Thanks, Chester, that looks good. Am I safely assuming that the Matlab runtime has been installed? Cheers, /Eugenio
> On 10 Jun 2021, at 21:31, Chester Kang <ckk...@unimelb.edu.au> wrote: > > 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-boun...@nmr.mgh.harvard.edu on behalf of > freesurfer-requ...@nmr.mgh.harvard.edu" > <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > >> External email: Please exercise caution >> >> Send Freesurfer mailing list submissions to >> freesurfer@nmr.mgh.harvard.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> >> https://secure-web.cisco.com/11QCqR7prxSgfCTvoUKKRK8tL2ls0hM_Sfukn_muBU55xcSMJPqXDZFUSjeQEc7GUksz7UA7hK4WrhUxAAdArGsQ_H7pjdgMBn9dbETcqUKC4nU357BLPcIjkc7x61EuAFLhIH-woON0i0o50lv4_Cci4otwMIPGJWJ7t4uPBcCf4yg1AOGzFogJh6Sj9cAunjzvngYZNEIiSps-Xk5vW9W1IDWpuAn6GXLsEa5i86eXXjQ_RHgOrIT_tbiKvXCUhNzjxH8YeiTRm-ieQB-UUCg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> .mgh.harvard.edu >> or, via email, send a message with subject or body 'help' to >> freesurfer-requ...@nmr.mgh.harvard.edu >> >> You can reach the person managing the list at >> freesurfer-ow...@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 (std...@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." <jiglesiasgonza...@mgh.harvard.edu> >> Subject: Re: [Freesurfer] Hippocampal Subfields error "no such file or >> directory"/"dyld library not loaded" >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <8419d11c-c916-4249-9983-557a25229...@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_m0IkJHWaqcVYgXiltKvmf2sZt9X-pyYSQmncbstu3rICy2Z7fHggRXk-aKCs7Fr-HTjpj0zQ6tCKLBMJ8qQlxpHWzL3Pl8OR-xTpN-F23znGzhgWE7K9yMHxIKC4JDu_uhiU4UqXswGp7DW6ImpICnIp2rAN9sjKc2johSTK9aRjCmaxJgCb5oKn4sJyy6IbRQBmyVceflyPgKIXagCBaIcBUNYGwHkmdx9RCUleJuy7MjerHcAPxmXS2QZAAA/http%3A%2F%2Fwww.jeiglesias.com >> s.com >> >>> On Jun 9, 2021, at 00:23, Chester Kang <ckk...@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@nmr.mgh.harvard.edu >>> >>> https://secure-web.cisco.com/11QCqR7prxSgfCTvoUKKRK8tL2ls0hM_Sfukn_muBU55xcSMJPqXDZFUSjeQEc7GUksz7UA7hK4WrhUxAAdArGsQ_H7pjdgMBn9dbETcqUKC4nU357BLPcIjkc7x61EuAFLhIH-woON0i0o50lv4_Cci4otwMIPGJWJ7t4uPBcCf4yg1AOGzFogJh6Sj9cAunjzvngYZNEIiSps-Xk5vW9W1IDWpuAn6GXLsEa5i86eXXjQ_RHgOrIT_tbiKvXCUhNzjxH8YeiTRm-ieQB-UUCg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> .mgh.harvard.edu >> >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Wed, 9 Jun 2021 13:09:17 +0000 >> From: "Lurie, Lucy" <llu...@email.unc.edu> >> Subject: [Freesurfer] Ill-Conditioned/Badly Scaled Matrix Error >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <3bcd8ea8-8da7-4a8a-ba82-8b7a4f2d2...@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-xG6RO1PJGAuLnAlN2Qa-m8h9EZGbO9Qo7QPQAiBVNevAoHlY-jf9z7dGHxurd8Oe8uw75EoTaRxQZ_Nl1ObEe1gsWQecXmO42TYy9xWhqpijv4wchCBs6bYGaIXNVDP3iaP_YqG99OQMWqyy3Zhq6_BwSFJYIw_edeT9Drrl9CQKiDWXReHaL-jQ4DUC7cHEyRW7ZG8OXH6a9M8dPLZcaM5Lxb8KEYCKOSgtBx3kUPo_h53ZU-lOQ/https%3A%2F%2Fcirclelab.unc.edu%2F >> e-web.cisco.com> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://secure-web.cisco.com/1hoC_DaHW0UiGr3lCXxXj-F1KZurvy-_5A9AqZmugILd0MQ_-Rmn3dA0aa-g3pMPvDBW74iS5nj2GDK0_xemg0DZgIK5xzLykuKCreeGRxJT1uW5mvsiprmBoVAP-n4l-Olb8WEGTBeKA-WJMgxecL-4AC65oPGSLN_ARRYf9VD56gOmt4ApqKA5dl_LHbNYaiE9M-E-L2xhxzvf7OvKvlwwVzBBq7MqOywKG4_K_rda2nDinCDVJy7zB5dn4CBDideY3i9-gEKJKz9BLwxuMag/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210609%2F59b9b5da%2Fattachment-0001.html. >> mgh.harvard.edu >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: eig_cgORCE_baselineORCE_teenCG.fsgd >> Type: application/octet-stream >> Size: 2848 bytes >> Desc: eig_cgORCE_baselineORCE_teenCG.fsgd >> Url : >> http://secure-web.cisco.com/123waNTw7ZTM74ngUZPaN9Q0HrWvygAfYiCbZuI5_54l-9H2uUkfmuQzPLUsNOSkwvVFU60DaseC3IqqYIGQt4-2gu8rfVujGpd9CZnmfka2QSfmt6ghjPXPEuv7bMhKjGJP4Scgzvw6BrTcY8UaSKkLhhaRTnZe9IngflB3IyfKtWmbHtLu8_kgIjmLXIsnnSwMGCRvjeQpkaYTM15WHJUtdfwJTD740qxPh1qezoW6g_2QDmabWsTNFLn7VhHQbX8517AXMM__dteRugp2k_g/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210609%2F59b9b5da%2Fattachment-0004.obj. >> mgh.harvard.edu >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: eig_cgORCE3042_slope.mtx >> Type: application/octet-stream >> Size: 11 bytes >> Desc: eig_cgORCE3042_slope.mtx >> Url : >> http://secure-web.cisco.com/1TgnsCB7_d5sh4wIKkRBdKTD-ao2LpdL3l7UCvS20A6ozafhxZ05LI5SIsDqMhdARAZoh9Yj--nWV38an446cg1rih9FfzjreJGxnoFGpvZXNNOgcB-PhdgiBne58Og07XtiYqo9IazuXsv2mCzexijH3ISZ8YsS0oEFw3znTtZumMDjUwX7AG_UyPPLCgecCYjmbQcaxY_aBJx48afPwEk0XkYtNZ8T7uN5gWKNWNTX2NnXv-oYb6S84HILQx1v14G_AY0kzkgVwZl42P7ApSw/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210609%2F59b9b5da%2Fattachment-0005.obj. >> mgh.harvard.edu >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: eig_teenCGqual_slope.mtx >> Type: application/octet-stream >> Size: 11 bytes >> Desc: eig_teenCGqual_slope.mtx >> Url : >> http://secure-web.cisco.com/1jlA_1fP2-c_2mD2w3plQMS-BeznYrqE4elzb8nlqnanzymJsTpNIe4ygYJX1KHIirqvFmalhYKlNtbpnZIVBQbmJnEC5L1lmhKHzr_XFI_4kEQl9Xjt9qT5x9YEH8LOeNjPp-wrmAo2tyxVHFWpoIfb5CQrp2LKQrNkI9PgNz3tmzei3XNaasrvsCggX5qEHXYZnXxux629-aA05jLzwSiWbz4oXLAQN42838lzY2liS1PUKNcQz_4reGJHWsdN9pl7p836ccHGkDrlI4MulKQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210609%2F59b9b5da%2Fattachment-0006.obj. >> mgh.harvard.edu >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: eig_cgORCEbaseline_slope.mtx >> Type: application/octet-stream >> Size: 11 bytes >> Desc: eig_cgORCEbaseline_slope.mtx >> Url : >> http://secure-web.cisco.com/1uwJmoZg9I6EyM30DKTVRG64vxfg_5UttbUSnDn5689xXZYE10TZbCFhZyGbys8pTsrYX-E-9VyyovNo8DVBe4C5jNCxzA-L6EK_OYU6mJhPhhbkDvm8aJ227VUFfNZpfZF7aQSaLy50hNeqpT58hRzxNFpIHZ8YfIgRcFXkHxDc9EGKCHvKJ4sMx_Bg3KvmXLgm8bPJD3SxEIZdlzvIeSMdn9b05ux2xEXwMpqyEQEfQ0DyTj3JD02hKcD6suljKJf9i4BjAtgZzVTsV8tOI0A/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210609%2F59b9b5da%2Fattachment-0007.obj. >> mgh.harvard.edu >> >> ------------------------------ >> >> Message: 3 >> Date: Wed, 9 Jun 2021 14:17:22 +0000 >> From: "Del Re, Elisabetta" <elisabetta_de...@hms.harvard.edu> >> Subject: [Freesurfer] LGI FS 7.1 >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Cc: Elisabetta del Re- Harvard <elisabettacde...@gmail.com> >> Message-ID: >> >> <bl0pr07mb4066c7fbfac7ed9625c69db5b3...@bl0pr07mb4066.namprd07.prod.outlo >> ok.com> >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> External Email - Use Caution >> >> Dear FS team, >> what are differences if any between LGI in FS 5.3 and 7.1? >> Thank you so much, >> best wishes, >> Elisabetta >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://secure-web.cisco.com/1thJbv-mQEwPKs_wMJ1yBqdA6x708duSBDyhE0cLwDEq9IN1bkyQMhUtK3bdW-ibxQay-fPXdkHjWAsK8zPdDYmHxT0TW68P0IJ9Wfaa_SUujI5xc7vFAkiTc3NAyXfxJXnbMqUGyEMRv3qLM915RhqCWaReCrnU9nG1JJ54msVtYZWyQ4Ohr78YGDC1mBbNd_FaN4gaZYgjk4zDIHuDk6DPBMYg6_nfhZDFTr1q7QbE281ao-UnQ8LN2KYcF3CkhJ2PRv4472ugwJB0heyWvvA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210609%2Fc561c3d7%2Fattachment-0001.html. >> mgh.harvard.edu >> >> ------------------------------ >> >> Message: 4 >> Date: Wed, 9 Jun 2021 16:38:05 +0200 (CEST) >> From: std...@virgilio.it >> Subject: [Freesurfer] mri_glmfit with pvr >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <1340792404.242762.1623249485...