hi, Doug

as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh

it shows me "Done mapping volume to surface" followed by "Segmentation fault"

may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty???

thanks kk

----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:19:21 AM Subject: Re: [Freesurfer] fMRI time series in surface space

Why not run the full preprocessing? It will do the sampling (and surface smoothing) for you. Alternatively, you can just use mri_vol2surf, then mris_fwhm to do the surface smoothing (you can also surface smooth in mri_vol2surf so you can do it all with one command). doug

On 05/24/2012 08:35 AM, Kushal Kapse wrote:

...

Hi Everyone,

I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation.

My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space?

Many thanks, kk

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

hi dough,

following is the terminal output which lead to segmentation fault.....

i checked the data space and it is not out of size

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault

----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Kushal Kapse" kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 3:53:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, please be sure to include the entire terminal output. These kinds of things are hard to track down from just the error msg. Also, how many time points are in the func.nii.gz? And are you sure that you are not running out of space on the disk? doug

On 05/25/2012 02:57 PM, Kushal Kapse wrote:

hi, Doug

as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh

it shows me "Done mapping volume to surface" followed by "Segmentation fault"

may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty???

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:19:21 AM Subject: Re: [Freesurfer] fMRI time series in surface space

Why not run the full preprocessing? It will do the sampling (and surface smoothing) for you. Alternatively, you can just use mri_vol2surf, then mris_fwhm to do the surface smoothing (you can also surface smooth in mri_vol2surf so you can do it all with one command). doug

On 05/24/2012 08:35 AM, Kushal Kapse wrote:

...

...

Hi Everyone,

I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation.

My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space?

Many thanks, kk

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

doug,

thanks doug....before i do that....i have two questions which may take care of "mri_vol2surf" issues

1- mri_vol2surf command needs to specify register.dat file........

i have been using register.dat file for vol2surf from reg-feat2anat output.....is that the register.dat file i am supposed to used?.....or if i am wrong, which register.dat file am i suppose to use....basically, where does tht file come from

2- vol2surf needs functional file as src and register.dat file....are these both supposed to be in same directory....because during processing it says "cannot find target reference for orig.mgz"......

please let me know

thanks kk

----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Kushal Kapse" kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug

On 05/25/2012 04:03 PM, Kushal Kapse wrote:

hi dough,

following is the terminal output which lead to segmentation fault.....

i checked the data space and it is not out of size

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 3:53:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, please be sure to include the entire terminal output. These kinds of things are hard to track down from just the error msg. Also, how many time points are in the func.nii.gz? And are you sure that you are not running out of space on the disk? doug

On 05/25/2012 02:57 PM, Kushal Kapse wrote:

...

hi, Doug

as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh

it shows me "Done mapping volume to surface" followed by "Segmentation fault"

may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty???

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:19:21 AM Subject: Re: [Freesurfer] fMRI time series in surface space

Why not run the full preprocessing? It will do the sampling (and surface smoothing) for you. Alternatively, you can just use mri_vol2surf, then mris_fwhm to do the surface smoothing (you can also surface smooth in mri_vol2surf so you can do it all with one command). doug

On 05/24/2012 08:35 AM, Kushal Kapse wrote:

...

...

Hi Everyone,

I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation.

My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space?

Many thanks, kk

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

@doug

no doug...this "orig.mgz"error was before segmentation fault error started showing up.....hence i wanna see if why it gave that ....lemme take a look and will keep u updated

----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Kushal Kapse" kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space

On 05/25/2012 04:30 PM, Kushal Kapse wrote:

doug,

thanks doug....before i do that....i have two questions which may take care of "mri_vol2surf" issues

1- mri_vol2surf command needs to specify register.dat file........

i have been using register.dat file for vol2surf from reg-feat2anat output.....is that the register.dat file i am supposed to used?.....or if i am wrong, which register.dat file am i suppose to use....basically, where does tht file come from

No, you are correct

2- vol2surf needs functional file as src and register.dat file....are these both supposed to be in same directory....because during processing it says "cannot find target reference for orig.mgz"......

They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where "subject" comes from the register.dat file. doug

please let me know

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug

On 05/25/2012 04:03 PM, Kushal Kapse wrote:

...

hi dough,

following is the terminal output which lead to segmentation fault.....

i checked the data space and it is not out of size

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 3:53:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, please be sure to include the entire terminal output. These kinds of things are hard to track down from just the error msg. Also, how many time points are in the func.nii.gz? And are you sure that you are not running out of space on the disk? doug

On 05/25/2012 02:57 PM, Kushal Kapse wrote:

...

hi, Doug

as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh

it shows me "Done mapping volume to surface" followed by "Segmentation fault"

may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty???

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:19:21 AM Subject: Re: [Freesurfer] fMRI time series in surface space

Why not run the full preprocessing? It will do the sampling (and surface smoothing) for you. Alternatively, you can just use mri_vol2surf, then mris_fwhm to do the surface smoothing (you can also surface smooth in mri_vol2surf so you can do it all with one command). doug

On 05/24/2012 08:35 AM, Kushal Kapse wrote:

...

...

Hi Everyone,

I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation.

My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space?

Many thanks, kk

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was

15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls

If either of those are not correct, then it will not determine the path correctly.

Does that orig.mgz file exist?

On 05/25/2012 04:50 PM, Kushal Kapse wrote:

i was talking about this issue....

mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness 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 /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file

i didnt understand when u said in last email "where "subject" comes from the register.dat file".....would you please explain me this

thanks kk

----- Original Message ----- From: "Kushal Kapse"kkapse@mail.med.upenn.edu To: "Douglas N Greve"greve@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space

@doug

no doug...this "orig.mgz"error was before segmentation fault error started showing up.....hence i wanna see if why it gave that ....lemme take a look and will keep u updated

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space

On 05/25/2012 04:30 PM, Kushal Kapse wrote:

...

doug,

thanks doug....before i do that....i have two questions which may take care of "mri_vol2surf" issues

1- mri_vol2surf command needs to specify register.dat file........

i have been using register.dat file for vol2surf from reg-feat2anat output.....is that the register.dat file i am supposed to used?.....or if i am wrong, which register.dat file am i suppose to use....basically, where does tht file come from

No, you are correct

...

2- vol2surf needs functional file as src and register.dat file....are these both supposed to be in same directory....because during processing it says "cannot find target reference for orig.mgz"......

They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where "subject" comes from the register.dat file. doug

...

please let me know

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug

On 05/25/2012 04:03 PM, Kushal Kapse wrote:

...

hi dough,

following is the terminal output which lead to segmentation fault.....

i checked the data space and it is not out of size

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 3:53:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, please be sure to include the entire terminal output. These kinds of things are hard to track down from just the error msg. Also, how many time points are in the func.nii.gz? And are you sure that you are not running out of space on the disk? doug

On 05/25/2012 02:57 PM, Kushal Kapse wrote:

...

hi, Doug

as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh

it shows me "Done mapping volume to surface" followed by "Segmentation fault"

may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty???

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:19:21 AM Subject: Re: [Freesurfer] fMRI time series in surface space

Why not run the full preprocessing? It will do the sampling (and surface smoothing) for you. Alternatively, you can just use mri_vol2surf, then mris_fwhm to do the surface smoothing (you can also surface smooth in mri_vol2surf so you can do it all with one command). doug

On 05/24/2012 08:35 AM, Kushal Kapse wrote:

...

...

Hi Everyone,

I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation.

My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space?

Many thanks, kk

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug

On 05/25/2012 04:56 PM, Kushal Kapse wrote:

orig.mgz file is on 15446_03908/mri/orig.mgz

yes the subject name and the directory path is correct....

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space

The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was

15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls

If either of those are not correct, then it will not determine the path correctly.

Does that orig.mgz file exist?

On 05/25/2012 04:50 PM, Kushal Kapse wrote:

...

i was talking about this issue....

mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness 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 /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file

i didnt understand when u said in last email "where "subject" comes from the register.dat file".....would you please explain me this

thanks kk

----- Original Message ----- From: "Kushal Kapse"kkapse@mail.med.upenn.edu To: "Douglas N Greve"greve@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space

@doug

no doug...this "orig.mgz"error was before segmentation fault error started showing up.....hence i wanna see if why it gave that ....lemme take a look and will keep u updated

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space

On 05/25/2012 04:30 PM, Kushal Kapse wrote:

...

doug,

thanks doug....before i do that....i have two questions which may take care of "mri_vol2surf" issues

1- mri_vol2surf command needs to specify register.dat file........

i have been using register.dat file for vol2surf from reg-feat2anat output.....is that the register.dat file i am supposed to used?.....or if i am wrong, which register.dat file am i suppose to use....basically, where does tht file come from

No, you are correct

...

