[Mne_analysis] Mne_analysis Digest, Vol 100, Issue 3

San-Yuan Lin lin.sanyuan at gmail.com
Sun May 8 21:30:52 EDT 2016
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Hi Alex,

Thank you. After I add —grid 3 (instead of 5) to mne_volume_source_space, the file did convert successfully.
A new problem is, with the following code to covert w file to mgz and then to nii.gz file format, I have error messages from mrInit and mrVista which request some informaion.

Here is the code:

mne_volume_data2mri --src $Data_DIR/$SUBJECT/$SsFileDir/$SsFileHead-vol-src.fif  --stc $Data_DIR/$SUBJECT/$SsFileDir/$SsFileHead-stc-lh.stc --out $Data_DIR/$SUBJECT/$SsFileDir/$SsFileHead-lh.stc.mgz 

mri_convert --out_orientation RAS  -rt nearest --reslice_like $SUBJECTS_Anatomy_DIR/$SUBJECT/HYJ_tag_FS4_T1.nii.gz --in_type mgz $Data_DIR/$SUBJECT/$SsFileDir/$SsFileHead-$PickTimeFileName-lh.w.mgz --out_type nifti1 $Data_DIR/$SUBJECT/$SsFileDir/$SsFileHead-$PickTimeFileName.w.nii.gz



And after these, I got the follow error messages:

[mrLoad]: mr.voxelSize has length<4: concatenating a "1" to it
[mrLoad]: mr.dims has length<4: concatenating a "1" to it
Warning: No freqdim field set in the nifti. Assuming freqdim = 1. Nifti stored at: /home/sanyuan/Documents/LSY_dev/MNE_practice/MEG/chi_hc/150715/run1_raw_sss-00150.0.w.nii.gz.hdr 
> In niftiApplyXform (line 99)
  In niftiApplyAndCreateXform (line 28)
  In mrInit (line 188) 
Warning: No phasedim field set in the nifti. Assuming phasedim = 2. Nifti stored at: /home/sanyuan/Documents/LSY_dev/MNE_practice/MEG/chi_hc/150715/run1_raw_sss-00150.0.w.nii.gz.hdr 
> In niftiApplyXform (line 106)
  In niftiApplyAndCreateXform (line 28)
  In mrInit (line 188) 
Index exceeds matrix dimensions.

Error in mrInit>mrInitInplaneTseries (line 345)
f.totalFrames = mr.dims(4);

Error in mrInit (line 221)
        mrInitInplaneTseries(func,scan);
 
>> mrVista
Warning: Matlab version 8.6.0.267246 (R2015b) is not yet supported in vistasoft. 
> In mrVista (line 62) 
Initializing Inplane view
Attaching menus
Warning: No freqdim field set in the nifti. Assuming freqdim = 1. Nifti stored at: /home/sanyuan/Documents/LSY_dev/MNE_practice/subjects/chi_hc/HYJ_tag_FS4_orig.nii.gz 
> In niftiApplyXform (line 99)
  In niftiApplyAndCreateXform (line 28)
  In viewSetAnatomy (line 45)
  In viewSet (line 191)
  In loadAnat (line 34)
  In openMontageWindow (line 165)
  In mrVista 
Warning: No phasedim field set in the nifti. Assuming phasedim = 2. Nifti stored at: /home/sanyuan/Documents/LSY_dev/MNE_practice/subjects/chi_hc/HYJ_tag_FS4_orig.nii.gz 
> In niftiApplyXform (line 106)
  In niftiApplyAndCreateXform (line 28)
  In viewSetAnatomy (line 45)
  In viewSet (line 191)
  In loadAnat (line 34)
  In openMontageWindow (line 165)
  In mrVista 
Reference to non-existent field 'scanParams'.

