065 >Possible problem with experimental design: Check for duplicate entries >and/or lack of range of continuous variables within a class. If you seek >help with this problem, make sure to send: >1. Your command line: mri_glmfit --y >lh.eig_cgORCE_baselineORCE_teenCG.thickness.10.mgh --fsgd >eig_cgORCE_baselineORCE_teenCG.fsgd dods --C eig_cgORCE3042_slope.mtx --C >eig_cgORCEbaseline_slope.mtx --C eig_teenCGqual_slope.mtx --surf >fsaverage lh --cortex --glmdir >lh.eig_cgORCE_baselineORCE_teenCGagesex.glmdir >2. The FSGD file (if using one) >3. And the design matrix > >Design matrix ------------------ >1.000 0.000 16.660 2.950 2.200 0.000; >1.000 0.000 16.960 1.900 2.600 0.000; >1.000 0.000 17.390 2.450 2.800 0.000; >1.000 1.000 17.130 2.300 2.500 0.000; >1.000 1.000 16.980 2.400 2.300 0.000; >1.000 0.000 17.690 2.200 2.900 0.000; >1.000 1.000 16.870 2.750 2.900 1.000; >1.000 0.000 17.570 2.550 1.700 0.000; >1.000 0.000 17.130 2.150 1.928 0.000; >1.000 1.000 17.650 2.750 2.200 0.000; >1.000 1.000 17.210 2.450 2.500 1.000; >1.000 0.000 15.610 3.100 1.565 1.000; >1.000 0.000 16.440 2.650 2.300 0.000; >1.000 1.000 17.350 2.400 2.600 0.000; >1.000 0.000 16.800 1.600 1.400 0.000; >1.000 1.000 17.980 2.200 2.300 1.000; >1.000 1.000 16.890 2.800 1.600 1.000; >1.000 0.000 16.760 1.100 1.300 0.000; >1.000 1.000 16.790 2.500 1.400 0.000; >1.000 1.000 16.620 2.900 2.800 0.000; >1.000 1.000 16.500 2.500 1.200 0.000; >1.000 1.000 16.290 2.700 3.200 0.500; >1.000 0.000 16.440 3.100 2.500 1.000; >1.000 0.000 17.540 2.100 2.100 1.000; >1.000 1.000 16.810 1.900 2.600 1.000; >1.000 0.000 17.110 2.650 2.400 0.000; >1.000 1.000 16.520 2.000 2.300 0.000; >1.000 1.000 16.520 3.100 3.400 1.000; >1.000 0.000 16.320 3.300 2.800 0.500; >1.000 0.000 16.380 3.200 1.900 1.000; >1.000 0.000 16.570 2.800 2.000 0.000; >1.000 1.000 16.250 2.200 1.600 0.000; >1.000 1.000 16.820 2.900 2.600 1.000; >1.000 0.000 16.580 2.600 2.800 0.000; >1.000 1.000 16.730 2.850 3.150 0.000; >1.000 