Hi Loic

if you are on the fsaverage surface you can save the -log10(p) values using save_mgh.m, then load them in freeview and threshold them or whatever

cheers Bruce On Mon, 20 May 2019, Loïc Daumail wrote:

External Email - Use Caution

Also, one more thing:

My data is on fsaverage5 resolution.

Thanks in advance,

Sincerely,

Loïc

Le lun. 20 mai 2019 à 09:49, Loïc Daumail loic.daumail@gmail.com a écrit : Dear Freesurfer community,

I obtained score matrices of surfaces after performing diffusion embedding map on fMRI data.

I am now using the SurfStat toolbox(Matlab) in order to obtain p-value maps to compare between two groups.

After obtaining the p-value map, I would like to label the surface in order to identify the regions of significant difference between both groups.

Would it be possible to use Freview in order to do it? If so, which format should I use for my SurfStatP output p-value map? How would you do it, (tools to convert into a specific format, surfaces and atlas to load on Freeview, which format for those ones)? I would be very grateful if you could detail a bit, as I am new to these tools!

Thanks in advance,

Loïc Daumail

sure. All the fsaverages are in the same space (they are subsets of fsaverage) On Mon, 20 May 2019, Loïc Daumail wrote:

External Email - Use Caution

Hi Bruce,

Thanks for your response. Is it also fine for fsaverage5 surface or I need to switch my data to fsaverage?

Thanks,

Sincerely,

Loïc

Le lun. 20 mai 2019 à 15:52, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit : Hi Loic

  if you are on the fsaverage surface you can save the -log10(p) values
  using save_mgh.m, then load them in freeview and threshold them or
  whatever

  cheers
  Bruce
  On Mon, 20 May 2019, Loïc Daumail wrote:

  >
  >         External Email - Use Caution        
  >
  > Also, one more thing:
  >
  > My data is on fsaverage5 resolution.
  >
  > Thanks in advance,
  >
  > Sincerely,
  >
  > Loïc
  >
  > Le lun. 20 mai 2019 à 09:49, Loïc Daumail <loic.daumail@gmail.com> a écrit :
  >       Dear Freesurfer community,
  >
  > I obtained score matrices of surfaces after performing diffusion embedding map on fMRI
  data.
  >
  > I am now using the SurfStat toolbox(Matlab) in order to obtain p-value maps to compare
  between
  > two groups.
  >
  > After obtaining the p-value map, I would like to label the surface in order to
  identify the
  > regions of significant difference between both groups.
  >
  > Would it be possible to use Freview in order to do it?
  > If so, which format should I use for my SurfStatP output p-value map?
  > How would you do it, (tools to convert into a specific format, surfaces and atlas to
  load on
  > Freeview, which format for those ones)?
  > I would be very grateful if you could detail a bit, as I am new to these tools!
  >
  > Thanks in advance,
  >
  > Loïc Daumail
  >
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

Hi Loïc,

you can load the atlases using `read_annotation` in Matlab, then of course use them for whatever purpose you like (including in surfstat). This code should get you started:

subjects_dir = '/data/mystudy'; subject_id = 'subject1'; hemi = 'lh';

aparc_file_this_hemi = fullfile(subjects_dir, subject_id, 'label', sprintf("%s.aparc.annot", hemi)); [vertices, label, colortable] = read_annotation(aparc_file_this_hemi); fprintf("Read aparc parcellation file '%s' containing %d regions.\n", aparc_file_this_hemi, length(colortable.struct_names)); for sidx = 1:length(colortable.struct_names) region = colortable.struct_names{sidx}; struct_code = colortable.table(sidx, 5); vertices_of_struct_roi = find(label == struct_code); fprintf("Found region '%s' with %d verts.\n", region, length(vertices_of_struct_roi)); end

To color the regions in surfstat, you would then need to set a colormap that has the correct number of colors (36 for Desikan, I think), using the colortable variable.

Best,

Tim

On May 23, 2019 at 11:35 AM Loïc Daumail loic.daumail@gmail.com wrote:

    External Email - Use Caution        

Hi Bruce,

I am coming back to this request as I was wondering: would it be possible to load freesurfer surface atlases in surfstat in order to label my surfaces? Is their format compatible? I saw surfstat only accepts a limited array of formats...

Thanks, Best,

Loïc

Le lun. 20 mai 2019 à 16:15, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit :

...

sure. All the fsaverages are in the same space (they are subsets of fsaverage) On Mon, 20 May 2019, Loïc Daumail wrote:

...

    External Email - Use Caution

Hi Bruce,

Thanks for your response. Is it also fine for fsaverage5 surface or I

need to switch my data to

...

fsaverage?

Thanks,

Sincerely,

Loïc

Le lun. 20 mai 2019 à 15:52, Bruce Fischl fischl@nmr.mgh.harvard.edu

a écrit :

...

  Hi Loic

  if you are on the fsaverage surface you can save the -log10(p)

values

...

  using save_mgh.m, then load them in freeview and threshold them or
  whatever

  cheers
  Bruce
  On Mon, 20 May 2019, Loïc Daumail wrote:

  >
  >         External Email - Use Caution
  >
  > Also, one more thing:
  >
  > My data is on fsaverage5 resolution.
  >
  > Thanks in advance,
  >
  > Sincerely,
  >
  > Loïc
  >
  > Le lun. 20 mai 2019 à 09:49, Loïc Daumail <

loic.daumail@gmail.com> a écrit :

...

  >       Dear Freesurfer community,
  >
  > I obtained score matrices of surfaces after performing diffusion

embedding map on fMRI

...

  data.
  >
  > I am now using the SurfStat toolbox(Matlab) in order to obtain

p-value maps to compare

...

  between
  > two groups.
  >
  > After obtaining the p-value map, I would like to label the

surface in order to

...

  identify the
  > regions of significant difference between both groups.
  >
  > Would it be possible to use Freview in order to do it?
  > If so, which format should I use for my SurfStatP output p-value

map?

...

