Freesurfer July 2019

freesurfer@nmr.mgh.harvard.edu

104 participants
165 discussions

Individual surface
by Alex Peng 12 Jul '19

12 Jul '19

External Email - Use Caution Hi FreeSurfer experts, I am having trouble with making individual surface as template. 1. I reconstructed a macaque T1 to his individual surface and I want to make it as my macaque template. However the vertices number of left hemi and right hemi are different. How can I revise them to have same vertices just like fsaverage template? 2. Since subcortical mask draw by myself, the generated medial wall regions on the surfaces are not smooth. Is there any way that allows me to smooth the medial wall region on surface space? 3. Currently, the generated surface have about 10k vertices on each hemi. How can I downsample them and get the transform matrix between them because I also want to project bold data to the downsampled surface. I have tried mris_decimate, it only gives me a downsampled surface without transform matrix. Thanks for your help. Appreciate it! X. Peng

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freeview
by Juan Rivas 12 Jul '19

12 Jul '19

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Fwd: Freeview
by Juan Rivas 12 Jul '19

12 Jul '19

External Email - Use Caution That is what happened: $ ldd /usr/local/bin/freeview | grep not ldd: /usr/local/bin/freeview: No such file or directory $ bash jcrn12@jcrn12-VirtualBox:~$ ldd /usr/local/bin/freeview | grep not ldd: /usr/local/bin/freeview: No such file or directory JC. ---------- Forwarded message --------- De: fsbuild <fsbuild(a)contbay.com> Date: lun., 15 jul. 2019 a las 14:19 Subject: Re: [Freesurfer] Freeview To: <freesurfer(a)nmr.mgh.harvard.edu> Cc: <jcrn12(a)gmail.com> Hello JC, Try this to see what libs are missing, $ ldd /usr/local/bin/freeview | grep not - R. On Jul 12, 2019, at 06:19, Juan Rivas <jcrn12(a)gmail.com> wrote: External Email - Use Caution Hi, thank you for your help. I tried again and once again it did not work. I am using Ubuntu 18 This is the message I get: $ freeview sh: 8: freeview: not found $ which freeview $ /usr/local/bin/freeview sh: 10: /usr/local/bin/freeview: not found $ which ldd /usr/bin/ldd $ ldd `which freeview` | grep not ldd: missing file arguments Try `ldd --help' for more information. Thank you very much, JC. El lun., 15 jul. 2019 a las 12:50, fsbuild (<fsbuild(a)contbay.com>) escribió: > Hello Juan, > > For CentOS try: > $ sudo yum install gcc-gfortran.x86_64 > … if that does not work then, > $ sudo yum install libgfortran.x86_64 > > For Ubuntu, > $sudo apt-get install gfortran > > One thing you might want to try first is to run the “ldd” command on the > freeview binary to see all/any libraries that are missing.... > > This should return the path to freeview, e.g., /usr/local/bin/freeview, > though your path may differ. > $ which freeview > /usr/local/bin/freeview > > - then check you have the ldd command, > $ which ldd > /usr/bin/ldd > > If the above returned paths for freeview and ldd, then run the ldd command > followed by the grep command to see what libraries are missing. Prior to > doing the install of libgfortran above, it should list libgfortran is > missing. > > $ ldd `which freeview` | grep not > > Also it would be good to know what linux you are running, e.g., CentOS 7, > Ubuntu 18, etc. > > - R. > > On Jul 15, 2019, at 12:39, Juan Rivas <jcrn12(a)gmail.com> wrote: > > External Email - Use Caution > > > > ---------- Forwarded message --------- > De: Juan Rivas <jcrn12(a)gmail.com> > Date: vie., 12 jul. 2019 a las 3:02 > Subject: Re: [Freesurfer] Freeview > To: fsbuild <fsbuild(a)contbay.com> > > > Hi, thank you for your answer. > I did what you recommended to me, and I get this message: > freeview: error while loading shared libraries: libgfortran.so.3: cannot > open shared object file: No such file or directory. > What could be the next step? > JC. > > El lun., 15 jul. 2019 a las 9:57, fsbuild (<fsbuild(a)contbay.com>) > escribió: > >> Hello JC, >> >> Your machine could be missing the qt5 libraries/files. >> >> On Ubuntu linux you can try installing them with, >> $ sudo apt-get install qt5-default qtcreator libqt5x11extras5-dev >> >> On CentOS linux, >> $ sudo yum install qt-create qt-config.x86_64 >> $ sudo yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel..x86_64 >> >> - R. >> >> On Jul 12, 2019, at 02:28, Juan Rivas <jcrn12(a)gmail.com> wrote: >> >> External Email - Use Caution >> >> Hello, I am trying to use freeview, but everytime I try I get this >> message: >> freeview: error while loading shared libraries: libQt5Widgets.so.5: >> cannot open shared object file: No such file or directory. >> How can I fix it? >> Thanks a lot, >> JC. >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freeview
by fsbuild 12 Jul '19

