Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] Flipped left to right hemisphere subjects
by Lutz,Olivia (BIDMC - Psychiatry) 22 Aug '18

22 Aug '18

Hi Doug, If you are talking about the brainmask, then yes that volume is left-right reversed as well as the nu.mgz. Thanks! Olivia Greve, Douglas N.,Ph.D.<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Mon, 20 Aug 2018 14:44:00 -0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…>? Is the volume actually left-right reversed? ________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Lutz,Olivia (BIDMC - Psychiatry) <ol...(a)bidmc.harvard.edu> Sent: Monday, August 20, 2018 4:55:24 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Flipped left to right hemisphere subjects Hi Doug and Bruce, thank you for the quick reply. As a follow-up question, we've edited our brainmasks for a dataset and want to flip some subjects left to right. I found instructions to flip the scans, however they are for the nu.mgz file (https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal) Is is possible to apply this mri_convert --in_orientation? command to change the left and right labels of the brainmask so we don't have to re-edit as opposed to applying it to the nu.mgz file and regenerating the brainmask? Thanks! Olivia ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

Histogram analysis capability via mri_segstats or other command-lines in Freesurfer?
by Yash Patel 22 Aug '18

22 Aug '18

Dear all, I am using mri_segstats to obtain intensity values from each of the 34 cortical parcellations in the Desikan-Killiany Atlas; this provides metrics such as mean, min, max, range, and standard deviation. Is there a way to extract information such as the *mode*, or information to create a histogram for each of the particular regions? Thank you, Yash

3 9

Calculating Gray Matter Density
by Andrew Jahn 22 Aug '18

22 Aug '18

External Email - Use Caution Hello, Does FreeSurfer have an option for calculating gray matter density during recon-all, or does one need to calculate it manually? In that case, what is the formula? The reason I would like to compute density is to replicate the effects show in this paper: http://www.jneurosci.org/content/early/2017/05/02/JNEUROSCI.3550-16.2017. I have seen other threads on FreeSurfer indicating that density is gray matter per unit volume, but it's unclear how to compute this. Thanks! -Andy

2 1

ERROR: make_roi_paths did not complete successfully!
by 付振荣 22 Aug '18

22 Aug '18

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to compute the local gfrification index(LGI), but is comes errors as below: my command line is: recon-all -lgi -s AD02 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /opt/freesurfer /usr/local/freesurfer/subjects/AD02/surf #-------------------------------------------- #@# Local Gyrification Index lh Wed Aug 22 20:15:25 CST 2018 mris_compute_lgi --i lh.pial ================= rm -Rf /usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> reading filled volume... closing volume... morphological closing done. writing outer surface... ================= mris_extract_main_component /usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ================= counting number of connected components... 64678 voxel in cpt #1: X=2 [v=64678,e=194028,f=129352] located at (-23.256193, -18.836494, 46.098969) For the whole surface: X=2 [v=64678,e=194028,f=129352] One single component has been found nothing to do done ================= mris_smooth -nw -n 30 /usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 64678 - 194028 + 129352 = 2 --> 0 holes F =2V-4: 129352 = 129356-4 (0) 2E=3F: 388056 = 388056 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_11463_.m'); exit ================= Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.03 sec) FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial-outer-smoothed ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.01 sec) deltaT = 6.5800 ================= make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/usr/local/freesurfer/subjects/AD02/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_11463_.m'); exit ================= Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> loading datas ... FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.03 sec) FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial-outer-smoothed ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.01 sec) preparing outer mesh structure ... face 5000 / 129352 face 10000 / 129352 face 15000 / 129352 face 20000 / 129352 face 25000 / 129352 face 30000 / 129352 face 35000 / 129352 face 40000 / 129352 face 45000 / 129352 face 50000 / 129352 face 55000 / 129352 face 60000 / 129352 face 65000 / 129352 face 70000 / 129352 face 75000 / 129352 face 80000 / 129352 face 85000 / 129352 face 90000 / 129352 face 95000 / 129352 face 100000 / 129352 face 105000 / 129352 face 110000 / 129352 face 115000 / 129352 face 120000 / 129352 face 125000 / 129352 mesh_outer = vertices: [64678x3 double] faces: [129352x3 double] facesOfVertex: [64678x1 struct] preparing pial mesh structure ... ...searching for mesh edges...done (165.42 sec). ... creating path file for vertex 1 / 64678 area file for outer ROIs saved at 1 {Improper assignment with rectangular empty matrix. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); } >> ERROR: make_roi_paths did not complete successfully! Linux lishuyu 4.4.0-97-generic #120-Ubuntu SMP Tue Sep 19 17:28:18 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s AD02 exited with ERRORS at Wed Aug 22 20:20:08 CST 2018 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I am looking forward for your reply! best! zhenrong fu beihang university,beijing, china