0.000 16.310 2.600 1.900 0.000; >1.000 1.000 17.010 1.700 2.400 0.000; >1.000 1.000 16.360 3.200 3.200 0.000; >1.000 1.000 16.490 2.400 1.525 0.000; >1.000 0.000 16.300 2.400 1.450 1.000; >1.000 0.000 16.060 2.200 1.300 0.000; >1.000 1.000 16.600 2.200 2.000 0.000; >1.000 0.000 16.720 3.300 2.500 0.000; >1.000 1.000 16.160 2.300 2.200 0.000; >1.000 1.000 16.140 2.800 1.850 0.000; >1.000 1.000 16.550 3.100 2.950 1.000; >1.000 1.000 17.300 3.450 2.700 1.000; >1.000 0.000 16.940 3.000 2.200 1.000; >1.000 1.000 16.550 2.700 2.850 0.000; >1.000 0.000 17.170 3.000 2.900 1.000; >1.000 0.000 17.150 2.800 2.450 0.000; >1.000 0.000 16.650 3.100 1.900 0.500; >1.000 0.000 16.070 2.700 2.900 1.000; >1.000 1.000 16.720 1.800 1.450 1.000; >1.000 0.000 16.150 2.900 1.000 0.000; >1.000 1.000 16.120 2.400 2.200 1.000; >1.000 1.000 17.540 2.600 2.600 0.000; >1.000 1.000 16.840 2.900 1.100 0.000; >1.000 1.000 15.790 3.100 1.600 1.000; >1.000 1.000 16.430 2.800 1.500 0.000; >1.000 0.000 16.390 3.300 2.700 1.000; >1.000 0.000 16.480 3.350 3.000 0.000; >1.000 1.000 16.930 3.000 1.000 0.000; >1.000 1.000 15.550 2.200 2.600 0.000; >1.000 1.000 17.080 2.900 1.500 0.000; >1.000 0.000 16.850 2.500 2.200 0.500; >1.000 1.000 16.700 2.200 1.800 0.000; >1.000 1.000 15.930 2.600 2.000 1.000; >1.000 1.000 16.080 2.600 1.200 0.500; >1.000 0.000 16.130 3.150 1.400 1.000; >1.000 1.000 16.250 3.100 1.400 1.000; >1.000 0.000 16.040 3.250 3.200 1.000; >1.000 0.000 16.040 3.500 2.900 1.000; >1.000 0.000 16.070 1.400 1.000 1.000; >1.000 0.000 16.550 3.200 2.300 1.000; >1.000 0.000 16.120 2.800 2.000 0.500; >1.000 1.000 16.450 3.150 1.400 1.000; >1.000 0.000 15.910 3.400 1.600 1.000; >1.000 1.000 15.700 3.000 2.400 1.000; > >Best, >Lucy Lurie (she/her/hers) >Doctoral Student, Clinical Psychology >Department of Psychology and Neuroscience >University of North Carolina at Chapel Hill >CIRCLE >Lab<https://secure-web.cisco.com/18i_Rf4fzTTcqPA2OQAm3_CnM6qhNKl6D-xG6RO1PJGAuL… >e-web.cisco.com> >

