Hello All,
I have a question regarding the actual command issued under the mris_preproc wrapper.
I noticed that when I ran the recon-all -qcache to resample the different anatomical measures like thickness etc to fsaverage, one of the step is the following -
mri_surf2surf --srcsubject 068 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval 068.1.mgh --sval ./lh.thickness --sfmt curv --noreshape --no-cortex
When I ran mris_preproc using the tutorial as specified here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup
the step similar to the one above is the following mri_surf2surf --srcsubject 068 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval 068.1.mgh --sval ./rh.VisStimBoth_rb.mgh --noreshape --no-cortex"
What does the "--sfmt curv" do ?
What happens if its included in the resampling of the functional data ? Should I ?
Please let me know.
Thanks
Ri
Hello FreeSurfer users,
I may be asking a stupid question but it really troubled me a while.
I converted dicom files to nift using dcm2niigui (MRIcron). In fslview, it displayed in RAS coordinates, but template of FSL are in LAS coordinates. Should I filp L-R before doing any further analysis? Besides, my structrual imagews were scanned in sagittal view, and after dcm2niigui transforation, it's in PIL coordinates in fslview. Should I reorient the image to LAS coordinates too? But the letters L R I S A P are labled correctly (at least A-P and I－S are correct), which means FSL can read in orientation information correctly. So I am confused whether I should reorient my data or not. I then processed strucutre images with Freesurfer, and the results from reoriented and not-reoriented images are different, so which one is correct?
Any help is appreciated, Thanks! --
Chunhui Chen
2010-05-04
Chunhui Chen _________________
Institute of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875
if the directions are labeled properly then you aer probably ok. In general you are better off just giving recon-all the dicom files as input and not doing any conversions beforehand.
cheers Bruce On Tue, 4 May 2010, chenchunhuichina wrote:
Hello FreeSurfer users,
I may be asking a stupid question but it really troubled me a while.
I converted dicom files to nift using dcm2niigui (MRIcron). In fslview, it displayed in RAS coordinates, but template of FSL are in LAS coordinates. Should I filp L-R before doing any further analysis? Besides, my structrual imagews were scanned in sagittal view, and after dcm2niigui transforation, it's in PIL coordinates in fslview. Should I reorient the image to LAS coordinates too? But the letters L R I S A P are labled correctly (at least A-P and I£S are correct), which means FSL can read in orientation information correctly. So I am confused whether I should reorient my data or not. I then processed strucutre images with Freesurfer, and the results from reoriented and not-reoriented images are different, so which one is correct?
Any help is appreciated, Thanks! --
Chunhui Chen
2010-05-04
Chunhui Chen _________________
Institute of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875
Hi, all Bruce has suggested that we can directly give recon-all dcm file as input. However, I have done recon-all with mgz file as input. Is that input file OK? For example, sub1 has 128 dcm files, 001~128, I just ran a syntax: mri_convert 001 sub1.mgz then the computer read 128 dcm files and convert them into sub1.mgz, then I ran recon-all with "sub1.mgz" as input file The version I used was freesurfer-Linux-centos4-stable-pub-v4.5.0 Besides, I have checked the aseg.stats and lh/rh.aparc.stats generated from different input files(dcm or mgz) in one subject, and find that they are completely the same. It must be a very stupid question, however, I need some confirmation. Too much Thanks! Jin
2010/5/4 Bruce Fischl fischl@nmr.mgh.harvard.edu
if the directions are labeled properly then you aer probably ok. In general you are better off just giving recon-all the dicom files as input and not doing any conversions beforehand.
cheers Bruce
On Tue, 4 May 2010, chenchunhuichina wrote:
Hello FreeSurfer users,
I may be asking a stupid question but it really troubled me a while.
I converted dicom files to nift using dcm2niigui (MRIcron). In fslview, it displayed in RAS coordinates, but template of FSL are in LAS coordinates. Should I filp L-R before doing any further analysis? Besides, my structrual imagews were scanned in sagittal view, and after dcm2niigui transforation, it's in PIL coordinates in fslview. Should I reorient the image to LAS coordinates too? But the letters L R I S A P are labled correctly (at least A-P and I－S are correct), which means FSL can read in orientation information correctly. So I am confused whether I should reorient my data or not. I then processed strucutre images with Freesurfer, and the results from reoriented and not-reoriented images are different, so which one is correct?
Any help is appreciated, Thanks! --
Chunhui Chen
2010-05-04
Chunhui Chen _________________
Institute of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875
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Yes, that's fine.
you don't need to reorient your data for FreeSurfer. Check the FSL site/list to see what there orientation requirements are
doug
chenchunhuichina wrote:
Hello FreeSurfer users, I may be asking a stupid question but it really troubled me a while.
I converted dicom files to nift using dcm2niigui (MRIcron). In fslview, it displayed in RAS coordinates, but template of FSL are in LAS coordinates. Should I filp L-R before doing any further analysis? Besides, my structrual imagews were scanned in sagittal view, and after dcm2niigui transforation, it's in PIL coordinates in fslview. Should I reorient the image to LAS coordinates too? But the letters L R I S A P are labled correctly (at least A-P and I－ S are correct), which means FSL can read in orientation information correctly. So I am confused whether I should reorient my data or not. I then processed strucutre images with Freesurfer, and the results from reoriented and not-reoriented images are different, so which one is correct?
Any help is appreciated, Thanks! -- Chunhui Chen 2010-05-04 Chunhui Chen _________________ Institute of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875
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