@mail1.virgilio.it> >> Content-Type: text/plain; charset="utf-8" >> >> 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/1AQW2Zmfaui0gjHDqfC-62qKrikS49RYbR7pNeQeTr2onenw4VdfUzxAD-yIGZ-RWjvqJqELbkeBxh-eEoHsrsM5sjWYXowa55h5HmDwS2HP-LGyy4SFdxgEGV4R5lhBK0pMIf8VhbvlMkoZpaRCGO9sEsN89fc0rgzYL83HiJvCE6vviDul0-oFKliOXHXlXxdd6kqkmidKljGOb8tcDOZX_cjdrLsH7G0YoQYuiemfio9U_qVDhfkyDU2t5DWXRvlVbn_e9Nkc3DJ7h0XjhCA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg18790.htmlOn >> b.cisco.com 6/3/2021 10:22 AM, 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" <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@nmr.mgh.harvard.edu >>>> >>>> https://secure-web.cisco.com/1eQw4HlVWpF4ZzzChk-hp9V02K-k7R250ksr-ZRpjXC5ESaaFuyzgAuTFAoGhyEgYrYKrou0EXi_1ri2KpbhLu0RDRiF8JbcjNXFPW9pDzwKVvda8OwJaDhfqmDKW60AffvShgjctqkjGDrtVh3d5g5ibXvHnKxBrCeDpGoDotLpWBCKfctMD7RKY5GYQlCh3Un1XOMnnDFI7_MF2lAwup2vGzl11XZ_ZrOq3M8ZZB588KJPu216UQ-0rXaUfyN9kqO2LvtMM_BKWPkbPWLv1wQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> web.cisco.com >>>> >>>> >>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@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/1C61OSNwGFU8-MmX4hWZetUP6ivnpYMPZsypGZ1hSjsNzy-brmGySww1ZGhhngrVj1qYbuwE6PRUUeJN-f9A8A1WZ7th0QNfdUhXE6D3hKAkvirUMUgcYjEpbpiqr5EEx-zEFztskyh0Z_s-qx-pZYihOqIa83wP01adMhu1ZWGzu3R2R5BlSU44Kyj-7-8tjs4X0m9YumA2POfACS1X8JuGCd9bbmRQnsPob9yGBPtkb0saYprAkjBM9vSEkN54Sqsr6uuBnkzUu9th-uPKp8g/http%3A%2F%2Fwww.nmr.mgh.harvard.edu%2Ffacility%2Ffiledrop%2Findex.html >>> eb.cisco.com >>> >>> >>> >>> 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/1SUkt2fsByhbVkrjyleWea7U8vPw7dJUUjO3n73A05t_91lBe900zX8Xj5BXS5FVVIPhPdXp82Z6tn-yeqKFAhUFk_5StCCsEPSU9TJVMOayzf4j0KrCyoFNj-C2OGDP0xFemZL4QAwmVXf6LLrOE9uXSoUkhZAdqVKfMGyQ69ZkTVjm5-iFg90fsEAVNWEfQKIfNgsAMcDyfxfoi3sAh7AkPp30_dgubiPt_de-c2xl98NuTVZv4kCbN3juzQ9BiEeSE28aMxZczxiclrU7Fxg/http%3A%2F%2Fwww.partners.org%2Fcomplianceline >>> eb.cisco.com . 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@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1eQw4HlVWpF4ZzzChk-hp9V02K-k7R250ksr-ZRpjXC5ESaaFuyzgAuTFAoGhyEgYrYKrou0EXi_1ri2KpbhLu0RDRiF8JbcjNXFPW9pDzwKVvda8OwJaDhfqmDKW60AffvShgjctqkjGDrtVh3d5g5ibXvHnKxBrCeDpGoDotLpWBCKfctMD7RKY5GYQlCh3Un1XOMnnDFI7_MF2lAwup2vGzl11XZ_ZrOq3M8ZZB588KJPu216UQ-0rXaUfyN9kqO2LvtMM_BKWPkbPWLv1wQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> b.cisco.com >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://secure-web.cisco.com/1Nr7WqvfUN_R1BTkCFXCXYTFypgKkEWg4kgeEDkp-4697UpeiPbP2d-_n0XUvMO6Bj9jAcL-o2BGcZ_JYsls-zS06_9_Cpx_U_X72WTbbug_r4XypT4h_Y9TaMMmKeC6acIQGzjRrTAVOGF42I53_xJLadMW56lzGNaz-0i204JO0zlnIODddFUj6jA3fLz7BVbIDfiPHdCknphmmZbnNe02x44pQBluELqsWTIam8c_j3qPLNSdQpgjt9jKwZdX8eRg9apoGTlhKnEL_wK_Uog/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210609%2F86b2df25%2Fattachment-0001.html. >> mgh.harvard.edu >> >> ------------------------------ >> >> Message: 5 >> Date: Wed, 9 Jun 2021 14:51:16 +0000 >> From: "Fischl, Bruce" <bfis...@mgh.harvard.edu> >> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> >> <bl0pr04mb6609fbc2dac7159f549ebf77ef...@bl0pr04mb6609.namprd04.prod.outlo >> ok.com> >> >> Content-Type: text/plain; charset="us-ascii" >> >> Great, so you are all set then? >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Alexopoulos, >> Dimitrios >> Sent: Tuesday, June 8, 2021 10:45 PM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces >> >> >> External Email - Use Caution >> >> External Email - Use Caution >> I simply added additional CPs to the original ones (on the left) . >> >> From: >> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.h >> arvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh. >> harvard.edu>> On Behalf Of Fischl, Bruce >> Sent: Tuesday, June 08, 2021 3:12 PM >> To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces >> >> * External Email - Caution * >> You mean before? It was because the normalization was making some of the >> WM intensities so bright that they