[Freesurfer] dt-recon output file format

Hi, Question for the developers. Is it possible to adjust the dt-recon tool such that the output files are in zipped NIFTI format (.nii.gz) in view of the enormous amount of data that is generated. It can accept .nii.gz files as input. Thank you in advance, Ed

Re: [Freesurfer] dt-recon output file format

Hi Ed, we should add this as the default, but for now you can just go into the dt_recon script and do a global replace of: .nii -- .niz cheers, Bruce On Tue, 9 Feb 2010, Ed Gronenschild wrote: Hi, Question for the developers. Is it possible to adjust the dt-recon tool such that the

[Freesurfer] FS Deformable Xform

Hello all, short time reader, first time poster... I have a question regarding the current FreeSurfer volumetric pipeline. This page: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferAnalysisPipelineOverview states that FreeSurfer has 5 stages and they are described in Fischl 2002,2004 (which

Re: [Freesurfer] dt-recon output file format

Bruce, Is it .niz or nii.gz? Ed On 9 Feb 2010, at 15:04, Bruce Fischl wrote: Hi Ed, we should add this as the default, but for now you can just go into the dt_recon script and do a global replace of: .nii -- .niz cheers, Bruce On Tue, 9 Feb 2010, Ed Gronenschild wrote: Hi,

Re: [Freesurfer] FS Deformable Xform

Hi Suresh, yes, there is a nonlinear volumetric registration that we compute described in the 2004 paper. We also do a series of intensity normalizations, which we also describe somewhat in the 2004 paper i think. The morph has a standard max posterior term, and also a density-based term that

Re: [Freesurfer] dt-recon output file format

actually, you're right, it's .nii.gz On Tue, 9 Feb 2010, Ed Gronenschild wrote: Bruce, Is it .niz or nii.gz? Ed On 9 Feb 2010, at 15:04, Bruce Fischl wrote: Hi Ed, we should add this as the default, but for now you can just go into the dt_recon script and do a global replace of:

[Freesurfer] ITI/ISI in optseq2

hello list, 1. Is there a way to make sure Optseq2 inserts a null after each event (and thus creating an ISI/ITI between every conditions)? If not - how is it possible to make sure there's a minimal ITI/ISI between each stimuli? 2. If defining an ITI is possible in optseq2, Is there a way to

Re: [Freesurfer] smooth pial surface in occipital pole region

Hi Yuning, it's hard to assess from a single slice, but you can try rerunning autorecon2-pial if you want. cheers Bruce On Tue, 9 Feb 2010 yzha...@artsci.wustl.edu wrote: Hi experts, I found that the pial surface in the occipital pole region tends to be smooth, after running recon-all.

[Freesurfer] Skull Stripping extra dura vasculature

Hello, I have a series of datasets with skull stripping issues - namely left over dura/vasculature in the occipital cortex, and some in frontal areas.(Attached is a jpeg of the type of issue. It's pervasive throughout the slices, across a handful of subject data.) I have rerun skull

Re: [Freesurfer] Skull Stripping extra dura vasculature

Hi Sherry, that's pretty tough. The dura is very bright and quite close to the gm. You may need to erase more of the dura Bruce On Tue, 9 Feb 2010, Sherri Novis wrote: Hello, I have a series of datasets with skull stripping issues - namely left over dura/vasculature in the occipital

Re: [Freesurfer] Skull Stripping extra dura vasculature

Hi Sherri, it's hard to say without seeing the images. If you want to send us the orig.mgz we can take a look. Can you also give us the details of the acquisition? Scanner, coil, TR/TE/flip/# of acquisitions, etc? Bruce On Tue, 9 Feb 2010, Sherri Novis wrote: Thanks Bruce. Is there

[Freesurfer] Editing Parcellations

Dear Freesurfer List I am trying to edit the parcellations using tkmedit, but I am unable to effect the Segmentation Brush label using the Configure Segmentation Brush window. Regardless of my selection, my drawing is labeled out of bounds. I don;t see an apply button or anything like

Re: [Freesurfer] Editing Parcellations

Hi Jennifer, do you mean editing the aseg.mgz? Can you send us the exact tkmedit command line? Bruce On Tue, 9 Feb 2010, Jennifer Bramen wrote: Dear Freesurfer List I am trying to edit the parcellations using tkmedit, but I am unable to effect the Segmentation Brush label using the

[Freesurfer] diagnostic level

Hi, there, Both mris_ca_label and mris_ca_train have a -v option which is called: diagnostic level. What is the meaning of this diagnostic level? Thanks! Guang _ Hotmail: Trusted email

Re: [Freesurfer] diagnostic level

actually that is incorrect in the help. It sets a diagnostic flag to spit out all the information it has about a specific vertex number that you give on the command line On Tue, 9 Feb 2010, Guang Zeng wrote: Hi, there, Both mris_ca_label and mris_ca_train have a -v option which is called:

Re: [Freesurfer] Pallidum Volume Assymetry in hemispheres and fs versions

Hi Jeff, the pallidum is quite small and quite low-contrast, so those numbers aren't surprising between versions that are that different. How do they look visually? Does either version look more accurate? It's amazing how just a couple of ambiguous voxels here and there can result in a 6-9%

[Freesurfer] Trouble installing freesurfer to a cluster

Hi, I am trying to install the freesurfer-Linux-suse-ia64-stable-pub-v4.5.0.tar to my user home directory (/home/knutsen) on the following Caltech cluster: Neuroecon Cluster 12 Dell Poweredge 1950 nodes 16 GB RAM per node Gigabit ethernet interconnect Matlab Distributed compute engine Rocks 5.1

Re: [Freesurfer] Trouble installing freesurfer to a cluster

hmmm, have you tried: chmod a+x /home/knutsen/freesurfer/bin/* not sure why they wouldn't be executable though. Bruce On Tue, 9 Feb 2010, Tamara Knutsen wrote: Hi, I am trying to install the freesurfer-Linux-suse-ia64-stable-pub-v4.5.0.tar to my user home directory (/home/knutsen) on the

[Freesurfer] recon-all analyze 7.5 format

Hi all, I've got .IMG and .HDR files in analyze 7.5 format, and ran recon-all -s subject -i file.img it doesn't seem to refer the .hdr file. What else should I do to use analyze format in Freesurfer? SG ___ Freesurfer mailing list