Re: [Freesurfer] PVE correction tool on Freesurfer 6

Hi Doug, Thanks a lot for the page! It was very helpful. I have a few questions about one of the commands and a question for one of the output files. 1) mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o

Re: [Freesurfer] TRACULA group stats visualization

Hi Anastasia, All subjects had both time-points (for DWI and T1-weighted recons). The recons were run following the standard longitudinal pipeline for FS. Would it matter that I ran the pipeline piecemeal (i.e. separate configuration files for each subject--see attached example)? In case you

Re: [Freesurfer] FreesurferNHP

We haven¹t yet released our NHP pipeline yet, mainly because the software support requirements are a bit higher and so it has made more sense to work with people as a part of collaborations. This is more of a question for the HCP Users list or an off-list inquiry because the FreeSurfer group

Re: [Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message

Hi Knut Jørgen - Can you please send your entire trac-all.log? Thanks! a.y On Mon, 11 Jul 2016, Knut J Bjuland wrote:   flirt.fsl -ref /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii -in

Re: [Freesurfer] Coordinates in TRACULA group analysis

Hi Anri - This may be a bug that was fixed at some point. Can you send me the scripts/trac-all.local-copy from one of your subjects? Thanks! a.y On Mon, 11 Jul 2016, Anri WATANABE wrote: Hi Anastasia,There is an error in .log files of left corticospinal tract in cvs template and I

Re: [Freesurfer] TRACULA tract group comparison p-values

Hi Barbara - Unfortunately we are very limited right now in our options for point set overlay display. I guess there's nothing that would be more suitable for displaying values that go all the way from negative to positive (which is what I suspect you have). I'll submit this request to

Re: [Freesurfer] Fwd: TRACULA stat extraction issue

Hi Shashwath - Unfortunately this is not possible right now, so you'd have to add those extra columns after you run it. a.y On Fri, 8 Jul 2016, Shashwath Meda wrote: Hi Anastasia - Yes thats what i figured, however the way our pipeline system is setup this was the most straightfoward way

Re: [Freesurfer] TRACULA group stats visualization

Hi Derek - Indeed this looks not to be in MNI coordinates, and I haven't been able to replicate the problem in our own longitudinal data. Did you by any chance have any subjects that had only a single time point? a.y On Thu, 7 Jul 2016, Derek Pisner wrote: > Sure thing. fmajor mean.txt file

Re: [Freesurfer] Freeview question

Yes, that worked Thank you. > Have you tried rebooting your computer? > > Best, > Ruopeng > >> On Jul 12, 2016, at 3:14 PM, pfot...@nmr.mgh.harvard.edu wrote: >> >> Hello FS Community, >> Lately, whenever I am trying to use freeview I get the following error >> message: >> >> freeview.bin:

Re: [Freesurfer] Freeview question

Have you tried rebooting your computer? Best, Ruopeng > On Jul 12, 2016, at 3:14 PM, pfot...@nmr.mgh.harvard.edu wrote: > > Hello FS Community, > Lately, whenever I am trying to use freeview I get the following error > message: > > freeview.bin: error while loading shared libraries:

[Freesurfer] Slight rotation when viewing brainmask.mgz in Freeview - why and is this a cause for concern?

Hello FS developers/users, When viewing brainmask.mgz in Freeview, for some subjects the brain is slightly (~10-20 degrees) rotated. By looking at the raw data, I see that their head position in the scanner was slightly skewed. I thought that brainmask.mgz is created after Talairach

[Freesurfer] Freeview question

Hello FS Community, Lately, whenever I am trying to use freeview I get the following error message: freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory Exit 127 The error started showing up after the cluster went

[Freesurfer] Visually inspecting subcortical segmentations + what command should be run to apply manual fixes to aseg.mgz voxels?

Hello FS developers/users, I have a two part question regarding subcortical segmentation: 1) To visually inspect if segmentation accurately captures structure boundaries (e.g., amygdala) I am using the norm.mgz file and overlaying it with the aseg.mgz file in Freeview. Is this correct? Or should

Re: [Freesurfer] mri_glmfit-sim

There were bugs in AlphaSim (not FSL randomise); these do not affect FS because FS is an independent implementation. FS does not use random field theory (RFT) but monte carlo simulation. The MC simulation does assume that the smoothing kernel is gaussian, so violations of that assumption will

[Freesurfer] CVS question

Hi, I want to compare two populations using CVS so I can cross-register multimodal maps (e.g. ASL, FA, QSM) for volumetric comparisons. I’ve gotten CVS to work very well registering one subject to another, it really is impressive However, using the --mni option, it doesn’t work so well,

[Freesurfer] Beta-Zero Correction - No Phase File

Hi, I'm working with a dataset that outputs only one file (not two separate mag and phase files) for the fieldmap. The data was also collected on non-Siemens scanners: Philips Ingenia and GE SIGNA HDx (not sure if this is the reason the fieldmaps are unpacking differently). I've attached the

Re: [Freesurfer] tcsh update

On ubuntu it would be something like: sudo apt-get update tcsh On 07/11/2016 01:55 PM, shi yao wang wrote: > Dear FS experts: > I am running FS in local computer and showing following error message > and program stopped at recon-all > > WARNING: tcsh v6.17.06 has an exit code bug! Please

[Freesurfer] mri_convert WARNING: files are not found to be different and cannot be sorted

Hello all, I have run mri_convert on a series of dicoms and received the following error for several of my images. As with the previous bug report for this I have run mri_info on my dicom series and it’s output is below. My main concern is since these dicoms are being jumbled up and I am not

Re: [Freesurfer] FreesurferNHP

Hi Peter, > On Jul 12, 2016, at 14:42 , Lauro, Peter wrote: > > Hello, > > I'm trying to reconstruct cortical surfaces from non-human primate MRIs. I > tried following the instructions/scripts listed here > (https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData), but I

Re: [Freesurfer] Regarding: Concatenating hippocampal to generate sig.mgh

Hi Sampada why not just take the volume of the hippocampus from the aseg.stats? Why do you want an mgz? You just want one number per subject, right? Bruce On Tue, 12 Jul 2016, Dr Sampada Sinha wrote: Dear Bruce,  Thanks for you for your response. I am trying to  generate an average

[Freesurfer] FreesurferNHP

Hello, I'm trying to reconstruct cortical surfaces from non-human primate MRIs. I tried following the instructions/scripts listed here ( https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData), but I was unable to make it work (I'm also running FS 5.3). I noticed on the Washington-Pipelines github

[Freesurfer] R: Re: Recon-all error after El Capitain update

This is the command and the error line. Thanks. Stefano recon-all -all -i $SUBJECTS_DIR/T1_STRUCT.nii.gz -subject SUBJECTS_DIR # INFO: fsaverage subject does not have perirhinal labels! \n cd /Applications/freesurfer/subjects/subject_prova/Control89;

Re: [Freesurfer] Regarding: Concatenating hippocampal to generate sig.mgh

Dear Bruce, Thanks for you for your response. I am trying to generate an average hippocampal volume and its correlation with HAM-D score in early and late onset depression (eod vs lod). One way I tried to do it was by binarizing and concatanating the hippocampal volumes and then run mri_glmfit.