Hi,

Thanks for your reply. I tried mri_surf2surf --reshape or many other methods but none of them could help.

Then based on your explanation, I tried *mri_convert *.nii.gz *.mgz*, and I could get data from mgz file, it really helps me, thank you!

Besides, I am interested in the difference of dimension between "-surface self"*(dim: -1 1 1)* and "-surface fsaverage"*(dim: 27307 1 6)*, why does the dimension of "-surface fsaverage" be set like this but "-surface self" do not? Is it possible to set the dimension of "-surface self" during preprocessing to make sure every number is less than 32k?

Best,

Bai Haohao

On Thu, Jul 6, 2017 at 7:07 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:

When the nifti standard was adopted, they used a short int to represent the dimensions. Unfortunately, this only allows for a maximum dimension of 32k, which is not big enough for surfaces. So I hacked the FS nifti format to put a -1 as the first dim at which point the FS code will go to another place in the header to get the spatial dimensions. It is possible to reshape the spatial dimensions as long as the largest prime factor is less than 32k (see mri_surf2surf with --reshape option). Other than that, you might ask the nibabel people to program the same hack.

On 6/25/17 6:48 AM, Bai Haohao wrote:

Hello Freesurfer experts,

I am running my data with preproc-sess to project my func data to individual anatomy file, and the command shows as below:

preproc-sess -sf ${Sesslist} -fsd "bold" -surface self lhrh -fwhm 0 -per-run -force

And the subjectname point to the subject dir that created after recon-all.

After the running completed, I try to load data from fmcpr.sm0.self.lh.nii.gz with nibabel, and I get this error info:

...

...

...

f.get_data()

Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/pymodules/python2.7/nibabel/spatialimages.py", line 341, in get_data return np.asanyarray(self._data) File "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py", line 512, in asanyarray return array(a, dtype, copy=False, order=order, subok=True) File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 55, in __array__ self._data = self._read_data() File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 60, in _read_data data = self.header.data_from_fileobj(fileobj) File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 486, in data_from_fileobj data = self.raw_data_from_fileobj(fileobj) File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 458, in raw_data_from_fileobj return array_from_file(shape, dtype, fileobj, offset) File "/usr/lib/pymodules/python2.7/nibabel/volumeutils.py", line 493, in array_from_file raise IOError(msg) IOError: Expected -1804 bytes, got 264809160 bytes from file "fmcpr.vol2surf.lh.nii.gz"

• could the file be damaged?

Then I check the file header by nibabel, and I get this:

...

...

...

print(f.get_header())

<class 'nibabel.nifti1.Nifti1Header'> object, endian='<' sizeof_hdr : 348 data_type : db_name : extents : 0 session_error : 0 regular : dim_info : 0 dim : [ 4 -1 1 1 451 1 1 1] intent_p1 : 0.0 intent_p2 : 0.0 intent_p3 : 0.0 intent_code : none datatype : float32 bitpix : 32 slice_start : 0 pixdim : [-1. 1. 1. 1. 2.00000072 1. 1.

1.    ]
   

vox_offset : 352.0 scl_slope : 0.0 scl_inter : 0.0 slice_end : 0 slice_code : unknown xyzt_units : 10 cal_max : 0.0 cal_min : 0.0 slice_duration : 0.0 toffset : 0.0 glmax : 0 glmin : 146790 descrip : FreeSurfer May 13 2013 aux_file : qform_code : scanner sform_code : scanner quatern_b : -0.0115927606821 quatern_c : -0.996071338654 quatern_d : -0.0864994972944 qoffset_x : 73344.5546875 qoffset_y : -1492.14978027 qoffset_z : -2311.28955078 srow_x : [ -9.99280393e-01 2.56918129e-02 2.79041883e-02 7.33445547e+04] srow_y : [ 2.04970520e-02 9.84766901e-01 -1.72667429e-01 -1.49214978e+03] srow_z : [ 3.19152586e-02 1.71971247e-01 9.84584868e-01 -2.31128955e+03] intent_name : magic : n+1

Note that the dim has value -1, but when I use -surface fsaverage, the dim is correct(show as below):

dim : [ 4 27307 1 6 451 1 1 1]

And I read the source code, the difference between self and fsaverage is appeared when running rawfunc2surf-sess, and log files are attached.

I have tried many commands to load data from fmcpr.sm0.self.lh.nii.gz, such as fslview, freeview, mri_convert, mri_surf2surf, ...

and only tksurfer could read this file by -timecourse fmcpr.sm0.self.lh.nii.gz.