1 0

hippocampal subfield segmentation
by Nillo, Ryan Michael R 21 Aug '18

21 Aug '18

External Email - Use Caution Hello FreeSurfer users, I want to segment hippocampal subfields, but did not have much luck running it. I downloaded the matlab compiler runtime according to this: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime. Now, there is a directory called MCRv80 in my FREESURFER_HOME. The first error says kvlAutoCrop: command not found. However, $FREESURFER_HOME.bin is on my path. Does anything seem incorrect? My path looks like this: /data/sugrue2/rnillo/tools:/data/sugrue2/rnillo:/netopt/afni:/working/sdl_analysis/software/dcm2niix/build/bin:/netopt/rhel7/versions/cmtk/lib/cmtk/bin:/working/sdl_analysis/software/vtk-dicom/build/bin:/netopt/dicom/bin:/working/sdl_analysis/software/ANTs/antsbin/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/mni/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin:/netopt/rhel7/versions/freesurfer/freesurfer-6.0.0/bin:/netopt/share/bin/local/sdl/fix:/netopt/rhel7/fsl/bin:/working/sdl_analysis/software/git_pipeline/CommandLineProg:/netopt/share/local/bin/sdl/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/local/bin:/usr/local/sbin:/working/sdl_analysis/software/git_unwarp:/working/sdl_analysis/software/parallel:/working/sdl_analysis/software/git_tools:/working/sdl_analysis/software/anaconda3/bin:/bin:/sbin:/usr/bin::/netopt/rhel7/bin:/netopt/rhel7/bin/local:/netopt/share/bin:/netopt/share/bin/local:/netopt/bin:/netopt/bin/local:/netopt/dicom/bin:/netopt/rhel7/matlab/bin:/netopt/ctf/bin:/netopt/share/hosts::/netopt/caret/bin:/netopt/afni:/netopt/freesurfer/bin/Linux:/netopt/freesurfer/bin/noarch:/netopt/sybase/12.5.3/OCS-12_5/bin:/netopt/rhel7/fsl/bin:/netopt/sge_n1ge6/bin/lx24-amd64:/netopt/rhel7/tivoli/tsm/client/ba/bin::/netopt/share/bin/local/sdl:/netopt/bin/local/brain:/netopt/share/bin/local/brain:/netopt/bin/local/ncl:/netopt/share/bin/local/ncl:. MatlabRuntime - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime> surfer.nmr.mgh.harvard.edu Matlab Runtime. The brainstem and hippocampal subfield modules in FreeSurfer 6.0 and the development version require the Matlab R2012b (v8.0) runtime (note that development versions from January 2018 onwards require the Matlab R2014b - v8.4 - runtime instead). ERROR MESSAGE: #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Tue Aug 21 13:45:25 PDT 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/runtime/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/bin/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/os/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/working/sdl_analysis/software/freesurfer6/freesurfer/bin: Warning: Unable to open display '10.48.0.125:0'. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG /working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlAutoCrop: line 3: kvlAutoCrop.bin: command not found gzip: /data/sugrue2/MTS/sub_0006_T1_20160920_1723/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1_autoEstimateAlveusML (line 158) MATLAB:badSwitchExpression #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Tue Aug 21 13:45:43 PDT 2018 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/runtime/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/bin/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/os/glnxa64:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/working/sdl_analysis/software/freesurfer6/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/working/sdl_analysis/software/freesurfer6/freesurfer/bin: Warning: Unable to open display '10.48.0.125:0'. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG /working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlApplyTransform: line 3: kvlApplyTransform.bin: command not found mv: cannot stat ‘imageDump_transformed.mgz’: No such file or directory /working/sdl_analysis/software/freesurfer6/freesurfer/bin/kvlAutoCrop: line 3: kvlAutoCrop.bin: command not found gzip: /data/sugrue2/MTS/sub_0006_T1_20160920_1723/tmp/hippoSF_T1_v10_right//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 550) Error in myMRIread>myMRIread_aux (line 92) Error in myMRIread (line 63) Error in segmentSubjectT1_autoEstimateAlveusML (line 158) MATLAB:badSwitchExpression Mahalo, Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging

2 2

Lesion segmentation
by Mo Izady 21 Aug '18

21 Aug '18

External Email - Use Caution Hi FreeSurfer experts, I have two questions; any hints are greatly appreciated: 1) What is considered lesion in subcortical segmentation? (tumor, MS, stroke, etc) 2) Would you pls share the reference to the algorithm that FreeSurfer uses for segmenting lesions? Thanks in advance! Mo Izady PhD Candidate in Neuroscience Arizona State University

2 3

vertex MNI305
by Trisanna Sprung-Much 21 Aug '18

21 Aug '18

External Email - Use Caution Hi there This might be a very silly question but I actually cannot find the answer in the email archive: Assuming I have loaded a label onto fsaverage in Freeview and want to get the MNI305 coordinate of that labelled vertex, am I simply using the x,y,z in brackets in the panel? I attach a photo of what I mean. Best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

4 8

Flipped left to right hemisphere subjects
by Lutz,Olivia (BIDMC - Psychiatry) 21 Aug '18

21 Aug '18

Hi Doug, Yes the brainmask volume is left-right reversed as well. Thanks! Olivia ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

AAL and freesurfer atlas concordance
by Venkateswaran Rajagopalan 21 Aug '18

21 Aug '18

External Email - Use Caution Dear All I have seen posts discussing about bringing AAL to freesurfer etc. I am wondering whether anyone has created a table of concordance between the regions in AAL to the freesurfer or the vice versa. If so can you please share with me. For my work I just want to know the mapping between the two atlases. Or is there any software or website (like the brain atlas concordance one) from where I can find the concordance between the two atlas regions Any help is greatly appreciated Thanks Venkat

1 1

Re: [Freesurfer] Flipped left to right hemisphere subjects
by Lutz,Olivia (BIDMC - Psychiatry) 20 Aug '18

20 Aug '18

Hi Doug and Bruce, thank you for the quick reply. As a follow-up question, we've edited our brainmasks for a dataset and want to flip some subjects left to right. I found instructions to flip the scans, however they are for the nu.mgz file (https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal) Is is possible to apply this mri_convert --in_orientation? command to change the left and right labels of the brainmask so we don't have to re-edit as opposed to applying it to the nu.mgz file and regenerating the brainmask? Thanks! Olivia ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

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