Re: [Freesurfer] Viewing Uncorrected Significance Map in Freeview

Try changing the thresholds (via the Configure button). When it first loads, the thresholds are set very low. When they get changed to your values (4,5), then there is nothing left and it looks like a blank brain. On 7/6/2019 9:38 AM, Marie Hill wrote: External Email - Use Caution Hi e

Re: [Freesurfer] How to Divide the Surface Parcellations of the Brain

Can you use mris_divide_parcellation On 7/8/2019 1:27 PM, Mahshid Fouladivanda wrote: External Email - Use Caution Dear Bruce, All the outputs are .nii and .gii I do not know if it is possible to convert it to the annotation! By the way, what is needed for creation of the annotation fi

Re: [Freesurfer] make_average_subject error: could not load norm volume from (null)

I think it is crashing outside of make_average_surface and make_average_volume, so the log files are not telling me what is going on. Can you capture the full terminal output? Also, you can try it with two subjects so that it runs faster (but it might not crash). On 7/10/2019 5:39 AM, Mads Jen

Re: [Freesurfer] A Question Regarding Topology Correction

It does not sound like something we can do, though I don't entirely follow everything that you wrote On 7/10/2019 11:07 PM, Maedeh Khalilian wrote: External Email - Use Caution Dear FreeSurfer experts, I know that FreeSurfer does segmentation, surface reconstruction and topology corre

Re: [Freesurfer] optseq2 parameters setup

On 7/15/2019 12:50 PM, Tugce Duran wrote: External Email - Use Caution Hi Dr. Greve, I am interested in designing the Face Name Associative Memory Exam (FNAME) fMRI task for our study. There are 80 face-name pairs that we will use and the duration can be between 3.5 and 4.75 secs. I

Re: [Freesurfer] Question about coordinates in Freesurfer

For question 1, try this https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems You did not say which MNI space you were dealing with (we use mni305, not 152). On 7/15/2019 12:02 PM, Zhi Li wrote: External Email - Use Caution Thank you very much, Tim. Any idea for the 1st question?

[Freesurfer] freeview

External Email - Use Caution I try again with fortran, uploaded it again, and now I get this message: jcrn12@jcrn12-VirtualBox:~$ freeview This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Reinstalling the application may fix th

[Freesurfer] Fwd: freeview

External Email - Use Caution libgfortran.so.3. No found. I día the fortran step as you indicated yo me. Thanks again, JC. -- Mensaje reenviado - De: fsbuild Fecha: El lun, 15 de jul. de 2019 a las 17:09 Asunto: Re: [Freesurfer] freeview Para: Cc: Did you try,

Re: [Freesurfer] freeview

External Email - Use Caution Did you try, $ ldd /usr/local/freesurfer/bin/freeview | grep not ? - R. On Jul 12, 2019, at 08:42, Juan Rivas wrote:External Email - Use CautionIt looks like freeview is in: jcrn12@jcrn12-VirtualBox:~$ /usr/local/

[Freesurfer] Fwd: freeview

External Email - Use Caution It looks like freeview is in: jcrn12@jcrn12-VirtualBox:~$ /usr/local/freesurfer/bin/freeview But when I try to use it, I can not do it, because: jcrn12@jcrn12-VirtualBox:~$ ldd freeview | grep not ldd: ./freeview: No such file or directory. Thank you fo

Re: [Freesurfer] Fwd: Fwd: Freeview

you need to run: ldd /usr/local/freesurfer/bin/freeview | grep not cheers Bruce On Fri, 12 Jul 2019, Juan Rivas wrote: External Email - Use Caution It does not work:jcrn12@jcrn12-VirtualBox:/usr/local/bin$ which freeview /usr/local/freesurfer/bin/freeview jcrn12@jcrn12-Vir

[Freesurfer] Fwd: Fwd: Freeview

External Email - Use Caution It does not work: jcrn12@jcrn12-VirtualBox:/usr/local/bin$ which freeview /usr/local/freesurfer/bin/freeview jcrn12@jcrn12-VirtualBox:/usr/local/bin$ ldd freeview | grep not ldd: ./freeview: No such file or directory JC -- Forwarded message ---

Re: [Freesurfer] Fwd: Freeview

External Email - Use Caution Sorry - from your previous mail, I mistakenly thought “which freeview” returned /usr/local/bin/freeview. If you can reproduce what you did before to run freeview from the command line where it tells you that it was not finding libgfortran, then “which

[Freesurfer] freeview

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.

