Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30095 discussions

error: mean: DIM must be an integer and a valid dimension / selxavg3-sess with octave
by Michael Schirner 12 Jan '17

12 Jan '17

Dear FreeSurfers, I just wanted to share a solution for an issue that can arise when running selxavg3-sess with octave instead of Matlab. In fast_selxavg3.m (which is called by selxavg3) there is a line (579 in my version) that computes the mean of an array by calling the mean function with the DIM argument, which specifies the dimension over which the average should be computed (4th dimension in this case): rho1mn.vol = mean(rho1.vol,4); This line will throw an error under octave if the number of dimensions of the array rho1.vol is smaller than 4. In Matlab it will simply return the array. To solve this issue for octave users one can use a simple if-else statement to check for the number of dimensions and return the unchanged volume if the number of dimensions is smaller than four or if the fourth dimension is a singleton, like this: if 4 > ndims(rho1.vol) || size(rho1.vol,4) == 1 rho1mn.vol = rho1.vol; else rho1mn.vol = mean(rho1.vol,4); end Best, Michael

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bbregister surfaces
by Christopher Markiewicz 12 Jan '17

12 Jan '17

Hi all, According to https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25476.html, bbregister uses the white matter surface and cortical thickness measures to perform its registrations, though there was some possibility of using the pial surface in further releases. I just want to verify that this is still the case, and the pial surface is not currently being used. Thanks, Chris Markiewicz

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Fwd: OHBM 2017 Call For Council Nominations
by Douglas N Greve 12 Jan '17

12 Jan '17

fyi -------- Forwarded Message -------- Subject: OHBM 2017 Call For Council Nominations Date: Thu, 12 Jan 2017 12:42:40 -0600 From: info(a)humanbrainmapping.org Reply-To: info(a)humanbrainmapping.org To: greve(a)nmr.mgh.harvard.edu Dear Douglas, The OHBM Nominating Committee is extending the deadline for members to submit Council nominations until *January 19, 2017. *Open positions include Chair-Elect, Secretary-Elect, Treasurer-Elect, Program Chair-Elect and Education Chair-Elect and the term of service begins in June 2017, and each term is for three years. Make**your nominations by completing the *Call for Nominations* <https://www.humanbrainmapping.org/i4a/forms/index.cfm?id=97> form no later than *Thursday, January 19^th at* *11:59 PM US CST*. Self-nominations are welcome and encouraged. The OHBM By-Laws <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3292>, Article 5 provides the framework and process for the election of new Council members. *OHBM Nominating Committee:* Tor Wager, Secretary Christian Grefkes, Secretary-Elect Tonya White, Past Secretary Alan Evans, Chair Bernard Mazoyer, Chair-Elect Karl Zilles, Past Chair You must, when making your nominations, specify a position you want the person to fill (Chair Elect, Treasurer Elect, Secretary Elect, Program Chair Elect, Education Chair-Elect). Please check with this person before you make the nomination to be sure they would be interested in serving. Once the final slate is prepared and distributed, members will be able to see a brief bio on each candidate and vote online via the OHBM website. The results of these elections will be announced during the Town Hall Meeting, Wednesday, June 29, 2017, during the OHBM Annual Meeting in Vancouver, Canada. All candidates identified on the ballot will be informed of the results prior to the Annual Meeting. Councilors are not eligible for re-election for any council position for three years after serving one term. Individuals who are currently ineligible as nominees due to service on Council within the past 3 years are listed below. Current 2016-2017 OHBM Council. <http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3313> *Not Eligible Until 2019/2020* * Karen Berman, 2015-2016 Chair * Jeannette Mumford, 2015-2016 Treasurer * Doug Greve, 2015-2016 Secretary * Jack Van Horn, 2015-2016 Program Chair * Niko Kriegeskorte, 2015-2016 Education Chair *Not Eligible Until 2018/2019* * Steve Smith, 2014-2015 Chair * Jia-Hong Gao, 2014-2015 Treasurer * Simon Eickhoff, 2014-2015 Secretary * Pedro Valdes Sosa, 2014-2015 Program Chair We look forward to your involvement in the identification and election of your association’s leadership. Please contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> with any questions. Sincerely, JoAnn Taie Executive Director Organization for Human Brain Mapping (OHBM) *Organization for Human Brain Mapping* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 Fax: 1 952-545-6073 www.humanbrainmapping.org <http://www.humanbrainmapping.org> info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <mailto:info@humanbrainmapping.org?subject=Opt%20Out%20of%20Emails>.