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mri_glmfit with pvr
by stdp82＠virgilio.it 10 Jun '21

10 Jun '21

External Email - Use Caution Thanks If I have 4 groups GroupDescriptorFile 1 Title XXX Class G1 Class G2 Class G3 Class G4 Input subj1 G1 Input subj2 G3 Input subj3 G2 Input subj4 G2 Input subj5 G4 .... Are the contrasts below corrected? G1_only_thick 1 0 0 0 G2_only_thick 1 0 0 0 G3_only_thick 1 0 0 0 G4_only_thick 1 0 0 0 G1+G2-G3+G4_thick 0.5 0.5 -0.5 -0.5 G3+G4+G2+G1_thick -0.5 -0.5 0.5 0.5 G1+G2+G3+G4_thick 0.25 0.25 0.25 0.25 Thanks Stefano Yes, you use a "per-vertex map" (--pvr option to mri_glmfit). See, example, this thread https://secure-web.cisco.com/1951sWOE8h4m5NbLCNqMyCAH8IOXE-lQF7pVtK2O9WlGr4… 6/3/2021 10:22 AM, std...(a)virgilio.it mailto:std...@virgilio.it wrote: > External Email - Use Caution Hi, how can I perform vertex by vertex (surface) analysis of covariance between functional connectivity data (FS-FAST) and cortical thickness, regressing out the effect of groups?My mean concern is how buid the fsgd file. Stefano > Great news, thank you, Doug! Best, aga On 8/3/11 5:02 PM, Douglas N Greve mailto:gr...@nmr.mgh.harvard.edu wrote: >Hi Aga, what you have done is correct, no need to include the pvr in the >fsgd. >doug > >Burzynska, Aga wrote: >> Dear all, >> I am trying to make group level analysis of functional data on the >>surface and add per-vertex regressors (PVR, here: cortical thickness) >>into the design. When I view the results I have the feeling that the PVR >>is not really included in the model: >> >> I am using the command: >> mri_glmfit --glmdir lh_output --y cope1_lh_4D.mgh --fsgd >>Group1versusGroup2.fsgd --pvr lh.thickness.10.mgh --C >>Group1only_thickness.mat --C Group2only_thickness.mat --C >>Group1minusGroup2_thickness.mat --C Group2minusGroup1_thickness.mat --C >>Group1plusGroup2_thickness.mat >> >> where >> cope1_lh_4D.mgh contains the concatenated sig.mgh images from the fixed >>level analysis (combining the runs) for each participant >> fsgd file contains: >> GroupDescriptorFile 1 >> Title Group1versusGroup2 >> Class Group1 >> Class Group2 >> Input 1109 Group1 >> Input 1110 Group1 >> Input 1111 Group1 >> Input 1112 Group1 >> ... >> Input 2280 Group2 >> Input 2282 Group2 >> Input 2283 Group2 >> Input 2284 Group2 >> >> The PVR is a file containing thickness maps for each participant, >>concatenated in the same order as for the functional data. >> >> So there are 2 main regressors (1 factor, 2 levels), but the contrast >>files contain 3 regressors (the third one is the PVE), for instance: >> Group1minusGroup2_thickness.mat contains 1 -1 0. >> >> Does it look correct? >> Should the pvr regressor be included in the fsdg file? How can I do it? >> >> Thank you very much for your help, >> Cheers, >> Aga >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1j7gX2AgIkSf91OBjYTSReZHX2EetZX7rsmwgY8OFEwb24… >> >> >> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center gr...(a)nmr.mgh.harvard.edu">>gr...(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: http://secure-web.cisco.com/1sv09XhDGpKH6GdjRo4NvJdoe1IvIDCTTvOgKXpkc6HwNAe… > > > >The information in this e-mail is intended only for the person to whom it >is >addressed. If you believe this e-mail was sent to you in error and the >e-mail >contains patient information, please contact the Partners Compliance >HelpLine at >http://secure-web.cisco.com/1bbniyuMe8EtHxhuwD0Cs4Y_OMwvdqAfwIF9xlQeUUwPtbb… . If the e-mail was sent to you in >error >but does not contain patient information, please contact the sender and >properly >dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1j7gX2AgIkSf91OBjYTSReZHX2EetZX7rsmwgY8OFEwb24…

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Re: [Freesurfer] mri_hippocampal-subfields error: MATLAB exited for no reason (Iglesias Gonzalez, Juan E.) Re: Freesurfer Digest, Vol 208, Issue 17
by 林鈺庭 10 Jun '21

