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.
]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
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