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"<gr...@nmr.mgh.harvard.edu>
> To: "Kushal Kapse"<kka...@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"<gr...@nmr.mgh.harvard.edu>
>> To: "Kushal Kapse"<kka...@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"<gr...@nmr.mgh.harvard.edu>
>>> To: "Kushal Kapse"<kka...@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"<gr...@nmr.mgh.harvard.edu>
>>>> To: "Kushal Kapse"<kka...@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"<gr...@nmr.mgh.harvard.edu>
>>>>> To: "Kushal Kapse"<kka...@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"<kka...@mail.med.upenn.edu>
>>>>>> To: "Douglas N Greve"<gr...@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"<gr...@nmr.mgh.harvard.edu>
>>>>>> To: "Kushal Kapse"<kka...@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"<gr...@nmr.mgh.harvard.edu>
>>>>>>> To: "Kushal Kapse"<kka...@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"<gr...@nmr.mgh.harvard.edu>
>>>>>>>> To: "Kushal Kapse"<kka...@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"<gr...@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.
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
