3 Apr
2012
3 Apr
'12
4:57 p.m.
sorry, this is going to take me a while to get to. We're running our FS course this week, so I have to resolve issues in the free time between talks, etc. doug
On 4/3/12 4:15 PM, Kaveh Kohan wrote:
Any thought on this? I am wondering there might be something wrong with FSL registration. I don't know what bbregister uses for registration but as far as I know "flirt" is unable to register 4d-image (such as fmri ) to 3D; it only accepts 3d as input and output. Is it possible to register freesurfer surface on the mean activation of fmri (therefore both 3d) and then sample from the surface on the fmri space?
Any reply is very appreciated.
On Mon, Apr 2, 2012 at 5:29 PM, Kaveh Kohan <kaveh.kohan@gmail.com mailto:kaveh.kohan@gmail.com> wrote:
No it did not work, mri_vol2surf still produces the same error (see below). In the link below, I have shared the freesurfer results (in the FREESURFER folder) plus fmri image (in the NITFI folder). I am wondering if there is anything wrong with my installation of the mri_vol2surf (stable 5). The data is anonymized. http://dl.dropbox.com/u/7895831/tp1.tar.gz --------------------------------- OUTPUT of mri_vol2surf ~$ mri_vol2surf --mov fMRI.nii.gz --reg bbregister/fmri-TO-orig.dat --hemi lh --o ./timeCourse.mgz srcvol = fMRI.nii.gz srcreg = bbregister/fmri-TO-orig.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /home/kayhan/test/myproject/control001/tp1/FREESURFER/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Segmentation fault ------------------------- On Mon, Apr 2, 2012 at 2:45 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: The new registration looks much better. The value I look at is the first value in the mincost file. For your data, it's about .6. This value will be between 0 and 1.1. There's no way to determine what a proper cut off is, but in your previous reg, the value as .9 or so, so .6 is probably fine. Did mri_vol2surf work with the new registration? doug On 04/02/2012 05:05 PM, Kaveh Kohan wrote: I re-ran the registration with FSL (initfsl option) and the results looks fine to me. I have attached the new log file. If the results look fine and it does not produce error, is there any way that I check that my registration failed? Is there any term that I should search for in the log file? Do you think that the whole problem could be because of the headers of the files? The de-identified data are already unloaded here. It contains the freesurfer results (in the FREESURFER foder) and the fmri image in the NIFTI folder. I would be appreciate if you can tell how to fix the problem with mri_vol2surf http://dl.dropbox.com/u/ 7895831/tp1.tar.gz <http://dl.dropbox.com/u/7895831/tp1.tar.gz> Thanks, On Mon, Apr 2, 2012 at 4:12 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard. edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: It looks like your registration failed (though it completed without error). Did you check it with tkregister? I don't think that would explain the segfault, but it is worth tracking it down. doug On 4/2/12 2:54 PM, Kaveh Kohan wrote: I have also attached the "fmri-TO-orig.dat.log" maybe that has some useful information about the previous step (bbregister) . On Mon, Apr 2, 2012 at 2:48 PM, Kaveh Kohan <kaveh.kohan@gmail.com <mailto:kaveh.kohan@gmail.com> <mailto:kaveh.kohan@gmail.com <mailto:kaveh.kohan@gmail.com>> > wrote: No, it does not; sorry for the confusion. I have attached a clean output below. I don't know what it means. May be there is something wrong with the format of the files. Do you need me to upload the freesurfer results and fMRI somewhere for you to inspect it? ------------ OUTPUT ~$ mri_vol2surf --mov fMRI.nii.gz --reg bbregister/fmri-TO-orig.dat --hemi lh --o ./timeCourse.mgz srcvol = fMRI.nii.gz srcreg = bbregister/fmri-TO-orig.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /home/kayhan/test/myproject/ control001/tp1/FREESURFER/ surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Segmentation fault ------------ On Mon, Apr 2, 2012 at 1:44 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard. edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: Hmmm, I don't know why it is doing that. Does it really print "using old" after the seg fault was that accidentally pasted in? It should not be printing that twice, maybe it's a clue. doug On 04/02/2012 10:26 AM, Kaveh Kohan wrote: I have tried and it did not work (the same seg fault, see below). It seems that it successfully performs the mapping but it fails in final step probably saving the results. Is the data format that I used OK? I am using Ubuntu 10.10, the version of "mri_vol2surf" is "stable5". Please let me knoe if more information is required. Thanks. ~$ mri_vol2surf --mov fMRI.nii.gz --reg bbregister/fmri-TO-orig.dat --hemi lh --o ./timeCourse.mgz srcvol = fMRI.nii.gz srcreg = bbregister/fmri-TO-orig.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /home/kayhan/test/myproject/ control001/tp1/FREESURFER/ surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface *Segmentation fault* using old On Sun, Apr 1, 2012 at 2:34 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh. harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> <mailto:fischl@nmr.mgh <mailto:fischl@nmr.mgh>. harvard.edu <http://harvard.edu> <mailto:fischl@nmr.mgh. harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote: Hi Kaveh use bbregister to register your functional data to the surface, then mri_vol2surf to sample it from the volume onto the surface and you should be all set. cheers Bruce On Sun, 1 Apr 2012, Kaveh Kohan wrote: Hi FreeSurfer Users, I am new to the Freesurfer, I have a question regarding mapping of the resting state fMRI time courses on the cortex area. I apologise in case my question is naive. please bear with me: Is it possible to have time-courses sampled from cortex? I mean how can I get corresponding time-course for each vertex on the cortex ? I know that FreeSurfer can produce mask for cortex are but I would like to have time-courses on the flattened (2D) map; ie assuming that cortex is flattened, each pixel of the 2D flattened image which resides in the cortex (I guess it corresponds to a vertex on the cortex manifold?) is time-series. I have ran recon-all on the T1. All of those operation were done using a third party packages that uses freesurfer namely CMTK (http://cmtk.org). I do not exactly know how to use "bbregister" to register the parcellation on the resting-state fMRI image? I would be thankful if you can help. Thanks The information in this e-mail is intended only for the person to whom it is addressed. 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