Freesurfer December 2017

freesurfer@nmr.mgh.harvard.edu

107 participants
172 discussions

Postdoctoral position available in the Poldrack Lab
by Chris Gorgolewski 04 Jan '18

04 Jan '18

Apologies for cross-posting. The Poldracklab at Stanford is looking to hire a postdoc with expertise in fMRI data analysis, starting as soon as possible. Our lab is a dynamic and collaborative group that includes basic cognitive neuroscience researchers focused on the study of decision making and executive function alongside methodological researchers focused on reproducible data analysis and data sharing. Stanford University is located in sunny northern California, deep in the heart of Silicon Valley and a short train ride to San Francisco. The postdoc will be able to contribute to a number of ongoing research projects in our lab and collaborating labs by analyzing fMRI data from those studies. In addition, the postdoc will have the opportunity to develop their own research program with the domain of scientific or methodological problems currently being investigated within the lab ( https://poldracklab.stanford.edu/projects) The successful candidate should: - Have a PhD in a relevant field of study and demonstrated experience with the processing and statistical analysis of fMRI data. - Have strong and demonstrated computer programming skills, including Python. Experience with Nipype is strongly preferred. Candidates will be asked to submit a link to their open source code repository for review. - Have strong skills in statistics and machine learning. - Have solid experience with computational data analysis, including strong UNIX/Linux skills and experience using high performance computing clusters. Experience with cloud computing platforms is also preferred. - Be dedicated to open source software development and data sharing. The Poldracklab is strongly committed to diversity in science, and we particularly welcome applications from members of traditionally underrepresented groups. Eligible candidates will be asked to complete a data analysis problem using a specified dataset and present a report of their results as well as sharing their analysis code, in order to demonstrate their expertise with data analysis. Interested candidates should email the following to russpold(a)stanford.edu: - A cover letter describing your background and research interests - CV (including a link to code repository, e.g. Github, Bitbucket) - Names and email addresses of two references

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Thresholding of Monte-Carlo simulation
by yoichiro takayanagi 03 Jan '18

03 Jan '18

Dear FS experts, I’m wondering whether the Monte-Carlo simulation accountｓ for spatial or intensity thresholds (or both). Thanks, Yoichiro Takayanagi

2 2

Concatenation of images
by Rosalia Dacosta Aguayo 02 Jan '18

02 Jan '18

Dear FreeSurfer team, Sorry for double posting, but I have realized that in my previous email I posted some ideas that were not intended for any list... Problem: I do not know how to concatenate the different files generated in order to perform a cortical thickness analysis. Any help on this issue would be very appreciated. Technical details: FreeSurfer version is the last release. I am working with Linux Mint. Warm regards, Rosalia

