Freesurfer August 2018

freesurfer@nmr.mgh.harvard.edu

104 participants
167 discussions

converting a color lookup table in csv to freesurfer format (.ctab)
by miracle ozzoude 23 Aug '18

23 Aug '18

External Email - Use Caution Hello, How can I convert a csv color lookup table to freesurfer format (.ctab)? My end goal is to use it to perform partial volume correction for an atlas/segmentation different from default freesurfer atlas. The atlas has a color lookup table however, mri_gtmpvc can't read it. The atlas is in nifti format and is based on MAPLEM. https://web.gin.g-node.org/doi/MALPEM_ADNI_data Thanks. best, Paul

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PSIR to refine pial surface?
by Vriend, Chris 23 Aug '18

23 Aug '18

External Email - Use Caution Dear Freesurfers, In our centre we acquire T1 MPRAGE scans and phase-sensitive inversion recovery (PSIR) scans. Because of its better contrast between brain and non-brain I thought that we could use this scan in the freesurfer pipeline (v6.0) to refine the pial surface. I've already tried to use the -FLAIRpial flag (even though it's obviously not a FLAIR) but that actually makes it worse. Does anyone know if it is at all possible or have any experience with using PSIR scans in freesurfer and can point me in the right direction? Thanks, Best wishes Chris [cid:image001.png@01D40E30.9B2FFEE0] Dr. C. Vriend | Assistant Professor Anatomy & Neurosciences - section Neuropsychiatry | Psychiatry Location VUmc | O|2 13W09 | De Boelelaan 1118, 1081 HZ Amsterdam T: + 31 (0) 6 25 69 49 12 | E: c.vriend(a)vumc.nl<mailto:c.vriend@vumc.nl> P: p/a sec. Anatomy & Neurosciences, postbus 7057, 1007 MB Amsterdam www.amsterdamumc.nl<http://www.amsterdamumc.nl> | www.vumc.nl<http://www.vumc.nl/> | http://www.neuroscience-amsterdam.nl/?page_id=189 _____________________________________________________ VUmc disclaimer: www.vumc.nl/disclaimer<http://www.vumc.nl/disclaimer>

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Low resolution voxels of T1-weighted data (FreeSurfer)
by Martin Juneja 23 Aug '18

23 Aug '18

External Email - Use Caution Hi FS experts, I came across this post https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-June/031245.html by Dr. Bruce Fischl, where it is mentioned that "*You won't be able to analyze the data unless **it is T1-weighted with voxels that are <1.3mm or so in any dimension."* However, I came across several papers in high impact journals, including papers published in Cerebral Cortex e.g. a very nice paper by Dr. Winkler https://academic.oup.com/cercor/article/28/2/738/4668693, other one is https://www.ncbi.nlm.nih.gov/pubmed/28183529, where the authors used voxels of size 1.3 mm or 1.33 mm. Could you please comment on this contradiction whether voxels of this large size or even larger than 1.33 mm can give decent/correct results, or it is not advisable at all? Thanks.

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Extract Cortical Thickness Values from ROI.nii
by Davide Momi 23 Aug '18

23 Aug '18

External Email - Use Caution Dear all, I've just completed the recon -all command and I would like to extract Cortical thickness values in subject space at vertex level (without any sort of normalization). Could you please give me an insight on how to do it? Thanks in advance Dav e

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memprage processing steps?
by Caspar M. Schwiedrzik 23 Aug '18

23 Aug '18

External Email - Use Caution Hi! I was wondering whether there is an overview / walkthrough for all the steps involved when working with MEMPRAGE? I am thinking dcmunpack, mri-concat / mri_average, flags for recon-all, mris_make_surfaces, etc. Any pointers would be appreciated. Thanks! Caspar

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selxavg3-sess contrasts error
by Francesca Strappini 22 Aug '18

22 Aug '18

External Email - Use Caution Hi, I'm trying to analyze a block-design experiment. I run selxavg3-sess: selxavg3-sess -s MS -analysis MS_VisLocDrawings.sm03.rh And I got this error message while computing the contrasts. Any idea what does it mean? outtop = /home/labs/malach/frastra/freesurfer/fsfast/visloc_drawing Extension format = nii.gz 1 animals-vs-fixation.mat 2 body_parts-vs-fixation.mat 3 faces-vs-fixation.mat 4 houses-vs-fixation.mat 5 scrambled_images-vs-fixation.mat 6 tools-vs-fixation.mat Unable to perform assignment because the indices on the left side are not compatible with the size of the right side. Error in fast_ldpar4 (line 97) par4(nthrow,1) = tonset; Error in flac_customize (line 121) [par partype] = fast_ldpar4(parpath); Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Thank you! -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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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.

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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

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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

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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

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Freesurfer August 2018