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 list
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


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.