2- vol2surf needs functional file as src and register.dat file....are these both supposed to be in same directory....because during processing it says "cannot find target reference for orig.mgz"......

They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where "subject" comes from the register.dat file. doug

...

please let me know

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug

On 05/25/2012 04:03 PM, Kushal Kapse wrote:

...

hi dough,

following is the terminal output which lead to segmentation fault.....

i checked the data space and it is not out of size

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 3:53:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, please be sure to include the entire terminal output. These kinds of things are hard to track down from just the error msg. Also, how many time points are in the func.nii.gz? And are you sure that you are not running out of space on the disk? doug

On 05/25/2012 02:57 PM, Kushal Kapse wrote:

...

hi, Doug

as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh

it shows me "Done mapping volume to surface" followed by "Segmentation fault"

may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty???

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:19:21 AM Subject: Re: [Freesurfer] fMRI time series in surface space

Why not run the full preprocessing? It will do the sampling (and surface smoothing) for you. Alternatively, you can just use mri_vol2surf, then mris_fwhm to do the surface smoothing (you can also surface smooth in mri_vol2surf so you can do it all with one command). doug

On 05/24/2012 08:35 AM, Kushal Kapse wrote:

...

> Hi Everyone, > > I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. > > My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? > > Many thanks, > kk _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with

tkregister2 --mov func.nii.gz --reg register.dat --surfs

doug

On 05/25/2012 05:45 PM, Kushal Kapse wrote:

well...

it seems the seg fault occured due to i was using a 4D func file and not 3d....does the vol2surf does only on 3d func data ?....how would i do that for 4D time series?

please let me know thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug

On 05/25/2012 04:56 PM, Kushal Kapse wrote:

...

orig.mgz file is on 15446_03908/mri/orig.mgz

yes the subject name and the directory path is correct....

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space

The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was

15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls

If either of those are not correct, then it will not determine the path correctly.

Does that orig.mgz file exist?

On 05/25/2012 04:50 PM, Kushal Kapse wrote:

...

i was talking about this issue....

mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness 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 /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file

i didnt understand when u said in last email "where "subject" comes from the register.dat file".....would you please explain me this

thanks kk

----- Original Message ----- From: "Kushal Kapse"kkapse@mail.med.upenn.edu To: "Douglas N Greve"greve@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space

@doug

no doug...this "orig.mgz"error was before segmentation fault error started showing up.....hence i wanna see if why it gave that ....lemme take a look and will keep u updated

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space

On 05/25/2012 04:30 PM, Kushal Kapse wrote:

...

doug,

thanks doug....before i do that....i have two questions which may take care of "mri_vol2surf" issues

1- mri_vol2surf command needs to specify register.dat file........

i have been using register.dat file for vol2surf from reg-feat2anat output.....is that the register.dat file i am supposed to used?.....or if i am wrong, which register.dat file am i suppose to use....basically, where does tht file come from

No, you are correct

...

2- vol2surf needs functional file as src and register.dat file....are these both supposed to be in same directory....because during processing it says "cannot find target reference for orig.mgz"......

They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where "subject" comes from the register.dat file. doug

...

please let me know

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug

On 05/25/2012 04:03 PM, Kushal Kapse wrote:

...

hi dough,

following is the terminal output which lead to segmentation fault.....

i checked the data space and it is not out of size

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 3:53:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, please be sure to include the entire terminal output. These kinds of things are hard to track down from just the error msg. Also, how many time points are in the func.nii.gz? And are you sure that you are not running out of space on the disk? doug

On 05/25/2012 02:57 PM, Kushal Kapse wrote:

...

hi, Doug

as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh

it shows me "Done mapping volume to surface" followed by "Segmentation fault"

may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty???

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 24, 2012 11:19:21 AM Subject: Re: [Freesurfer] fMRI time series in surface space

Why not run the full preprocessing? It will do the sampling (and surface smoothing) for you. Alternatively, you can just use mri_vol2surf, then mris_fwhm to do the surface smoothing (you can also surface smooth in mri_vol2surf so you can do it all with one command). doug

On 05/24/2012 08:35 AM, Kushal Kapse wrote: >> Hi Everyone, >> >> I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. >> >> My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? >> >> Many thanks, >> kk > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

Not that I can think of. Did you try that new version?

On 05/25/2012 05:58 PM, Kushal Kapse wrote:

yes ..the registration is nicely aligned and i did check the green-lines alignment in tkregister2

is their any other reason for it showing segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:52:41 PM Subject: Re: [Freesurfer] fMRI time series in surface space

it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with

tkregister2 --mov func.nii.gz --reg register.dat --surfs

doug

On 05/25/2012 05:45 PM, Kushal Kapse wrote:

...

well...

it seems the seg fault occured due to i was using a 4D func file and not 3d....does the vol2surf does only on 3d func data ?....how would i do that for 4D time series?

please let me know thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug

On 05/25/2012 04:56 PM, Kushal Kapse wrote:

...

orig.mgz file is on 15446_03908/mri/orig.mgz

yes the subject name and the directory path is correct....

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space

The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was

15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls

If either of those are not correct, then it will not determine the path correctly.

Does that orig.mgz file exist?

On 05/25/2012 04:50 PM, Kushal Kapse wrote:

...

i was talking about this issue....

mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness 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 /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file

i didnt understand when u said in last email "where "subject" comes from the register.dat file".....would you please explain me this

thanks kk

----- Original Message ----- From: "Kushal Kapse"kkapse@mail.med.upenn.edu To: "Douglas N Greve"greve@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space

@doug

no doug...this "orig.mgz"error was before segmentation fault error started showing up.....hence i wanna see if why it gave that ....lemme take a look and will keep u updated

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space

On 05/25/2012 04:30 PM, Kushal Kapse wrote:

...

doug,

thanks doug....before i do that....i have two questions which may take care of "mri_vol2surf" issues

1- mri_vol2surf command needs to specify register.dat file........

i have been using register.dat file for vol2surf from reg-feat2anat output.....is that the register.dat file i am supposed to used?.....or if i am wrong, which register.dat file am i suppose to use....basically, where does tht file come from

No, you are correct

...

2- vol2surf needs functional file as src and register.dat file....are these both supposed to be in same directory....because during processing it says "cannot find target reference for orig.mgz"......

They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where "subject" comes from the register.dat file. doug

...

please let me know

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug

On 05/25/2012 04:03 PM, Kushal Kapse wrote:

...

hi dough,

following is the terminal output which lead to segmentation fault.....

i checked the data space and it is not out of size

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 3:53:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, please be sure to include the entire terminal output. These kinds of things are hard to track down from just the error msg. Also, how many time points are in the func.nii.gz? And are you sure that you are not running out of space on the disk? doug

On 05/25/2012 02:57 PM, Kushal Kapse wrote: > hi, Doug > > as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows > > mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh > > it shows me "Done mapping volume to surface" followed by "Segmentation fault" > > > may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty??? > > > thanks > kk > > > ----- Original Message ----- > From: "Douglas N Greve"greve@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Sent: Thursday, May 24, 2012 11:19:21 AM > Subject: Re: [Freesurfer] fMRI time series in surface space > > Why not run the full preprocessing? It will do the sampling (and surface > smoothing) for you. Alternatively, you can just use mri_vol2surf, then > mris_fwhm to do the surface smoothing (you can also surface smooth in > mri_vol2surf so you can do it all with one command). > doug > > On 05/24/2012 08:35 AM, Kushal Kapse wrote: >>> Hi Everyone, >>> >>> I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. >>> >>> My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? >>> >>> Many thanks, >>> kk >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>

I don't think it ever supported w files ... you can use mgh /mgz format. It will also produce nifti files, but they might not always be legal nifti files. FreeSurfer will always be able to work with them, but other software packages might not. doug

On 5/25/12 8:19 PM, Kushal Kapse wrote:

doug,

did try new version..it worked fine...but seems tht new version doesnt support .w as output format; like in the tutorial online.....what output format does the new version vol2surf likes?

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:59:59 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Not that I can think of. Did you try that new version?

On 05/25/2012 05:58 PM, Kushal Kapse wrote:

...

yes ..the registration is nicely aligned and i did check the green-lines alignment in tkregister2

is their any other reason for it showing segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:52:41 PM Subject: Re: [Freesurfer] fMRI time series in surface space

it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with

tkregister2 --mov func.nii.gz --reg register.dat --surfs

doug

On 05/25/2012 05:45 PM, Kushal Kapse wrote:

...

well...

it seems the seg fault occured due to i was using a 4D func file and not 3d....does the vol2surf does only on 3d func data ?....how would i do that for 4D time series?

please let me know thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug

On 05/25/2012 04:56 PM, Kushal Kapse wrote:

...

orig.mgz file is on 15446_03908/mri/orig.mgz

yes the subject name and the directory path is correct....