  > How would you do it, (tools to convert into a specific format,

surfaces and atlas to

...

  load on
  > Freeview, which format for those ones)?
  > I would be very grateful if you could detail a bit, as I am new

to these tools!

...

  >
  > Thanks in advance,
  >
  > Loïc Daumail
  >
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

Afaik SurfStat is not maintained anymore and I think it's been this way for quite a while now. Maybe someone else knows better?

The website is at http://www.math.mcgill.ca/keith/surfstat/ and it says 'Updated 26 September 2008'. I'm not sure whether that's really true, but at least for the last 14 months (the only time frame I know about), there have not been any changes to that website or any new releases of SurfStat.

Tim

On May 23, 2019 at 4:36 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Loic

sorry, can you ask whoever maintains surfstat? Or maybe someone else on the list knows? I don't. You can label surfaces manually with the dev version of freeview if you want.

cheers Bruce

On Thu, 23 May 2019, Loïc Daumail wrote:

...

External Email - Use Caution

Hi Bruce,

I am coming back to this request as I was wondering: would it be possible to load freesurfer surface atlases in surfstat in order to label my surfaces? Is their format compatible? I saw surfstat only accepts a limited array of formats...

Thanks, Best,

Loïc

Le lun. 20 mai 2019 à 16:15, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit : sure. All the fsaverages are in the same space (they are subsets of fsaverage) On Mon, 20 May 2019, Loïc Daumail wrote:

  >
  >         External Email - Use Caution        
  >
  > Hi Bruce,
  >
  > Thanks for your response. Is it also fine for fsaverage5 surface or I need to switch
  my data to
  > fsaverage?
  >
  > Thanks,
  >
  > Sincerely,
  >
  > Loïc
  >
  > Le lun. 20 mai 2019 à 15:52, Bruce Fischl <fischl@nmr.mgh.harvard.edu> a écrit :
  >       Hi Loic
  >
  >       if you are on the fsaverage surface you can save the -log10(p) values
  >       using save_mgh.m, then load them in freeview and threshold them or
  >       whatever
  >
  >       cheers
  >       Bruce
  >       On Mon, 20 May 2019, Loïc Daumail wrote:
  >
  >       >
  >       >         External Email - Use Caution        
  >       >
  >       > Also, one more thing:
  >       >
  >       > My data is on fsaverage5 resolution.
  >       >
  >       > Thanks in advance,
  >       >
  >       > Sincerely,
  >       >
  >       > Loïc
  >       >
  >       > Le lun. 20 mai 2019 à 09:49, Loïc Daumail <loic.daumail@gmail.com> a écrit :
  >       >       Dear Freesurfer community,
  >       >
  >       > I obtained score matrices of surfaces after performing diffusion embedding map
  on fMRI
  >       data.
  >       >
  >       > I am now using the SurfStat toolbox(Matlab) in order to obtain p-value maps to
  compare
  >       between
  >       > two groups.
  >       >
  >       > After obtaining the p-value map, I would like to label the surface in order to
  >       identify the
  >       > regions of significant difference between both groups.
  >       >
  >       > Would it be possible to use Freview in order to do it?
  >       > If so, which format should I use for my SurfStatP output p-value map?
  >       > How would you do it, (tools to convert into a specific format, surfaces and
  atlas to
  >       load on
  >       > Freeview, which format for those ones)?
  >       > I would be very grateful if you could detail a bit, as I am new to these
  tools!
  >       >
  >       > Thanks in advance,
  >       >
  >       > Loïc Daumail
  >       >
  >       >
  >       >_______________________________________________
  >       Freesurfer mailing list
  >       Freesurfer@nmr.mgh.harvard.edu
  >       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

External Email - Use Caution

Hi Loïc,

that does not look correct, the data is definitely off. I'm not sure where the variables `mean_rest` and `surf.b` come from in your code, and I suspect that something is wrong with them.

In the meantime, I got interested in this myself and put together some code that will load the Desikan data for both hemispheres and display it in surfstat. Feel free to use it, there also is an example screenshot of the results:

https://github.com/dfsp-spirit/comp_neuro_science/tree/master/surfstat_desik...

Best,

Tim

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

On May 27, 2019 at 11:01 AM Loïc Daumail loic.daumail@gmail.com wrote:

    External Email - Use Caution        

Hi Tim,

Thanks a lot for your help, indeed, this is exactly what I needed! I wrote this : " subjects_dir = '/home/loic/Documents/recon_all_success/freesurfer/'; subject_id = 'sub-004'; hemi = 'lh';

aparc_file_this_hemi = fullfile(subjects_dir, subject_id, 'label', sprintf("%s.aparc.annot", hemi)); [vertices, label, colortable] = read_annotation(aparc_file_this_hemi); fprintf("Read aparc parcellation file '%s' containing %d regions.\n", aparc_file_this_hemi, length(colortable.struct_names)); for sidx = 1:length(colortable.struct_names) region = colortable.struct_names{sidx}; struct_code = colortable.table(sidx, 5); vertices_of_struct_roi = find(label == struct_code); fprintf("Found region '%s' with %d verts.\n", region, length(vertices_of_struct_roi)); end fig1 = figure(); SurfStatView(mean_rest, surf.b); SurfStatColormap(colortable.table(:,1:3)/255); " However, the image I obtain seems a bit fuzzy...( see attached) Is it because of my data?

Thanks in advance,

Loïc

Le jeu. 23 mai 2019 à 17:20, Tim Schäfer ts+ml@rcmd.org a écrit :

...

    External Email - Use Caution

Afaik SurfStat is not maintained anymore and I think it's been this way for quite a while now. Maybe someone else knows better?

The website is at http://www.math.mcgill.ca/keith/surfstat/ and it says 'Updated 26 September 2008'. I'm not sure whether that's really true, but at least for the last 14 months (the only time frame I know about), there have not been any changes to that website or any new releases of SurfStat.

Tim

...

On May 23, 2019 at 4:36 PM Bruce Fischl fischl@nmr.mgh.harvard.edu

wrote:

...