12 Jul '19

External Email - Use Caution Hello Juan, For CentOS try:$ sudo yum install gcc-gfortran.x86_64… if that does not work then,$ sudo yum install libgfortran.x86_64 For Ubuntu,$sudo apt-get install gfortran One thing you might want to try first is to run the “ldd” command on the freeview binary to see all/any libraries that are missing.... This should return the path to freeview, e.g., /usr/local/bin/freeview, though your path may differ. $ which freeview/usr/local/bin/freeview - then check you have the ldd command, $ which ldd/usr/bin/ldd If the above returned paths for freeview and ldd, then run the ldd command followed by the grep command to see what libraries are missing..  Prior to doing the install of libgfortran above, it should list libgfortran is missing. $ ldd `which freeview` | grep not Also it would be good to know what linux you are running, e.g., CentOS 7, Ubuntu 18, etc. - R. On Jul 15, 2019, at 12:39, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        ---------- Forwarded message ---------De: Juan Rivas <jcrn12(a)gmail.com>Date: vie., 12 jul. 2019 a las 3:02Subject: Re: [Freesurfer] FreeviewTo: fsbuild <fsbuild(a)contbay.com>Hi, thank you for your answer.I did what you recommended to me, and I get this message:freeview: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory.What could be the next step?JC.El lun., 15 jul. 2019 a las 9:57, fsbuild (<fsbuild(a)contbay.com>) escribió:Hello JC,Your machine could be missing the qt5 libraries/files.On Ubuntu linux you can try installing them with,$ sudo apt-get install qt5-default qtcreator libqt5x11extras5-devOn CentOS linux,$ sudo yum install qt-create qt-config.x86_64$ sudo yum install qt5-qtx11extras.x86_64 qt5-qtx11extras-devel.x86_64- R.On Jul 12, 2019, at 02:28, Juan Rivas <jcrn12(a)gmail.com> wrote:        External Email - Use Caution        Hello, I am trying to use freeview, but everytime I try I get this message:freeview: error while loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: No such file or directory.How can I fix it?Thanks a lot,JC._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freeview
by Juan Rivas 12 Jul '19

12 Jul '19

External Email - Use Caution Hello, I am trying to use freeview, but everytime I try I get this message: freeview: error while loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: No such file or directory. How can I fix it? Thanks a lot, JC.

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mri_gtmpvc -- Failed tissue type check
by Lois Gomez, Cristina 11 Jul '19

11 Jul '19

Hi Freesurfers, I am having trouble with one subject's PVC (we process many cases and never had this issue before). When running mri_gtmpvc I get a 'Failed tissue type check' error. I've seen that other people have reported similar errors in the past, but I haven't found any advice on how to trouble-shoot this. We have longitudinal PET data with two tracers for this subject, so it is very important for us to get this fixed. Any advice? Thank you, Cristina

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Fwd: A Question Regarding Topology Correction
by Maedeh Khalilian 11 Jul '19

11 Jul '19

External Email - Use Caution From: "Maedeh Khalilian" <M.Khalilian(a)sutech.ac.ir> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Date: Thu, 11 Jul 2019 07:37:05 +0430 Subject: A Question Regarding Topology Correction Dear FreeSurfer experts, I know that FreeSurfer does segmentation, surface reconstruction and topology correction through its routine pipeline using "recon-all" . However, I have some T2w brain MR images and I have done the segmentation and extracted WM, GM, and CSF with my own algorithm. Now I need to remove back to back (i.e. a part of topology correction) which is caused in sulci due to the segmentation. In other word, after doing my segmentation, I wanna open the closed concavities in CSF that were open originally. Now I wanna know if I can do the topology correction using FreeSurfer while I have done the segmentation by myself? I would be grateful if you could help me with that. Best, Maedeh

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Different template between FSFAST and SPM?
by Zhi Li 11 Jul '19

11 Jul '19

External Email - Use Caution Dear Freesurfer experts, Now I am using both FSFAST and SPM to preprocessed my functional image data. In FSFAST, I replaced the subcortical template with the whole brain in the folder "mri.2mm", to get the whole brain volumetric data. I have also diluted the whole brain template in FSFAST. However, as showed in attached files, the resampled data in FSFAST seems smaller than that of SPM. May I ask if it is normal? Would the mask creation step in FSFAST caused this difference? I read from a previous PPT which said "FSL BET run on the template" in mask creation. As far as I know, the default parameter in BET may strip some part of prefrontal lobe sometime. If FSFAST apply BET or similar algorithm to strip skull, may I ask how could I change the parameter? Looking forward to your kind suggestions. Thanks and best wishes, Lizhi

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FW: Trouble viewing files on tkmedit
by Valerio, Kate 11 Jul '19

11 Jul '19

External Email - Use Caution I was attempting to view some of our images and kept receiving this error message (shown below). I tried looking online and saw some comments about not having a compatible version of XQuartz and the MacOS but they both seem be compatible versions and this was not a problem last week. XQuartz version is XQuartz 2.7.11 and the OS is Mojave 10.14.5. Are there any other errors that could cause this problem? ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... Thank you so much for your help. Best Kate Valerio

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Freesurfer versions & Amygdala Subnuclei.
by Jamie Hanson 10 Jul '19

10 Jul '19

External Email - Use Caution Dear Freesurfer List- I had a (hopefully) quick question about amygdala subnuclei segmentation. I know that the subnuclei routine is only available in the dev versions of Freesurfer, but can data already processed with stable v6.0.0 be used (with said script)? Basically, we have a number of subjects previously processed in the stable release and just wanted to complete amygdala subnuclei segmentation; is that any issue with mixing v.6 and the dev version to complete this? (Or should we reprocess everything in the dev version for this new project?) Thanks much, and all the best, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org

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Freesurfer July 2019