Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

merge in a sigle label the results obetained in fs-fast
by stdp82＠virgilio.it 21 Sep '17

21 Sep '17

Hi list, I would to merge (separatelly pos and neg) in a sigle .label which contain all the clusters which represent the seed-cortical connectivity after fs-fast analysis.I aim to avoid to extraxt manually single label for cluster by tksurfer. Thanks, Stefano

2 1

Error in Qcache
by Emmanuel Nwosu 21 Sep '17

21 Sep '17

Hi All, I will want to know if this error on this link https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051464.ht… was resolved. I am having a similar problem while sampling to the fsaverage. Thanks Kind regards Emmanuel

2 1

recon-all question
by STACEY M SCHAEFER 21 Sep '17

21 Sep '17

Hello, I want to run recon-all again on scans that have already been hand-edited, the appropriate recon-all flags ran, and resulting output checked and approved. The images look good, but when the hippocampal subfield routine was later run on the images, it crashed, leaving an error in the recon-all.log. We want to be anal, and make sure there is no error again after running recon-all. In other words, we want the last line in the recon-all.log to reflect that the images all completed successfully. Is there a recommended flag (or flags) at this point? In other words, there are no additional edits to incorporate in the recon-all job, but we also don't want the earlier edits, control points, etc. ignored in this last rerun of recon-all. Thank you for your help! Stacey Stacey M. Schaefer, Ph.D. Center for Healthy Minds University of Wisconsin-Madison 625 W Washington Ave Madison WI 53703 608-263-9321

2 1

Longitudinal increase in thickness/volume
by Huang, Caleb (NIH/NINDS) [F] 21 Sep '17

21 Sep '17

Hello, I'm tracking atrophy in the precentral region. I've run the subjects through the longitudinal stream. Because of time constraints, I've mostly focused on editing the precentral regions as well as any significant errors outside of the region. I've observed increases in thickness of up to 0.1mm in the precentral region. In some cases there's an increase in volume as well. Upon inspection though, the precentral wm/pial surfaces look fine. Is this a normal range of error? Thank you, -Caleb

2 1

Mris_volume
by Fereshte 21 Sep '17

21 Sep '17

Dear FreeSurfer Developers Using "mris_volume surface_file_name " now i can't see any output files and 381271.851642 is shown in the command terminal, i have no idea what the problem is. Could you please help? Thank you!

2 3

longitudinal freesurfer- different scanners
by Michelle VanTieghem 21 Sep '17

21 Sep '17

Hello, Would it be ok to use the longitudinal pipeline for scans that were acquired on different scanners (e.g time 1 and time 2 on the same scanner, time 3 on different scanner)? Would the longitudinal pipeline help to account for different scanners, since it creates the average base image for all 3 time points? or is this not recommended? Thank you, Michelle -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

3 5

Longitudinal processing -qcache ERROR
by Lisa Delalande 21 Sep '17

21 Sep '17

Hi everyone, During my PhD, I'm using some longitudinal data and at the setp called "BASE" but when i want to make a qcache processing with the last version of FreeSurfer (i.e. 6.0)(command used : "*recon-all -base template_1-02 -qcache*") it doesn't work. I have a error message : "Error : cannot find /.../template_1-02/surf/*lh.w-g.pct.mgh*" I would like to kown if you know where the problem comes ? And what can I do to fix it ? Thank you, Best regards, Lisa

2 1

Newborn MRI segmentation
by Paula Diniz 21 Sep '17

21 Sep '17

Hi experts! I want to perform recon-all pipeline on newborn MRI data. How I can do this? Which atlas you recommend? Any news about infant pipeline? Thanks!! Paula Diniz