2 3

OpenGL link errors
by Melvin Robinson 02 Jan '18

02 Jan '18

I posted this to the Freesurfer github site, but didn't exactly know if that was the most appropriate place. The Freesurfer build fails at this command: libtool: link: g++ -fdata-sections -ffunction-sections -Wl,--gc-sections -Wl,-Map -Wl,ld_map.txt -Wl,--no-demangle -o mris_show mris_show.o /usr/lib64/libuuid.so -L/home/melrobin/packages/centos6-x86_64-packages/qt/current/lib -L/usr/lib64 -L/usr/X11R6/lib64 -L/home/melrobin/packages/centos6-x86_64-packages//mni/current/lib -L/home/melrobin/packages/centos6-x86_64-packages//vxl/current/lib -L/home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit ../utils/libutils.a ../minc_substitute/libminc_substitute.a ../fsgdf/libfsgdf.a ../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a ../glut/libglut.a -L/lib64 -lX11 -lXmu /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKIO.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKAlgorithms.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKCommon.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKNumerics.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKMetaIO.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKniftiio.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKNrrdIO.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkpng.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitksys.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitktiff.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkv3p_netlib.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkzlib.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkgdcm.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkopenjpeg.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkjpeg8.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkjpeg12.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libitkjpeg16.a /home/melrobin/packages/centos6-x86_64-packages//itk/current/lib/InsightToolkit/libITKDICOMParser.a -lz -lm -lcrypt -ldl -lpthread /home/melrobin/packages/centos6-x86_64-packages//mni/current/lib/libvolume_io.a /home/melrobin/packages/centos6-x86_64-packages//mni/current/lib/libminc.a /home/melrobin/packages/centos6-x86_64-packages//mni/current/lib/libnetcdf.a -lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib and produces lots of these types of errors /home/melrobin/packages/freesurfer/mris_show/mris_show.c:878: undefined reference to glViewport' mris_show.o: In functionspecial_key_handler': /home/melrobin/packages/freesurfer/mris_show/mris_show.c:923: undefined reference to glMatrixMode' /home/melrobin/packages/freesurfer/mris_show/mris_show.c:937: undefined reference toglRotatef' /home/melrobin/packages/freesurfer/mris_show/mris_show.c:955: undefined reference to glRotatef' /home/melrobin/packages/freesurfer/mris_show/mris_show.c:945: undefined reference toglRotatef' /home/melrobin/packages/freesurfer/mris_show/mris_show.c:951: undefined reference to glRotatef' /home/melrobin/packages/freesurfer/mris_show/mris_show.c:933: undefined reference toglRotatef' The build seems not to include the OpenGL libraries when building mris_show as you can see from the link line. I'm trying to trace this up the Autotools chain, but need some help. I can work a little more on a fix with a little guidance telling me where to look.

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mri_gtmpvc & mri_gtmseg errors - failed tissue type check
by Makaretz, Sara Johanna 02 Jan '18

02 Jan '18

Hi Doug, I ran mri_gtmseg on a subject & got no errors, and the gtmseg.mgz/apas+head.mgz outputs looked fine: $Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $ mri_gtmseg --s $s etc, exited fine Then I tried running mri_gtmpvc, and got a 'failed tissue type check' error: [weckl:FDG_2017-11-15] (nmr-stable6-env) cat MR_2017-11-07/pvc.psf06/mri_gtmpvc.log $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR $SUBJECTS_DIR mri_gtmpvc --auto-mask 11 .001 --rbv --mgx .25 --lgtm --threads 8 --seg gtmseg.mgz --no-rescale --save-input --i $PET_DIR/MeanPET.nii --reg $PET_DIR/reg.pet2t1.lta --psf 6 --o $PET_DIR/pvc.psf06 --default-seg-merge sysname Linux hostname weckl.nmr.mgh.harvard.edu machine x86_64 user makaretz vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Loading seg for gtm $SUBJECTS_DIR/$s/mri/gtmseg.mgz Loading ctab $SUBJECTS_DIR/$s/mri/gtmseg.ctab Reading $SUBJECTS_DIR/$s/mri/gtmseg.lta Failed tissue type check [weckl:FDG_2017-11-15] (nmr-stable6-env) I tried re-running mri_gtmseg and adding --keep-cc, as recommended in this thread (I left out --no-xcerseg since I think it's now the default): https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043523.… But I got a different error, where it's trying to write to a file called (null): [weckl:FDG_2017-11-15] (nmr-stable6-env) mri_gtmseg --s $s --keep-cc $Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $ cwd $PET_DIR cmdline mri_gtmseg --s $s--keep-cc sysname Linux hostname weckl.nmr.mgh.harvard.edu machine x86_64 user makaretz subject $s USF 2 OutputUSF 2 apasfile apas+head.mgz wmannotfile NULL ctxannotfile aparc.annot ctxlhbase 1000 ctxrhbase 2000 SubSegWM 0 KeepHypo 0 KeepCC 1 dmax 5.000000 nlist 0 lhmin 1000 lhmax 1900 rhmin 2000 rhmax 2900 Starting MRIgtmSeg() Starting MRIgtmSeg() USF=2 Loading $SUBJECTS_DIR/$s/mri/apas+head.mgz Loading surfaces t = 2.1280 Loading annotations t = 6.2390 Not segmenting WM reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Relabeling any unlateralized hypointenities as lateralized hypointenities MRIrelabelHypoHemi(): looping over volume nthreads = 1 Relabeling any hypointensities as WM MRIunsegmentWM(): looping over volume nthreads = 1 Upsampling segmentation USF = 2 t = 32.3010 MRIhiresSeg(): filling unknowns with 257 Beginning cortical segmentation using aparc.annot t = 83.9890 MRIannot2CorticalSeg(): looping over volume nthreads = 1 MRIannot2CorticalSeg(): found 1517 unknown, filled with 257 Not subsegmenting WM Found 115 segs in the final list MRIgtmSeg() done, t = 358.8340 Computing colortable WARNING: segid 29 Left-undetermined tissue type is not set Writing output file to $SUBJECTS_DIR/$s/mri/(null) unknown file type for file ($SUBJECTS_DIR/$s/mri/(null)) [weckl:FDG_2017-11-15] (nmr-stable6-env) I think I ruled out the usual operator errors (typos/SUBJECTS_DIR/permissions). Do you have any advice? Thank you in advance for any help! Sara