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space

The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was

15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls

If either of those are not correct, then it will not determine the path correctly.

Does that orig.mgz file exist?

On 05/25/2012 04:50 PM, Kushal Kapse wrote:

...

i was talking about this issue....

mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness 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 /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file

i didnt understand when u said in last email "where "subject" comes from the register.dat file".....would you please explain me this

thanks kk

----- Original Message ----- From: "Kushal Kapse"kkapse@mail.med.upenn.edu To: "Douglas N Greve"greve@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space

@doug

no doug...this "orig.mgz"error was before segmentation fault error started showing up.....hence i wanna see if why it gave that ....lemme take a look and will keep u updated

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space

On 05/25/2012 04:30 PM, Kushal Kapse wrote:

...

doug,

thanks doug....before i do that....i have two questions which may take care of "mri_vol2surf" issues

1- mri_vol2surf command needs to specify register.dat file........

i have been using register.dat file for vol2surf from reg-feat2anat output.....is that the register.dat file i am supposed to used?.....or if i am wrong, which register.dat file am i suppose to use....basically, where does tht file come from

No, you are correct

...

2- vol2surf needs functional file as src and register.dat file....are these both supposed to be in same directory....because during processing it says "cannot find target reference for orig.mgz"......

They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where "subject" comes from the register.dat file. doug

...

please let me know

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug

On 05/25/2012 04:03 PM, Kushal Kapse wrote: > hi dough, > > following is the terminal output which lead to segmentation fault..... > > i checked the data space and it is not out of size > > > > > mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz > srcvol = pitt1_cpw-e_4.05_059.nii.gz > srcreg = register.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > ProjFrac = 0.5 > thickness = thickness > reshape = 0 > interp = trilinear > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white > Done reading source surface > Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness > Done > Mapping Source Volume onto Source Subject Surface > 1 0.5 0.5 0.5 > using old > Done mapping volume to surface > Segmentation fault > > > ----- Original Message ----- > From: "Douglas N Greve"greve@nmr.mgh.harvard.edu > To: "Kushal Kapse"kkapse@mail.med.upenn.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Friday, May 25, 2012 3:53:31 PM > Subject: Re: [Freesurfer] fMRI time series in surface space > > Hi Kushal, please be sure to include the entire terminal output. These > kinds of things are hard to track down from just the error msg. Also, > how many time points are in the func.nii.gz? And are you sure that you > are not running out of space on the disk? > doug > > On 05/25/2012 02:57 PM, Kushal Kapse wrote: >> hi, Doug >> >> as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows >> >> mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh >> >> it shows me "Done mapping volume to surface" followed by "Segmentation fault" >> >> >> may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty??? >> >> >> thanks >> kk >> >> >> ----- Original Message ----- >> From: "Douglas N Greve"greve@nmr.mgh.harvard.edu >> To: freesurfer@nmr.mgh.harvard.edu >> Sent: Thursday, May 24, 2012 11:19:21 AM >> Subject: Re: [Freesurfer] fMRI time series in surface space >> >> Why not run the full preprocessing? It will do the sampling (and surface >> smoothing) for you. Alternatively, you can just use mri_vol2surf, then >> mris_fwhm to do the surface smoothing (you can also surface smooth in >> mri_vol2surf so you can do it all with one command). >> doug >> >> On 05/24/2012 08:35 AM, Kushal Kapse wrote: >>>> Hi Everyone, >>>> >>>> I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. >>>> >>>> My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? >>>> >>>> Many thanks, >>>> kk >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>>

hi doug,

as per our last conversation of 4d time series on surface, i did mri_vol2surf as per tutorial on wiki..i used the new mri_vol2surf which u send me....this was my command:

mri_vol2surf.linux --src func.nii.gz --reg register.dat --hemi lh --out spm001-lh.w --out_type paint

but i cant find output anywhere....ALSO, i tried having output in mgh and mgz format...but the output doesnt work...

i opened tkesurfer and tried to check the output...it doesnt show any activation on surface......can you plz give ur thought on this

thanks kk

----- Original Message ----- From: "Douglas Greve" greve@nmr.mgh.harvard.edu To: "Kushal Kapse" kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 8:23:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space

I don't think it ever supported w files ... you can use mgh /mgz format. It will also produce nifti files, but they might not always be legal nifti files. FreeSurfer will always be able to work with them, but other software packages might not. doug

On 5/25/12 8:19 PM, Kushal Kapse wrote:

doug,

did try new version..it worked fine...but seems tht new version doesnt support .w as output format; like in the tutorial online.....what output format does the new version vol2surf likes?

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:59:59 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Not that I can think of. Did you try that new version?

On 05/25/2012 05:58 PM, Kushal Kapse wrote:

...

yes ..the registration is nicely aligned and i did check the green-lines alignment in tkregister2

is their any other reason for it showing segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:52:41 PM Subject: Re: [Freesurfer] fMRI time series in surface space

it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with

tkregister2 --mov func.nii.gz --reg register.dat --surfs

doug

On 05/25/2012 05:45 PM, Kushal Kapse wrote:

...

well...

it seems the seg fault occured due to i was using a 4D func file and not 3d....does the vol2surf does only on 3d func data ?....how would i do that for 4D time series?

please let me know thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug

On 05/25/2012 04:56 PM, Kushal Kapse wrote:

...

orig.mgz file is on 15446_03908/mri/orig.mgz

yes the subject name and the directory path is correct....

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space

The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was

15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls

If either of those are not correct, then it will not determine the path correctly.

Does that orig.mgz file exist?

On 05/25/2012 04:50 PM, Kushal Kapse wrote:

...

i was talking about this issue....

mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness 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 /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file

i didnt understand when u said in last email "where "subject" comes from the register.dat file".....would you please explain me this

thanks kk

----- Original Message ----- From: "Kushal Kapse"kkapse@mail.med.upenn.edu To: "Douglas N Greve"greve@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space

@doug

no doug...this "orig.mgz"error was before segmentation fault error started showing up.....hence i wanna see if why it gave that ....lemme take a look and will keep u updated

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space

On 05/25/2012 04:30 PM, Kushal Kapse wrote:

...

doug,

thanks doug....before i do that....i have two questions which may take care of "mri_vol2surf" issues

1- mri_vol2surf command needs to specify register.dat file........

i have been using register.dat file for vol2surf from reg-feat2anat output.....is that the register.dat file i am supposed to used?.....or if i am wrong, which register.dat file am i suppose to use....basically, where does tht file come from

No, you are correct

...

2- vol2surf needs functional file as src and register.dat file....are these both supposed to be in same directory....because during processing it says "cannot find target reference for orig.mgz"......

They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where "subject" comes from the register.dat file. doug

...

please let me know

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug

On 05/25/2012 04:03 PM, Kushal Kapse wrote: > hi dough, > > following is the terminal output which lead to segmentation fault..... > > i checked the data space and it is not out of size > > > > > mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz > srcvol = pitt1_cpw-e_4.05_059.nii.gz > srcreg = register.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > ProjFrac = 0.5 > thickness = thickness > reshape = 0 > interp = trilinear > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white > Done reading source surface > Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness > Done > Mapping Source Volume onto Source Subject Surface > 1 0.5 0.5 0.5 > using old > Done mapping volume to surface > Segmentation fault > > > ----- Original Message ----- > From: "Douglas N Greve"greve@nmr.mgh.harvard.edu > To: "Kushal Kapse"kkapse@mail.med.upenn.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Friday, May 25, 2012 3:53:31 PM > Subject: Re: [Freesurfer] fMRI time series in surface space > > Hi Kushal, please be sure to include the entire terminal output. These > kinds of things are hard to track down from just the error msg. Also, > how many time points are in the func.nii.gz? And are you sure that you > are not running out of space on the disk? > doug > > On 05/25/2012 02:57 PM, Kushal Kapse wrote: >> hi, Doug >> >> as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows >> >> mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh >> >> it shows me "Done mapping volume to surface" followed by "Segmentation fault" >> >> >> may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty??? >> >> >> thanks >> kk >> >> >> ----- Original Message ----- >> From: "Douglas N Greve"greve@nmr.mgh.harvard.edu >> To: freesurfer@nmr.mgh.harvard.edu >> Sent: Thursday, May 24, 2012 11:19:21 AM >> Subject: Re: [Freesurfer] fMRI time series in surface space >> >> Why not run the full preprocessing? It will do the sampling (and surface >> smoothing) for you. Alternatively, you can just use mri_vol2surf, then >> mris_fwhm to do the surface smoothing (you can also surface smooth in >> mri_vol2surf so you can do it all with one command). >> doug >> >> On 05/24/2012 08:35 AM, Kushal Kapse wrote: >>>> Hi Everyone, >>>> >>>> I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. >>>> >>>> My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? >>>> >>>> Many thanks, >>>> kk >>> _______________________________________________ >>> 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.