Error in dtGet (line 123)
            val = dt.scanParams(varargin{1}).cropSize;

Error in viewGetTimeSeries (line 58)
                val = dtGet(dataTYPES(1),'Func Size', scan);

Error in viewGet (line 317)
        val = viewGetTimeSeries(vw,param,varargin{:});

Error in labelInplaneLR (line 65)
if Rdim == viewGet(vw,'slicedim')

Error in openMontageWindow (line 186)
INPLANE{s} = labelInplaneLR(INPLANE{s}); %This assumes that the LR data is saved in mrSESSION

Error in mrVista
 
>> mrInit
***** [mrInit] Initializing Session LSY_dev ***** (06-May-2016 16:10:17)
freq_dim not set correctly in NIFTI header.
phase_dim not set correctly in NIFTI header.
[mrLoad]: mr.voxelSize has length<4: concatenating a "1" to it
[mrLoad]: mr.dims has length<4: concatenating a "1" to it
Warning: No freqdim field set in the nifti. Assuming freqdim = 1. Nifti stored at:
/home/sanyuan/Documents/LSY_dev/MNE_practice/subjects/chi_hc/mri/ribbon.nii 
> In niftiApplyXform (line 99)
  In niftiApplyAndCreateXform (line 28)
  In mrInit (line 188) 
Warning: No phasedim field set in the nifti. Assuming phasedim = 2. Nifti stored at:
/home/sanyuan/Documents/LSY_dev/MNE_practice/subjects/chi_hc/mri/ribbon.nii 
> In niftiApplyXform (line 106)
  In niftiApplyAndCreateXform (line 28)
  In mrInit (line 188) 
Index exceeds matrix dimensions.

Error in mrInit>mrInitInplaneTseries (line 345)
f.totalFrames = mr.dims(4);

Error in mrInit (line 221)
        mrInitInplaneTseries(func,scan);


I found no way to fill in missing information when converting the files.
Could you help me to find out might be the cause or step I missed?