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[freesurfer] version differences for pial matter / skull strip?
by Michelle VanTieghem 02 Jan '18

02 Jan '18

Hello, I have posted several times about problems with skull-stripping with our dataset. We have tried gcut and multiple other options in other packages (AFNI, FSL, ANTS) to remove skull from structural images in our dataset with little success. Recently, a colleague suggested this may be due to versions: that 6.0 deals with skull stripping much better than 5.3. I wanted to ask if indeed this could be the case before I go install 6.0 and re-run everything in my study. Thank you, Michelle -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

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About the contrast matrix in LME toolbox
by Gong, Liang 02 Jan '18

02 Jan '18

Dear LME developer and expert, I am using LME recently, based on longitudinal brain structural data, but I have two confusions in using it. 1) I followed the tutorial at: https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels However, I don't actually understand the Contrast matrix design in this tool. In the example the contrast C matrix is a 3*14, is there any explain about this matrix design? For my study, I want to explore 3 treatment (2 therapy methods and 1 waitlist) effects on the brain structural, If I want to explore the main effect of treatment, how could I write the Contrast matrix, and whether I can explore each treatment effect on the brain structural? And how can explore the time*treatment effect contrast matrix? 2) For the mass-univariate analysis, the example C matrix is 3*17, and it will explore the group differences in the rate of change over time among the four groups, and if I get the four group difference maps, How can I know the difference between each two groups? If I need to do the another qdec file and do the following steps as mris_preproc and mri_surf2surf? Thank you very much! Best, Gallen

2 1

Question about an error during recon-all process
by 박경일 01 Jan '18

01 Jan '18

Dear experts, I am sorry for asking again. I have some problems in running recon-all. Recon-all process was shut down with this error message ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string." I guess this is because of low resolution or small size of images. is it right? Thank you so much for you help in advance. FYI, log file is attached. Kyung

2 3

Feat
by N Saf 01 Jan '18

01 Jan '18

Dear FreeSurfer experts, I am trying to view the Feat on volume and surface by following commands: tkmedit bert orig.mgz -aux brain.mgz -overlay ./fbert1.feat/stats/zstat1.nii.gz -overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat -fthresh 2.3 –fmax 4.3 -seg aparc+aseg.mgz and tksurfer bert rh inflated -overlay ./fbert1.feat/stats/zstat1.nii.gz -overlay-reg ./fbert1.feat/reg/freesurfer/anat2exf.register.dat -fthresh 2.3 -fmid 3.3 -fslope 1 it works but thats my question: Is it possible to do the same thing with freeview ? I can not convert above commands in a way which be meaningful for freeview. many thanks to any help you can provide me. BRG, Nazanin

2 2

Can I use FS to detect white matter lesion using FLARE imaging?
by shi yao wang 31 Dec '17

31 Dec '17

Dear FS experts: Can I use FS to detect white matter lesion using FLARE imaging? Where can I find the command. Thanks Lawrence Radiology Department Emory University

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Freesurfer December 2017