Hi Loic

sorry, can you ask whoever maintains surfstat? Or maybe someone else on

the

...

list knows? I don't. You can label surfaces manually with the dev

version

...

of freeview if you want.

cheers Bruce

On Thu, 23 May 2019, Loïc Daumail wrote:

...

    External Email - Use Caution

Hi Bruce,

I am coming back to this request as I was wondering: would it be possible to load freesurfer surface atlases in surfstat in

order to label my surfaces?

...

...

Is their format compatible? I saw surfstat only accepts a limited

array of formats...

...

...

Thanks, Best,

Loïc

Le lun. 20 mai 2019 à 16:15, Bruce Fischl fischl@nmr.mgh.harvard.edu

a écrit :

...

...

  sure. All the fsaverages are in the same space (they are subsets

of

...

...

  fsaverage)
  On Mon, 20 May 2019, Loïc Daumail wrote:

  >
  >         External Email - Use Caution
  >
  > Hi Bruce,
  >
  > Thanks for your response. Is it also fine for fsaverage5

surface or I need to switch

...

...

  my data to
  > fsaverage?
  >
  > Thanks,
  >
  > Sincerely,
  >
  > Loïc
  >
  > Le lun. 20 mai 2019 à 15:52, Bruce Fischl <

fischl@nmr.mgh.harvard.edu> a écrit :

...

...

  >       Hi Loic
  >
  >       if you are on the fsaverage surface you can save the

-log10(p) values

...

...

  >       using save_mgh.m, then load them in freeview and

threshold them or

...

...

  >       whatever
  >
  >       cheers
  >       Bruce
  >       On Mon, 20 May 2019, Loïc Daumail wrote:
  >
  >       >
  >       >         External Email - Use Caution
  >       >
  >       > Also, one more thing:
  >       >
  >       > My data is on fsaverage5 resolution.
  >       >
  >       > Thanks in advance,
  >       >
  >       > Sincerely,
  >       >
  >       > Loïc
  >       >
  >       > Le lun. 20 mai 2019 à 09:49, Loïc Daumail <

loic.daumail@gmail.com> a écrit :

...

...

  >       >       Dear Freesurfer community,
  >       >
  >       > I obtained score matrices of surfaces after performing

diffusion embedding map

...

...

  on fMRI
  >       data.
  >       >
  >       > I am now using the SurfStat toolbox(Matlab) in order

to obtain p-value maps to

...

...

  compare
  >       between
  >       > two groups.
  >       >
  >       > After obtaining the p-value map, I would like to label

the surface in order to

...

...

  >       identify the
  >       > regions of significant difference between both groups.
  >       >
  >       > Would it be possible to use Freview in order to do it?
  >       > If so, which format should I use for my SurfStatP

output p-value map?

...

...

  >       > How would you do it, (tools to convert into a specific

format, surfaces and

...

...

  atlas to
  >       load on
  >       > Freeview, which format for those ones)?
  >       > I would be very grateful if you could detail a bit, as

I am new to these

...

...

  tools!
  >       >
  >       > Thanks in advance,
  >       >
  >       > Loïc Daumail
  >       >
  >       >
  >       >_______________________________________________
  >       Freesurfer mailing list
  >       Freesurfer@nmr.mgh.harvard.edu
  >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

...

  >
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

Hi Tim,

Your link works perfectly, it's awesome! Thanks a lot,

Best,

Loïc

Le lun. 27 mai 2019 à 11:43, Loïc Daumail loic.daumail@gmail.com a écrit :

Hi Tim,

'mean_rest' is a diffusion embedding map, which contains scores for every vertex on fsaverage5 surface resolution. 'surf.b' is the pial surface of both hemispheres of fsaverage5... I also tried forjust lh hemisphere, but it gives me the same result...

Thanks for the link!

Best,

Loïc

Le lun. 27 mai 2019 à 11:20, Tim Schäfer ts+ml@rcmd.org a écrit :

...

    External Email - Use Caution

Hi Loïc,

that does not look correct, the data is definitely off. I'm not sure where the variables `mean_rest` and `surf.b` come from in your code, and I suspect that something is wrong with them.

In the meantime, I got interested in this myself and put together some code that will load the Desikan data for both hemispheres and display it in surfstat. Feel free to use it, there also is an example screenshot of the results:

https://github.com/dfsp-spirit/comp_neuro_science/tree/master/surfstat_desik...

Best,

Tim

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

...

On May 27, 2019 at 11:01 AM Loïc Daumail loic.daumail@gmail.com

wrote:

...

    External Email - Use Caution

Hi Tim,

Thanks a lot for your help, indeed, this is exactly what I needed! I wrote this : " subjects_dir = '/home/loic/Documents/recon_all_success/freesurfer/'; subject_id = 'sub-004'; hemi = 'lh';

aparc_file_this_hemi = fullfile(subjects_dir, subject_id, 'label', sprintf("%s.aparc.annot", hemi)); [vertices, label, colortable] = read_annotation(aparc_file_this_hemi); fprintf("Read aparc parcellation file '%s' containing %d regions.\n", aparc_file_this_hemi, length(colortable.struct_names)); for sidx = 1:length(colortable.struct_names) region = colortable.struct_names{sidx}; struct_code = colortable.table(sidx, 5); vertices_of_struct_roi = find(label == struct_code); fprintf("Found region '%s' with %d verts.\n", region, length(vertices_of_struct_roi)); end fig1 = figure(); SurfStatView(mean_rest, surf.b); SurfStatColormap(colortable.table(:,1:3)/255); " However, the image I obtain seems a bit fuzzy...( see attached) Is it because of my data?

Thanks in advance,

Loïc

Le jeu. 23 mai 2019 à 17:20, Tim Schäfer ts+ml@rcmd.org a écrit :

...

    External Email - Use Caution

Afaik SurfStat is not maintained anymore and I think it's been this

way

...

...

for quite a while now. Maybe someone else knows better?

The website is at http://www.math.mcgill.ca/keith/surfstat/ and it

says

...

...

'Updated 26 September 2008'. I'm not sure whether that's really true,

but

...

