Freesurfer June 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
140 discussions

nalysis of covariance between functional connectivity data (FS-FAST) and cortical thickness
by stdp82＠virgilio.it 04 Jun '21

04 Jun '21

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

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A problem about Freesurfer
by 胡俊涛 04 Jun '21

04 Jun '21

External Email - Use Caution Can I use Freesurfer to process MRI image data of mice? Thank you!

2 1

freesurfer-7.1.1-centos8.rpm :: problems
by Eric Deveaud 04 Jun '21

04 Jun '21

External Email - Use Caution Hello, I installed freesurfer-7.11 from centos8 rpm on stock docker centos8 image: there is some problems // misses with this installation 1) some scripts are python and uses /usr/bin/env python which is not available by default on centos8 currently freesurfer rpm specfile should have a dependency to python2, and associated python required modules, ie: dipy graph_tools holoviews plotly statsmodels pyyaml in that case, following files sheebang should be modified slicedelay dsh mcparams2reg rca-config2csh shebang should be /usr/bin/env python2 instead of /usr/bin/env python other solution will be to port those scripts to python3 and use fspython 2) some scripts are tclsh ones but no tclsh installed. eg unpackimadir2, unpacksdcmdir. fsgfget please add tcl rpm dependency to rpm specfile 3) tools depending on MRC matlab runtime segmentSubjectT2_autoEstimateAlveusML segmentSubjectT1_autoEstimateAlveusML segmentSubject segmentSubjectT1T2_autoEstimateAlveusML SegmentThalamicNuclei SegmentSubfieldsT1Longitudinal irepifitvol.glnx64 and fs_spmreg.glnxa64 are linked versus libmwmclmcrrt.so.8.3 which is not provided by mcr runtime R2014b but version 8.4 is. and by the way libncurses-devel is required as rpm dependency 4) some tools uses commands that are not available show_tal, tal_compare uses mri_show which is not avaialble 5) qdec tcl have invalid environement configuration Singularity> qdec Tcl_Init error: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 /usr/local/freesurfer/7.1.1-1/lib/tcl8.4 /usr/local/freesurfer/lib/tcl8.4 /usr/local/freesurfer/7.1.1-1/library /usr/local/freesurfer/library /usr/local/freesurfer/tcl8.4.6/library /usr/local/tcl8.4.6/library /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 you may want to add $FREESURFER_HOME/lib/tktools/tcl8.4 to TCL_LIBRARY regards Eric

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Re: [Freesurfer] mri_hippocampal-subfields error: MATLAB exited for no reason (Iglesias Gonzalez, Juan E.)
by 林鈺庭 04 Jun '21

