[Neuroimaging] 回复： Fwd: [Freesurfer] negative header afterpreproc-sess
Bai Haohao
744652457 at qq.com
Fri Jul 28 12:55:42 EDT 2017
Hi,
Thank you for your reply in email and github, I will try the newest version of nibabel to see if this problem can be fixed.
It really helps me a lot, thank you:)
Best,
Bai Haohao
------------------ 原始邮件 ------------------
发件人: "Christopher Markiewicz";<effigies at bu.edu>;
发送时间: 2017年7月28日(星期五) 晚上11:18
收件人: "Neuroimaging analysis in Python"<neuroimaging at python.org>;
主题: Re: [Neuroimaging] Fwd: [Freesurfer] negative header afterpreproc-sess
Hi Bai,
You can try setting the FSF_OUTPUT_FORMAT environment variable to 'mgz' (in $FREESURFER_HOME/FreeSurferEnv.sh).
I haven't tried this, and there may be code that presumes NIfTI inputs, but I would assume it would be fine with MGH/MGZ formats.
Chris
On Fri, Jul 28, 2017 at 10:59 AM, Bai Haohao <jarblank1200 at gmail.com> wrote:
Hello,
Thanks for your replies, and I agree with your idea that Nifti1 standard should be replaced by Nifti2, or do not save file into Nifti1 format.
However, I have tried convert input data format from "*.nii.gz" to "*.mgz", and delete origin *.nii.gz file, then running "preproc-sess", and I found freesurfer would detect the format of the input, and convert "*.mgz" to "*.nii.gz", finally I got Nifti1 data, with negative dim.
Maybe there has an argument that could specify output format and convert output file format manually could solve it, but I think it would be helpful for other people who meet the same situation as me if nibabel could support reading these kind of data.
Thanks for your opinions again, and I believe we hold the same view:)
Best,
Bai Haohao
On Thu, Jul 27, 2017 at 11:59 PM, Christopher Markiewicz <effigies at bu.edu> wrote:
I agree with this viewpoint from a user/standards perspective. AFAIK only FreeSurfer and nibabel support the surface hacks, and both also support the .mgh format, so there's no real advantage to using NIfTI here. For interoperability, other formats are more appropriate. I also think it's reasonable to encourage FreeSurfer to move toward writing NIfTI-2 when hacks are necessary to generate NIfTI-1 files.
From a nibabel-as-multitool perspective, while I understand the concern about propagating broken formats, I also think we should be able to read images as created by existing packages, as long as doing so doesn't harm our ability to read standard-conforming files.
Chris
On Thu, Jul 27, 2017 at 10:18 AM, Reynolds, Richard C. (NIH/NIMH) [E] <reynoldr at mail.nih.gov> wrote:
This seems like an appropriate case to be using the
NIFTI-2 standard, which uses 64-bit values rather than
the 16-bits for NIFTI-1 (which was done just to keep it
similar to ANALYZE).
For that matter, GIFTI was made to be the surface
alternative to NIFTI, and FreeSurfer supports it, as does
nibabel, it seems.
Even without those options, it seems like FreeSurfer
can still output what you want in a useful format.
Breaking the NIFTI-1 standard is causing you trouble.
Maybe propagating that is not necessary.
- rick
From: Bai Haohao <jarblank1200 at gmail.com>
Sent: Thursday, July 27, 2017 9:41:13 AM
To: neuroimaging at python.org
Subject: [Neuroimaging] Fwd: [Freesurfer] negative header after preproc-sess
Dear nibabel experts,
I forward this email to nibabel mailing list because I think it is related to nibabel, even this problem is caused by nifti standard and freesurfer.
I am using nibabel to load data after freesurfer "preproc-sess -suface self" and I get negative dim(-1 1 1, see origin email for detail), which makes nibabel.get_data() failed, but freesurfer first level analysis can be done successfully, in my view it means freesurfer can get data from this bad header.
I find a way to solve it is by using "mri_convert *.nii.gz *.mgz", then nibabel could get data from *.mgz. But I think if nibabel could support getting data from negative header file would be more helpful.
Just some undevelopped thoughts, I hope I express it clearly.
Best,
Bai Haohao
---------- Forwarded message ----------
From: Douglas Greve <greve at nmr.mgh.harvard.edu>
Date: Thu, Jul 6, 2017 at 7:07 AM
Subject: Re: [Freesurfer] negative header after preproc-sess
To: freesurfer at nmr.mgh.harvard.edu
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
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