...

at least for the last 14 months (the only time frame I know about),

there

...

...

have not been any changes to that website or any new releases of

SurfStat.

...

...

Tim

...

On May 23, 2019 at 4:36 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu

...

wrote:

...

Hi Loic

sorry, can you ask whoever maintains surfstat? Or maybe someone

else on

...

...

the

...

list knows? I don't. You can label surfaces manually with the dev

version

...

of freeview if you want.

cheers Bruce

On Thu, 23 May 2019, Loïc Daumail wrote:

...

    External Email - Use Caution

Hi Bruce,

I am coming back to this request as I was wondering: would it be possible to load freesurfer surface atlases in

surfstat in

...

...

order to label my surfaces?

...

...

Is their format compatible? I saw surfstat only accepts a limited

array of formats...

...

...

Thanks, Best,

Loïc

Le lun. 20 mai 2019 à 16:15, Bruce Fischl <

fischl@nmr.mgh.harvard.edu>

...

...

a écrit :

...

...

  sure. All the fsaverages are in the same space (they are

subsets

...

...

of

...

...

  fsaverage)
  On Mon, 20 May 2019, Loïc Daumail wrote:

  >
  >         External Email - Use Caution
  >
  > Hi Bruce,
  >
  > Thanks for your response. Is it also fine for fsaverage5

surface or I need to switch

...

...

  my data to
  > fsaverage?
  >
  > Thanks,
  >
  > Sincerely,
  >
  > Loïc
  >
  > Le lun. 20 mai 2019 à 15:52, Bruce Fischl <

fischl@nmr.mgh.harvard.edu> a écrit :

...

...

  >       Hi Loic
  >
  >       if you are on the fsaverage surface you can save the

-log10(p) values

...

...

  >       using save_mgh.m, then load them in freeview and

threshold them or

...

...

  >       whatever
  >
  >       cheers
  >       Bruce
  >       On Mon, 20 May 2019, Loïc Daumail wrote:
  >
  >       >
  >       >         External Email - Use Caution
  >       >
  >       > Also, one more thing:
  >       >
  >       > My data is on fsaverage5 resolution.
  >       >
  >       > Thanks in advance,
  >       >
  >       > Sincerely,
  >       >
  >       > Loïc
  >       >
  >       > Le lun. 20 mai 2019 à 09:49, Loïc Daumail <

loic.daumail@gmail.com> a écrit :

...

...

  >       >       Dear Freesurfer community,
  >       >
  >       > I obtained score matrices of surfaces after

performing

...

...

diffusion embedding map

...

...

  on fMRI
  >       data.
  >       >
  >       > I am now using the SurfStat toolbox(Matlab) in

order

...

...

to obtain p-value maps to

...

...

  compare
  >       between
  >       > two groups.
  >       >
  >       > After obtaining the p-value map, I would like to

label

...

...

the surface in order to

...

...

  >       identify the
  >       > regions of significant difference between both

groups.

...

...

...

...

  >       >
  >       > Would it be possible to use Freview in order to

do it?

...

...

...

...

  >       > If so, which format should I use for my SurfStatP

output p-value map?

...

...

  >       > How would you do it, (tools to convert into a

specific

...

...

format, surfaces and

...

...

  atlas to
  >       load on
  >       > Freeview, which format for those ones)?
  >       > I would be very grateful if you could detail a

bit, as

...

...

I am new to these

...

...

  tools!
  >       >
  >       > Thanks in advance,
  >       >
  >       > Loïc Daumail
  >       >
  >       >
  >       >_______________________________________________
  >       Freesurfer mailing list
  >       Freesurfer@nmr.mgh.harvard.edu
  >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

...

  >
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

...

...

...

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main,

Germany

...

...

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Loïc

the .mgz file should having dimensions nvertices x 1 x 1 for freeview to know it is a surface overlay I believe

cheers Bruce

On Thu, 20 Jun 2019, Loïc Daumail wrote:

External Email - Use Caution

Hi Bruce,

I am reaching out to you, as I am trying to load the surface scalar values of diffusion embedding for overlay on a pial surface in Freeview.

I used save_mgh to save a scalar matrix containing surface embedding values in an .mgz format. However I can't load it in freeview, be either only half of the matrix data (one hemisphere I assume) or the whole matrix saved in the same file.

Is there anything specific I need to do in order to be able to visualize a scalar overlay on a surface? Is .mgz a wrong format for scalar values? I also tried with .nii.gz, or .mgh. I am not even sure save_mgh can do all this...

Thanks in advance,

Sincerely,

Loïc

Le lun. 27 mai 2019 à 11:54, Loïc Daumail loic.daumail@gmail.com a écrit : Hi Tim,

Your link works perfectly, it's awesome! Thanks a lot,

Best,

Loïc

Le lun. 27 mai 2019 à 11:43, Loïc Daumail loic.daumail@gmail.com a écrit : Hi Tim,

'mean_rest' is a diffusion embedding map, which contains scores for every vertex on fsaverage5 surface resolution. 'surf.b' is the pial surface of both hemispheres of fsaverage5... I also tried forjust lh hemisphere, but it gives me the same result...

Thanks for the link!

Best,

Loïc

Le lun. 27 mai 2019 à 11:20, Tim Schäfer ts+ml@rcmd.org a écrit :         External Email - Use Caution

  Hi Loïc,

  that does not look correct, the data is definitely off. I'm not sure where
  the variables `mean_rest` and `surf.b` come from in your code, and I suspect
  that something is wrong with them.