04 Jun '21

External Email - Use Caution Dear Eugenio, Yes, it happened to each subjects. Therefore, we'd contacted MATLAB tech support, and fix the problem. (turns out it resulted from the incompatibility of MATLAB R2014b and macOS Big Sur 11. We now construct the Docker container on Mac to build the Linux system to run the module) However it came up with new error: *Making Unknown map to reduced label 13Computing hyperparameters for estimation of Gaussian parametersEstimating typical intensities of alveusError using ksdensity>parse_args (line 162)X must be a non-empty vector.Error in ksdensity (line 114)Error in segmentSubjectT1_autoEstimateAlveusML (line 969)stats:ksdensity:VectorRequired1Linux 2981d0ea233a 5.10.25-linuxkit #1 SMP Tue Mar 23 09:27:39 UTC 2021 x86_64 x86_64 x86_64 GNU/LinuxT1 hippocampal subfields exited with ERRORS at Fri Jun 4 07:26:27 UTC 2021For more details, see the log file /data/S013/scripts/hippocampal-subfields-T1.log* I've attached hippocampal-subfields-T1.log here. We're truly grateful! Best regards, Josephine <freesurfer-request(a)nmr.mgh.harvard.edu> 於 2021年5月29日週六下午3:26寫道： > 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/1MoS_SoUN2CuP9nhdPAApUJCj-XIvBHefNefy9g33Njlps… > 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: mri_hippocampal-subfields error: MATLAB exited for no > reason (Iglesias Gonzalez, Juan E.) (Iglesias Gonzalez, Juan E.) > 2. Re: Hippocampal Subfield error (Daniel Davidson Callow) > 3. Re: Hippocampal Subfield error (Iglesias Gonzalez, Juan E.) > 4. Re: Hippocampal Subfield error (Daniel Davidson Callow) > 5. mri_glmfit-sim with grf (ERROR: need --csd with --csd-out) > (Di?genes Bispo) > 6. Group comparison with MD (Antti Cajanus) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 28 May 2021 19:29:14 +0000 > From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] mri_hippocampal-subfields error: MATLAB > exited for no reason (Iglesias Gonzalez, Juan E.) > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <7A66B3DD-56D6-4754-B9B5-84A215B1F480(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Multiple subjects or all of them? > > Juan Eugenio Iglesias > Senior research fellow > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > http://secure-web.cisco.com/1pE3k87UhoxvKjc11wQZjMDTYqKuASKmhlXVprr_YosR6_6… > > > On May 28, 2021, at 12:26, ??? <ytlin923(a)g.ntu.edu.tw> wrote: > > > > External Email - Use Caution > > > > Dear Dear FreeSurfer Developers, > > > > (We?re the message 3) > > This happened to multiple subjects. Our computer got 16GB MHz DDR4 , We > thought it met the requirements to run the module based on the > documentation on freesurfer wiki , or didn?t it? :( > > > > > > Best regards, > > Josephine > > > >> freesurfer-request(a)nmr.mgh.harvard.edu ? 2021?5?29? ??12:03 ??? > >> 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/19MxmZ-YngtXyjI8JhMif3nT9Tvss_ZmhVPTJcv7XmEmCX… > >> 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. (no subject) (Daniel Davidson Callow) > >> 2. Hippocampal Subfield error (Daniel Davidson Callow) > >> 3. Re: mri_hippocampal-subfields error: MATLAB existed for no > >> reason (Iglesias Gonzalez, Juan E.) > >> 4. Re: Choosing projfrac/projdist and checking mri_vol2surf > >> output (M Pope) > >> 5. Re: Hippocampal Subfield error (Iglesias Gonzalez, Juan E.) > >> 6. PVC to calculate myelin maps (Marina Fern?ndez) > >> 7. Re: PVC to calculate myelin maps (Glasser, Matthew) > >> 8. PVC to calculate myelin maps (Marina Fern?ndez) > >> 9. Re: PVC to calculate myelin maps (Glasser, Matthew) > >> 10. (no subject) (Francisca Ferreira) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Fri, 28 May 2021 07:52:44 -0400 > >> From: Daniel Davidson Callow <dcallow(a)umd.edu> > >> Subject: [Freesurfer] (no subject) > >> To: freesurfer(a)nmr.mgh.harvard.edu > >> Message-ID: > >> <CAFMVdsfJ9Scx1sQ+CC6BMobLtKQT6501=vTR9KKxVA4OB_rOxg(a)mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> External Email - Use Caution > >> > >> Hello, > >> > >> I am running into errors when running > >> > >> segmentHA_T2.sh ${subj} > >> /data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1 > >> > >> Approximately 10% of my subjects are being processed but for some > reason, > >> the majority fail to execute. Here is an output from the error log. > >> ------------------------------ > >> USER dcallow > >> HOST compute-4-32.bswift.umd.edu > >> < > http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzV… > > > >> PROCESSID 4033 > >> PROCESSOR x86_64 > >> OS Linux > >> Linux compute-4-32.bswift.umd.edu > >> < > http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzV… > > > >> 2.6.32-754.35.1.el6.x86_64 > >> #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux > >> ------------------------------ > >> > >> #-------------------------------------------- > >> #@# Hippocampal Subfields processing (T1+T2) left Thu May 27 21:39:51 > EDT > >> 2021 > >> ------------------------------------------ > >> Setting up environment variables > >> --- > >> INFO: error loading libraries in default configuration, trying with MCR > >> libraries only > >> LD_LIBRARY_PATH is > >> > .:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//runtime/glnxa64:/data/bswift-0/software/freesurfer/7.1.0-1//MCRv84//bin/glnxa64:/data/bswift-0$Registering > >> norm.mgz to additional volume > >> makeIsotropic WARNING: not different enough, won't reslice! > >> No more processes. > >> ERROR: could not open > >> > /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh > >> for reading > >> ERROR: loading > >> > /data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh > >> as MGH > >> Warning: File > >> > '/data/bswift-1/dcallow/aging/freesurfer/HCA8537992_V1_MR/tmp/hippoSF_T1T2_v21_T2_left/23207174_T2resampledLikeT1__353506.mgh' > >> not found. > >> [^H> In myMRIread at 64 > >> In segmentSubjectT1T2_autoEstimateAlveusML at 207]^H > >> Attempt to reference field of