Freesurfer September 2019

freesurfer@nmr.mgh.harvard.edu

93 participants
143 discussions

Question about how to build .gca files from non-human atlas and images
by arsene ella 06 Sep '19

06 Sep '19

External Email - Use Caution *Dear **Freesurfer experts,* *I’ve built an atlas of structures of a non-human average brain and now **I would like to build **its** .gca files from scratch. **From the Freesurfer mailing list, I saw that this is possible using **rebuild_gca_atlas.csh* *which trains labelled brai**ns (**seg_edited.mgz**) and their intensity volumes (it is said to use the **norm.mgz** for this purpose) from several subjects through **mri_ca_train**. **My questions are :**1) How to normalize my native intensity volume to a **norm.mgz** volume without .gca and .lta files asking by **mri_ca_normalize **?**Y**ou’ve suggested to give **mri_ca_normalize** a flag to tell it to use a manual segmentation instead of the gca by trying **-seg <manual seg volume>**. Then the gca name won't matter - it should ignore it… I tried this as followed :**let : **- **Brain_Template_T1_MPR.mgz ** be my intensity native volume**- **Brain_Cortex_Atlas.mgz* * be my manual segmented volume**- **Brain_Template_T1_MPR_norm.mgz* * be **my **norm** output** volume* *Command lines :**mri_ca_normalize** Brain_Template_T1_MPR.mgz **-seg** Brain_Cortex_Atlas.mgz Brain_Template_T1_MPR_norm.mgz**gave the following error message :**reading 1 input volume**reading atlas from '-seg'...**GCAread(-seg): could not open file**No such file or directory**mri_ca_normalize: could not open GCA -seg.**No such file or directory* *mri_ca_normalize* *-seg ** Brain_Cortex_Atlas.mgz Brain_Template_T1_MPR.mgz Brain_Template_T1_MPR_norm.mgz**gave the following message and stopped:**using segmentation volume /home/arsene/Bureau/FS_GCA/FS_SHEEP_CGA/Brain_Cortex_Atlas.mgz to generate control points...**usage: mri_ca_normalize [<options>] <inbrain1> <inbrain2> ... <atlas> <transform file> <output1> <output2> ...* *What is wrong with theses **mri_ca_normalize* *commands ?* *2) My second question is to know how to transfert labels from my* *manual seg**mented** volume **(ex : **atlas.mgz**) to each single image volume (ex : vol1**.mgz**) ?**You’ve suggested to use **mri_label2label**, but **I didn’t see anything allowing me to do a **volume_to_volume** transfert **from **its **–help**…** If I got it wrong, could you suggest a command ?* *cheers* *Arsene*

2 3

Morphological Features, Description & References
by Loske, Philipp 06 Sep '19

06 Sep '19

External Email - Use Caution Hello FreeSurfer Developers, I have a question about references and descriptions to all the morphological features available in aparc.stats, extracted from structural MRI. I am using all the different features (SurfArea, GrayVol, ThickAvg, ThickStd, MeanCurv, GausCurv, FoldInd, CurvInd) for the 68 cortical regions available from the Desikan Kiliany atlas. I have been trying to find references to how these features are measured or derived, but couldn't find a proper list of references to each of the features. I a lot of references here https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation, with detailed descriptions on surface reconstruction and how cortical thickness is measured, but couldn't find a detailed explanation on the other features, especially curvature values. I think I have been able to find out what each of the measurements mean and how they are calculated in principle, through searching the internet a lot, but with no direct link to FreeSurfer. For instance, I know you can calculate the curvature values from the principle curvatures, but how does FS estimate those form the reconstructed Surface? And which one of the two surfaces does it use? White-pial or pial-csf surface? I found https://brainder.org/ really helpful, but it says for example that a new way of measuring cortical volume was implemented in FS 6.0.0, so does that mean for previous versions FS uses the Thickness x SurfaceArea method? Would be great if you can help me with this, or point me to the correct website I might just have missed during my search. Best wishes Philipp The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.