Hi Kushal, you cannot use .w file for 4D outputs. Use this cmd:

mri_vol2surf.linux --src func.nii.gz --reg register.dat --hemi lh --out spm001.mgh

doug

On 5/29/12 8:46 AM, Kushal Kapse wrote:

hi doug,

as per our last conversation of 4d time series on surface, i did mri_vol2surf as per tutorial on wiki..i used the new mri_vol2surf which u send me....this was my command:

mri_vol2surf.linux --src func.nii.gz --reg register.dat --hemi lh --out spm001-lh.w --out_type paint

but i cant find output anywhere....ALSO, i tried having output in mgh and mgz format...but the output doesnt work...

i opened tkesurfer and tried to check the output...it doesnt show any activation on surface......can you plz give ur thought on this

thanks kk

----- Original Message ----- From: "Douglas Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 8:23:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space

I don't think it ever supported w files ... you can use mgh /mgz format. It will also produce nifti files, but they might not always be legal nifti files. FreeSurfer will always be able to work with them, but other software packages might not. doug

On 5/25/12 8:19 PM, Kushal Kapse wrote:

...

doug,

did try new version..it worked fine...but seems tht new version doesnt support .w as output format; like in the tutorial online.....what output format does the new version vol2surf likes?

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:59:59 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Not that I can think of. Did you try that new version?

On 05/25/2012 05:58 PM, Kushal Kapse wrote:

...

yes ..the registration is nicely aligned and i did check the green-lines alignment in tkregister2

is their any other reason for it showing segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:52:41 PM Subject: Re: [Freesurfer] fMRI time series in surface space

it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with

tkregister2 --mov func.nii.gz --reg register.dat --surfs

doug

On 05/25/2012 05:45 PM, Kushal Kapse wrote:

...

well...

it seems the seg fault occured due to i was using a 4D func file and not 3d....does the vol2surf does only on 3d func data ?....how would i do that for 4D time series?

please let me know thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug

On 05/25/2012 04:56 PM, Kushal Kapse wrote:

...

orig.mgz file is on 15446_03908/mri/orig.mgz

yes the subject name and the directory path is correct....

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space

The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was

15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls

If either of those are not correct, then it will not determine the path correctly.

Does that orig.mgz file exist?

On 05/25/2012 04:50 PM, Kushal Kapse wrote:

...

i was talking about this issue....

mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness 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 /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file

i didnt understand when u said in last email "where "subject" comes from the register.dat file".....would you please explain me this

thanks kk

----- Original Message ----- From: "Kushal Kapse"kkapse@mail.med.upenn.edu To: "Douglas N Greve"greve@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space

@doug

no doug...this "orig.mgz"error was before segmentation fault error started showing up.....hence i wanna see if why it gave that ....lemme take a look and will keep u updated

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space

On 05/25/2012 04:30 PM, Kushal Kapse wrote: > doug, > > thanks doug....before i do that....i have two questions which may take care of "mri_vol2surf" issues > > > 1- mri_vol2surf command needs to specify register.dat file........ > > i have been using register.dat file for vol2surf from reg-feat2anat output.....is that the register.dat file i am supposed to used?.....or if i am wrong, which register.dat file am i suppose to use....basically, where does tht file come from No, you are correct > 2- vol2surf needs functional file as src and register.dat file....are these both supposed to be in same directory....because during processing it says "cannot find target reference for orig.mgz"...... They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where "subject" comes from the register.dat file. doug > please let me know > > thanks > kk > > ----- Original Message ----- > From: "Douglas N Greve"greve@nmr.mgh.harvard.edu > To: "Kushal Kapse"kkapse@mail.med.upenn.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Friday, May 25, 2012 4:08:35 PM > Subject: Re: [Freesurfer] fMRI time series in surface space > > Hi Kushal, can you try this version of vol2surf? > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux > If that still fails, please tar up the subject and functional and upload > it to our file drop system at the end of this email. > doug > > On 05/25/2012 04:03 PM, Kushal Kapse wrote: >> hi dough, >> >> following is the terminal output which lead to segmentation fault..... >> >> i checked the data space and it is not out of size >> >> >> >> >> mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz >> srcvol = pitt1_cpw-e_4.05_059.nii.gz >> srcreg = register.dat >> srcregold = 0 >> srcwarp unspecified >> surf = white >> hemi = lh >> ProjFrac = 0.5 >> thickness = thickness >> reshape = 0 >> interp = trilinear >> float2int = round >> GetProjMax = 0 >> INFO: float2int code = 0 >> INFO: changing type to float >> Done loading volume >> Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white >> Done reading source surface >> Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness >> Done >> Mapping Source Volume onto Source Subject Surface >> 1 0.5 0.5 0.5 >> using old >> Done mapping volume to surface >> Segmentation fault >> >> >> ----- Original Message ----- >> From: "Douglas N Greve"greve@nmr.mgh.harvard.edu >> To: "Kushal Kapse"kkapse@mail.med.upenn.edu >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Friday, May 25, 2012 3:53:31 PM >> Subject: Re: [Freesurfer] fMRI time series in surface space >> >> Hi Kushal, please be sure to include the entire terminal output. These >> kinds of things are hard to track down from just the error msg. Also, >> how many time points are in the func.nii.gz? And are you sure that you >> are not running out of space on the disk? >> doug >> >> On 05/25/2012 02:57 PM, Kushal Kapse wrote: >>> hi, Doug >>> >>> as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows >>> >>> mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh >>> >>> it shows me "Done mapping volume to surface" followed by "Segmentation fault" >>> >>> >>> may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty??? >>> >>> >>> thanks >>> kk >>> >>> >>> ----- Original Message ----- >>> From: "Douglas N Greve"greve@nmr.mgh.harvard.edu >>> To: freesurfer@nmr.mgh.harvard.edu >>> Sent: Thursday, May 24, 2012 11:19:21 AM >>> Subject: Re: [Freesurfer] fMRI time series in surface space >>> >>> Why not run the full preprocessing? It will do the sampling (and surface >>> smoothing) for you. Alternatively, you can just use mri_vol2surf, then >>> mris_fwhm to do the surface smoothing (you can also surface smooth in >>> mri_vol2surf so you can do it all with one command). >>> doug >>> >>> On 05/24/2012 08:35 AM, Kushal Kapse wrote: >>>>> Hi Everyone, >>>>> >>>>> I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. >>>>> >>>>> My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? >>>>> >>>>> Many thanks, >>>>> kk >>>> _______________________________________________ >>>> 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.

it does not produce a .w file the output is spm001.mgh

On 5/29/12 9:00 AM, Kushal Kapse wrote:

hi doug/bruce:

it still says it cannot find .w file....please check at the bottom ....

[kkapse@dendrite 15546_03908]$ /home/kkapse/mri_vol2surf.linux --src func.nii.gz --reg register.dat --hemi rh --out spm001.mgh srcvol = func.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /15546_03908/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 10737 Writing to spm001.mgh Dim: 147942 1 1 [kkapse@dendrite 15546_03908]$ qsurfer -stat spm001 -hemi lh -subject 15546_03908 ERROR: cannot find 15546_03908/spm001-lh.w

thanks kk

----- Original Message ----- From: "Douglas Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, May 29, 2012 8:54:40 AM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, you cannot use .w file for 4D outputs. Use this cmd:

mri_vol2surf.linux --src func.nii.gz --reg register.dat --hemi lh --out spm001.mgh

doug

On 5/29/12 8:46 AM, Kushal Kapse wrote:

...

hi doug,

as per our last conversation of 4d time series on surface, i did mri_vol2surf as per tutorial on wiki..i used the new mri_vol2surf which u send me....this was my command:

mri_vol2surf.linux --src func.nii.gz --reg register.dat --hemi lh --out spm001-lh.w --out_type paint

but i cant find output anywhere....ALSO, i tried having output in mgh and mgz format...but the output doesnt work...

i opened tkesurfer and tried to check the output...it doesnt show any activation on surface......can you plz give ur thought on this

thanks kk

----- Original Message ----- From: "Douglas Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 8:23:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space

I don't think it ever supported w files ... you can use mgh /mgz format. It will also produce nifti files, but they might not always be legal nifti files. FreeSurfer will always be able to work with them, but other software packages might not. doug

On 5/25/12 8:19 PM, Kushal Kapse wrote:

...

doug,

did try new version..it worked fine...but seems tht new version doesnt support .w as output format; like in the tutorial online.....what output format does the new version vol2surf likes?