no longer looked like white matter >> (more like fat or something) >> >> Bruce >> >> From: >> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.h >> arvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh. >> harvard.edu>> On Behalf Of Alexopoulos, Dimitrios >> Sent: Tuesday, June 8, 2021 4:08 PM >> To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces >> >> >> External Email - Use Caution >> >> External Email - Use Caution >> Bruce, that did the trick, with additional CPs to the WM. See below. >> I'm still not sure why some occipital brain was removed in the brainmask. >> >> >> [cid:image001.jpg@01D75D1D.5C3FD180][cid:image002.jpg@01D75D1D.5C3FD180] >> >> >> >> From: >> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.h >> arvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh. >> harvard.edu>> On Behalf Of Fischl, Bruce >> Sent: Monday, June 07, 2021 5:30 PM >> To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces >> >> * External Email - Caution * >> It's really hard to say without looking at your data. You have to be >> careful not to accidentally add CPs outside of brain though as that can >> mess everything up >> Bruce >> >> From: >> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.h >> arvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh. >> harvard.edu>> On Behalf Of Alexopoulos, Dimitrios >> Sent: Monday, June 7, 2021 6:24 PM >> To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces >> >> >> External Email - Use Caution >> >> External Email - Use Caution >> Thx Bruce, I'll edit the CPs as you suggest. >> >> How do you explain brain in the updated brainmask being removed in the >> occipital region? I made no edits or changes in that area?. >> Do I need to edit the brainmask by cloning to the T1? >> >> From: >> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.h >> arvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh. >> harvard.edu>> On Behalf Of Fischl, Bruce >> Sent: Monday, June 07, 2021 3:58 PM >> To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] FW: WM or Pial edits to correct surfaces >> >> * External Email - Caution * >> p.s. if you are still struggling with this after trying to be more >> conservative we can take a look. The other thing you can try if you want >> to keep your current CP placement is to also add some to the interior of >> the WM (where things are getting to be in the 130s and 140s). This will >> limit the spatial extent of the influence of the CPs that are on the thin >> strands >> >> From: >> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.h >> arvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh. >> harvard.edu>> On Behalf Of Alexopoulos, Dimitrios >> Sent: Monday, June 7, 2021 4:46 PM >> To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: [Freesurfer] FW: WM or Pial edits to correct surfaces >> >> >> External Email - Use Caution >> >> External Email - Use Caution >> As a followup to my previous post, here is the aparc+aseg in that same >> region. >> >> [cid:image002.jpg@01D75D1D.5C3FD180][cid:image003.png@01D75D1D.5C3FD180] >> >> >> From: >> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.h >> arvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh. >> harvard.edu>> On Behalf Of Alexopoulos, Dimitrios >> Sent: Monday, June 07, 2021 3:26 PM >> To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces >> >> * External Email - Caution * >> >> External Email - Use Caution >> Bruce, >> >> Thanks for the recommenadtion. I editerd several regions by being more >> aggressive with CPs, whose palcements are shown in >> The snapshots below. The images on the left of each row below are the >> original FS ouputs and on the right are the updated outputs with the CPs >> added and running