I want to figure out how could I fix it, and any suggestion would be helpful.

Thanks in advance,

Bai Haohao

Version info: System: ubuntu-16.04.1-server-amd64 Freesurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP nibabel: python-nibabel 1.2.2-1

---

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi,

Thanks for your reply, and I get these dims by using nibabel, simply like this:

*import nibabel as nib* *print(nib.load(*.nii.gz).get_header())*

then it would return header info about *.nii.gz, and dim info is included in it. I tried load and get header both from *fmcpr.up.sm0.self.lh.nii.gz* and* fmcpr.up.sm0.fsaverage.lh.nii.gz*, and only self data has this negative dim issue and cannot be read by *nib.get_data()*, fsaverage data has normal dim and can be read.

Besides, I tried your advice and email to nibabel mailing list, they replied to me just as what Christopher said, that is to encourage FreeSurfer to move toward writing NIfTI-2.

Best,

Bai Haohao

On Fri, Jul 28, 2017 at 1:11 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

where are you getting those dims?

On 07/27/2017 09:24 AM, Bai Haohao wrote:

...

Hi,

Thanks for your reply. I tried mri_surf2surf --reshape or many other methods but none of them could help.

Then based on your explanation, I tried *mri_convert *.nii.gz *.mgz*, and I could get data from mgz file, it really helps me, thank you!

Besides, I am interested in the difference of dimension between "-surface self"*(dim: -1 1 1)* and "-surface fsaverage"*(dim: 27307 1 6)*, why does the dimension of "-surface fsaverage" be set like this but "-surface self" do not? Is it possible to set the dimension of "-surface self" during preprocessing to make sure every number is less than 32k?

Best,

Bai Haohao

On Thu, Jul 6, 2017 at 7:07 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

When the nifti standard was adopted, they used a short int to
represent the dimensions. Unfortunately, this only allows for a
maximum dimension of 32k, which is not big enough for surfaces. So
I hacked the FS nifti format to put a -1 as the first dim at which
point the FS code will go to another place in the header to get
the spatial dimensions. It is possible to reshape the spatial
dimensions as long as the largest prime factor is less than 32k
(see mri_surf2surf with --reshape option). Other than that, you
might ask the nibabel people to program the same hack.


On 6/25/17 6:48 AM, Bai Haohao wrote:

...

Hello Freesurfer experts,

I am running my data with preproc-sess to project my func data to
individual anatomy file, and the command shows as below:

    preproc-sess -sf ${Sesslist} -fsd "bold" -surface self lhrh
    -fwhm 0 -per-run -force


And the subjectname point to the subject dir that created after
recon-all.

After the running completed, I try to load data from
fmcpr.sm0.self.lh.nii.gz with nibabel, and I get this error info:

    >>> f.get_data()
    Traceback (most recent call last):
      File "<stdin>", line 1, in <module>
      File
    "/usr/lib/pymodules/python2.7/nibabel/spatialimages.py", line
    341, in get_data
        return np.asanyarray(self._data)
      File
    "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py",
    line 512, in asanyarray
        return array(a, dtype, copy=False, order=order, subok=True)
      File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py",
    line 55, in __array__
        self._data = self._read_data()
      File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py",
    line 60, in _read_data
        data = self.header.data_from_fileobj(fileobj)
      File "/usr/lib/pymodules/python2.7/nibabel/analyze.py",
    line 486, in data_from_fileobj
        data = self.raw_data_from_fileobj(fileobj)
      File "/usr/lib/pymodules/python2.7/nibabel/analyze.py",
    line 458, in raw_data_from_fileobj
        return array_from_file(shape, dtype, fileobj, offset)
      File "/usr/lib/pymodules/python2.7/nibabel/volumeutils.py",
    line 493, in array_from_file
        raise IOError(msg)
    IOError: Expected -1804 bytes, got 264809160 bytes from file
    "fmcpr.vol2surf.lh.nii.gz"
     - could the file be damaged?