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:59:59 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Not that I can think of. Did you try that new version?

On 05/25/2012 05:58 PM, Kushal Kapse wrote:

...

yes ..the registration is nicely aligned and i did check the green-lines alignment in tkregister2

is their any other reason for it showing segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:52:41 PM Subject: Re: [Freesurfer] fMRI time series in surface space

it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with

tkregister2 --mov func.nii.gz --reg register.dat --surfs

doug

On 05/25/2012 05:45 PM, Kushal Kapse wrote:

...

well...

it seems the seg fault occured due to i was using a 4D func file and not 3d....does the vol2surf does only on 3d func data ?....how would i do that for 4D time series?

please let me know thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug

On 05/25/2012 04:56 PM, Kushal Kapse wrote:

...

orig.mgz file is on 15446_03908/mri/orig.mgz

yes the subject name and the directory path is correct....

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space

The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was

15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls

If either of those are not correct, then it will not determine the path correctly.

Does that orig.mgz file exist?

On 05/25/2012 04:50 PM, Kushal Kapse wrote: > i was talking about this issue.... > > mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz > srcvol = func.nii.gz > srcreg unspecified > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > ProjFrac = 0.5 > thickness = thickness > 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 /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. > mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file > > > i didnt understand when u said in last email "where "subject" comes from the register.dat file".....would you please explain me this > > thanks > kk > > ----- Original Message ----- > From: "Kushal Kapse"kkapse@mail.med.upenn.edu > To: "Douglas N Greve"greve@nmr.mgh.harvard.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Friday, May 25, 2012 4:39:47 PM > Subject: Re: [Freesurfer] fMRI time series in surface space > > @doug > > no doug...this "orig.mgz"error was before segmentation fault error started showing up.....hence i wanna see if why it gave that ....lemme take a look and will keep u updated > > ----- Original Message ----- > From: "Douglas N Greve"greve@nmr.mgh.harvard.edu > To: "Kushal Kapse"kkapse@mail.med.upenn.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Friday, May 25, 2012 4:33:20 PM > Subject: Re: [Freesurfer] fMRI time series in surface space > > > > On 05/25/2012 04:30 PM, Kushal Kapse wrote: >> doug, >> >> thanks doug....before i do that....i have two questions which may take care of "mri_vol2surf" issues >> >> >> 1- mri_vol2surf command needs to specify register.dat file........ >> >> i have been using register.dat file for vol2surf from reg-feat2anat output.....is that the register.dat file i am supposed to used?.....or if i am wrong, which register.dat file am i suppose to use....basically, where does tht file come from > No, you are correct >> 2- vol2surf needs functional file as src and register.dat file....are these both supposed to be in same directory....because during processing it says "cannot find target reference for orig.mgz"...... > They do not have to be. I did not see that error below. Is that > something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where > "subject" comes from the register.dat file. > doug >> please let me know >> >> thanks >> kk >> >> ----- Original Message ----- >> From: "Douglas N Greve"greve@nmr.mgh.harvard.edu >> To: "Kushal Kapse"kkapse@mail.med.upenn.edu >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Friday, May 25, 2012 4:08:35 PM >> Subject: Re: [Freesurfer] fMRI time series in surface space >> >> Hi Kushal, can you try this version of vol2surf? >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux >> If that still fails, please tar up the subject and functional and upload >> it to our file drop system at the end of this email. >> doug >> >> On 05/25/2012 04:03 PM, Kushal Kapse wrote: >>> hi dough, >>> >>> following is the terminal output which lead to segmentation fault..... >>> >>> i checked the data space and it is not out of size >>> >>> >>> >>> >>> mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz >>> srcvol = pitt1_cpw-e_4.05_059.nii.gz >>> srcreg = register.dat >>> srcregold = 0 >>> srcwarp unspecified >>> surf = white >>> hemi = lh >>> ProjFrac = 0.5 >>> thickness = thickness >>> reshape = 0 >>> interp = trilinear >>> float2int = round >>> GetProjMax = 0 >>> INFO: float2int code = 0 >>> INFO: changing type to float >>> Done loading volume >>> Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white >>> Done reading source surface >>> Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness >>> Done >>> Mapping Source Volume onto Source Subject Surface >>> 1 0.5 0.5 0.5 >>> using old >>> Done mapping volume to surface >>> Segmentation fault >>> >>> >>> ----- Original Message ----- >>> From: "Douglas N Greve"greve@nmr.mgh.harvard.edu >>> To: "Kushal Kapse"kkapse@mail.med.upenn.edu >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Sent: Friday, May 25, 2012 3:53:31 PM >>> Subject: Re: [Freesurfer] fMRI time series in surface space >>> >>> Hi Kushal, please be sure to include the entire terminal output. These >>> kinds of things are hard to track down from just the error msg. Also, >>> how many time points are in the func.nii.gz? And are you sure that you >>> are not running out of space on the disk? >>> doug >>> >>> On 05/25/2012 02:57 PM, Kushal Kapse wrote: >>>> hi, Doug >>>> >>>> as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows >>>> >>>> mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh >>>> >>>> it shows me "Done mapping volume to surface" followed by "Segmentation fault" >>>> >>>> >>>> may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty??? >>>> >>>> >>>> thanks >>>> kk >>>> >>>> >>>> ----- Original Message ----- >>>> From: "Douglas N Greve"greve@nmr.mgh.harvard.edu >>>> To: freesurfer@nmr.mgh.harvard.edu >>>> Sent: Thursday, May 24, 2012 11:19:21 AM >>>> Subject: Re: [Freesurfer] fMRI time series in surface space >>>> >>>> Why not run the full preprocessing? It will do the sampling (and surface >>>> smoothing) for you. Alternatively, you can just use mri_vol2surf, then >>>> mris_fwhm to do the surface smoothing (you can also surface smooth in >>>> mri_vol2surf so you can do it all with one command). >>>> doug >>>> >>>> On 05/24/2012 08:35 AM, Kushal Kapse wrote: >>>>>> Hi Everyone, >>>>>> >>>>>> I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. >>>>>> >>>>>> My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? >>>>>> >>>>>> Many thanks, >>>>>> kk >>>>> _______________________________________________ >>>>> 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.

tksurfer subjectname lh inflated -overlay spm001.mgh

You can then scroll through the different time points with the overlay configuration

On 5/29/12 9:35 AM, Kushal Kapse wrote:

so if i have output as .mgh file....how can i check the output on surface...i try tksurfer and it just shows inflated surface....the qsurfer doesnt load coz it keeps looking for .w file format.......is there any change in commands to make so that i can visualize the output of functionaltosurface..i have been trying numerous ways looking at the output by working on tutorial of "functional to surface resampling"...but havent been successful.......please lemme know

thanks kk

----- Original Message ----- From: "Douglas Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, May 29, 2012 9:29:50 AM Subject: Re: [Freesurfer] fMRI time series in surface space

it does not produce a .w file the output is spm001.mgh

On 5/29/12 9:00 AM, Kushal Kapse wrote:

...

hi doug/bruce:

it still says it cannot find .w file....please check at the bottom ....

[kkapse@dendrite 15546_03908]$ /home/kkapse/mri_vol2surf.linux --src func.nii.gz --reg register.dat --hemi rh --out spm001.mgh srcvol = func.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /15546_03908/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 10737 Writing to spm001.mgh Dim: 147942 1 1 [kkapse@dendrite 15546_03908]$ qsurfer -stat spm001 -hemi lh -subject 15546_03908 ERROR: cannot find 15546_03908/spm001-lh.w

thanks kk

----- Original Message ----- From: "Douglas Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, May 29, 2012 8:54:40 AM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, you cannot use .w file for 4D outputs. Use this cmd:

mri_vol2surf.linux --src func.nii.gz --reg register.dat --hemi lh --out spm001.mgh

doug

On 5/29/12 8:46 AM, Kushal Kapse wrote:

...

hi doug,

as per our last conversation of 4d time series on surface, i did mri_vol2surf as per tutorial on wiki..i used the new mri_vol2surf which u send me....this was my command:

mri_vol2surf.linux --src func.nii.gz --reg register.dat --hemi lh --out spm001-lh.w --out_type paint

but i cant find output anywhere....ALSO, i tried having output in mgh and mgz format...but the output doesnt work...

i opened tkesurfer and tried to check the output...it doesnt show any activation on surface......can you plz give ur thought on this

thanks kk

----- Original Message ----- From: "Douglas Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 8:23:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space

I don't think it ever supported w files ... you can use mgh /mgz format. It will also produce nifti files, but they might not always be legal nifti files. FreeSurfer will always be able to work with them, but other software packages might not. doug

On 5/25/12 8:19 PM, Kushal Kapse wrote:

...

doug,

 did try new version..it worked fine...but seems tht new version doesnt support .w as output format; like in the tutorial online.....what output format does the new version vol2surf likes?