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pial surface vs. aparc segmentation inconsistency
by Gabor Perlaki 12 Jan '17

12 Jan '17

Dear all, In some of our subjects the border of ctx_lh_parahippocampal (green color) is inconsistent with the border of pial surface (red color) in the sense that some small region within the pial surface is segmented as cerebellum (orange) coming from the subcortical segmentation stream. This problem is present in all three planes. It is hard to decide whether the colored border of ctx_lh_parahippocampal or the pial surface is more realistic, but it would be nice to know which one is used for the parahippocampal statistics in lh.aparc.stats file. Do I need to correct for this inaccuracy? How should I correct this type of missegmentation? Best Regards, Gabor <petzinger.gabor(a)gmail.com>

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Re: [Freesurfer] autorecon1 crash (with nu_correct).
by Jamie Hanson 12 Jan '17

12 Jan '17

Hello Zeke, I included the terminal output error for the stable version of Freesurfer, but get the same error with the dev version. Here's an example, pasted below: Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1 INFO: SUBJECTS_DIR is /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award Actual FREESURFER_HOME /usr/local/pkg/freesurfer-dev Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/pkg/freesurfer-dev/bin/recon-all' -> '/home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/scripts/recon-all.local-copy' #-------------------------------------------- #@# MotionCor Wed Jan 11 20:49:48 EST 2017 Found 1 runs /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig/001.mgz /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107 mri_convert /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz --conform mri_convert.bin /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -0.971961, -0.235142) j_ras = (0, -0.235142, 0.971961) k_ras = (1, -1.11022e-16, -1.66533e-16) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz... mri_add_xform_to_header -c /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/transforms/talairach.xfm /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Jan 11 20:50:00 EST 2017 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri /usr/local/pkg/freesurfer-dev//bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Wed Jan 11 20:50:00 EST 2017 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.130158 /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.130158/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.130158/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.130158/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Jan 11 20:50:03 EST 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.130158/nu0.mnc ./tmp.mri_nu_correct.mni.130158/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.130158/0/ -iterations 1000 -distance 50 Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/pkg/freesurfer//mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 10107 exited with ERRORS at Wed Jan 11 20:50:03 EST 2017 For more details, see the log file /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10107/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ===== The MNI tools are from 2010, but as noted at the start, the Freesurfer version is "Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1" (which I believe is the most recent dev version). Other thoughts or things to work on? Thanks much! Best, Jamie. On Wed, Jan 11, 2017 at 6:28 PM, Z K <zkaufman(a)nmr.mgh.harvard.edu> wrote: > Hello Jamie, > > Are you absolutely sure your using the dev version of freeseurfer? It > looks like from the output you pasted below their is possibly some mixing > of the old and new versions (it says MNI was built in 2010 - should be much > more recent than that). Try starting with a fresh terminal window and > sourcing freesurfer and see what happens. If the problem persists I will > look deeper into the issue upon my return. > > > On Jan 11, 2017, at 10:15 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > wrote: > > > > I'm suspecting that there is an error or incompatibility in the MNI > > software (where we get nu_correct). Unforutnately, the person who would > > handle this (Zeke) is away until next Wed. Can it wait until then? > > > > > > > >> On 01/11/2017 04:58 PM, Jamie Hanson wrote: > >> > >> Is it happening on all subjects or just some of them? > >> > >> > >> all of them... > >> > >> > >> > >> > >> > >> On 01/11/2017 03:45 PM, Jamie Hanson wrote: > >> > >> Apologies my email must have clipped it out. > >> I pasted it below. > >> > >> > >> > >> ======= > >> > >> Hello Freesurfer List, > >> > >> I was running into issues processing subjects, with errors > >> just getting through the autorecon1 step of the pipeline. My > >> terminal outputs the following: > >> > >> ==== > >> > >> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri > >> /usr/local/pkg/freesurfer-dev//bin/mri_nu_correct.mni > >> --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters > >> 1000 --distance 50 > >> nIters 1 > >> $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ > >> Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 > >> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux > >> Tue Jan 10 12:53:44 EST 2017 > >> Program nu_correct, built from: > >> Package MNI N3, version 1.10, compiled by nicks@minerva > >> (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 > >> /usr/bin/bc > >> tmpdir is ./tmp.mri_nu_correct.mni.129237 > >> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri > >> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.129237/nu0.mnc > >> -odt float > >> mri_convert.bin orig.mgz > >> ./tmp.mri_nu_correct.mni.129237/nu0.mnc -odt float > >> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > >> reading from orig.mgz... > >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > >> i_ras = (-1, -1.32349e-23, -1.32349e-23) > >> j_ras = (0, 1.49012e-08, -1) > >> k_ras = (0, 1, 1.49012e-08) > >> changing data type from uchar to float (noscale = 0)... > >> writing to ./tmp.mri_nu_correct.mni.129237/nu0.mnc... > >> > >> -------------------------------------------------------- > >> Iteration 1 Tue Jan 10 12:53:47 EST 2017 > >> nu_correct -clobber ./tmp.mri_nu_correct.mni.129237/nu0.mnc > >> ./tmp.mri_nu_correct.mni.129237/nu1.mnc -tmpdir > >> ./tmp.mri_nu_correct.mni.129237/0/ -iterations 1000 -distance 50 > >> Can't use 'defined(@array)' (Maybe you should just omit the > >> defined()?) at > >> /usr/local/pkg/freesurfer//mni/bin/nu_estimate_np_and_em line > 165. > >> nu_correct: crashed while running nu_estimate_np_and_em > >> (termination status=65280) > >> ERROR: nu_correct > >> Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 > >> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux > >> > >> recon-all -s 10007 exited with ERRORS at Tue Jan 10 12:53:47 > >> EST 2017 > >> > >> For more details, see the log file > >> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/ > 10007/scripts/recon-all.log > >> To report a problem, see > >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > >> > >> ==== > >> > >> Searching the FS list, I saw that I originally thought this > >> was an incompatibility with the current stable Freesurfer > >> version and the most recent MNI tools. To troubleshoot that > >> issue, I installed the dev version of Freesurfer (as noted by > >> this thread: > >> https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/ > 2016-September/047734.html > >> <https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/ > 2016-September/047734.html> > >> <https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/ > 2016-September/047734.html > >> <https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/ > 2016-September/047734.html>>). > >> The error however still persists (even using the dev version). > >> Anyone else run into this issue or have thoughts about > >> troubleshooting it? Thanks much! > >> > >> Best, > >> Jamie. > >> > >> -- > >> Jamie Hanson > >> Assistant Professor, Psychology > >> Research Scientist, Learning Research and Development Center > >> University of Pittsburgh > >> Personal website: jamiehanson.org <http://jamiehanson.org> > >> <http://jamiehanson.org/> > >> > >> > >> On Wed, Jan 11, 2017 at 3:42 PM, Douglas N Greve > >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >> <mailto:greve@nmr.mgh.harvard.edu > >> <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > >> > >> please include previous correspondence. we get a lot of > emails > >> here and can't remember the context of each one. > >> > >> thanks > >> > >> > >> On 01/11/2017 03:17 PM, Jamie Hanson wrote: > >> > >> > >> I'm seeing it for multiple subjects, same issue. I > >> can't get > >> passed the autorecon1 steps. Any thoughts? > >> > >> > >> -- Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >> <mailto:greve@nmr.mgh.harvard.edu > >> <mailto:greve@nmr.mgh.harvard.edu>> > >> Phone Number: 617-724-2358 <tel:617-724-2358> > >> <tel:617-724-2358 <tel:617-724-2358>> > >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > >> <tel:617-726-7422>> > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> <https://gate.nmr.mgh.harvard.edu/filedrop2> > >> <https://gate.nmr.mgh.harvard.edu/filedrop2 > >> <https://gate.nmr.mgh.harvard.edu/filedrop2>> > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >> > >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > >> Outgoing: > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >> > >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> > >> > >> > >> > >> 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://www.partners.org/complianceline > >> <http://www.partners.org/complianceline> > >> <http://www.partners.org/complianceline > >> <http://www.partners.org/complianceline>> . If the e-mail was > sent > >> to you in error > >> but does not contain patient information, please contact the > >> sender and properly > >> dispose of the e-mail. > >> > >> > >> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > >> Phone Number: 617-724-2358 <tel:617-724-2358> > >> Fax: 617-726-7422 <tel:617-726-7422> > >> > >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> <https://gate.nmr.mgh.harvard.edu/filedrop2> > >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >> Outgoing: > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >> > >> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >

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Editing annot files
by Martin Juneja 12 Jan '17

12 Jan '17

Hi, I was wondering if there is any way to edit annot file e.g. I would like to edit *lh.Yeo2011_7Networks_N1000.annot* file in such a way when I overlay this file in freeview, I just display limbic network from Yeo 7 network atlas and hide other 6 networks. I would prefer to use MATLAB for this but would really appreciate any other simple way to do that. Thanks.

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Viewing Atlas for Cortical Parcellations
by Tamara Tavares 12 Jan '17

12 Jan '17

Hello, I was wondering whether it is possible to view the atlases that are used to construct the cortical surface ROIs in a visualization program? Thank you in advance for your help. Best, Tamara

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Cannot allocate memory error
by Aziz Nanthaamornphong 12 Jan '17

12 Jan '17

Hi experts, I ran the command $recon-all -all -subjid 0696 I have got these error messages *CORRECTING DEFECT 46 (vertices=66623, convex hull=8931)* *Excessive topologic defect encountered: could not allocate 322592700 edges for retessellation* *Cannot allocate memory* *Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux* I am not sure if this problem came from the insufficient memory on my computer. Otherwise, please let me suggestions for solving this problem. Thank you, Aziz.

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Fwd: Error of fsaverage unknown during mri_glmfit
by Xiuyi Wang 12 Jan '17

12 Jan '17

Hello FreeSurfer Developers, I am attempting to repeat the group analysis with the tutorial data on FreeSurfer website, as described on the FsTutorial/GroupAnalysis ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) But I received an error message when running the mri_glmfit command lines. At first, the command lines that I types: mri_glmfit --y xiuyi_lh_thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx \ —-surf fsaverage lh \—-cortex —glmdir xiuyi_lh.gender_age.glmdir Errors: MRISread(/Users/xiuyi/Documents/tutorial_data/buckner_data/tutorial_subjs/ group_analysis_tutorial/glm/fsaverage/surf/lh. —-cortex): could not open file No such file or directory mri_glmfit: could not read surface /Users/xiuyi/Documents/tutorial_data/ buckner_data/tutorial_subjs/group_analysis_tutorial/glm/fsaverage/surf/lh. —-cortex No such file or directory Then I changed the command lines, replacing "surf fsaverage lh.white" with "surf fsaverage lh". The exact command lines are: mri_glmfit --y xiuyi_lh_thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx \ —-surf fsaverage lh.white \—-cortex —glmdir xiuyi_lh.gender_age.glmdir The error message is: gdfReadHeader: reading gender_age.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 57.175 26.6006 Class Means of each Continuous Variable 1 genderFemale 59.1429 2 genderMale 55.0000 INFO: gd2mtx_method is dods *ERROR: Option fsaverage unknown.* I have searched the list and found this type of error has been reported by another person but no reply was found.(https://mail.nmr.mgh. harvard.edu/pipermail//freesurfer/2010-May/014401.html) 1) FreeSurfer Version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Flatform: macOS Sierra version 10:12 Thank you for your reply. Xiuyi

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pial surface vs. aparc segmentation inconsistency
by Gabor Perlaki 12 Jan '17

12 Jan '17

Somehow, my earlier post is unvisible on the maillist, therefore I send it again without the attached image. Dear all, In some of our subjects the border of ctx_lh_parahippocampal (green color) is inconsistent with the border of pial surface (red color) in the sense that some small region within the pial surface is segmented as cerebellum (orange) coming from the subcortical segmentation stream. This problem is present in all three planes. It is hard to decide whether the colored border of ctx_lh_parahippocampal or the pial surface is more realistic, but it would be nice to know which one is used for the parahippocampal statistics in lh.aparc.stats file. Do I need to correct for this inaccuracy? How should I correct this type of missegmentation? Best Regards, Gabor <petzinger.gabor(a)gmail.com>

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2005

2004

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