non-structure array. > >> > >> Error in segmentSubjectT1T2_autoEstimateAlveusML (line 211) > >> > >> > >> > >> MATLAB:nonStrucReference > >> @#@FSTIME 2021:05:27:21:39:51 > >> run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 e 334.41 S 1.15 U > 8.61 > >> P 2% M 818424 F 0 R 185834 W 0 c 2541 w 20306 I 0 O 216480 L > $@#@FSLOADPOST > >> 2021:05:27:21:45:25 run_segmentSubjectT1T2_autoEstimateAlveusML.sh N 17 > >> 31.22 29.74 28.95 > >> Linux compute-4-32.bswift.umd.edu > >> < > http://secure-web.cisco.com/1ypL43FxiKSZvppDyGttq1kG6jN0GRt9e8cgB2S5Z-8zCzV… > > > >> 2.6.32-754.35.1.el6.x86_64 > >> #1 SMP Wed Sep 16 06:48:01 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux > >> > >> T2 hippocampal subfields exited with ERRORS at Thu May 27 21:45:25 EDT > 2021 > >> > >> I am also getting a matlab_crash_dump file > >> > >> ------------------------------------------------------------------------ > >> Segmentation violation detected at Thu May 27 21:51:52 2021 > >> ------------------------------------------------------------------------ > >> > >> Configuration: > >> Crash Decoding : Disabled > >> Current Visual : None > >> Default Encoding : US-ASCII > >> GNU C Library : 2.12 stable > >> MATLAB Architecture: glnxa64 > >> MATLAB Root : /export/rel60_shadow/ > >> glue.umd.edu/software/matlab/2014b/Linux > >> MATLAB Version : 8.4.0.150421 (R2014b) > >> Operating System : Linux 2.6.32-754.30.2.el6.x86_64 #1 SMP Fri May 29 > >> 04:45:43 EDT 2020 x86_64 > >> Processor ID : x86 Family 6 Model 62 Stepping 4, GenuineIntel > >> Software OpenGL : 0 > >> Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java > >> HotSpot(TM) 64-Bit Server VM mixed mode > >> Window System : No active display > >> > >> Fault Count: 1 > >> > >> > >> Abnormal termination: > >> Segmentation violation > >> > >> Stack Trace (from fault): > >> [ 0] 0x00007f2b30f06213 > >> /lib64/libpthread.so.0+00033299 pthread_join+00000035 > >> [ 1] 0x00007f2a9f4d847d > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 2] 0x00007f2a9f4d8cac > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 3] 0x00007f2a9f5cae63 > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 4] 0x00007f2a9f5af896 > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 5] 0x00007f2a9f5a6b8d > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 6] 0x00007f2a9f5a6fd0 > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 7] 0x00007f2a9f5aad00 > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 8] 0x00007f2a9f5a5c3c > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 9] 0x00007f2a9f44fb03 > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 10] 0x00007f2a9f42b9cc > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 11] 0x00007f2a9f42b132 > >> > /tmp/MCR_1785852174/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlGEMSMatlab.mexa64+0$[ > >> 12] 0x00007f2b21dcfc0a /export/rel60_shadow/ > >> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00150538 > >> mexRunMexFile+00000090 > >> [ 13] 0x00007f2b21dcc5c4 /export/rel60_shadow/ > >> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00136644 > >> [ 14] 0x00007f2b21dcd414 /export/rel60_shadow/ > >> glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmex.so+00140308 > >> [ 15] 0x00007f2b232ff329 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+0… > >> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 16] 0x00007f2b2260fb70 > >> /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 17] 0x00007f2b225bfe02 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 18] 0x00007f2b225c2022 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 19] 0x00007f2b225c7f87 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 20] 0x00007f2b225c36ff /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 21] 0x00007f2b225c4334 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 22] 0x00007f2b2263952e /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 23] 0x00007f2b232ff329 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+0… > >> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 24] 0x00007f2b2260fb70 > >> /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 25] 0x00007f2b225bfe02 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 26] 0x00007f2b225c2022 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 27] 0x00007f2b225c7f87 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 28] 0x00007f2b225c36ff /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 29] 0x00007f2b225c4334 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 30] 0x00007f2b2263952e /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 31] 0x00007f2b232ff329 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_dispatcher.so+0… > >> _ZN8Mfh_file11dispatch_fhEiPP11mxArray$[ 32] 0x00007f2b225ecbf0 > >> /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 33] 0x00007f2b225ec449 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> [ 34] 0x00007f2b2252ffd6 /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> inCallFcnWithTrap+00000086 > >> [ 35] 0x00007f2b225b3c0b /export/rel60_shadow/ > >> > glue.umd.edu/software/matlab/2014b/Linux/bin/glnxa64/libmwm_interpreter.so+… > >> > >> This error was detected while a MEX-file was running. If the MEX-file > >> is not an official MathWorks function, please examine its source code > >> for errors. Please consult the External Interfaces Guide for information > >> on debugging MEX-files. > >> > >> If this problem is reproducible, please submit a Service Request via: > >> > http://secure-web.cisco.com/1lsmxJ1l6wT0WmnW3q7zuS6JngCO6upWHYdXR6E3TNhC0oD… > >> > >> A technical support engineer might contact you with further information. > >> > >> Any insight or help you can provide is greatly appreciated. > >> *Daniel Callow* > >> *PhD Student, Neuroscience and Cognitive Science* > >> Exercise for Brain Health Lab > >> University of Maryland, College Park > >> dcallow(a)umd.edu <dcallow(a)gmail.com> > >> 443-254-6298 > >>