recon-all -all. >> >> . >> >> Original >> >> With CPs >> >> In row 1 the the pial and white surrfaces in the frontal pole region in >> many cases look much better. The WM has pushed the pial out correctly. >> >> [cid:image004.jpg@01D75D1D.5C3FD180][cid:image005.jpg@01D75D1D.5C3FD180] >> >> >> >> Row 2: >> >> Not so good a result when adding CPS. The frontal pole pial got pulled >> out correctly but the WM surface is incorrect. Suggrestions to correct? >> I aslo noticed that several WM voxels in the updated regions are >110 up >> to 130-140. Is this expected? >> >> [cid:image006.png@01D75D1D.5C3FD180][cid:image007.jpg@01D75D1D.5C3FD180] >> >> >> Row 3: >> >> CPs appear to have captured more WM and the pial got pushed out correctly >> in the lateral orbital region. In this example I'm not sure why the >> occipital pole has data removed in the brainmask. I simply reran >> recoon-all -all incorporating the updated control,dat. >> Do I need to add back brain by cloning with the T1? >> >> [cid:image008.jpg@01D75D1D.5C3FD180][cid:image009.jpg@01D75D1D.5C3FD180] >> >> >> >> >> >> From: >> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.h >> arvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh. >> harvard.edu>> On Behalf Of Fischl, Bruce >> Sent: Sunday, June 06, 2021 12:59 PM >> To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces >> >> * External Email - Caution * >> Usually you can do this iteratively. Find some voxels that are clearly >> wm, but whose intensity is <110 and add some cps there then rerun. In the >> image below you could put some near the red cursor, which looks darker >> than the wm more superior >> >> From: >> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.h >> arvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh. >> harvard.edu>> On Behalf Of Alexopoulos, Dimitrios >> Sent: Sunday, June 6, 2021 1:57 PM >> To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces >> >> >> External Email - Use Caution >> >> External Email - Use Caution >> Bruce, >> >> Below are snapshots of the brainmask and surfaces in that problematic >> region. >> I tried to add some CPs but generally did not because the WM is not >> visible and/or intensity values are ~70. The cortex is just darker in >> this region. >> >> >> [cid:image010.png@01D75D1D.5C3FD180][cid:image011.png@01D75D1D.5C3FD180] >> [cid:image012.jpg@01D75D1D.5C3FD180] >> >> >> From: >> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.h >> arvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh. >> harvard.edu>> On Behalf Of Fischl, Bruce >> Sent: Sunday, June 06, 2021 10:52 AM >> To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces >> >> * External Email - Caution * >> Where did you try putting control points? If I understand what you are >> seeing I would add them to the body of the wm near temporal pole, then >> check in the brain.mgz to make sure that the intensities have been >> increased enough (where you put the CPs it should be close to 110, and >> the WM should be >90 or so most places depending on the details of your >> acquisition ) >> >> Cheers >> Bruce >> >> From: >> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.h >> arvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh. >> harvard.edu>> On Behalf Of Alexopoulos, Dimitrios >> Sent: Saturday, June 5, 2021 2:20 PM >> To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces >> >> >> External Email - Use Caution >> >> External Email - Use Caution >> Greg, >> >> I tried what you recommended. I ran several iterations with >> PlaceT1PialSurf --max-cbv-dist 6 (8 and 10), with and without controls >> points. No meaningful changes occur with pulling out the pial and adding >> CPs. In fact the CPS may cause more harm since