  In the meantime, I got interested in this myself and put together some code
  that will load the Desikan data for both hemispheres and display it in
  surfstat. Feel free to use it, there also is an example screenshot of the
  results:

   
   https://github.com/dfsp-spirit/comp_neuro_science/tree/master/surfstat_desikan

  Best,

  Tim

  --
  Dr. Tim Schäfer
  Postdoc Computational Neuroimaging
  Department of Child and Adolescent Psychiatry, Psychosomatics and
  Psychotherapy
  University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

  > On May 27, 2019 at 11:01 AM Loïc Daumail <loic.daumail@gmail.com> wrote:
  >
  >
  >         External Email - Use Caution       
  >
  > Hi Tim,
  >
  > Thanks a lot for your help, indeed, this is exactly what I needed!
  > I wrote this :
  > "
  > subjects_dir = '/home/loic/Documents/recon_all_success/freesurfer/';
  > subject_id = 'sub-004';
  > hemi = 'lh';
  >
  > aparc_file_this_hemi = fullfile(subjects_dir, subject_id, 'label',
  > sprintf("%s.aparc.annot", hemi));
  > [vertices, label, colortable] = read_annotation(aparc_file_this_hemi);
  > fprintf("Read aparc parcellation file '%s' containing %d regions.\n",
  > aparc_file_this_hemi, length(colortable.struct_names));
  > for sidx = 1:length(colortable.struct_names)
  >      region = colortable.struct_names{sidx};
  >      struct_code = colortable.table(sidx, 5);
  >      vertices_of_struct_roi = find(label == struct_code);
  >     fprintf("Found region '%s' with %d verts.\n", region,
  > length(vertices_of_struct_roi));
  > end
  > fig1 = figure();
  > SurfStatView(mean_rest, surf.b);
  > SurfStatColormap(colortable.table(:,1:3)/255);
  > "
  > However, the image I obtain seems a bit fuzzy...( see attached)
  > Is it because of my data?
  >
  > Thanks in advance,
  >
  > Loïc
  >
  >
  > Le jeu. 23 mai 2019 à 17:20, Tim Schäfer <ts+ml@rcmd.org> a écrit :
  >
  > >         External Email - Use Caution
  > >
  > > Afaik SurfStat is not maintained anymore and I think it's been this way
  > > for quite a while now. Maybe someone else knows better?
  > >
  > > The website is at http://www.math.mcgill.ca/keith/surfstat/ and it says
  > > 'Updated 26 September 2008'. I'm not sure whether that's really true,
  but
  > > at least for the last 14 months (the only time frame I know about),
  there
  > > have not been any changes to that website or any new releases of
  SurfStat.
  > >
  > > Tim
  > >
  > > > On May 23, 2019 at 4:36 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu>
  > > wrote:
  > > >
  > > >
  > > > Hi Loic
  > > >
  > > > sorry, can you ask whoever maintains surfstat? Or maybe someone else
  on
  > > the
  > > > list knows? I don't. You can label surfaces manually with the dev
  > > version
  > > > of freeview if you want.
  > > >
  > > > cheers
  > > > Bruce
  > > >
  > > >
  > > > On Thu, 23 May 2019, Loïc
  > > > Daumail wrote:
  > > >
  > > > >
  > > > >         External Email - Use Caution
  > > > >
  > > > > Hi Bruce,
  > > > >
  > > > > I am coming back to this request as I was wondering:
  > > > > would it be possible to load freesurfer surface atlases in surfstat
  in
  > > order to label my surfaces?
  > > > > Is their format compatible? I saw surfstat only accepts a limited
  > > array of formats...
  > > > >
  > > > > Thanks,
  > > > > Best,
  > > > >
  > > > > Loïc
  > > > >
  > > > > Le lun. 20 mai 2019 à 16:15, Bruce Fischl
  <fischl@nmr.mgh.harvard.edu>
  > > a écrit :
  > > > >       sure. All the fsaverages are in the same space (they are
  subsets
  > > of
  > > > >       fsaverage)
  > > > >       On Mon, 20 May 2019, Loïc Daumail wrote:
  > > > >
  > > > >       >
  > > > >       >         External Email - Use Caution
  > > > >       >
  > > > >       > Hi Bruce,
  > > > >       >
  > > > >       > Thanks for your response. Is it also fine for fsaverage5
  > > surface or I need to switch
  > > > >       my data to
  > > > >       > fsaverage?
  > > > >       >
  > > > >       > Thanks,
  > > > >       >
  > > > >       > Sincerely,
  > > > >       >
  > > > >       > Loïc
  > > > >       >
  > > > >       > Le lun. 20 mai 2019 à 15:52, Bruce Fischl <
  > > fischl@nmr.mgh.harvard.edu> a écrit :
  > > > >       >       Hi Loic
  > > > >       >
  > > > >       >       if you are on the fsaverage surface you can save the
  > > -log10(p) values
  > > > >       >       using save_mgh.m, then load them in freeview and
  > > threshold them or
  > > > >       >       whatever
  > > > >       >
  > > > >       >       cheers
  > > > >       >       Bruce
  > > > >       >       On Mon, 20 May 2019, Loïc Daumail wrote:
  > > > >       >
  > > > >       >       >
  > > > >       >       >         External Email - Use Caution
  > > > >       >       >
  > > > >       >       > Also, one more thing:
  > > > >       >       >
  > > > >       >       > My data is on fsaverage5 resolution.
  > > > >       >       >
  > > > >       >       > Thanks in advance,
  > > > >       >       >
  > > > >       >       > Sincerely,
  > > > >       >       >
  > > > >       >       > Loïc
  > > > >       >       >
  > > > >       >       > Le lun. 20 mai 2019 à 09:49, Loïc Daumail <
  > > loic.daumail@gmail.com> a écrit :
  > > > >       >       >       Dear Freesurfer community,
  > > > >       >       >
  > > > >       >       > I obtained score matrices of surfaces after
  performing
  > > diffusion embedding map
  > > > >       on fMRI
  > > > >       >       data.
  > > > >       >       >
  > > > >       >       > I am now using the SurfStat toolbox(Matlab) in order
  > > to obtain p-value maps to
  > > > >       compare
  > > > >       >       between
  > > > >       >       > two groups.
  > > > >       >       >
  > > > >       >       > After obtaining the p-value map, I would like to
  label
  > > the surface in order to
  > > > >       >       identify the
  > > > >       >       > regions of significant difference between both
  groups.
  > > > >       >       >
  > > > >       >       > Would it be possible to use Freview in order to do
  it?
  > > > >       >       > If so, which format should I use for my SurfStatP
  > > output p-value map?
  > > > >       >       > How would you do it, (tools to convert into a
  specific
  > > format, surfaces and
  > > > >       atlas to
  > > > >       >       load on
  > > > >       >       > Freeview, which format for those ones)?
  > > > >       >       > I would be very grateful if you could detail a bit,
  as
  > > I am new to these
  > > > >       tools!
  > > > >       >       >
  > > > >       >       > Thanks in advance,
  > > > >       >       >
  > > > >       >       > Loïc Daumail
  > > > >       >       >
  > > > >       >       >
  > > > >       >       >_______________________________________________
  > > > >       >       Freesurfer mailing list
  > > > >       >       Freesurfer@nmr.mgh.harvard.edu
  > > > >       >
  > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  > > > >       >
  > > > >       >
  > > > >       >_______________________________________________
  > > > >       Freesurfer mailing list
  > > > >       Freesurfer@nmr.mgh.harvard.edu
  > > > >       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  > > > >
  > > > >
  > > > >_______________________________________________
  > > > Freesurfer mailing list
  > > > Freesurfer@nmr.mgh.harvard.edu
  > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  > >
  > > --
  > > Dr. Tim Schäfer
  > > Postdoc Computational Neuroimaging
  > > Department of Child and Adolescent Psychiatry, Psychosomatics and
  > > Psychotherapy
  > > University Hospital Frankfurt, Goethe University Frankfurt am Main,
  Germany
  > >
  > > _______________________________________________
  > > Freesurfer mailing list
  > > Freesurfer@nmr.mgh.harvard.edu
  > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  > _______________________________________________
  > Freesurfer mailing list
  > Freesurfer@nmr.mgh.harvard.edu
  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