Then I check the file header by nibabel, and I get this:


    >>> print(f.get_header())
    <class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
    sizeof_hdr  : 348
    data_type :
    db_name :
    extents : 0
    session_error : 0
    regular :
    dim_info  : 0
    dim : [  4  -1   1   1 451   1   1   1]
    intent_p1 : 0.0
    intent_p2 : 0.0
    intent_p3 : 0.0
    intent_code : none
    datatype  : float32
    bitpix  : 32
    slice_start : 0
    pixdim  : [-1.          1.          1.    1.
     2.00000072  1.  1.
      1.        ]
    vox_offset  : 352.0
    scl_slope : 0.0
    scl_inter : 0.0
    slice_end : 0
    slice_code  : unknown
    xyzt_units  : 10
    cal_max : 0.0
    cal_min : 0.0
    slice_duration  : 0.0
    toffset : 0.0
    glmax : 0
    glmin : 146790
    descrip : FreeSurfer May 13 2013
    aux_file  :
    qform_code  : scanner
    sform_code  : scanner
    quatern_b : -0.0115927606821
    quatern_c : -0.996071338654
    quatern_d : -0.0864994972944
    qoffset_x : 73344.5546875
    qoffset_y : -1492.14978027
    qoffset_z : -2311.28955078
    srow_x  : [ -9.99280393e-01   2.56918129e-02   2.79041883e-02
      7.33445547e+04]
    srow_y  : [  2.04970520e-02   9.84766901e-01  -1.72667429e-01
     -1.49214978e+03]
    srow_z  : [  3.19152586e-02   1.71971247e-01   9.84584868e-01
     -2.31128955e+03]
    intent_name :
    magic : n+1




Note that the dim has value -1, but when I use -surface
fsaverage, the dim is correct(show as below):

    dim             : [    4 27307     1     6   451     1     1
        1]


And I read the source code, the difference between self and
fsaverage is appeared when running rawfunc2surf-sess, and log
files are attached.

I have tried many commands to load data from
fmcpr.sm0.self.lh.nii.gz, such as fslview, freeview, mri_convert,
mri_surf2surf, ...

and only tksurfer could read this file by -timecourse
fmcpr.sm0.self.lh.nii.gz.

I want to figure out how could I fix it, and any suggestion would
be helpful.

Thanks in advance,

Bai Haohao


Version info:
System: ubuntu-16.04.1-server-amd64
Freesurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP
nibabel: python-nibabel  1.2.2-1



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

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.

harvard.edu>

...

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>


The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline
<http://www.partners.org/complianceline> . If the e-mail was sent
to you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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

Hi,

Thanks for your reply, and I contacted with nibabel team based on your advice.

They advice me to update my nibabel to the newest version, and now these data can be got properly:)

Besides, I'm interested in the different dimension between `-surface self' and `-surface fsaverage`, they both have vertex more than 32k, but every dimension of fsaverage is not beyond 32k.

Does it mean if the target surface is fsaverage, then the dimension would be reshaped automatically? And can the dimension of `surface -self` be reshaped like that?

Best,

Bai Haohao

On Mon, Jul 31, 2017 at 10:10 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:

If this is surface data, then there is nothing that we can do right now. One possibility is to read the data into matlab with the FS MRIread.m, then write it out in nifti2 using some other tool

On 7/28/17 10:26 AM, Bai Haohao wrote:

Hi,

Thanks for your reply, and I get these dims by using nibabel, simply like this:

*import nibabel as nib* *print(nib.load(*.nii.gz).get_header())*

then it would return header info about *.nii.gz, and dim info is included in it. I tried load and get header both from *fmcpr.up.sm0.self.lh.nii.gz* and* fmcpr.up.sm0.fsaverage.lh.nii.gz*, and only self data has this negative dim issue and cannot be read by *nib.get_data()*, fsaverage data has normal dim and can be read.

Besides, I tried your advice and email to nibabel mailing list, they replied to me just as what Christopher said, that is to encourage FreeSurfer to move toward writing NIfTI-2.

Best,

Bai Haohao

On Fri, Jul 28, 2017 at 1:11 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:

...

where are you getting those dims?

On 07/27/2017 09:24 AM, Bai Haohao wrote:

...

Hi,

Thanks for your reply. I tried mri_surf2surf --reshape or many other methods but none of them could help.

Then based on your explanation, I tried *mri_convert *.nii.gz *.mgz*, and I could get data from mgz file, it really helps me, thank you!

Besides, I am interested in the difference of dimension between "-surface self"*(dim: -1 1 1)* and "-surface fsaverage"*(dim: 27307 1 6)*, why does the dimension of "-surface fsaverage" be set like this but "-surface self" do not? Is it possible to set the dimension of "-surface self" during preprocessing to make sure every number is less than 32k?

Best,

Bai Haohao

On Thu, Jul 6, 2017 at 7:07 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

When the nifti standard was adopted, they used a short int to
represent the dimensions. Unfortunately, this only allows for a
maximum dimension of 32k, which is not big enough for surfaces. So
I hacked the FS nifti format to put a -1 as the first dim at which
point the FS code will go to another place in the header to get
the spatial dimensions. It is possible to reshape the spatial
dimensions as long as the largest prime factor is less than 32k
(see mri_surf2surf with --reshape option). Other than that, you
might ask the nibabel people to program the same hack.