2 1

Re: [Freesurfer] Freeview aborts under centos6
by Markus Gschwind 21 Sep '17

21 Sep '17

Dear Andrew, So the sys admin has changed the libraries. however, it did not change anything. Freeview aborts without comment. Below the command you asked for the result. Any other ideas? What other info would you like to get? Sorry for that persisting problem! And thanks for your help! Markus ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/libvtk* lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so -> libvtkalglib.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 -> libvtkalglib.so.5.6.0 -rwxr-xr-x 1 sagon unige 146394 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so -> libvtkCommon.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 -> libvtkCommon.so.5.6.0 -rwxr-xr-x 1 sagon unige 3703594 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so -> libvtkCommonTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 -> libvtkCommonTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 1499456 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 26 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so -> libvtkDICOMParser.so.5.6.0 lrwxrwxrwx 1 sagon unige 26 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6 -> libvtkDICOMParser.so.5.6.0 -rwxr-xr-x 1 sagon unige 145360 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so -> libvtkexoIIc.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 -> libvtkexoIIc.so.5.6.0 -rwxr-xr-x 1 sagon unige 312372 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so -> libvtkFiltering.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 -> libvtkFiltering.so.5.6.0 -rwxr-xr-x 1 sagon unige 4502701 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6.0 lrwxrwxrwx 1 sagon unige 27 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so -> libvtkFilteringTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 27 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 -> libvtkFilteringTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 2185191 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 19 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so -> libvtkftgl.so.5.6.0 lrwxrwxrwx 1 sagon unige 19 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 -> libvtkftgl.so.5.6.0 -rwxr-xr-x 1 sagon unige 60005 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6.0 lrwxrwxrwx 1 sagon unige 31 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so -> libvtkGenericFiltering.so.5.6.0 lrwxrwxrwx 1 sagon unige 31 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 -> libvtkGenericFiltering.so.5.6.0 -rwxr-xr-x 1 sagon unige 294583 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6.0 lrwxrwxrwx 1 sagon unige 34 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so -> libvtkGenericFilteringTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 34 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6 -> libvtkGenericFilteringTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 153307 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 23 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphics.so -> libvtkGraphics.so.5.6.0 lrwxrwxrwx 1 sagon unige 23 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6 -> libvtkGraphics.so.5.6.0 -rwxr-xr-x 1 sagon unige 8696621 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6.0 lrwxrwxrwx 1 sagon unige 26 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so -> libvtkGraphicsTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 26 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 -> libvtkGraphicsTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 2517761 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so -> libvtkHybrid.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 -> libvtkHybrid.so.5.6.0 -rwxr-xr-x 1 sagon unige 3436930 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so -> libvtkHybridTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so.5.6 -> libvtkHybridTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 1085658 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImaging.so -> libvtkImaging.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6 -> libvtkImaging.so.5.6.0 -rwxr-xr-x 1 sagon unige 4169350 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6.0 lrwxrwxrwx 1 sagon unige 25 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so -> libvtkImagingTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 25 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 -> libvtkImagingTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 883379 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 17 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so -> libvtkIO.so.5.6.0 lrwxrwxrwx 1 sagon unige 17 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6 -> libvtkIO.so.5.6.0 -rwxr-xr-x 1 sagon unige 6095744 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6.0 lrwxrwxrwx 1 sagon unige 20 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so -> libvtkIOTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 20 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 -> libvtkIOTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 1268771 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtklibxml2.so -> libvtklibxml2.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtklibxml2.so.5.6 -> libvtklibxml2.so.5.6.0 -rwxr-xr-x 1 sagon unige 1769914 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtklibxml2.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so -> libvtkmetaio.