  _______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

Me again,

Also, here is how I save the matrix on matlab:

M = nan(4,4); save_mgh('freeview_overlay', ['/home/loic/Documents/emb_output/mgh_format/lh_emb_' char(subjectsList(1)) '_' char(statesList(1)) '.mgz'], M);

Thanks,

Sincerely,

Loïc

Le ven. 21 juin 2019 à 12:25, Loïc Daumail loic.daumail@gmail.com a écrit :

Hi Bruce,

Thanks for your tip. Unfortunately, I am still running through an error... I have a matrix of 18715 elements regarding both hemispheres. The size of fsaverage5 is 20484 I believe, so I filled the remaining elements with zeros, and also tried with rand().

The other issue is that I am not so sure which part of the matrix is for lh and the other one for rh. Thus, I divided 18715/2 and took the 9357 first elements of the 18715 matrix. Then filled it with zeros or random values to reach 10242.

Then I saved it with save_mgh function and tried to load it with freeview using the following command line: freeview -f ~/Documents/recon_all_success/freesurfer/fsaverage5/surf/lh.pial:overlay=~/Documents/emb_output/mgh_format/lh_emb_sub-002_compassion.mgz

I am getting the following error: " Did not find any volume info 2 [0]PETSC ERROR:

---

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig... ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message

---

[0]PETSC ERROR: Signal received! [0]PETSC ERROR:

---

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:

---

[0]PETSC ERROR: Unknown Name on a linux-gnu named loic-HP-ZBook-17 by loic Fri Jun 21 12:15:53 2019 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR:

---

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0"

Any idea of what could be wrong in my process?

Thanks

Sincerely,

Loïc

Le jeu. 20 juin 2019 à 19:39, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit :

...

Hi Loïc

the .mgz file should having dimensions nvertices x 1 x 1 for freeview to know it is a surface overlay I believe

cheers Bruce

On Thu, 20 Jun 2019, Loïc Daumail wrote:

...

    External Email - Use Caution

Hi Bruce,

I am reaching out to you, as I am trying to load the surface scalar

values of diffusion embedding

...

for overlay on a pial surface in Freeview.

I used save_mgh to save a scalar matrix containing surface embedding

values in an .mgz format.

...

However I can't load it in freeview, be either only half of the matrix

data (one hemisphere I

...

assume) or the whole matrix saved in the same file.

Is there anything specific I need to do in order to be able to

visualize a scalar overlay on a

...

surface? Is .mgz a wrong format for scalar values? I also tried with

.nii.gz, or .mgh. I am not even

...

sure save_mgh can do all this...

Thanks in advance,

Sincerely,

Loïc

Le lun. 27 mai 2019 à 11:54, Loïc Daumail loic.daumail@gmail.com a

écrit :

...

  Hi Tim,

Your link works perfectly, it's awesome! Thanks a lot,

Best,

Loïc

Le lun. 27 mai 2019 à 11:43, Loïc Daumail loic.daumail@gmail.com a

écrit :

...

  Hi Tim,

'mean_rest' is a diffusion embedding map, which contains scores for

every vertex on

...

fsaverage5 surface resolution. 'surf.b' is the pial surface of both hemispheres of fsaverage5... I

also tried forjust

...

lh hemisphere, but it gives me the same result...

Thanks for the link!

Best,

Loïc

Le lun. 27 mai 2019 à 11:20, Tim Schäfer ts+ml@rcmd.org a écrit : External Email - Use Caution

  Hi Loïc,

  that does not look correct, the data is definitely off. I'm not

sure where

...

  the variables `mean_rest` and `surf.b` come from in your code,

and I suspect

...

  that something is wrong with them.

  In the meantime, I got interested in this myself and put together

some code

...

  that will load the Desikan data for both hemispheres and display

it in

...

  surfstat. Feel free to use it, there also is an example

screenshot of the

...

  results:

https://github.com/dfsp-spirit/comp_neuro_science/tree/master/surfstat_desik...

...

  Best,

  Tim

  --
  Dr. Tim Schäfer
  Postdoc Computational Neuroimaging
  Department of Child and Adolescent Psychiatry, Psychosomatics and
  Psychotherapy
  University Hospital Frankfurt, Goethe University Frankfurt am

Main, Germany

...