On 6/25/17 6:48 AM, Bai Haohao wrote:

...

Hello Freesurfer experts,

I am running my data with preproc-sess to project my func data to
individual anatomy file, and the command shows as below:

    preproc-sess -sf ${Sesslist} -fsd "bold" -surface self lhrh
    -fwhm 0 -per-run -force


And the subjectname point to the subject dir that created after
recon-all.

After the running completed, I try to load data from
fmcpr.sm0.self.lh.nii.gz with nibabel, and I get this error info:

    >>> f.get_data()
    Traceback (most recent call last):
      File "<stdin>", line 1, in <module>
      File
    "/usr/lib/pymodules/python2.7/nibabel/spatialimages.py", line
    341, in get_data
        return np.asanyarray(self._data)
      File
    "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py",
    line 512, in asanyarray
        return array(a, dtype, copy=False, order=order, subok=True)
      File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py",
    line 55, in __array__
        self._data = self._read_data()
      File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py",
    line 60, in _read_data
        data = self.header.data_from_fileobj(fileobj)
      File "/usr/lib/pymodules/python2.7/nibabel/analyze.py",
    line 486, in data_from_fileobj
        data = self.raw_data_from_fileobj(fileobj)
      File "/usr/lib/pymodules/python2.7/nibabel/analyze.py",
    line 458, in raw_data_from_fileobj
        return array_from_file(shape, dtype, fileobj, offset)
      File "/usr/lib/pymodules/python2.7/nibabel/volumeutils.py",
    line 493, in array_from_file
        raise IOError(msg)
    IOError: Expected -1804 bytes, got 264809160 bytes from file
    "fmcpr.vol2surf.lh.nii.gz"
     - could the file be damaged?


Then I check the file header by nibabel, and I get this:


    >>> print(f.get_header())
    <class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
    sizeof_hdr  : 348
    data_type :
    db_name :
    extents : 0
    session_error : 0
    regular :
    dim_info  : 0
    dim : [  4  -1   1   1 451   1   1   1]
    intent_p1 : 0.0
    intent_p2 : 0.0
    intent_p3 : 0.0
    intent_code : none
    datatype  : float32
    bitpix  : 32
    slice_start : 0
    pixdim  : [-1.          1.          1.    1.
     2.00000072  1.  1.
      1.        ]
    vox_offset  : 352.0
    scl_slope : 0.0
    scl_inter : 0.0
    slice_end : 0
    slice_code  : unknown
    xyzt_units  : 10
    cal_max : 0.0
    cal_min : 0.0
    slice_duration  : 0.0
    toffset : 0.0
    glmax : 0
    glmin : 146790
    descrip : FreeSurfer May 13 2013
    aux_file  :
    qform_code  : scanner
    sform_code  : scanner
    quatern_b : -0.0115927606821
    quatern_c : -0.996071338654
    quatern_d : -0.0864994972944
    qoffset_x : 73344.5546875
    qoffset_y : -1492.14978027
    qoffset_z : -2311.28955078
    srow_x  : [ -9.99280393e-01   2.56918129e-02   2.79041883e-02
      7.33445547e+04]
    srow_y  : [  2.04970520e-02   9.84766901e-01  -1.72667429e-01
     -1.49214978e+03]
    srow_z  : [  3.19152586e-02   1.71971247e-01   9.84584868e-01
     -2.31128955e+03]
    intent_name :
    magic : n+1




Note that the dim has value -1, but when I use -surface
fsaverage, the dim is correct(show as below):

    dim             : [    4 27307     1     6   451     1     1
        1]


And I read the source code, the difference between self and
fsaverage is appeared when running rawfunc2surf-sess, and log
files are attached.

I have tried many commands to load data from
fmcpr.sm0.self.lh.nii.gz, such as fslview, freeview, mri_convert,
mri_surf2surf, ...

and only tksurfer could read this file by -timecourse
fmcpr.sm0.self.lh.nii.gz.

I want to figure out how could I fix it, and any suggestion would
be helpful.

Thanks in advance,

Bai Haohao


Version info:
System: ubuntu-16.04.1-server-amd64
Freesurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP
nibabel: python-nibabel  1.2.2-1



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

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.har

vard.edu>

...