the intensities are around >> 60-70. >> >> The issue appears to be intensity-gradient related. The raw T1 has a >> mild intensity inhomogeneity where the anterior is darker than posterior >> regions, including darker cortex especially in frontal pole cortex. The >> N3 gain field correction does not appear to have had much on an effect. >> This is illustrated in the images below. Raw T1 (left), brainmask, >> brainmask/pial surface. >> >> [cid:image013.jpg@01D75D1D.5C3FD180][cid:image014.jpg@01D75D1D.5C3FD180][c >> id:image015.jpg@01D75D1D.5C3FD180] >> >> >> Are there other options with the N3 correction in freesurfer? >> >> Can we input another T1 which has been pre-processed using another >> method, perhaps using ANTS N4, which appears to do better with the gain >> field correction. >> >> Jim >> >> >> From: >> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.h >> arvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh. >> harvard.edu>> On Behalf Of Alexopoulos, Dimitrios >> Sent: Friday, May 28, 2021 1:08 PM >> To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces >> >> * External Email - Caution * >> >> External Email - Use Caution >> Thanks Doug. Will try with difference distances. Where is the expert file >> placed? >> >> From: >> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.h >> arvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh. >> harvard.edu>> On Behalf Of Douglas N. Greve >> Sent: Thursday, May 27, 2021 5:25 PM >> To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] WM or Pial edits to correct surfaces >> >> * External Email - Caution * >> There might be a couple things happening. First, I would try adding a few >> control points in that area; make sure they are in true WM in voxels that >> have a value less than 110 on the brain.mgz file. This might help push >> the white surface further out (the WM in that gyrus is very thin). It >> might also help push the pial surface out. The next thing you can try is >> to increase the maximum distance over which the edge is searched for. >> These young subjects have very plump/thick cortices. You can do that with >> an expert options file. Create a text file with the following content: >> >> PlaceT1PialSurf --max-cbv-dist 6 >> >> Where "6" tells it to search 6 mm rather than the default 5. You may need >> to play with the number >> >> You can then run recon-all with >> >> recon-all -s subject -expert yourexpertoptions.txt -pial -lh >> >> The above command will run just the pial of just the lh hemi, so you >> should have your answer in a few minutes >> On 5/27/2021 2:19 PM, Alexopoulos, Dimitrios wrote: >> >> External Email - Use Caution >> >> External Email - Use Caution >> >> >> Hi users, >> >> We're having some issues with running some of our 2-3yo data (0.8mm >> isotropic) through FS7 with and without the -hires flag. >> >> There are persistent issues with the frontal lobe regions where the pial >> has not extended to outer surface as illustrated below. >> The WM surface contour look reasonable but the pial has underestimated >> the outer cortex resulting in an incorrect surface (below). >> >> I don't think control points will work (low intensity values in the >> 50-60s), and no WM to add to the WM.mgz. >> Any suggestion on how to push the pial surface out to capture the >> cortical surface?? >> >> Thx. >> Jim >> >> [cid:image016.png@01D75D1D.5C3FD180] [cid:image017.jpg@01D75D1D.5C3FD180] >> [cid:image018.png@01D75D1D.5C3FD180] [cid:image019.png@01D75D1D.5C3FD180] >> >> &nb sp; >> [cid:image020.png@01D75D1D.5C3FD180][cid:image021.jpg@01D75D1D.5C3FD180] >> >> ________________________________ >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. 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