[Freesurfer] Fwd: Freeview

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.

[Freesurfer] optseq2 parameters setup

External Email - Use Caution Hi Dr. Greve, I am interested in designing the Face Name Associative Memory Exam (FNAME) fMRI task for our study. There are 80 face-name pairs that we will use and the duration can be between 3.5 and 4.75 secs. I have used the following command: opt

Re: [Freesurfer] Freeview

External Email - Use Caution 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 wrote:External Email - Use CautionHi, thank you for your help. I tried again and

Re: [Freesurfer] general installation and configuration questions (new user!)

External Email - Use Caution Hello Robin, I believe folks use the freesurfer binary archive expanded/installed on file servers that are remotely mounted, e.g., thru NFS, so everyone can share a common installation.  IT/dev-ops can implement that in different ways, e.g., maybe th

[Freesurfer] Freeview

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 $ wh

Re: [Freesurfer] Freeview

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 free

[Freesurfer] Freeview

External Email - Use Caution -- Forwarded message - De: Juan Rivas Date: vie., 12 jul. 2019 a las 3:02 Subject: Re: [Freesurfer] Freeview To: fsbuild Hi, thank you for your answer. I did what you recommended to me, and I get this message: freeview: error while l

Re: [Freesurfer] Question about coordinates in Freesurfer

External Email - Use Caution Thank you very much, Tim. Any idea for the 1st question? Thanks and best wishes, Lizhi On Sat, 13 Jul 2019 at 09:18, Tim Schäfer wrote: > External Email - Use Caution > > Dear Lizhi, > > on your 2nd question: a rough explanation is on the F

Re: [Freesurfer] Freeview

External Email - Use Caution 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 yu

[Freesurfer] Freeview

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] MRI Technologist Job Posting at The Ohio State University

External Email - Use Caution Hello, The Center for Cognitive and Behavioral Brain Imaging (CCBBI) at The Ohio State University is seeking to hire a Magnetic Resonance Imaging (MRI) Technologist. Please see attached document for full description. Best Regards, The Clinical Neurosc

Re: [Freesurfer] Create no-skull brain with gray matter mask

The ribbon.mgz file should be about the same (but for both hemis) On 7/15/2019 9:36 AM, Bruce Fischl wrote: Hi Marina if you have a pial surface you can use mris_fill to fill the interior then use that as a mask cheers Bruce On Mon, 15 Jul 2019, Marina Fernández wrote: External Emai

Re: [Freesurfer] CSF mask

that or see here https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 7/15/2019 9:39 AM, Bruce Fischl wrote: you can do this with mri_convert: mri_convert -rl native_volume.mgz -rt nearest apas+head.mgz apas+head.native.mgz cheers Bruce On Mon, 15 Jul 2019, Laboratorio de Neurocie

Re: [Freesurfer] CSF mask

you can do this with mri_convert: mri_convert -rl native_volume.mgz -rt nearest apas+head.mgz apas+head.native.mgz cheers Bruce On Mon, 15 Jul 2019, Laboratorio de Neurociencia Funcional wrote: External Email - Use Caution Thank you, Doug. The voxel resolution of the apa

Re: [Freesurfer] Create no-skull brain with gray matter mask

Hi Marina if you have a pial surface you can use mris_fill to fill the interior then use that as a mask cheers Bruce On Mon, 15 Jul 2019, Marina Fernández wrote: External Email - Use Caution Dear experts, I need to get a no-skull brain. The automated no-skull brain has m

Re: [Freesurfer] CSF mask

External Email - Use Caution Thank you, Doug. The voxel resolution of the apas+head.mgz file is 1mm3. Would it be possible to obtain the same file but with the native resolution? Best, Jose El lun., 15 jul. 2019 a las 6:01, Greve, Douglas N.,Ph.D. (< dgr...@mgh.harvard.edu>) escr

[Freesurfer] general installation and configuration questions (new user!)

External Email - Use Caution Hi folks, I am new to the Freesurfer world and I have a couple of questions about installing the application, specifically around the 10Gb "footprint" of data, after unpacking the archive file. So I have run through the installation and configuratio

[Freesurfer] Create no-skull brain with gray matter mask

External Email - Use Caution Dear experts, I need to get a no-skull brain. The automated no-skull brain has many errors and I was thinking that I could create it taking into account the gray matter mask (we segment manually, so the mask is accurate) in such a way that everything o