3 2

mri_glmfit error
by Gwang-Won Kim 06 Sep '19

06 Sep '19

2 1

qcache after running recon-all post correction processing
by Swanson,Clayton 06 Sep '19

06 Sep '19

External Email - Use Caution Hi FreeSurfer folks, I searched through the archives and was unable to find the answer I was looking for. I have recently run recon-all on all our subjects (55 participants separated into two groups), then went through and corrected, saved and re-ran recon-all using the following command “recon-all -autorecon2-cp -autorecon3 -subjid Subj_020”. I neglected to add one additional command, the -qcache command for the second round of recon-all’s which I have already run for all participants. Because I am going to be comparing the two groups and doing group analysis what is the most appropriate way to proceed? Should I re-run the participants again although this time with the -qcache command? Or, what would be the most logical and efficient next step? Thanks for the help, Clayton ________________________________ Clayton Swanson MS Graduate Research Assistant & PhD Student Sensorimotor Neuroimaging Laboratory Colorado State University Office: (970) 491-6160 Clayton.Swanson(a)colostate.edu<mailto:Clayton.Swanson@colostate.edu>

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ERROR reading /<my data path>/fsaverage/label/lh.BA1_exvivo.label with recon-all.log
by liuxingze1993 06 Sep '19

06 Sep '19

External Email - Use Caution Hello，Dear FreeSurfer Developers, Hi, I'm attempting to follow the steps descripted on ‘Practice Working with Data’ (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice) with our own data, but I’ve met the same problem several times when I programing the command ‘recon-all -all’: SUBJECTS_DIR /media/dell/AA32E/Data_prac/220liujiayue/20181217 FREESURFER_HOME /usr/local/freesurfer Loading source label Invalid argument ERROR reading /media/dell/AA32E/Data_prac/220liujieyue/20181217/fsaverage/label/lh.BA1_exvivo.label I've searched the ‘lh.BA1_exvivo.label’ file in the related path and no such file here. Maybe I need to reinstall the freesurfer? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu14.04 LTS 3) uname -a: Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank u for viewing, and I will be waiting here for your professional advice !

2 1

qdec contrast and data extraction
by Maximo, Jose Omar 06 Sep '19

06 Sep '19

External Email - Use Caution Hi, Which specific file should I load? I see cluster.mgh, cluster.summary, sign.ocn.annot, sig.ocn.mgh, sig.vertex.mgh, and pdf.dat. How can I extract the values from fsaverage space? Basically, what is the correct way to extract values from these significant clusters? Many thanks, Omar Date: Tue, 3 Sep 2019 15:15:02 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] qdec contrast and data extraction To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <2286f9bf-37a4-1be9-2252-0bccc833a218(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" You might have done something wrong along the way. When you run the montecarlo correction, it will create a file with the thickness values in it for each cluster. the first thing to do is to load that and see if you see the expected differences. The other thing is to not go back into native space to extract the numbers. There are several operations that happen as it moves into fsaverage space and in preparation for group analysis (interpolation, and smoothing); sometimes these make a big difference. if the ROI is small, it may not map accurately back into the native space (and you should not need to draw it in the first place) On 8/30/2019 11:36 AM, Maximo, Jose Omar wrote: External Email - Use Caution Hi, I have a question: My design is 2 groups (HC and Patients in that respective order) and 2 nuisance factors (age and eTIV). When I look at the average volume difference between the 2 groups, I get blue and red clusters. I presume the color coding is where each group is greater than the other (Blue = Patients > HC and Red = HC > Patients). Then, I processed to extract individual values from each cluster in order to plot them. When I extract data from the blue clusters and plot them, the two groups show no difference in thickness at all, whereas when I look at volume, HC show more than patients in blue clusters (see attached figure). I would assume that both figures would show patients > HC based on the negative statistic. Am I interpreting the colors wrong? Or am I doing something wrong? These are my steps 1) After applying montecarlo correction, I drew my ROIs to extract the data from; 2) map it onto every single subject; and then 3) used mris_anatomical_stats to extract the data from each subject. Any suggestions are welcome. Best, Omar Jose O. Maximo, Ph.D. | Postdoctoral Fellow Department of Psychiatry & Behavioral Neurobiology UAB School of Medicine University of Alabama at Birmingham Cell Phone: (619) 252-3492 Email: jomaximo(a)uabmc.edu<mailto:jomaximo@uabmc.edu>

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Problem with lGI
by Avi Gharehgazlou 06 Sep '19