  > On May 27, 2019 at 11:01 AM Loïc Daumail <

loic.daumail@gmail.com> wrote:

...

  >
  >
  >         External Email - Use Caution
  >
  > Hi Tim,
  >
  > Thanks a lot for your help, indeed, this is exactly what I

needed!

...

  > I wrote this :
  > "
  > subjects_dir =

'/home/loic/Documents/recon_all_success/freesurfer/';

...

  > subject_id = 'sub-004';
  > hemi = 'lh';
  >
  > aparc_file_this_hemi = fullfile(subjects_dir, subject_id,

'label',

...

  > sprintf("%s.aparc.annot", hemi));
  > [vertices, label, colortable] =

read_annotation(aparc_file_this_hemi);

...

  > fprintf("Read aparc parcellation file '%s' containing %d

regions.\n",

...

  > aparc_file_this_hemi, length(colortable.struct_names));
  > for sidx = 1:length(colortable.struct_names)
  >      region = colortable.struct_names{sidx};
  >      struct_code = colortable.table(sidx, 5);
  >      vertices_of_struct_roi = find(label == struct_code);
  >     fprintf("Found region '%s' with %d verts.\n", region,
  > length(vertices_of_struct_roi));
  > end
  > fig1 = figure();
  > SurfStatView(mean_rest, surf.b);
  > SurfStatColormap(colortable.table(:,1:3)/255);
  > "
  > However, the image I obtain seems a bit fuzzy...( see attached)
  > Is it because of my data?
  >
  > Thanks in advance,
  >
  > Loïc
  >
  >
  > Le jeu. 23 mai 2019 à 17:20, Tim Schäfer <ts+ml@rcmd.org> a

écrit :

...

  >
  > >         External Email - Use Caution
  > >
  > > Afaik SurfStat is not maintained anymore and I think it's

been this way

...

  > > for quite a while now. Maybe someone else knows better?
  > >
  > > The website is at http://www.math.mcgill.ca/keith/surfstat/

and it says

...

  > > 'Updated 26 September 2008'. I'm not sure whether that's

really true,

...

  but
  > > at least for the last 14 months (the only time frame I know

about),

...

  there
  > > have not been any changes to that website or any new releases

of

...

  SurfStat.
  > >
  > > Tim
  > >
  > > > On May 23, 2019 at 4:36 PM Bruce Fischl <

fischl@nmr.mgh.harvard.edu>

...

  > > wrote:
  > > >
  > > >
  > > > Hi Loic
  > > >
  > > > sorry, can you ask whoever maintains surfstat? Or maybe

someone else

...

  on
  > > the
  > > > list knows? I don't. You can label surfaces manually with

the dev

...

  > > version
  > > > of freeview if you want.
  > > >
  > > > cheers
  > > > Bruce
  > > >
  > > >
  > > > On Thu, 23 May 2019, Loïc
  > > > Daumail wrote:
  > > >
  > > > >
  > > > >         External Email - Use Caution
  > > > >
  > > > > Hi Bruce,
  > > > >
  > > > > I am coming back to this request as I was wondering:
  > > > > would it be possible to load freesurfer surface atlases

in surfstat

...

  in
  > > order to label my surfaces?
  > > > > Is their format compatible? I saw surfstat only accepts a

limited

...

  > > array of formats...
  > > > >
  > > > > Thanks,
  > > > > Best,
  > > > >
  > > > > Loïc
  > > > >
  > > > > Le lun. 20 mai 2019 à 16:15, Bruce Fischl
  <fischl@nmr.mgh.harvard.edu>
  > > a écrit :
  > > > >       sure. All the fsaverages are in the same space

(they are

...

  subsets
  > > of
  > > > >       fsaverage)
  > > > >       On Mon, 20 May 2019, Loïc Daumail wrote:
  > > > >
  > > > >       >
  > > > >       >         External Email - Use Caution
  > > > >       >
  > > > >       > Hi Bruce,
  > > > >       >
  > > > >       > Thanks for your response. Is it also fine for

fsaverage5

...

  > > surface or I need to switch
  > > > >       my data to
  > > > >       > fsaverage?
  > > > >       >
  > > > >       > Thanks,
  > > > >       >
  > > > >       > Sincerely,
  > > > >       >
  > > > >       > Loïc
  > > > >       >
  > > > >       > Le lun. 20 mai 2019 à 15:52, Bruce Fischl <
  > > fischl@nmr.mgh.harvard.edu> a écrit :
  > > > >       >       Hi Loic
  > > > >       >
  > > > >       >       if you are on the fsaverage surface you can

save the

...

  > > -log10(p) values
  > > > >       >       using save_mgh.m, then load them in

freeview and

...

  > > threshold them or
  > > > >       >       whatever
  > > > >       >
  > > > >       >       cheers
  > > > >       >       Bruce
  > > > >       >       On Mon, 20 May 2019, Loïc Daumail wrote:
  > > > >       >
  > > > >       >       >
  > > > >       >       >         External Email - Use Caution
  > > > >       >       >
  > > > >       >       > Also, one more thing:
  > > > >       >       >
  > > > >       >       > My data is on fsaverage5 resolution.
  > > > >       >       >
  > > > >       >       > Thanks in advance,
  > > > >       >       >
  > > > >       >       > Sincerely,
  > > > >       >       >
  > > > >       >       > Loïc
  > > > >       >       >
  > > > >       >       > Le lun. 20 mai 2019 à 09:49, Loïc Daumail

<

...

  > > loic.daumail@gmail.com> a écrit :
  > > > >       >       >       Dear Freesurfer community,
  > > > >       >       >
  > > > >       >       > I obtained score matrices of surfaces

after

...

  performing
  > > diffusion embedding map
  > > > >       on fMRI
  > > > >       >       data.
  > > > >       >       >
  > > > >       >       > I am now using the SurfStat

toolbox(Matlab) in order

...

