[Mne_analysis] Mne_analysis Digest, Vol 100, Issue 3
Alexandre Gramfort
alexandre.gramfort at telecom-paristech.fr
Mon May 9 00:52:42 EDT 2016
hi Sanyuan,
can you share a full script with all the commands?
For the sample data we scripts we used are:
https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_meg_volume_tutorial.sh
or in python:
https://github.com/mne-tools/mne-scripts/blob/master/sample-data/run_meg_volume_tutorial.py
HTH
Alex
On Mon, May 9, 2016 at 3:30 AM, San-Yuan Lin <lin.sanyuan at gmail.com> wrote:
> 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
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> HelpLine at
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> ------------------------------
>
> 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
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>
>
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> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
> HelpLine at
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>
> ------------------------------
>
> 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
>
>
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