Best,
Sanyuan



> mne_analysis-request at nmr.mgh.harvard.edu 於 2016年5月4日 下午9:54 寫道:
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> Today's Topics:
> 
>   1. Creating bem meshes with mne_watershed_bem -
>      mne_convert_surface not found (milton_avila at usp.br)
>   2. Re: Creating bem meshes with mne_watershed_bem -
>      mne_convert_surface not found (Alexandre Gramfort)
>   3. Error message from mne_volume_data2mri: w file	vertex number
>      out of range (San-Yuan Lin)
>   4. Re: Error message from mne_volume_data2mri: w file vertex
>      number out of range (Alexandre Gramfort)
>   5. Re: Creating bem meshes with mne_watershed_bem -
>      mne_convert_surface not found (milton_avila at usp.br)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 3 May 2016 18:11:38 -0300 (BRT)
> From: milton_avila at usp.br
> Subject: [Mne_analysis] Creating bem meshes with mne_watershed_bem -
> 	mne_convert_surface not found
> To: mne_analysis at nmr.mgh.harvard.edu
> Message-ID: <1368681712.9206796.1462309898045.JavaMail.root at usp.br>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear MNE users, 
> 
> I am trying to create BEM meshes using 
> mne_watershed_bem. 
> 
> I raises the following error: 
> 
> Running subprocess: mne_convert_surface --surf S07_brain_surface --mghmri /media/milton/Dados/MRI/S07/mri/T1.mgz --surfout S07_brain_surface --replacegeom 
> Command not found: mne_convert_surface 
> Traceback (most recent call last): 
> File "pre_process.py", line 257, in <module> 
> mne.bem.make_watershed_bem(subj, subjects_dir=mri_path, overwrite=True) 
> File "<string>", line 2, in make_watershed_bem 
> File "/home/milton/anaconda2/lib/python2.7/site-packages/mne/utils.py", line 551, in verbose 
> return function(*args, **kwargs) 
> File "/home/milton/anaconda2/lib/python2.7/site-packages/mne/bem.py", line 1015, in make_watershed_bem 
> run_subprocess(cmd, env=env, stdout=sys.stdout, stderr=sys.stderr) 
> File "<string>", line 2, in run_subprocess 
> File "/home/milton/anaconda2/lib/python2.7/site-packages/mne/utils.py", line 551, in verbose 
> return function(*args, **kwargs) 
> File "/home/milton/anaconda2/lib/python2.7/site-packages/mne/utils.py", line 804, in run_subprocess 
> p = subprocess.Popen(command, *args, **kwargs) 
> File "/home/milton/anaconda2/lib/python2.7/subprocess.py", line 710, in __init__ 
> errread, errwrite) 
> File "/home/milton/anaconda2/lib/python2.7/subprocess.py", line 1335, in _execute_child 
> raise child_exception 
> OSError: [Errno 2] No such file or directory 
> 
> 
> The files created: 
> <subj>_brain_surface 
> <subj>_inner_skull_surface 
> <subj>_outer_skull_surface 
> <subj>_inner_skin_surface 
> 
> The files NOT created: 
> inner_skull.surf, 
> outer_skull.surf 
> outer_skin.surf 
> 
> Does anybody know what is going on? 
> Thanks in advance 
> Milton 
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> 
> ------------------------------
> 
> Message: 2
> Date: Wed, 4 May 2016 13:52:07 +0200
> From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr>
> Subject: Re: [Mne_analysis] Creating bem meshes with mne_watershed_bem
> 	- mne_convert_surface not found
> To: Discussion and support forum for the users of MNE Software
> 	<mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> 	<CADeotZq5poNMMvrCJj88G-=nON-WoT1WpW4Re0Hsu9eJ10Ze=w at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> hi Milton,
> 
> do you have the problem with all your subjects?
> 
> if so can you try with the latest version of mne-python code?
> 
> I recently had to fix this code that was not creating properly the sym links.
> 
> Alex
> 
> 
> On Tue, May 3, 2016 at 11:11 PM,  <milton_avila at usp.br> wrote:
>> Dear MNE users,
>> 
>> I am trying to create BEM meshes using
>> mne_watershed_bem.
>> 
>> I raises the following error:
>> 
>> Running subprocess: mne_convert_surface --surf S07_brain_surface --mghmri
>> /media/milton/Dados/MRI/S07/mri/T1.mgz --surfout S07_brain_surface
>> --replacegeom