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>


The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline
<http://www.partners.org/complianceline> . If the e-mail was sent
to you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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

---

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Yes, it is on my to-do list :)

On 07/27/2017 11:42 AM, Christopher Markiewicz wrote:

Hi Doug,

I wonder if there's a plan to move to NIfTI-2 as the default encoding for .nii(.gz) images that would can't be encoded in a standard-conforming NIfTI-1? I believe all of the major packages support NIfTI-2 in their latest releases (with the possible exception of ANTs, which I don't believe handles surface data in any event).

Chris Markiewwicz ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu Sent: Wednesday, July 5, 2017 7:07:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] negative header after preproc-sess

When the nifti standard was adopted, they used a short int to represent the dimensions. Unfortunately, this only allows for a maximum dimension of 32k, which is not big enough for surfaces. So I hacked the FS nifti format to put a -1 as the first dim at which point the FS code will go to another place in the header to get the spatial dimensions. It is possible to reshape the spatial dimensions as long as the largest prime factor is less than 32k (see mri_surf2surf with --reshape option). Other than that, you might ask the nibabel people to program the same hack.

On 6/25/17 6:48 AM, Bai Haohao wrote: Hello Freesurfer experts,

I am running my data with preproc-sess to project my func data to individual anatomy file, and the command shows as below:

preproc-sess -sf ${Sesslist} -fsd "bold" -surface self lhrh -fwhm 0 -per-run -force

And the subjectname point to the subject dir that created after recon-all.

After the running completed, I try to load data from fmcpr.sm0.self.lh.nii.gz with nibabel, and I get this error info:

...

...

...

f.get_data()

Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/pymodules/python2.7/nibabel/spatialimages.py", line 341, in get_data return np.asanyarray(self._data) File "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py", line 512, in asanyarray return array(a, dtype, copy=False, order=order, subok=True) File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 55, in __array__ self._data = self._read_data() File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 60, in _read_data data = self.header.data_from_fileobj(fileobj) File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 486, in data_from_fileobj data = self.raw_data_from_fileobj(fileobj) File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 458, in raw_data_from_fileobj return array_from_file(shape, dtype, fileobj, offset) File "/usr/lib/pymodules/python2.7/nibabel/volumeutils.py", line 493, in array_from_file raise IOError(msg) IOError: Expected -1804 bytes, got 264809160 bytes from file "fmcpr.vol2surf.lh.nii.gz"

• could the file be damaged?

Then I check the file header by nibabel, and I get this:

...

...

...

print(f.get_header())

<class 'nibabel.nifti1.Nifti1Header'> object, endian='<' sizeof_hdr : 348 data_type : db_name : extents : 0 session_error : 0 regular : dim_info : 0 dim : [ 4 -1 1 1 451 1 1 1] intent_p1 : 0.0 intent_p2 : 0.0 intent_p3 : 0.0 intent_code : none datatype : float32 bitpix : 32 slice_start : 0 pixdim : [-1. 1. 1. 1. 2.00000072 1. 1.

1.    ]
   

vox_offset : 352.0 scl_slope : 0.0 scl_inter : 0.0 slice_end : 0 slice_code : unknown xyzt_units : 10 cal_max : 0.0 cal_min : 0.0 slice_duration : 0.0 toffset : 0.0 glmax : 0 glmin : 146790 descrip : FreeSurfer May 13 2013 aux_file : qform_code : scanner sform_code : scanner quatern_b : -0.0115927606821 quatern_c : -0.996071338654 quatern_d : -0.0864994972944 qoffset_x : 73344.5546875 qoffset_y : -1492.14978027 qoffset_z : -2311.28955078 srow_x : [ -9.99280393e-01 2.56918129e-02 2.79041883e-02 7.33445547e+04] srow_y : [ 2.04970520e-02 9.84766901e-01 -1.72667429e-01 -1.49214978e+03] srow_z : [ 3.19152586e-02 1.71971247e-01 9.84584868e-01 -2.31128955e+03] intent_name : magic : n+1

Note that the dim has value -1, but when I use -surface fsaverage, the dim is correct(show as below):

dim : [ 4 27307 1 6 451 1 1 1]

And I read the source code, the difference between self and fsaverage is appeared when running rawfunc2surf-sess, and log files are attached.

I have tried many commands to load data from fmcpr.sm0.self.lh.nii.gz, such as fslview, freeview, mri_convert, mri_surf2surf, ...

and only tksurfer could read this file by -timecourse fmcpr.sm0.self.lh.nii.gz.

I want to figure out how could I fix it, and any suggestion would be helpful.

Thanks in advance,

Bai Haohao

Version info: System: ubuntu-16.04.1-server-amd64 Freesurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP nibabel: python-nibabel 1.2.2-1

---

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

---

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