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Cortical Thickness Measures for MTL
by Kidwai, Ambereen 03 Jun '21

03 Jun '21

External Email - Use Caution Hello, I have been manually tracing the entorhinal cortex, dividing it into the antero-lateral entorhinal and posterior-medial entorhinal cortex. I am looking for a way to get cortical thickness measures for this region. I have a few questions relating to this: 1. Is it possible to import my manually traced labels (traced in ITK-snap) into freesurfer and then get the thickness measures for these labels? 2. Is it possible to edit the aparc or aseg in order to divide the entorhinal cortex into the two regions that I am delineating? 3. If neither of the above options are possible, is there any other way to get cortical thickness measures for manual segmentation of this region? I appreciate any help or insight you can give me. Best regards, Amber Kidwai Research Assistant Functional Neuroimaging of Memory Laboratory Center for Vital Longevity | University of Texas at Dallas 1600 Viceroy Drive Suite 800 Dallas, TX 75235 Cell: (214) 675 3612 [Description: Description: CVL_logo] ____________________________________________________________________

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Tracula registration failure
by Marena Manierka 03 Jun '21

03 Jun '21

External Email - Use Caution To the Tracula team: I am attempting to complete my first project using the Tracula pipeline on a mixed dataset of autism, schizophrenia, and control adult brains. I ran the tracula prep, bedp and path steps for the autistic subject in question without receiving any error messages. However, when I attempt to view the registration of the FA.bbr.nii.gz image to the MNI brain the registered image appears as a completely white, roughly brain-shaped mask. This has not occurred with other subjects from the dataset. I have attached a screenshot from freeview for reference. When I load the subject's dtifit_FA.nii.gz in freeview it appears to be relatively normal. Is this a fatal error in the registration process, and is there any way to correct it? I have also attached the log file for the subject in case this is helpful. Thank you for your help, Marena -- Marena Manierka, B.Sc Graduate Student, Integrative Program in Neuroscience Department of Psychology, MSS 414/ MS0296 University of Nevada, Reno marena.manierka(a)gmail.com

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Recon-all running on a loop
by DIANA ORTEGA CRUZ 03 Jun '21

