5 Apr
2012
5 Apr
'12
9:59 a.m.
Hi Kaveh,
yes, you can create a 2d patch using tksurfer to cut it out, then mris_flatten to flatten it.
cheers Bruce On Thu, 5 Apr 2012, Kaveh Kohan wrote:
Thank you for all replies. One more question to bother you. in :
http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/fsrecon.ppt
In this tutorial, in the page 40 it reads "Flattening not done as part of standard reconstruction". Is it possible to get the 2D flat patch too (page 40 and 41)? I can embed the graph in 2D space but I am not sure it produces the same results.
Thanks again,
On Tue, Apr 3, 2012 at 8:36 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: read_surf.m will do the trick, but be sure to use 1-based indices! And note that the timeCourse.mgz you read is almost certainly a surface overlay with 137654 vertices and 236 time points, so if you read the surface f.vol(1,j,1,:) would be the timecourse for the jth index returned by read_surf
cheers, Bruce On Tue, 3 Apr 2012, Kaveh Kohan wrote: I think I figure out the problem with "mri_vol2surf". It seems that there is a bug in the executable. I switched to the older version of freesurfer (from 5.1 to 5.0) and it just works! I am not sure how to check the results. In matlab I used: >> f = MRIread('timeCourse.mgz'); >> size(f.vol) 1 137654 1 236 it should be OK, right? It seems that there are 137654 voxels. BTW, how can I read the graph structure of the vertex, ie x,y,z of each vertex, which neighbors of each vertex etc? In case you want to know the spec. of the sytem: ~$ uname -a Linux pc71 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux maybe the mri_vol2surf is not compatible with this machine? about the tar file, I just downloaded, it no probelm: ~$ wget http://dl.dropbox.com/u/7895831/tp1.tar.gz . kayhan kayhan 336958635 2012-04-03 20:09 tp1.tar.gz ~$ tar xvzf tp1.tar.gz If you still unable to download it let me know I will find another way to upload it. Thanks, On Tue, Apr 3, 2012 at 6:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: Can you double check that tar file? I get an error when I try to untar it -rw-r----- 1 greve greve 96469167 Apr 3 18:58 tp1.tar.gz On 04/03/2012 04:15 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. If you believe > this e-mail was > sent to you in > error and the e-mail > contains patient > information, please > contact the Partners > Compliance HelpLine at > http://www.partners.org/ complianceline > <http://www.partners.org/ complianceline > <http://www.partners.org/ complianceline > <http://www.partners.org/complianceline>>> . 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If you believe this > e-mail was sent to > you in error and > the e-mail > contains patient information, please > contact the > Partners > Compliance HelpLine at > http://www.partners.org/ complianceline > <http://www.partners.org/ complianceline > <http://www.partners.org/complianceline>> . If the > > e-mail was sent to > > you in error > but does not contain patient > information, please > contact the > sender and properly > dispose of the e-mail. > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard. edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/ > <http://surfer.nmr.mgh.harvard.edu/> fswiki/BugReporting > <http://surfer.nmr.mgh. harvard.edu/fswiki/ > BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > FileDrop: www.nmr.mgh.harvard.edu/ > <http://www.nmr.mgh.harvard.edu/> > facility/filedrop/index.html > <http://www.nmr.mgh.harvard. > edu/facility/filedrop/index. html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/ fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/ > facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. 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