10 Jun '21

External Email - Use Caution Dear Developer and Eugenio, Thank you for the suggestion! I tried to cd into FreeSurfer root or the specific folder which contains the data (i.e., /usr/local/freesurfer/subjects/S013 or /usr/local/freesurfer/subjects), and also tried to make the optional argument to override the subjects directory (i.e., /usr/local/freesurfer/subjects/S013 or /usr/local/freesurfer/subjects) However, even doing so, there's still no .txt file to be written since couldn't find it in any of the folders. ( we applied the 'find' command, too) Could you way in any more suggestions? Thank you in advance! Here're the terminal commands: *[root@d7d0454589af S013]# quantifyHAsubregions.sh hippoSf T1 results013.txtGathering results from subjects in: /usr/local/freesurfer/subjectsUsing the prefix name: hippoSfUsing the suffix name: T1And writing them to: results013.txt[root@d7d0454589af S013]# cd ..[root@d7d0454589af subjects]# ls -ltotal 12316-rw-rw-r-- 1 root root 1512 Jul 23 2020 READMEdrwx--S--- 11 root root 4096 Jun 7 06:32 S013drwxrwsr-x 6 root root 4096 Nov 11 2008 V1_averagedrwxrwsr-x 10 root root 4096 Jul 23 2020 bertdrwxrwsr-x 12 root root 4096 Mar 13 2012 cvs_avg35drwxrwsr-x 13 root root 4096 Apr 14 2015 cvs_avg35_inMNI152drwxrwsr-x 8 root root 4096 Nov 13 2015 fsaveragedrwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage3drwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage4drwxrwsr-x 8 root root 4096 May 31 2011 fsaverage5drwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage6drwxrwsr-x 12 root root 4096 Aug 20 2012 fsaverage_symdrwxrwsr-x 6 root root 4096 Mar 30 2010 lh.EC_averagedrwxrwsr-x 6 root root 4096 Mar 30 2010 rh.EC_average-rw-rw-r-- 1 root root 6280209 Jul 23 2020 sample-001.mgz-rw-rw-r-- 1 root root 6269785 Jul 23 2020 sample-002.mgz[root@d7d0454589af subjects]# cd S013[root@d7d0454589af S013]# quantifyHAsubregions.sh hippoSf T1 results013.txt /usr/local/freesurfer/subjects/S013Gathering results from subjects in: /usr/local/freesurfer/subjects/S013Using the prefix name: hippoSfUsing the suffix name: T1And writing them to: results013.txt[root@d7d0454589af S013]# cd ..[root@d7d0454589af subjects]# ls -ltotal 12316-rw-rw-r-- 1 root root 1512 Jul 23 2020 READMEdrwx--S--- 11 root root 4096 Jun 7 06:32 S013drwxrwsr-x 6 root root 4096 Nov 11 2008 V1_averagedrwxrwsr-x 10 root root 4096 Jul 23 2020 bertdrwxrwsr-x 12 root root 4096 Mar 13 2012 cvs_avg35drwxrwsr-x 13 root root 4096 Apr 14 2015 cvs_avg35_inMNI152drwxrwsr-x 8 root root 4096 Nov 13 2015 fsaveragedrwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage3drwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage4drwxrwsr-x 8 root root 4096 May 31 2011 fsaverage5drwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage6drwxrwsr-x 12 root root 4096 Aug 20 2012 fsaverage_symdrwxrwsr-x 6 root root 4096 Mar 30 2010 lh.EC_averagedrwxrwsr-x 6 root root 4096 Mar 30 2010 rh.EC_average-rw-rw-r-- 1 root root 6280209 Jul 23 2020 sample-001.mgz-rw-rw-r-- 1 root root 6269785 Jul 23 2020 sample-002.mgz[root@d7d0454589af subjects]# quantifyHAsubregions.sh hippoSf T1 results013.txtGathering results from subjects in: /usr/local/freesurfer/subjectsUsing the prefix name: hippoSfUsing the suffix name: T1And writing them to: results013.txt[root@d7d0454589af subjects]# ls -ltotal 12316-rw-rw-r-- 1 root root 1512 Jul 23 2020 READMEdrwx--S--- 11 root root 4096 Jun 7 06:32 S013drwxrwsr-x 6 root root 4096 Nov 11 2008 V1_averagedrwxrwsr-x 10 root root 4096 Jul 23 2020 bertdrwxrwsr-x 12 root root 4096 Mar 13 2012 cvs_avg35drwxrwsr-x 13 root root 4096 Apr 14 2015 cvs_avg35_inMNI152drwxrwsr-x 8 root root 4096 Nov 13 2015 fsaveragedrwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage3drwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage4drwxrwsr-x 8 root root 4096 May 31 2011 fsaverage5drwxrwsr-x 8 root root 4096 Sep 22 2009 fsaverage6drwxrwsr-x 12 root root 4096 Aug 20 2012 fsaverage_symdrwxrwsr-x 6 root root 4096 Mar 30 2010 lh.EC_averagedrwxrwsr-x 6 root root 4096 Mar 30 2010 rh.EC_average-rw-rw-r-- 1 root root 6280209 Jul 23 2020 sample-001.mgz-rw-rw-r-- 1 root root 6269785 Jul 23 2020 sample-002.mgz* Best regards, Josephine

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Fw: Problem when using freesurfer
by Yuqian Chen 09 Jun '21

