[Freesurfer] blend own template into FS pipeline

Hi FreeSurfer experts, We are dealing with a sample of children MRI and we want to introduce our own templates into the pipeline instead of the MNI/tailarach. Any advice or guidance you can provide on how to go about doing this would be much appreciate it. Thanks, Kev

Re: [Freesurfer] blend own template into FS pipeline

On Mon, 25 Feb 2013, Schumman Resonance wrote: Hi FreeSurfer experts, We are dealing with a sample of children MRI and we want to introduce our own templates into the pipeline instead of the MNI/tailarach. Any advice or guidance you can provide on how to go about doing this would be much

[Freesurfer] Estimate of number of manual edits and time to complete in 100subject sample

This is a question for the FS community in general, I gather there is variability around this, but rather than an exact number and time, I was hoping for an estimate on how many scans would I expect to require manual edits(any of the check points recommended in the tutorials) as well as an

[Freesurfer] mri_convert mnc to nii

Hi freesurfers, I want to convert minc files to nii to work with them in ITK-SNAP segmentation software. I have used mri_convert binary, but the orientation on the nii images is completely wonky. Any advice in terms of how to use the --in_orientation argument --out_orientation argument flags?

Re: [Freesurfer] TAR fs files

g. That file is mostly irrelevant > in any case > > cheers > Bruce > > > On Wed, 12 Jul 2017, Schumman > Resonance wrote: > > > Hi freesurfers, > > I'm compressing FS files for storage, and while runnig TAR I got this > > message for all the f

[Freesurfer] TAR fs files

Hi freesurfers, I'm compressing FS files for storage, and while runnig TAR I got this message for all the files in the directory I'm compressing: "tar: data/sbj001_post_anat.nii.gz/mri/transforms/talairach.m3z.inv.y.mgz: file changed as we read it" Any thoughts on whether this message is making

[Freesurfer] content of "subjects_dir"

Dear free surfer community, Silly question here. I note the default "subjects_dir" in freesurfer contains a bunch of directories and files. If I set the environment so that my "subjects_dir" is not the default location, do I need to move any of the files in the original location to the new one?

[Freesurfer] Freeview error

Hi, Newbie question. When I try to upload a surface to Freview I get the following error: [0]PETSC ERROR: [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job:

Re: [Freesurfer] Freeview error

the full command line and screen output? > Cheers > Bruce > > On May 27, 2017, at 11:45 PM, Schumman Resonance <schumm...@gmail.com> > wrote: > > Hi, > > Newbie question. > > When I try to upload a surface to Freview

[Freesurfer] Untar and sh files in dev version

External Email - Use Caution Hi, Couple of newbie questions. I downloaded the dev version of freesurfer and did: tar xvzf freesurfer-linux-centos6_x86_64-dev.tar.gz to get gzip: stdin: unexpected end of file tar: Unexpected EOF in archive tar: Unexpected EOF in archive

Re: [Freesurfer] Untar and sh files in dev version

; > and then take a look at the files. > > - Rob > > On Aug 10, 2018, at 10:25 PM, Schumman Resonance > wrote: > > External Email - Use Caution > > Hi, > > Couple of newbie questions. I downloaded the dev version of freesurfer > and did: > tar xvzf > fr

Re: [Freesurfer] Untar and sh files in dev version

86_64-stable-pub-v6.0.0.tar.gz> > > Then you will need 5 GB of space to uncompress it. I would add the v > option so you can see the expansion in progress, > > $ tar zxvpf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz > > - Rob > > > On Aug 11, 2018, at 2:55 AM

[Freesurfer] Stats2table_bash.sh script

External Email - Use Caution Hi, I'm trying to run the Stats2table_bash.sh script from Jamaan Alghamdi & Dr. Vanessa Sluming. And I get This error: File "/Applications/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects

Re: [Freesurfer] Stats2table_bash.sh script

s bert > > It looks like the subjects option expects the name for at least one > subjects (data), > but the help output says you can list more than one subjects name as the > argument to > —subjects > > On Aug 12, 2018, at 12:31 PM, Schumman Resonance >

Re: [Freesurfer] Untar and sh files in dev version

, > > Andrew > > > > *From: * on behalf of Schumman > Resonance > *Reply-To: *FS Help > *Date: *Saturday, August 11, 2018 at 9:24 AM > *To: *FS Help > *Subject: *Re: [Freesurfer] Untar and sh files in dev version > > > > *External Email -

[Freesurfer] is untar existing runtime2012b.tar.gz sufficient?

Hi, I was following the steps on the wiki to run the hipposubfields stream and it mentioned runtime needs to be downloaded. However, I noticed in my free surfer home the tar file runtime2012b.tar.gz. Would untaring this existing file in fresurfer homer put the libraries required in the MCR