06 Sep '19

External Email - Use Caution Hi, I have ran the lGI flag many times in the past. However, now that I am trying to run the flag on a new group of participants I get the below error. Will you please tell me how I can fix this? Thanks so much, Avi New invocation of recon-all Fri Aug 30 16:47:49 EDT 2019 /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01 /usr/local/freesurfer/bin/recon-all -s MR160-114-0370_01 -localGI -openmp 2 subjid MR160-114-0370_01 setenv SUBJECTS_DIR /d/mjt/9/users/avideh/data/recon FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux apollo.sickkids.ca 4.15.0-50-generic #54-Ubuntu SMP Mon May 6 18:46:08 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 16384 kbytes maxproc 321903 maxlocks unlimited maxsignal 321903 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 82473464 18994140 26581924 374636 36897400 62364472 Swap: 8388604 1922560 6466044 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Aug 30 16:47:51 EDT 2019 mris_compute_lgi --i lh.pial ================= rm -Rf /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/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('/d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2019 The MathWorks, Inc. R2019a Update 4 (9.6.0.1150989) 64-bit (glnxa64) June 26, 2019 For online documentation, see https://www.mathworks.com/support For product information, visit www.mathworks.com. >> reading filled volume... closing volume... { Undefined variable "matlab" or class "matlab.graphics.chart.internal.datachk". Error in isosurface (line 76) data = matlab.graphics.chart.internal.datachk(data); Error in make_outer_surface (line 49) [f,v] = isosurface(BW2,100); } >> -------------------------------------------------------------------------------- std::terminate() detected at Fri Aug 30 16:48:20 2019 -0400 -------------------------------------------------------------------------------- Configuration: Crash Decoding : Disabled - No sandbox or build area path Crash Mode : continue (default) Default Encoding : US-ASCII Deployed : false Desktop Environment : MATE GNU C Library : 2.27 stable MATLAB Architecture : glnxa64 MATLAB Entitlement ID : 1261621 MATLAB Root : /usr/local/MATLAB/R2019a MATLAB Version : 9.6.0.1150989 (R2019a) Update 4 Operating System : Ubuntu 18.04.3 LTS Process ID : 2352 Processor ID : x86 Family 6 Model 44 Stepping 2, GenuineIntel Session Key : 75ad7f0e-24cf-4356-844c-9536f142fca0 Static TLS mitigation : Disabled: Unable to open display Window System : No active display Fault Count: 1 Abnormal termination: std::terminate() Register State (captured): RAX = 0000000000000000 RBX = 00007fee6ea82d98 RCX = 000000000000000a RDX = 00007fee6ea63e00 RSP = 00007fee4bff84a0 RBP = 00007fee4bff8860 RSI = 00007fee6ea2b3c6 RDI = 00007fee4bff84b0 R8 = 000000000000ffff R9 = 00007fee70e04740 R10 = 0000000000000000 R11 = 0000000000000005 R12 = 00007fee6ea72d08 R13 = 00007fee4bff8c20 R14 = 00007fee4bff9110 R15 = 00007fee4bff90e0 RIP = 00007fee6e97b1ae EFL = 00007fee6e8ab270 CS = 7480 FS = 71d8 GS = 7fee Stack Trace (captured): [ 0] 0x00007fee6e972713 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwfl.so+00829203 [ 1] 0x00007fee6e97290c /usr/local/MATLAB/R2019a/bin/glnxa64/libmwfl.so+00829708 _ZN10foundation4core4diag15stacktrace_base7captureEm+00000028 [ 2] 0x00007fee6e975052 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwfl.so+00839762 [ 3] 0x00007fee64201553 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01213779 [ 4] 0x00007fee64204157 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01225047 [ 5] 0x00007fee6420438a /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01225610 [ 6] 0x00007fee64204951 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01227089 [ 7] 0x00007fee642058d7 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01231063 [ 8] 0x00007fee70b1f3a6 /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00582566 [ 9] 0x00007fee70b1e3d9 /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00578521 [ 10] 0x00007fee70b1ed2d /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00580909 __gxx_personality_v0+00000717 [ 11] 0x00007fee70889f03 /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libgcc_s.so.1+00065283 [ 12] 0x00007fee7088a26b /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libgcc_s.so.1+00066155 _Unwind_RaiseException+00000251 [ 13] 0x00007fee70b1f5fb /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00583163 __cxa_throw+00000091 [ 14] 0x00007fee66376e22 /usr/local/MATLAB/R2019a/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoFoundation.so.48+00900642 _ZN4Poco10MemoryPool7releaseEPv+00000162 [ 15] 0x00007fee66966e5f /usr/local/MATLAB/R2019a/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoNet.so.48+00638559 _ZN4Poco3Net19HTTPHeaderStreamBufD2Ev+00000031 [ 16] 0x00007fee66967253 /usr/local/MATLAB/R2019a/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoNet.so.48+00639571 _ZN4Poco3Net21HTTPHeaderInputStreamD1Ev+00000067 [ 17] 0x00007fee6695abc7 /usr/local/MATLAB/R2019a/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoNet.so.48+00588743 _ZN4Poco3Net17HTTPClientSession15receiveResponseERNS0_12HTTPResponseE+00000199 [ 18] 0x00007fee58a7c827 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/../../../../bin/glnxa64/libmwflhttpclient.so+00141351 [ 19] 0x00007fee58a76d38 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/../../../../bin/glnxa64/libmwflhttpclient.so+00118072 [ 20] 0x00007fee58a7117d /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/../../../../bin/glnxa64/libmwflhttpclient.so+00094589 _ZNK10foundation10httpclient16WebServiceClient23doWebServiceTransactionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS8_S8_St4lessIS8_ESaISt4pairIS8_S8_EEES9_RNS1_18WebServiceResponseEiS9_+00000061 [ 21] 0x00007fee58a72409 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/../../../../bin/glnxa64/libmwflhttpclient.so+00099337 _ZNK10foundation10httpclient16WebServiceClient25makeWebServiceTransactionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS8_S8_St4lessIS8_ESaISt4pairIS8_S8_EEES9_RNS1_18WebServiceResponseEiiS9_+00000121 [ 22] 0x00007fee58c02387 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00590727 [ 23] 0x00007fee58c0675b /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00608091 [ 24] 0x00007fee58be9a68 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00490088 [ 25] 0x00007fee58c6beaa /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+01023658 [ 26] 0x00007fee58bf090a /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00518410 [ 27] 0x00007fee6ef5f7ad /usr/local/MATLAB/R2019a/bin/glnxa64/libmwms.so+02697133 [ 28] 0x00007fee58bf0586 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00517510 [ 29] 0x00007fee6fe54bdd /usr/local/MATLAB/R2019a/bin/glnxa64/libmwboost_thread.so.1.65.1+00080861 [ 30] 0x00007fee70e196db /lib/x86_64-linux-gnu/libpthread.so.0+00030427 [ 31] 0x00007fee705aa88f /lib/x86_64-linux-gnu/libc.so.6+01185935 clone+00000063 [ 32] 0x0000000000000000 <unknown-module>+00000000 ** This crash report has been saved to disk as /home/avideh/matlab_crash_dump.2352-1 ** MATLAB is exiting because of fatal error Killed ERROR: make_outer_surface did not create output file '/d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux apollo.sickkids.ca 4.15.0-50-generic #54-Ubuntu SMP Mon May 6 18:46:08 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s MR160-114-0370_01 exited with ERRORS at Fri Aug 30 16:48:21 EDT 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2 1

(revised) mri_glmfit error
by Gwang-Won Kim 06 Sep '19

06 Sep '19

1 0

Using mask image
by Gwang-Won Kim 05 Sep '19

05 Sep '19

2 1

How to generate a solid volume from lh/rh.pial-outer-smoothed
by Jingya Miao 05 Sep '19

05 Sep '19

External Email - Use Caution Hello Freesurfer Developers, I am trying to generate a solid volume out of the lh/rh.pial-outer-smoothed file. I was able to get just the surface in .nii format by using: mri_surf2vol --hemi lh --surf pial-outer-smoothed --mkmask --reg mri/register.dat --o surfsmoothed.nii --template mri/T1.nii --subject BerA I also attempted to use --fillribbon mri_surf2vol --surfval $SUBJECTS_DIR/Berger_Andrew/surf/lh.pial-outer-smoothed --fillribbon --reg mri/register.dat --o smoothedfill.nii --template T1.nii --subject BerA gdiagno = -1 ERROR: cannot recognize the type of /Users/mah.ali/freesurfer/subjects/Ber A/surf/lh.pial-outer-smoothed I am wondering what would be a good way to generate a solid volume out of the pill-outer-smoothed files. Thank you, Miao

2 1

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Freesurfer September 2019