Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

GC-DG
by 郑凤莲 03 Jan '18

03 Jan '18

Hi professor, I am using FS 6.0 for hippocampal subfield. I have a doubt what is the full name of GC-DG? I didn't find it in the wiki. Sincerely, Zheng

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Scan sequences and parameters in hippocampus segmentation.
by Qin weiting 03 Jan '18

03 Jan '18

Dear FreeSurfer experts, I'm sorry that English is not my mother language. I have met some trouble in choosing the scan sequences and parameters of data collecting in hippocampus segmentation, I have read the MORPHOMETRY PROTOCOLS on FreeSurfer Wiki, but our lab only has GE Discovery MR 750W instead of Siemens MRI. How should the T1 and T2 scan sequences and parameters be designed on a GE MR 750W? Thank you very much！ Best, Qin weiting

1 0

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

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AnatomiCuts in tracula
by Knut J Bjuland 03 Jan '18

03 Jan '18

Dear Freesurfer expert I have used Tracula and I read that AnatomiCuts could improve Tracula performance. Can I use AnatomiCuts with Tracula in Freesurfer 6.0 or developer version. If this is not the case, will it be released in Freesurfer 6.1 Best regards Knut Jørgen Bjuland PhD

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Does this analysis work for new born baby
by Ting Li 03 Jan '18

03 Jan '18

Dear Stuff, Happy new year. Does Freesurfer work for new born baby MRI or not? If I want to use it for baby MRI, what should I pay attention to? Thanks a lot! Best wishes, Ting

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FSAVERAGE - RECON-All
by Savaş Aker 03 Jan '18

03 Jan '18

Dear all, I would like to learn the following: I ran recon-all -all command, and now want to use only parcellation results of Desikan-Killiany Atlas or Destrieux (mean curvature, cortical thickness, etc.). So I will use values under STATS folder (e.g. lh.aparc or Lh.aparc.2009 for mean curvature and thickness) and do my own statistical analysis with these values. To make it clear, I will NOT continue on qdec for statistical analysis. So I did NOT run -qchache command for preparing my data for qdec (so my data was not sampled to fsaverage). Considering these, do I still use fsaverage in any stage of my analysis (running recon-all without qchace option)? I want to use only results of e.g. Desikan-Killiany Atlas, and do not want my data to be resampled to fsaverage. Thanks, Savas

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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

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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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Re: [Freesurfer] mris_convert error in finding file: fread error
by Douglas Greve 02 Jan '18

02 Jan '18

Hi Joao, please remember to send to the list. We don't have anything to merge two hemis together. Manybe the other software has this functionality. On 1/2/18 11:11 AM, João V. Dornas wrote: > Hi Douglass, > > thank you for your response. > > I created two surfaces overlay files like this: > > lh.mgz > rh.mgz > > I can load and view the information using FreeView. > > I need to merge these files as a single surface file to load them > together at the same time in another software. > > This other software accepts Freesurfer ASC, Freesurfer BINARY, Text > files and Gifti. > > Do you mind to give me a hint in how I could accomplish this? > > thank you very much, > > best regards, > > João V. Dornas >

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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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