>> Command not found: mne_convert_surface
>> Traceback (most recent call last):
>>  File "pre_process.py", line 257, in <module>
>>    mne.bem.make_watershed_bem(subj, subjects_dir=mri_path, overwrite=True)
>>  File "<string>", line 2, in make_watershed_bem
>>  File "/home/milton/anaconda2/lib/python2.7/site-packages/mne/utils.py",
>> line 551, in verbose
>>    return function(*args, **kwargs)
>>  File "/home/milton/anaconda2/lib/python2.7/site-packages/mne/bem.py", line
>> 1015, in make_watershed_bem
>>    run_subprocess(cmd, env=env, stdout=sys.stdout, stderr=sys.stderr)
>>  File "<string>", line 2, in run_subprocess
>>  File "/home/milton/anaconda2/lib/python2.7/site-packages/mne/utils.py",
>> line 551, in verbose
>>    return function(*args, **kwargs)
>>  File "/home/milton/anaconda2/lib/python2.7/site-packages/mne/utils.py",
>> line 804, in run_subprocess
>>    p = subprocess.Popen(command, *args, **kwargs)
>>  File "/home/milton/anaconda2/lib/python2.7/subprocess.py", line 710, in
>> __init__
>>    errread, errwrite)
>>  File "/home/milton/anaconda2/lib/python2.7/subprocess.py", line 1335, in
>> _execute_child
>>    raise child_exception
>> OSError: [Errno 2] No such file or directory
>> 
>> 
>> The files created:
>> <subj>_brain_surface
>> <subj>_inner_skull_surface
>> <subj>_outer_skull_surface
>> <subj>_inner_skin_surface
>> 
>> The files NOT created:
>> inner_skull.surf,
>> outer_skull.surf
>> outer_skin.surf
>> 
>> Does anybody know what is going on?
>> Thanks in advance
>> Milton
>> 
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> 
>> 
>> 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.
>> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Wed, 4 May 2016 20:15:25 +0800
> From: San-Yuan Lin <lin.sanyuan at gmail.com>
> Subject: [Mne_analysis] Error message from mne_volume_data2mri: w file
> 	vertex number out of range
> To: mne_analysis at nmr.mgh.harvard.edu
> Message-ID: <00E0A193-8C19-4660-85BC-CE5012E323B4 at gmail.com>
> Content-Type: text/plain; charset=big5
> 
> Hi All,
> 
> I?ve tried to convert w file into niifi format for mrVista by using the following code, and got "w file vertex number out of range.? message from mne_volume_data2mri. Does anyone know the meaning of this message?
> 
> (I used ico 5 for both source space and forward model.)
> 
> Here is the code I used:
> 
> mne_volume_source_space --mindist 3 --surf $SUBJECTS_Anatomy_DIR/$SUBJECT/surf/lh.sphere --bem $SUBJECTS_Anatomy_DIR/$SUBJECT/bem/$SsFileHead-bem.fif --mri $SUBJECTS_Anatomy_DIR/$SUBJECT/mri/T1.mgz --src $Data_DIR/$SUBJECT/$SsFileDir/$SsFileHead-vol-lh-src.fif 
> 
> mne_volume_data2mri --scale 0.1 --src $Data_DIR/$SUBJECT/$SsFileDir/$SsFileHead-vol-lh-src.fif  --w $Data_DIR/$SUBJECT/$SsFileDir/$SsFileHead-w-$PickTimeFileName-lh.w --out $Data_DIR/$SUBJECT/$SsFileDir/$SsFileHead-$PickTimeFileName-lh.w.mgz
> 
> 
> Thanks,
> Sanyuan
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Wed, 4 May 2016 14:17:33 +0200
> From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr>
> Subject: Re: [Mne_analysis] Error message from mne_volume_data2mri: w
> 	file vertex number out of range
> To: Discussion and support forum for the users of MNE Software
> 	<mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> 	<CADeotZoFg39zcDXbzOQ43T=44SoH+Fkogd0N2tF-TT0S2k6Aow at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> hi Sanyuan,
> 
> ico5 refers to a surface/cortical source space. Could it be the issue
> as you want to manipulate volume grids?
> 
> Alex
> 
> On Wed, May 4, 2016 at 2:15 PM, San-Yuan Lin <lin.sanyuan at gmail.com> wrote:
>> Hi All,
>> 
>> I?ve tried to convert w file into niifi format for mrVista by using the following code, and got "w file vertex number out of range.? message from mne_volume_data2mri. Does anyone know the meaning of this message?
>> 
>> (I used ico 5 for both source space and forward model.)
>> 
>> Here is the code I used:
>> 