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:59:59 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Not that I can think of. Did you try that new version?

On 05/25/2012 05:58 PM, Kushal Kapse wrote:

...

yes ..the registration is nicely aligned and i did check the green-lines alignment in tkregister2

is their any other reason for it showing segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:52:41 PM Subject: Re: [Freesurfer] fMRI time series in surface space

it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with

tkregister2 --mov func.nii.gz --reg register.dat --surfs

doug

On 05/25/2012 05:45 PM, Kushal Kapse wrote:

...

well...

it seems the seg fault occured due to i was using a 4D func file and not 3d....does the vol2surf does only on 3d func data ?....how would i do that for 4D time series?

please let me know thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug

On 05/25/2012 04:56 PM, Kushal Kapse wrote: > orig.mgz file is on 15446_03908/mri/orig.mgz > > yes the subject name and the directory path is correct.... > > ----- Original Message ----- > From: "Douglas N Greve"greve@nmr.mgh.harvard.edu > To: "Kushal Kapse"kkapse@mail.med.upenn.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Friday, May 25, 2012 4:52:37 PM > Subject: Re: [Freesurfer] fMRI time series in surface space > > The register.dat file is a text file. The first line has the name of the > subject. It looks like the subject name was > > 15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls > > If either of those are not correct, then it will not determine the path correctly. > > Does that orig.mgz file exist? > > > On 05/25/2012 04:50 PM, Kushal Kapse wrote: >> i was talking about this issue.... >> >> mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz >> srcvol = func.nii.gz >> srcreg unspecified >> srcregold = 0 >> srcwarp unspecified >> surf = white >> hemi = lh >> ProjFrac = 0.5 >> thickness = thickness >> 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 /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. >> mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file >> >> >> i didnt understand when u said in last email "where "subject" comes from the register.dat file".....would you please explain me this >> >> thanks >> kk >> >> ----- Original Message ----- >> From: "Kushal Kapse"kkapse@mail.med.upenn.edu >> To: "Douglas N Greve"greve@nmr.mgh.harvard.edu >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Friday, May 25, 2012 4:39:47 PM >> Subject: Re: [Freesurfer] fMRI time series in surface space >> >> @doug >> >> no doug...this "orig.mgz"error was before segmentation fault error started showing up.....hence i wanna see if why it gave that ....lemme take a look and will keep u updated >> >> ----- Original Message ----- >> From: "Douglas N Greve"greve@nmr.mgh.harvard.edu >> To: "Kushal Kapse"kkapse@mail.med.upenn.edu >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Friday, May 25, 2012 4:33:20 PM >> Subject: Re: [Freesurfer] fMRI time series in surface space >> >> >> >> On 05/25/2012 04:30 PM, Kushal Kapse wrote: >>> doug, >>> >>> thanks doug....before i do that....i have two questions which may take care of "mri_vol2surf" issues >>> >>> >>> 1- mri_vol2surf command needs to specify register.dat file........ >>> >>> i have been using register.dat file for vol2surf from reg-feat2anat output.....is that the register.dat file i am supposed to used?.....or if i am wrong, which register.dat file am i suppose to use....basically, where does tht file come from >> No, you are correct >>> 2- vol2surf needs functional file as src and register.dat file....are these both supposed to be in same directory....because during processing it says "cannot find target reference for orig.mgz"...... >> They do not have to be. I did not see that error below. Is that >> something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where >> "subject" comes from the register.dat file. >> doug >>> please let me know >>> >>> thanks >>> kk >>> >>> ----- Original Message ----- >>> From: "Douglas N Greve"greve@nmr.mgh.harvard.edu >>> To: "Kushal Kapse"kkapse@mail.med.upenn.edu >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Sent: Friday, May 25, 2012 4:08:35 PM >>> Subject: Re: [Freesurfer] fMRI time series in surface space >>> >>> Hi Kushal, can you try this version of vol2surf? >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux >>> If that still fails, please tar up the subject and functional and upload >>> it to our file drop system at the end of this email. >>> doug >>> >>> On 05/25/2012 04:03 PM, Kushal Kapse wrote: >>>> hi dough, >>>> >>>> following is the terminal output which lead to segmentation fault..... >>>> >>>> i checked the data space and it is not out of size >>>> >>>> >>>> >>>> >>>> mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz >>>> srcvol = pitt1_cpw-e_4.05_059.nii.gz >>>> srcreg = register.dat >>>> srcregold = 0 >>>> srcwarp unspecified >>>> surf = white >>>> hemi = lh >>>> ProjFrac = 0.5 >>>> thickness = thickness >>>> reshape = 0 >>>> interp = trilinear >>>> float2int = round >>>> GetProjMax = 0 >>>> INFO: float2int code = 0 >>>> INFO: changing type to float >>>> Done loading volume >>>> Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white >>>> Done reading source surface >>>> Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness >>>> Done >>>> Mapping Source Volume onto Source Subject Surface >>>> 1 0.5 0.5 0.5 >>>> using old >>>> Done mapping volume to surface >>>> Segmentation fault >>>> >>>> >>>> ----- Original Message ----- >>>> From: "Douglas N Greve"greve@nmr.mgh.harvard.edu >>>> To: "Kushal Kapse"kkapse@mail.med.upenn.edu >>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>> Sent: Friday, May 25, 2012 3:53:31 PM >>>> Subject: Re: [Freesurfer] fMRI time series in surface space >>>> >>>> Hi Kushal, please be sure to include the entire terminal output. These >>>> kinds of things are hard to track down from just the error msg. Also, >>>> how many time points are in the func.nii.gz? And are you sure that you >>>> are not running out of space on the disk? >>>> doug >>>> >>>> On 05/25/2012 02:57 PM, Kushal Kapse wrote: >>>>> hi, Doug >>>>> >>>>> as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows >>>>> >>>>> mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh >>>>> >>>>> it shows me "Done mapping volume to surface" followed by "Segmentation fault" >>>>> >>>>> >>>>> may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty??? >>>>> >>>>> >>>>> thanks >>>>> kk >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: "Douglas N Greve"greve@nmr.mgh.harvard.edu >>>>> To: freesurfer@nmr.mgh.harvard.edu >>>>> Sent: Thursday, May 24, 2012 11:19:21 AM >>>>> Subject: Re: [Freesurfer] fMRI time series in surface space >>>>> >>>>> Why not run the full preprocessing? It will do the sampling (and surface >>>>> smoothing) for you. Alternatively, you can just use mri_vol2surf, then >>>>> mris_fwhm to do the surface smoothing (you can also surface smooth in >>>>> mri_vol2surf so you can do it all with one command). >>>>> doug >>>>> >>>>> On 05/24/2012 08:35 AM, Kushal Kapse wrote: >>>>>>> Hi Everyone, >>>>>>> >>>>>>> I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. >>>>>>> >>>>>>> My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? >>>>>>> >>>>>>> Many thanks, >>>>>>> kk >>>>>> _______________________________________________ >>>>>> 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.

hi doug/freesurfer users

after doing mri_vol2surf.....i went and imported the files in matlab by using f=MRIread ('filename.mgh') for the original functional (func.nii) file and spm001lh.mgh file...it seems the original func files has nvoxels=204800 and spm001lh file has nvolxels=118234.....for mri_vol2surf i used the flag --noreshape

1>>i m not understanding why is there a decrease in voxels for functional-surface mapping of time series??

2>>if i want to pick certain activation voxel in functional and look at its dimension/vertex position on surface; how would i do tht in matlab..... for eg: a voxel (12, 24, 64) would be what and how on its surface?

please let me know

thanks kk

----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Kushal Kapse" kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:59:59 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Not that I can think of. Did you try that new version?

On 05/25/2012 05:58 PM, Kushal Kapse wrote:

yes ..the registration is nicely aligned and i did check the green-lines alignment in tkregister2

is their any other reason for it showing segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:52:41 PM Subject: Re: [Freesurfer] fMRI time series in surface space

it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with

tkregister2 --mov func.nii.gz --reg register.dat --surfs

doug

On 05/25/2012 05:45 PM, Kushal Kapse wrote:

...

well...

it seems the seg fault occured due to i was using a 4D func file and not 3d....does the vol2surf does only on 3d func data ?....how would i do that for 4D time series?

please let me know thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug

On 05/25/2012 04:56 PM, Kushal Kapse wrote:

...

orig.mgz file is on 15446_03908/mri/orig.mgz

yes the subject name and the directory path is correct....

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space

The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was

15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls

If either of those are not correct, then it will not determine the path correctly.

Does that orig.mgz file exist?