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 -> libvtkmetaio.so.5.6.0 -rwxr-xr-x 1 sagon unige 643391 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so -> libvtkNetCDF.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 -> libvtkNetCDF.so.5.6.0 -rwxr-xr-x 1 sagon unige 257185 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6.0 lrwxrwxrwx 1 sagon unige 18 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so -> libvtkpng.so.5.6.0 lrwxrwxrwx 1 sagon unige 18 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 -> libvtkpng.so.5.6.0 -rwxr-xr-x 1 sagon unige 168598 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6.0 lrwxrwxrwx 1 sagon unige 20 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkproj4.so -> libvtkproj4.so.5.6.0 lrwxrwxrwx 1 sagon unige 20 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkproj4.so.5.6 -> libvtkproj4.so.5.6.0 -rwxr-xr-x 1 sagon unige 335939 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkproj4.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so -> libvtkRendering.so.5.6.0 lrwxrwxrwx 1 sagon unige 24 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 -> libvtkRendering.so.5.6.0 -rwxr-xr-x 1 sagon unige 6120907 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6.0 lrwxrwxrwx 1 sagon unige 27 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so -> libvtkRenderingTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 27 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6 -> libvtkRenderingTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 2278760 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksqlite.so -> libvtksqlite.so.5.6.0 lrwxrwxrwx 1 sagon unige 21 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6 -> libvtksqlite.so.5.6.0 -rwxr-xr-x 1 sagon unige 709297 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6.0 lrwxrwxrwx 1 sagon unige 18 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so -> libvtksys.so.5.6.0 lrwxrwxrwx 1 sagon unige 18 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 -> libvtksys.so.5.6.0 -rwxr-xr-x 1 sagon unige 305372 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so -> libvtkverdict.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0 -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0 lrwxrwxrwx 1 sagon unige 30 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so -> libvtkVolumeRendering.so.5.6.0 lrwxrwxrwx 1 sagon unige 30 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 -> libvtkVolumeRendering.so.5.6.0 -rwxr-xr-x 1 sagon unige 4500213 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6.0 lrwxrwxrwx 1 sagon unige 33 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so -> libvtkVolumeRenderingTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 33 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6 -> libvtkVolumeRenderingTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 420713 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so -> libvtkWidgets.so.5.6.0 lrwxrwxrwx 1 sagon unige 22 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 -> libvtkWidgets.so.5.6.0 -rwxr-xr-x 1 sagon unige 2425484 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6.0 lrwxrwxrwx 1 sagon unige 25 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so -> libvtkWidgetsTCL.so.5.6.0 lrwxrwxrwx 1 sagon unige 25 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 -> libvtkWidgetsTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 1227320 Sep 14 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6.0 -rwxr-xr-x 1 sagon unige 89056 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so -rwxr-xr-x 1 sagon unige 89056 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 -rwxr-xr-x 1 sagon unige 89056 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ 6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6.0 2017-09-19 20:10 GMT+02:00 Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu>: > I've attached a tar of the vtk library (vtk.tar.gz). To reinstall this, > the sys admin should run: > > tar -xzvf vtk.tar.gz > rm -rf $FREESURFER_HOME/lib/vtk > mv vtk $FREESURFER_HOME/lib/ > > after doing this, running the following command should display a bunch of > symbolic links: > ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/libvtk* > > If that's the case, hopefully freeview will run... or at least throw a > different error > > best > Andrew > ________________________________________ > From: Hoopes, Andrew > Sent: Tuesday, September 19, 2017 1:56 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Freeview aborts under centos6 > > Hi Markus, okay - I'll directly send you a tar of the vtk library. A > reinstall of vtk might work, because those shared objects that we > distribute are usually sym-linked > > Can you also send the fs buildstamp? You can get this by running the > command ‘bugr’ after sourcing freesurfer > > Andrew > > On Sep 19, 2017, at 11:02 AM, Markus Gschwind <markus.gschwind(a)gmail.com< > mailto:markus.gschwind@gmail.com>> wrote: > > Dear Andrew, > > after the System admin executed your proposed commands, it stays the same, > Freeview aborts. > > Is there anything else we could try? > > Thank you and best wishes, > > Markus > > 2017-09-15 20:06 GMT+02:00 Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu<mailto: > AHOOPES(a)mgh.harvard.edu>>: > Hm okay thanks - I’m curious what happens when you run: > > cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 > # backup the shared objects > mv libvtkverdict.so libvtkverdict.so.bk > mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk > # link them to 5.6 > ln -s libvtkverdict.so.5.6.0 libvtkverdict.so > ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6 > > then do you get the same error from freeview? > > -Andrew > > On Sep 15, 2017, at 12:10 PM, Markus Gschwind <markus.gschwind(a)gmail.com< > mailto:markus.gschwind@gmail.com>> wrote: > > Dear Andrew, > > The command gives this result: > > [gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<< > $LD_LIBRARY_PATH) | grep libvtkverdict.so > /sbin/ldconfig: Can't stat /usr/lib/jvm/java-1.7.0- > openjdk-1.7.0.71.x86_64/jre/lib/amd64/server: No such file or directory > /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6: > duplicate hwcap 1 nosegneg > /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6: > duplicate hwcap 1 nosegneg > /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.6.2.el6.aufs21.x86_64.conf:6: > duplicate hwcap 1 nosegneg > /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6: > duplicate hwcap 1 nosegneg > /sbin/ldconfig: Path `/usr/lib64' given more than once > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkalglib.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 > is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkWidgets.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 > is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 > is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkGenericFiltering.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 > is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkmetaio.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkHybrid.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkFilteringTCL.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkRendering.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkverdict.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkCommonTCL.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libmpistubs.so.5.6 > is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 > is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 is not a symbolic link > libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0 > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkRenderingTCL.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkexoIIc.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkCommon.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkFiltering.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtksqlite.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkGraphics.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkHybridTCL.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkproj4.so.5.6 > is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6 > is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtklibxml2.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkDICOMParser.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkImaging.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6 is not a symbolic link > /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/ > lib/vtk-5.6/libMapReduceMPI.so.5.6 is not a symbolic link > > > Thanks for your help!! > > Markus > > 2017-09-15 17:49 GMT+02:00 Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu<mailto: > AHOOPES(a)mgh.harvard.edu>>: > Hi Markus, > > What is the output when you run the following: (this will list libraries > you have access to) > > /sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep > libvtkverdict.so > > best, > Andrew > > On Sep 15, 2017, at 3:33 AM, Markus Gschwind <markus.gschwind(a)gmail.com< > mailto:markus.gschwind@gmail.com>> wrote: > > Hi experts, > > I am installing freeusrfer on our cluster which is running Centos6. > > [gschwind@login1 ~]$ uname -a > Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 > UTC 2017 x86_64 x86_64 x86_64 GNU/Linux > > > Freeview aborts without any other complaint. > > [gschwind@login1 ~]$ freeview > Abort > > When running freeview.bin it complains about a libraries error: > > [gschwind@login1 ~]$ freeview.bin > freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: > cannot open shared object file: No such file or directory > > I searched the archives and found this info to be given, > > [gschwind@login1 ~]$ ls -l $FREESURFER_HOME/lib/vtk/lib/ > vtk-5.6/*libvtkverdict* > -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ > 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so > -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ > 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 > -rwxr-xr-x 1 sagon unige 189017 Aug 17 2010 /opt/ebsofts/Core/FreeSurfer/ > 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0 > > > I then integrated this into bashrc > > export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6 > > however, the problem persists. > > Any help is highly appreciated! > > Thanks you! > Markus > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 . 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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 . 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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

1 0

TRACULA trac-all prep error
by Fred Sampedro 21 Sep '17

21 Sep '17

Dear TRACULA users, I'm trying to preprocess a DTI subject in TRACULA which has an already reconed-all error-free T1. I followed the tutorial, but trac-all -prep exited with errors very fast. Please find attached the log and error files, and the dmrirc. Also bvals and bvecs (were obtained from dcm2nii). The raw dti.nii.gz has 16 volumes, the first being b0 and then 15 directions. Any ideas on what could be happening would be much appreciated, Thanks a lot in advance, Fred-

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