09 Jun '21

External Email - Use Caution Dear Sir or Madam, Hope you are doing well! Thank you very much for your contribution to the freesurfer software which offers great help to research in the neuroimaging area. However, I met a problem when using it and I hope you can help me with it. The freesurfer version I use is freesurfer-linux-centos7_x86_64-7.1.1.tar.gz. I hope to implement AnatomiCuts with my own data which is tractography data (.vtk) reconstructed from HCP dataset with ukf tractography method. When I tried to run the dmri_AnatomiCuts command (the complete command is: dmri_AnatomiCuts -s wmparc.nii.gz -f 100307_ukf_pp.vtk -c 100 -n 14 -e 50 -o output -d s), the following messages appears: ups ups ups ups ups ups ... queue emplace 3894 queue emplace 0 It seems that the algorithm is running. But it just stays here and I cannot get the final results even with input data of only 100 fibers divided into 2 clusters. I am really confused what is going on here. Are there any special requirements for the input data? Your help will be greatly appreciated. Regards, Yuqian

1 0

Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"
by Chester Kang 09 Jun '21

09 Jun '21

External Email - Use Caution Hello FreeSurfer Developers, I am trying to run subfield segmentation of the hippocampus using Freesurfer v7.1.0. Recon-all has been previously run on all subjects, however with a different version of Freesurfer (v5.3.0). Getting the error(s): "No such file or directory" and on further investigation "dyld: Library not loaded: @rpath/libmwlaunchermain.dylib" I've searched the archive but could not find a solution. Could someone please help? Below are details of the system and unsuccessful troubleshooting attempts. Regards, Chester FreeSurfer version: 7.1.0 Platform: Mac OS 10.13.3 hippocampal-subfields-T1.log is below: Things that have been checked/tried or troubleshooting attempted: - SIP protection is disabled (csrutil status shows "disabled") - Checked that there are files and correct permissions in the "lib/gcc/lib" and the "MCRv84" folders - tried to unset DYLD_LIBRARY_PATH (in the SetUpFreeSurfer.sh) - checked the DYLD_LIBRARY_PATH value and run a step directly (both with "" empty value and the values below) $ echo $DYLD_LIBRARY_PATH .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib $ /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML dyld: Library not loaded: @rpath/libmwlaunchermain.dylib Referenced from: /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML Reason: image not found Abort trap: 6 === hippocampal-subfields-T1.log === "... ------------------------------ USER chester HOST selma.nnf.unimelb.edu.au PROCESSID 17656 PROCESSOR x86_64 OS Darwin ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64 ------------------------------ freesurfer-darwin-macOS-7.1.0-20200511-813297b setenv SUBJECTS_DIR /data/netapp02/work/chester/global_pass_all cd /data/netapp02/work/chester/global_pass_all /Applications/freesurfer_v7.1.0/bin/segmentHA_T1.sh 1002310 #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Tue 8 Jun 2021 15:25:15 AEST ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/freesurfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib /Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: No such file or directory Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue Dec 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64 T1 hippocampal subfields exited with ERRORS at Tue 8 Jun 2021 15:25:16 AEST ..."

2 1

recon-all errors
by Mark Wagshul 09 Jun '21

09 Jun '21

External Email - Use Caution Hi. I'm trying to run recon-all, with T1 and FLAIR images and running into errors, which seem to be associated with the FLAIR refinement of the pial surface. recon-all -s 2019-10049-045-SP -FLAIR 2019-10049-045-SP/VISIT_1/RAW/105_3D_FLAIR_SAGBrain.nii.gz -FLAIRpial -all 1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) cat /proc/version: Linux version 2.6.32-696.6.3.el6.694g0000.x86_64 (root(a)-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) ) #1 SMP Wed Jul 12 02:19:57 UTC 2017 3) uname -a: Linux loginnode2 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log attached Thanks! Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.org<mailto:mark.wagshul@einsteinmed.org> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