On 05/25/2012 04:50 PM, Kushal Kapse wrote:

...

i was talking about this issue....

mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness 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 /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file

i didnt understand when u said in last email "where "subject" comes from the register.dat file".....would you please explain me this

thanks kk

----- Original Message ----- From: "Kushal Kapse"kkapse@mail.med.upenn.edu To: "Douglas N Greve"greve@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space

@doug

no doug...this "orig.mgz"error was before segmentation fault error started showing up.....hence i wanna see if why it gave that ....lemme take a look and will keep u updated

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space

On 05/25/2012 04:30 PM, Kushal Kapse wrote:

...

doug,

thanks doug....before i do that....i have two questions which may take care of "mri_vol2surf" issues

1- mri_vol2surf command needs to specify register.dat file........

i have been using register.dat file for vol2surf from reg-feat2anat output.....is that the register.dat file i am supposed to used?.....or if i am wrong, which register.dat file am i suppose to use....basically, where does tht file come from

No, you are correct

...

2- vol2surf needs functional file as src and register.dat file....are these both supposed to be in same directory....because during processing it says "cannot find target reference for orig.mgz"......

They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where "subject" comes from the register.dat file. doug

...

please let me know

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug

On 05/25/2012 04:03 PM, Kushal Kapse wrote:

...

hi dough,

following is the terminal output which lead to segmentation fault.....

i checked the data space and it is not out of size

mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz srcvol = pitt1_cpw-e_4.05_059.nii.gz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white Done reading source surface Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 3:53:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, please be sure to include the entire terminal output. These kinds of things are hard to track down from just the error msg. Also, how many time points are in the func.nii.gz? And are you sure that you are not running out of space on the disk? doug

On 05/25/2012 02:57 PM, Kushal Kapse wrote: > hi, Doug > > as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows > > mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh > > it shows me "Done mapping volume to surface" followed by "Segmentation fault" > > > may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty??? > > > thanks > kk > > > ----- Original Message ----- > From: "Douglas N Greve"greve@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Sent: Thursday, May 24, 2012 11:19:21 AM > Subject: Re: [Freesurfer] fMRI time series in surface space > > Why not run the full preprocessing? It will do the sampling (and surface > smoothing) for you. Alternatively, you can just use mri_vol2surf, then > mris_fwhm to do the surface smoothing (you can also surface smooth in > mri_vol2surf so you can do it all with one command). > doug > > On 05/24/2012 08:35 AM, Kushal Kapse wrote: >>> Hi Everyone, >>> >>> I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. >>> >>> My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? >>> >>> Many thanks, >>> kk >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>

hi fellas,

i m doing a trial group analysis using qdec i performed make_average_subject for 5 subjects fixed factor= gender; continuous= age, mean thickness, nuisance factors= age thickness, dof=4

it shows

ERROR: QdecGlmDesign::Create: zero factors!

may i please know what 'factors' is it talking about as i have clearly imported qdec.table.dat

thanks kk ----- Original Message ----- From: "Douglas Greve" greve@nmr.mgh.harvard.edu To: "Kushal Kapse" kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, May 29, 2012 6:45:07 PM Subject: Re: [Freesurfer] fMRI time series in surface space

It's no longer in the volume, it is on the surface. It should have as many voxels as there are vertices in the surface

On 5/29/12 5:55 PM, Kushal Kapse wrote:

hi doug/freesurfer users

after doing mri_vol2surf.....i went and imported the files in matlab by using f=MRIread ('filename.mgh') for the original functional (func.nii) file and spm001lh.mgh file...it seems the original func files has nvoxels=204800 and spm001lh file has nvolxels=118234.....for mri_vol2surf i used the flag --noreshape

1>>i m not understanding why is there a decrease in voxels for functional-surface mapping of time series??

2>>if i want to pick certain activation voxel in functional and look at its dimension/vertex position on surface; how would i do tht in matlab..... for eg: a voxel (12, 24, 64) would be what and how on its surface?

please let me know

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:59:59 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Not that I can think of. Did you try that new version?

On 05/25/2012 05:58 PM, Kushal Kapse wrote:

...

yes ..the registration is nicely aligned and i did check the green-lines alignment in tkregister2

is their any other reason for it showing segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:52:41 PM Subject: Re: [Freesurfer] fMRI time series in surface space

it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with

tkregister2 --mov func.nii.gz --reg register.dat --surfs

doug

On 05/25/2012 05:45 PM, Kushal Kapse wrote:

...

well...

it seems the seg fault occured due to i was using a 4D func file and not 3d....does the vol2surf does only on 3d func data ?....how would i do that for 4D time series?

please let me know thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug

On 05/25/2012 04:56 PM, Kushal Kapse wrote:

...

orig.mgz file is on 15446_03908/mri/orig.mgz

yes the subject name and the directory path is correct....

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space

The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was

15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls

If either of those are not correct, then it will not determine the path correctly.

Does that orig.mgz file exist?

On 05/25/2012 04:50 PM, Kushal Kapse wrote:

...

i was talking about this issue....

mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness 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 /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file

i didnt understand when u said in last email "where "subject" comes from the register.dat file".....would you please explain me this

thanks kk

----- Original Message ----- From: "Kushal Kapse"kkapse@mail.med.upenn.edu To: "Douglas N Greve"greve@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space

@doug

no doug...this "orig.mgz"error was before segmentation fault error started showing up.....hence i wanna see if why it gave that ....lemme take a look and will keep u updated

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space

On 05/25/2012 04:30 PM, Kushal Kapse wrote:

...

doug,

thanks doug....before i do that....i have two questions which may take care of "mri_vol2surf" issues

1- mri_vol2surf command needs to specify register.dat file........

i have been using register.dat file for vol2surf from reg-feat2anat output.....is that the register.dat file i am supposed to used?.....or if i am wrong, which register.dat file am i suppose to use....basically, where does tht file come from

No, you are correct

...

2- vol2surf needs functional file as src and register.dat file....are these both supposed to be in same directory....because during processing it says "cannot find target reference for orig.mgz"......

They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where "subject" comes from the register.dat file. doug

...

please let me know

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:08:35 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Hi Kushal, can you try this version of vol2surf? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux If that still fails, please tar up the subject and functional and upload it to our file drop system at the end of this email. doug

On 05/25/2012 04:03 PM, Kushal Kapse wrote: > hi dough, > > following is the terminal output which lead to segmentation fault..... > > i checked the data space and it is not out of size > > > > > mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz > srcvol = pitt1_cpw-e_4.05_059.nii.gz > srcreg = register.dat > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > ProjFrac = 0.5 > thickness = thickness > reshape = 0 > interp = trilinear > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > INFO: changing type to float > Done loading volume > Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white > Done reading source surface > Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness > Done > Mapping Source Volume onto Source Subject Surface > 1 0.5 0.5 0.5 > using old > Done mapping volume to surface > Segmentation fault > > > ----- Original Message ----- > From: "Douglas N Greve"greve@nmr.mgh.harvard.edu > To: "Kushal Kapse"kkapse@mail.med.upenn.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Friday, May 25, 2012 3:53:31 PM > Subject: Re: [Freesurfer] fMRI time series in surface space > > Hi Kushal, please be sure to include the entire terminal output. These > kinds of things are hard to track down from just the error msg. Also, > how many time points are in the func.nii.gz? And are you sure that you > are not running out of space on the disk? > doug > > On 05/25/2012 02:57 PM, Kushal Kapse wrote: >> hi, Doug >> >> as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows >> >> mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh >> >> it shows me "Done mapping volume to surface" followed by "Segmentation fault" >> >> >> may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty??? >> >> >> thanks >> kk >> >> >> ----- Original Message ----- >> From: "Douglas N Greve"greve@nmr.mgh.harvard.edu >> To: freesurfer@nmr.mgh.harvard.edu >> Sent: Thursday, May 24, 2012 11:19:21 AM >> Subject: Re: [Freesurfer] fMRI time series in surface space >> >> Why not run the full preprocessing? It will do the sampling (and surface >> smoothing) for you. Alternatively, you can just use mri_vol2surf, then >> mris_fwhm to do the surface smoothing (you can also surface smooth in >> mri_vol2surf so you can do it all with one command). >> doug >> >> On 05/24/2012 08:35 AM, Kushal Kapse wrote: >>>> Hi Everyone, >>>> >>>> I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. >>>> >>>> My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? >>>> >>>> Many thanks, >>>> kk >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>>

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hi doug,

we i am working parallel with tutorial and working on our own data....

----- Original Message ----- From: "Douglas N Greve" greve@nmr.mgh.harvard.edu To: "Kushal Kapse" kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, May 31, 2012 5:15:06 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Have you tried doing the tutorial?