>> mne_volume_source_space --mindist 3 --surf $SUBJECTS_Anatomy_DIR/$SUBJECT/surf/lh.sphere --bem $SUBJECTS_Anatomy_DIR/$SUBJECT/bem/$SsFileHead-bem.fif --mri $SUBJECTS_Anatomy_DIR/$SUBJECT/mri/T1.mgz --src $Data_DIR/$SUBJECT/$SsFileDir/$SsFileHead-vol-lh-src.fif
>> 
>> mne_volume_data2mri --scale 0.1 --src $Data_DIR/$SUBJECT/$SsFileDir/$SsFileHead-vol-lh-src.fif  --w $Data_DIR/$SUBJECT/$SsFileDir/$SsFileHead-w-$PickTimeFileName-lh.w --out $Data_DIR/$SUBJECT/$SsFileDir/$SsFileHead-$PickTimeFileName-lh.w.mgz
>> 
>> 
>> Thanks,
>> Sanyuan
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> 
>> 
>> 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.
> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Wed, 4 May 2016 10:54:47 -0300 (BRT)
> From: milton_avila at usp.br
> Subject: Re: [Mne_analysis] Creating bem meshes with mne_watershed_bem
> 	- mne_convert_surface not found
> To: Discussion and support forum for the users of MNE Software
> 	<mne_analysis at nmr.mgh.harvard.edu>
> Message-ID: <364624205.9382566.1462370087867.JavaMail.root at usp.br>
> Content-Type: text/plain; charset="utf-8"
> 
> H i Alex! 
> Thanks for the reply. 
> 
> No success. I got the same error. 
> It is happening with the only subject I have. 
> Milton 
> ----- Mensagem original -----
> 
>> De: "Alexandre Gramfort" <alexandre.gramfort at telecom-paristech.fr>
>> Para: "Discussion and support forum for the users of MNE Software"
>> <mne_analysis at nmr.mgh.harvard.edu>
>> Enviadas: Quarta-feira, 4 de Maio de 2016 8:52:07
>> Assunto: Re: [Mne_analysis] Creating bem meshes with
>> mne_watershed_bem - mne_convert_surface not found
> 
>> hi Milton,
> 
>> do you have the problem with all your subjects?
> 
>> if so can you try with the latest version of mne-python code?
> 
>> I recently had to fix this code that was not creating properly the
>> sym links.
> 
>> Alex
> 
>> On Tue, May 3, 2016 at 11:11 PM, <milton_avila at usp.br> wrote:
>>> Dear MNE users,
>>> 
>>> I am trying to create BEM meshes using
>>> mne_watershed_bem.
>>> 
>>> I raises the following error:
>>> 
>>> Running subprocess: mne_convert_surface --surf S07_brain_surface
>>> --mghmri
>>> /media/milton/Dados/MRI/S07/mri/T1.mgz --surfout S07_brain_surface
>>> --replacegeom
>>> Command not found: mne_convert_surface
>>> Traceback (most recent call last):
>>> File "pre_process.py", line 257, in <module>
>>> mne.bem.make_watershed_bem(subj, subjects_dir=mri_path,
>>> overwrite=True)
>>> File "<string>", line 2, in make_watershed_bem
>>> File
>>> "/home/milton/anaconda2/lib/python2.7/site-packages/mne/utils.py",
>>> line 551, in verbose
>>> return function(*args, **kwargs)
>>> File
>>> "/home/milton/anaconda2/lib/python2.7/site-packages/mne/bem.py",
>>> line
>>> 1015, in make_watershed_bem
>>> run_subprocess(cmd, env=env, stdout=sys.stdout, stderr=sys.stderr)
>>> File "<string>", line 2, in run_subprocess
>>> File
>>> "/home/milton/anaconda2/lib/python2.7/site-packages/mne/utils.py",
>>> line 551, in verbose
>>> return function(*args, **kwargs)
>>> File
>>> "/home/milton/anaconda2/lib/python2.7/site-packages/mne/utils.py",
>>> line 804, in run_subprocess
>>> p = subprocess.Popen(command, *args, **kwargs)
>>> File "/home/milton/anaconda2/lib/python2.7/subprocess.py", line
>>> 710, in
>>> __init__
>>> errread, errwrite)
>>> File "/home/milton/anaconda2/lib/python2.7/subprocess.py", line
>>> 1335, in
>>> _execute_child
>>> raise child_exception
>>> OSError: [Errno 2] No such file or directory
>>> 
>>> 
>>> The files created:
>>> <subj>_brain_surface
>>> <subj>_inner_skull_surface
>>> <subj>_outer_skull_surface
>>> <subj>_inner_skin_surface
>>> 
>>> The files NOT created:
>>> inner_skull.surf,
>>> outer_skull.surf
>>> outer_skin.surf
>>> 
>>> Does anybody know what is going on?
>>> Thanks in advance
>>> Milton
>>> 
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>> 
>>> 
>>> 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.
>>> 
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
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