2 7

Re: [Freesurfer] 'help: aparcstats2table'
by Nolan, Jackson 08 Jun '21

08 Jun '21

Hello again, Thank you for sending the screenshot and additional information. It looks like your directory structure is correct. It also looks like you are correct about the python version causing your error. That utility is written in Python 2.7, and it appears that your environment is sourcing some version of Python 3. (You can confirm this by running the command 'python --version' in your terminal). You need to check that you have a version of Python2.7 installed, and then add that to your path. To check that you have a version of Python2.7: run the command 'which python2'. If a version of Python2.7 is installed, the path to it will be printed in the terminal. If no version of is found, you will need to install one. To source that python version (add it to your path): run 'export PATH="</path/to/python2.7/>":$PATH' Best, Jackson ________________________________ From: Zeynep Boz <zeynep.boz(a)omu.edu.tr> Sent: Friday, June 4, 2021 2:00 PM To: Nolan, Jackson <JNOLAN5(a)mgh.harvard.edu> Subject: Re: 'help: aparcstats2table' External Email - Use Caution Dear Jackson, I run these commands "FreesurferWork on my computer" in the directory containing that subject. My subject is H1_deneme in named directory FreesurferWork According to the comments I read, I think this error may be related to the phyton version, but of course you know better. Attached I am sending you a screenshot of the terminal and the folders with the file directories. Thank you for your support I wish you good work Dr. Zeynep YÜKSEL Ondokuz Mayis University Vocational School of Health Services, Medical İmaging 55139, Atakum, Samsun, Turkey Tel: +903623121919 Ext:5261 ________________________________ Kimden: "Nolan, Jackson" <JNOLAN5(a)mgh.harvard.edu> Kime: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu>, "zeynep boz" <zeynep.boz(a)omu.edu.tr> Gönderilenler: 2 Haziran Çarşamba 2021 23:20:11 Konu: Re: 'help: aparcstats2table' Hello Dr. Zeynep, Are you running those commands in the directory containing that subject? The script needs the file path to the subject, and absolute paths tend to work better than relative paths. If you have specified these are still getting those errors, please send your full terminal output with the command run and all error messages. Best, Jackson ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Zeynep Boz <zeynep.boz(a)omu.edu.tr> Sent: Saturday, May 29, 2021 3:15 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] 'help: aparcstats2table' External Email - Use Caution Hello, I am using Ubuntu 18.05 version and Freesurfer6 version. I've completed all the recon-all parts without any problems, but I'm having trouble with the "aparcstats2table" part. The command "aparcstats2table --subject H1_deneme --hemi lh --meas thickness --tablefile lh.thicknes.xlsx" gives the following error: File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' On the command "asegstats2table --subjects H1_deneme H1 --common-segs --meas volume --stats = aseg.stats --table = segstats.txt" gives the following error: File "/usr/local/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' Thank you in advance for your support Dr.Zeynep YÜKSEL Ondokuz Mayis University Vocational School of Health Services, Medical İmaging 55139, Atakum, Samsun, Turkey Tel: +903623121919 Ext:5261 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

1 0

Streaks of random colors when opening segmented files
by Ken Takeoka 08 Jun '21

08 Jun '21

External Email - Use Caution Dear FreeSurfer Developers, I currently use FreeSurfer to segment fetal brain MRIs, but I keep encountering this issue: sometimes when I open freeview and load the volumes, there appears streaks of gray with the “Grayscale” setting, and then with the “LookUp Table” setting there are streaks of color below or above the head. These colors are random, and too many to manually erase by hand. I have tried using the “Replace label” function to change these colors to 0, but that has not always worked or took way too long. I wonder what the issue here may be? Could it be the process of opening the file, closing the file after I’m finished, or some error within the system itself? As of now, I am taking measures by creating and saving backup copies (as files these streaks would not be useful for volumetric analysis), but it would be helpful to know the potential causes and steps to resolve/prevent the issue. 1. Freesurfer version: freesurfer-linux-centos7_x86_64-7.1.0-2020511-813297b 2. Platform: Using VirtualBox on Windows 10 (following these instructions: https://secure-web.cisco.com/198hW-Y_5CqOaKNqjYM3bPRnMVo3rBeETnC_0DhCJ_55_S…) I think Ubuntu 18. 3. I have trouble finding the log file within my files, but I hope that is okay since I have not really done much coding except opening freeview, changing directories, and renaming files. I am not sure if this is related, but I always see this error message when starting up Ubuntu (see image below): [drm:vmw_host_log [vmwgfx]] *ERROR* Failed to send host log message 4. Images description: Streaks of color on grayscale and also on LookUp Table. The “Show existing labels” column also includes labels I have not touched at all. Sincerely, Ken Takeoka

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