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
You should register the fMRI to the anatomical with bbregister. Run it with --help for more info, also see the wiki tutorial on fMRI integration. You can then sample the time series to the surface with mri_vol2surf doug
On 4/1/12 1:52 PM, 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Thank you very much for the replies.
I checked the wiki and tutorial and I have successfully registered fMRI on the T1 images; the results were reasonable after checking with tkregister2. However, the "mri_vol2surf" fails producing "Segmentation fault", I don't know how to resolve it. Here is how I ran the whole process:
export SUBJECTS_DIR=/home/kayhan/test/myproject/control001/tp1 cd ${SUBJECTS_DIR}/NIFTI bbregister --mov fMRI.nii.gz --bold --s FREESURFER --init-fsl --reg bbregister/fmri-TO-orig.dat --fslmat bbregister/fmri-TO-orig.mat
FREESURFER is the place the freesurfer files are. I have checked the results of the bbregister and it was fine. Here is how I called "mri_vol2surf" :
~$ mri_vol2surf --mov fMRI.nii.gz --regheader FREESURFER --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 Computing registration from header. Using /home/kayhan/test/myproject/control001/tp1/FREESURFER/mri/orig.mgz as target reference. 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*
I would be thankful if you can help.
Thanks,
On Sun, Apr 1, 2012 at 2:34 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
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/**compliancelinehttp://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.
You should not use --regheader with --reg, but that should not have caused a seg fault. I'm not sure what went wrong, but try removing --regheader and see if it works. doug
On 4/2/12 2:38 AM, Kaveh Kohan wrote:
Thank you very much for the replies.
I checked the wiki and tutorial and I have successfully registered fMRI on the T1 images; the results were reasonable after checking with tkregister2. However, the "mri_vol2surf" fails producing "Segmentation fault", I don't know how to resolve it. Here is how I ran the whole process:
export SUBJECTS_DIR=/home/kayhan/test/myproject/control001/tp1 cd ${SUBJECTS_DIR}/NIFTI bbregister --mov fMRI.nii.gz --bold --s FREESURFER --init-fsl --reg bbregister/fmri-TO-orig.dat --fslmat bbregister/fmri-TO-orig.mat
FREESURFER is the place the freesurfer files are. I have checked the results of the bbregister and it was fine. Here is how I called "mri_vol2surf" :
~$ mri_vol2surf --mov fMRI.nii.gz --regheader FREESURFER --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 Computing registration from header. Using /home/kayhan/test/myproject/control001/tp1/FREESURFER/mri/orig.mgz as target reference. 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*
I would be thankful if you can help.
Thanks,
On Sun, Apr 1, 2012 at 2:34 PM, Bruce Fischl <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> . 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.eduwrote:
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/ compliancelinehttp://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.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 . 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.
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>> 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> . 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
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.eduwrote:
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.edufischl@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>>. 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.______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu>
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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/**compliancelinehttp://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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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 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
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.edufischl@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>>. 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.______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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/**compliancelinehttp://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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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> 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>> 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>>> 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>> . 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. ______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> ______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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> . 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> 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>
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
Thanks,
On Mon, Apr 2, 2012 at 4:12 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
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 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> 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<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>>. 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. ______________________________ _________________Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh. harvard.eduFreesurfer@nmr.mgh.harvard.edu
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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/ compliancelinehttp://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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/ fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/ facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
Thanks,
On Mon, Apr 2, 2012 at 4:12 PM, Douglas Greve <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>> 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>> 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>>> 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>> . 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. ______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> ______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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> . 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> 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>
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.eduwrote:
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.gzhttp://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 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**> 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 <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<fischl@nmr.mgh.harvard.edu><mailto:fischl@nmr.mgh. harvard.edu <mailto:fischl@nmr.mgh.**harvard.edu<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>>>. 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. ______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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<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<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 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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 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
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.gzhttp://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 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**> 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 <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<fischl@nmr.mgh.harvard.edu><mailto:fischl@nmr.mgh. harvard.edu <mailto:fischl@nmr.mgh.**harvard.edu<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>>>. 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. ______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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>>. 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 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<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 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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. 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>>> . 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. ______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>. harvard.edu <http://harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> ______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>. harvard.edu <http://harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> 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>> . 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>
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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>>> . 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. ______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>. harvard.edu <http://harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> ______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>. harvard.edu <http://harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> 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>> . 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>
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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.eduwrote:
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 itcompleted
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>>> . 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. ______________________________ _________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh <mailto:Freesurfer@nmr.mgh>. harvard.edu <http://harvard.edu> <mailto:Freesurfer@nmr.mgh. harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E%3E
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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>> . 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%3E%3E
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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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.commailto: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> > 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
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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
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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
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
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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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.eduwrote:
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.gzhttp://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.commailto: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 isanonymized.
http://dl.dropbox.com/u/**7895831/tp1.tar.gz<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<greve@nmr.mgh.harvard.edu>wrote:
The new registration looks much better. The value I look atis
the first value in the mincost file. For your data, it'sabout
.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 previousreg,
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 newlog
file. If the results look fine and it does not produce error, is there any way that I check that myregistration
failed? Is there any term that I should search for inthe
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 FREESURFERfoder)
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<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<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard. edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>>>>wrote:
It looks like your registration failed (though itcompleted
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>**> > wrote: No, it does not; sorry for the confusion. I have attached a clean output below. I don't know what itmeans.
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 SubjectSurface
1 0 0 0 using old Done mapping volume to surface Segmentation fault ------------ On Mon, Apr 2, 2012 at 1:44 PM, Douglas NGreve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard. edu <mailto:greve@nmr.mgh.harvard.**edu<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 wasthat
accidentally pasted in? It should not be printing that twice, maybe it's a clue. doug On 04/02/2012 10:26 AM, Kaveh Kohanwrote:
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 finalstep
probably saving the results. Is the dataformat
that I used OK? I am using Ubuntu 10.10, the versionof
"mri_vol2surf" is "stable5". Pleaselet
me knoe if more information is required.Thanks.
~$ mri_vol2surf --mov fMRI.nii.gz--reg
bbregister/fmri-TO-orig.dat --hemilh
--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 2:34PM,
Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.**harvard.edu<fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh. harvard.edu <mailto:fischl@nmr.mgh.**harvard.edu<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<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 fMRItime
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 pixelof
the 2D flattened image which resides in the cortex (I guess itcorresponds
to a vertex on the cortex manifold?) istime-series.
I have ran recon-allon
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 knowhow
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<http://www.partners.org/complianceline>>>>. If
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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>>> . 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. > > > > > ______________________________ > _________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh. harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh > <mailto:Freesurfer@nmr.mgh>. harvard.edu > <http://harvard.edu> > > <mailto:Freesurfer@nmr.mgh. harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > https://mail.nmr.mgh.harvard. > edu/mailman/listinfo/ freesurfer > <https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ > freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > ______________________________ > _________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh. harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh > <mailto:Freesurfer@nmr.mgh>. harvard.edu > <http://harvard.edu> > > <mailto:Freesurfer@nmr.mgh. harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ > freesurfer > <https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ > freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > 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>> . 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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