03 Jun '21

External Email - Use Caution Dear FreeSurfer team, My name is Diana Ortega, I am a Neuroscience PhD student at Universidad Politécnica of Madrid. I run a job to compute recon-all in parallel for 30 subjects remotely on a supercomputer at my research institution. This job finished due to timeout, and all subjects but one finished without errors. However, one of the subjects was not finished and it appears as if it was stuck on a loop. Its recon-all.log is constantly adding new lines (the file is 20GB in size), and from *recon-all-status.log* it appears to be stuck in the "Fix Topology" step. Have you ever encountered a similar situation? Would you know why this could have occurred? Here are the details: FreeSurfer version: 7.1.1-centos8_x86_64 Operative System: CentOS8 Hardware: Supercomputer - 68 nodes of Lenovo ThinkSystem SD530 <https://secure-web.cisco.com/1Bch1AH1AvTKzQqcdunZ0FIqTIHtdhvL6XMYZuyZxpRjtV…> Line run for that subject: recon-all -subjid NoUMA0233 -i filepath.nii -all -qcache -parallel -openmp 16 When opening *recon-all.log*, it keeps adding the following lines: Remesher::removeTria( 240873 ) Remesher::removeTria( 240876 ) NEXTIDX : 88755 Remesher::removeCollapsedTrias( 88755 , 120326 ) v_to_t[vidx] : Trias are identical : ... removing ... When opening the error.log of the complete job, there are several lines of this error: rm: No match. Any advice will be of great help! Thanks a big lot! Best, Diana Ortega Cruz. PhD Student Laboratory for Clinical Neuroscience Centro de Tecnología Biomédica - Universidad Politécnica de Madrid

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Labels #601-#628
by A.R. Sekar 03 Jun '21

03 Jun '21

External Email - Use Caution Hello Experts, I am trying to isolate ROIs using labels #601-#628 however I am getting the following output and it is the same for each label. Any idea what is wrong here? Thanks for your help! Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol raparc+aseg.nii --outprefix raparc+aseg_labels --L $label 601 Input file: raparc+aseg.nii Output prefix: raparc+aseg_labels mri_convert raparc+aseg.nii raparc+aseg.nii.gz reading from raparc+aseg.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to raparc+aseg.nii.gz... Label of interest: 601 Number of voxels and volume for label 601 is = (0, 0.000000mm^3) mri_binarize --i raparc+aseg.nii.gz --match 601 --o raparc+aseg_labels_label601.mgz 7.1.1 cwd /Users/akilasekar/Desktop/B301001 cmdline mri_binarize --i raparc+aseg.nii.gz --match 601 --o raparc+aseg_labels_label601.mgz sysname Darwin hostname Akilas-MacBook-Air.local machine x86_64 user akilasekar input raparc+aseg.nii.gz frame 0 nErode3d 0 nErode2d 0 output raparc+aseg_labels_label601.mgz Binarizing based on matching values nMatch 1 0 601 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Count: -1 -1.642760 5242880 -0.000019 mri_binarize done Regards, Akila

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freesurfer-7.1.1 :: mcparams2reg is python2 script
by Eric Deveaud 03 Jun '21

03 Jun '21

External Email - Use Caution Hello, While installing freesurfer-7.1.1 for centos via rpm (freesurfer-CentOS8-7.1.1-1.x86_64.rpm) I had the following problem: /usr/local/freesurfer/7.1.1-1/bin/mcparams2reg is a python script that use /usr/bin/env python, not fspython which is 3.6.8 either python2 should added as rpm requirement, either mcparams2reg should ported to python3 regards Eric

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freesurfer-7.1.1 "" anatomiCutsUtils :: missing lzma python module
by Eric Deveaud 03 Jun '21

03 Jun '21

External Email - Use Caution Hello, freesurfer-centos8-7.1.1 rpm installa in singularity container Singularity> anatomiCutsUtils -h /usr/local/freesurfer/7.1.1-1/python/packages/pandas/compat/__init__.py:117: UserWarning: Could not import the lzma module. Your installed Python is incomplete. Attempting to use lzma compression will result in a RuntimeError. warnings.warn(msg) Traceback (most recent call last): File "/usr/local/freesurfer/7.1.1-1/python/scripts/anatomiCutsUtils", line 19, in <module> import graph_tools as gt ModuleNotFoundError: No module named 'graph_tools' regards Eric

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Freesurfer June 2021