[Mne_analysis] Mne_analysis Digest, Vol 100, Issue 7
San-Yuan Lin
lin.sanyuan at gmail.com
Mon May 9 21:05:59 EDT 2016
Hi Alex,
Please find in attachment the script I wrote.
Thanks a lot.
Best,
Sanyuan
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> mne_analysis-request at nmr.mgh.harvard.edu ? 2016?5?10? ??12:00 ???
>
> Send Mne_analysis mailing list submissions to
> mne_analysis at nmr.mgh.harvard.edu
>
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Mne_analysis digest..."
>
>
> Today's Topics:
>
> 1. Re: Mne_analysis Digest, Vol 100, Issue 3 (Alexandre Gramfort)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 9 May 2016 06:52:42 +0200
> From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr>
> Subject: Re: [Mne_analysis] Mne_analysis Digest, Vol 100, Issue 3
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> <CADeotZpjg2ekJjwAbQnt_YTvoVF8mNL_gn+LnpCfSFmv799nYw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> 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 ? 2016?5?4? ??9:54 ???
>>
>> Send Mne_analysis mailing list submissions to
>> mne_analysis at nmr.mgh.harvard.edu
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> or, via email, send a message with subject or body 'help' to
>> mne_analysis-request at nmr.mgh.harvard.edu
>>
>> You can reach the person managing the list at
>> mne_analysis-owner at nmr.mgh.harvard.edu
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Mne_analysis digest..."
>>
>>
>> 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
>> -------------- next part --------------
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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
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