On 05/31/2012 04:34 PM, Kushal Kapse wrote:

hi fellas,

i m doing a trial group analysis using qdec i performed make_average_subject for 5 subjects fixed factor= gender; continuous= age, mean thickness, nuisance factors= age thickness, dof=4

it shows

ERROR: QdecGlmDesign::Create: zero factors!

may i please know what 'factors' is it talking about as i have clearly imported qdec.table.dat

thanks kk ----- Original Message ----- From: "Douglas Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, May 29, 2012 6:45:07 PM Subject: Re: [Freesurfer] fMRI time series in surface space

It's no longer in the volume, it is on the surface. It should have as many voxels as there are vertices in the surface

On 5/29/12 5:55 PM, Kushal Kapse wrote:

...

hi doug/freesurfer users

after doing mri_vol2surf.....i went and imported the files in matlab by using f=MRIread ('filename.mgh') for the original functional (func.nii) file and spm001lh.mgh file...it seems the original func files has nvoxels=204800 and spm001lh file has nvolxels=118234.....for mri_vol2surf i used the flag --noreshape

1>>i m not understanding why is there a decrease in voxels for functional-surface mapping of time series??

2>>if i want to pick certain activation voxel in functional and look at its dimension/vertex position on surface; how would i do tht in matlab..... for eg: a voxel (12, 24, 64) would be what and how on its surface?

please let me know

thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:59:59 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Not that I can think of. Did you try that new version?

On 05/25/2012 05:58 PM, Kushal Kapse wrote:

...

yes ..the registration is nicely aligned and i did check the green-lines alignment in tkregister2

is their any other reason for it showing segmentation fault

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:52:41 PM Subject: Re: [Freesurfer] fMRI time series in surface space

it works for 4D, we do it all the time. Is the registration good? Did you check it visually with tkregister2? You can visualize it with

tkregister2 --mov func.nii.gz --reg register.dat --surfs

doug

On 05/25/2012 05:45 PM, Kushal Kapse wrote:

...

well...

it seems the seg fault occured due to i was using a 4D func file and not 3d....does the vol2surf does only on 3d func data ?....how would i do that for 4D time series?

please let me know thanks kk

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 5:09:31 PM Subject: Re: [Freesurfer] fMRI time series in surface space

Sorry, I just noticed that your command line is wrong. But that is not the one that is seg faulting. The one that seg faults is the correct command doug

On 05/25/2012 04:56 PM, Kushal Kapse wrote:

...

orig.mgz file is on 15446_03908/mri/orig.mgz

yes the subject name and the directory path is correct....

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:52:37 PM Subject: Re: [Freesurfer] fMRI time series in surface space

The register.dat file is a text file. The first line has the name of the subject. It looks like the subject name was

15546_03908 and your SUBJECTS_DIR was /data/mgi_structural/penn/controls

If either of those are not correct, then it will not determine the path correctly.

Does that orig.mgz file exist?

On 05/25/2012 04:50 PM, Kushal Kapse wrote:

...

i was talking about this issue....

mri_vol2surf --src func.nii.gz --ref orig.mgz --regheader register.dat --hemi lh --projfrac 0.5 --out lhfunc.nii.gz srcvol = func.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness 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 /data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz as target reference. mghRead(/data/mgi_structural/penn/controls/15546_03908//register.dat/mri/orig.mgz, -1): could not open file

i didnt understand when u said in last email "where "subject" comes from the register.dat file".....would you please explain me this

thanks kk

----- Original Message ----- From: "Kushal Kapse"kkapse@mail.med.upenn.edu To: "Douglas N Greve"greve@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:39:47 PM Subject: Re: [Freesurfer] fMRI time series in surface space

@doug

no doug...this "orig.mgz"error was before segmentation fault error started showing up.....hence i wanna see if why it gave that ....lemme take a look and will keep u updated

----- Original Message ----- From: "Douglas N Greve"greve@nmr.mgh.harvard.edu To: "Kushal Kapse"kkapse@mail.med.upenn.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 4:33:20 PM Subject: Re: [Freesurfer] fMRI time series in surface space

On 05/25/2012 04:30 PM, Kushal Kapse wrote: > doug, > > thanks doug....before i do that....i have two questions which may take care of "mri_vol2surf" issues > > > 1- mri_vol2surf command needs to specify register.dat file........ > > i have been using register.dat file for vol2surf from reg-feat2anat output.....is that the register.dat file i am supposed to used?.....or if i am wrong, which register.dat file am i suppose to use....basically, where does tht file come from No, you are correct > 2- vol2surf needs functional file as src and register.dat file....are these both supposed to be in same directory....because during processing it says "cannot find target reference for orig.mgz"...... They do not have to be. I did not see that error below. Is that something new? It's looking for $SUBJECTS_DIR/subject/mri/orig.mgz where "subject" comes from the register.dat file. doug > please let me know > > thanks > kk > > ----- Original Message ----- > From: "Douglas N Greve"greve@nmr.mgh.harvard.edu > To: "Kushal Kapse"kkapse@mail.med.upenn.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Friday, May 25, 2012 4:08:35 PM > Subject: Re: [Freesurfer] fMRI time series in surface space > > Hi Kushal, can you try this version of vol2surf? > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2surf.linux > If that still fails, please tar up the subject and functional and upload > it to our file drop system at the end of this email. > doug > > On 05/25/2012 04:03 PM, Kushal Kapse wrote: >> hi dough, >> >> following is the terminal output which lead to segmentation fault..... >> >> i checked the data space and it is not out of size >> >> >> >> >> mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.nii.gz >> srcvol = pitt1_cpw-e_4.05_059.nii.gz >> srcreg = register.dat >> srcregold = 0 >> srcwarp unspecified >> surf = white >> hemi = lh >> ProjFrac = 0.5 >> thickness = thickness >> reshape = 0 >> interp = trilinear >> float2int = round >> GetProjMax = 0 >> INFO: float2int code = 0 >> INFO: changing type to float >> Done loading volume >> Reading surface /data/mgi_structural/penn/controls/11186_03197/surf/lh.white >> Done reading source surface >> Reading thickness /data/mgi_structural/penn/controls/11186_03197/surf/lh.thickness >> Done >> Mapping Source Volume onto Source Subject Surface >> 1 0.5 0.5 0.5 >> using old >> Done mapping volume to surface >> Segmentation fault >> >> >> ----- Original Message ----- >> From: "Douglas N Greve"greve@nmr.mgh.harvard.edu >> To: "Kushal Kapse"kkapse@mail.med.upenn.edu >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Friday, May 25, 2012 3:53:31 PM >> Subject: Re: [Freesurfer] fMRI time series in surface space >> >> Hi Kushal, please be sure to include the entire terminal output. These >> kinds of things are hard to track down from just the error msg. Also, >> how many time points are in the func.nii.gz? And are you sure that you >> are not running out of space on the disk? >> doug >> >> On 05/25/2012 02:57 PM, Kushal Kapse wrote: >>> hi, Doug >>> >>> as per conversation yday, i did perform mri_vol2surf on a functional volume to map it in surface space as follows >>> >>> mri_vol2surf --mov func.nii.gz --reg register.dat --projfrac 0.5 --interp trilinear --hemi lh --o lh.func.mgh >>> >>> it shows me "Done mapping volume to surface" followed by "Segmentation fault" >>> >>> >>> may i please know why it states segmentation fault as i have no clue of which segmentation on vol2surf is faulty??? >>> >>> >>> thanks >>> kk >>> >>> >>> ----- Original Message ----- >>> From: "Douglas N Greve"greve@nmr.mgh.harvard.edu >>> To: freesurfer@nmr.mgh.harvard.edu >>> Sent: Thursday, May 24, 2012 11:19:21 AM >>> Subject: Re: [Freesurfer] fMRI time series in surface space >>> >>> Why not run the full preprocessing? It will do the sampling (and surface >>> smoothing) for you. Alternatively, you can just use mri_vol2surf, then >>> mris_fwhm to do the surface smoothing (you can also surface smooth in >>> mri_vol2surf so you can do it all with one command). >>> doug >>> >>> On 05/24/2012 08:35 AM, Kushal Kapse wrote: >>>>> Hi Everyone, >>>>> >>>>> I am new to FreeSurfer, and having some issues with what I believe should be a pretty basic operation. >>>>> >>>>> My goal is to register a 4D functional time series to FS average space for further connectivity analysis in Matlab (similar to the recent Yeo et al. J Neurophysiology paper). We have run recon-all without problems on the structural data, but I am having trouble getting the whole functional time series into surface space. When I perform FS-FAST just from pre processing till automatic registration of func-struc, "register.dof6.dat" is produced, which includes input registration matrix. Is their any way to apply this registration matrix to the 4D time series directly, so that the output is in FS average template surface (rather than volumetric) space? >>>>> >>>>> Many thanks, >>>>> kk >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>>

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