Re: [Freesurfer] Morphing Buckner2011 MNI152 to subject's space {Disarmed}

External Email - Use Caution Hi Katherine, Yes. This is still the best way if you have already run recon-all. Regards, Thomas On Sat, Oct 6, 2018 at 8:21 AM Katherine Damme wrote: > Hello, > > I have a tone of FS people who have been run through Recon-all and I am > happy

Re: [Freesurfer] Morphing Buckner2011 MNI152 to subject's space {Disarmed}

External Email - Use Caution Hello, I have a tone of FS people who have been run through Recon-all and I am happy with the output but I would like to expand the existing labels to include the Buckner 7 tight labels. Is this still the best way to update my subject labels to

Re: [Freesurfer] nu_correct disk i/o issues

Dear *, we also run Freesurfer on a cluster and are starting to use singularity, so naturally I'm curious about this issue. I was able to reproduce the error with a clean singularity run (-c -e). Then, I rebuilt a container to start nu_correct with "strace -f -e open,write" and I believe I found

Re: [Freesurfer] Definition of circular label centered on peak vertex

you can create a label with just that vertex, then use mri_label2label to dilate it, then use mri_segstats specifying the label with --slabel, using beta as input (--i), and specifying the output as --avfwf. Run it with --help to get more info On 10/5/18 11:10 AM, Milde, Christopher wrote:

Re: [Freesurfer] Error running setup_configure

You’re attempting to build the dev version of freesurfer, in which case you should follow the build instructions on this page - https://surfer.nmr.mgh.harvard.edu/fswiki/BuildGuide. If you’d like to build freesurfer 6, you’ll have to checkout the "stable6" git branch before running

[Freesurfer] How to convert enhanced dicom format

External Email - Use Caution Greeting, Our radiology department recently installed a Siemens Vida system. It apparently exports in "enhanced dicom” format, which doesn't work with any of my software. Does anyone know anything about this format? Cheers, Jason

Re: [Freesurfer] nu_correct disk i/o issues

Not that I know of, but this is not a native FS script, it comes from the MNI, so it could be doing something we don't understand. Can you do an experiment for us? Can you run it outside of the container using reprozip (or something equivalent) to see all the files it touches? On 10/5/18 5:31

[Freesurfer] Error running setup_configure

External Email - Use Caution We are attempting to build Freesurfer 6 on CentOS 7 x76_64. After cloning the git repo we see the following when running ./setup_configure configure.in:3866: the top level Makefile.am: error: required file './NEWS' not found Makefile.am: error:

[Freesurfer] Definition of circular label centered on peak vertex

External Email - Use Caution Dear FS experts I`m interested in extracting beta values from a FSFAST analysis performed in the subject`s native space. The beta values shall be extracted from a circular label around the peak vertex. How can you define a circular label centered

Re: [Freesurfer] Definition of circular label centered on peak vertex

Hi Chris if you can find the peak vertex you can create a single vertex label from it, then use mri_label2label --dilate N to create an approximation of an N-radius circle cheers Bruce On Fri, 5 Oct 2018, Milde, Christopher wrote: External Email - Use Caution Dear FS

[Freesurfer] nu_correct disk i/o issues

External Email - Use Caution We are trying to run recon_all inside an fmriprep singularity container, but are running into an issue with nu_correct. It says it cannot write to disk, however there is plenty of space on the tmpdir and output dir. Does this script try to write to any

Re: [Freesurfer] QAtools for Freesurfer version6?

External Email - Use Caution I guess this: https://surfer.nmr.mgh.harvard.edu/fswiki/QATools But it's outdated, I also gave it a try recently and tried to contact the author without success. It worked for v5, but is not compatible with v6 output. (If you search the list