  > > to obtain p-value maps to
  > > > >       compare
  > > > >       >       between
  > > > >       >       > two groups.
  > > > >       >       >
  > > > >       >       > After obtaining the p-value map, I would

like to

...

  label
  > > the surface in order to
  > > > >       >       identify the
  > > > >       >       > regions of significant difference between

both

...

  groups.
  > > > >       >       >
  > > > >       >       > Would it be possible to use Freview in

order to do

...

  it?
  > > > >       >       > If so, which format should I use for my

SurfStatP

...

  > > output p-value map?
  > > > >       >       > How would you do it, (tools to convert

into a

...

  specific
  > > format, surfaces and
  > > > >       atlas to
  > > > >       >       load on
  > > > >       >       > Freeview, which format for those ones)?
  > > > >       >       > I would be very grateful if you could

detail a bit,

...

  as
  > > I am new to these
  > > > >       tools!
  > > > >       >       >
  > > > >       >       > Thanks in advance,
  > > > >       >       >
  > > > >       >       > Loïc Daumail
  > > > >       >       >
  > > > >       >       >
  > > > >       >

---

  > > > >       >       Freesurfer mailing list
  > > > >       >       Freesurfer@nmr.mgh.harvard.edu
  > > > >       >
  > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  > > > >       >
  > > > >       >
  > > > >       >_______________________________________________
  > > > >       Freesurfer mailing list
  > > > >       Freesurfer@nmr.mgh.harvard.edu
  > > > >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  > > > >
  > > > >
  > > > >_______________________________________________
  > > > Freesurfer mailing list
  > > > Freesurfer@nmr.mgh.harvard.edu
  > > >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  > >
  > > --
  > > Dr. Tim Schäfer
  > > Postdoc Computational Neuroimaging
  > > Department of Child and Adolescent Psychiatry, Psychosomatics

and

...

  > > Psychotherapy
  > > University Hospital Frankfurt, Goethe University Frankfurt am

Main,

...

  Germany
  > >
  > > _______________________________________________
  > > Freesurfer mailing list
  > > Freesurfer@nmr.mgh.harvard.edu
  > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  > _______________________________________________
  > Freesurfer mailing list
  > Freesurfer@nmr.mgh.harvard.edu
  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

  _______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

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External Email - Use Caution

Hi Bruce and Doug,

To respond to your questions: I projected the BOLD data on the surface using mri_vol2surf function. Then obtained a .mgz file of size 10242 x 1 x 1 x 200.

Then I performed diffusion embedding (unsupervised dimensionality reduction technique) on this .mgz file, whose output was a .npy file. I then loaded this file into a matrix on python, which size was 1 x 18715 x 5. I then saved this file as a .mat file. Then loaded it on matlab, and kept only 1 x 18715 x 1 part of the matrix, and stored it into a zeros(1, 20484). Then kept only the part from (0:10242) and used save_mgh function to save this data into a .mgz file Looking at the info of my .mgz file created with save_mgh, I see that the file doesn't seem to include the data:

" mri_info lh_emb_sub-002_compassion.mgz Volume information for lh_emb_sub-002_compassion.mgz type: MGH dimensions: 1 x 16 x 1 voxel sizes: -nan, -nan, -nan type: FLOAT (3) fov: -nan dof: 1 xstart: -nan, xend: -nan ystart: -nan, yend: -nan zstart: -nan, zend: -nan TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -nan, y_r = -nan, z_r = -nan, c_r = -nan : x_a = -nan, y_a = -nan, z_a = -nan, c_a = -nan : x_s = -nan, y_s = -nan, z_s = -nan, c_s = -nan

talairach xfm : Orientation : III Primary Slice Direction: axial

voxel to ras transform: -nan -nan -nan -nan -nan -nan -nan -nan -nan -nan -nan -nan 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -nan

ras to voxel transform: mat = NULL! MatrixFree: NULL mat POINTER! " It seems that save_mgh function requires tclsh package, as when I ran save_mgh for the first time with this command line: save_mgh('freeview_overlay', ['/home/loic/Documents/emb_output/mgh_format/emb_' char(subjectsList(1)) '_' char(statesList(1)) '.MGZ'], M);

I was getting this message in return in the matlab window: " /usr/share/modules/init/bash: line 36: /usr/bin/tclsh: No such file or directory /usr/share/modules/init/bash: line 58: export: _moduleraw: not a function /usr/share/modules/init/bash: line 60: export: module: not a function " Checking into the '/usr/bin/tclsh' directory, the only package called/related to tclsh was 'tclsh8.6'. I thus changed the name from 'tclsh8.6' to 'tclsh'.

Then tried to save the matrix again with save_mgh function. Now I don't see the error message anymore. However I still get a .mgz file with nans, as seen in the previous mri_info message above.

Would any of you have an advice on how I could make this work, in order to visualize this .mgz file on the left hemisphere pial surface in Freeview?

Thanks in advance,

Sincerely,

Loïc

Le ven. 21 juin 2019 à 16:24, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit :

I don't think it matters but I would use eye instead of nan for M. But the critical issue is where you get your data and what dimensions it has cheers Bruce

On Fri, 21 Jun 2019, Loïc Daumail wrote:

...

    External Email - Use Caution

Me again,

Also, here is how I save the matrix on matlab:

M = nan(4,4); save_mgh('freeview_overlay',

['/home/loic/Documents/emb_output/mgh_format/lh_emb_'

...

char(subjectsList(1)) '_' char(statesList(1)) '.mgz'], M);

Thanks,

Sincerely,

Loïc

Le ven. 21 juin 2019 à 12:25, Loïc Daumail loic.daumail@gmail.com a

écrit :

...

  Hi Bruce,

Thanks for your tip. Unfortunately, I am still running through an

error...

...

I have a matrix of 18715 elements regarding both hemispheres. The size of fsaverage5 is 20484 I believe, so I filled the remaining

elements with zeros, and

...

also tried with rand().

The other issue is that I am not so sure which part of the matrix is for

lh and the other one

...

for rh. Thus, I divided 18715/2 and took the 9357 first elements of the

18715 matrix. Then

...

filled it with zeros or random values to reach 10242.

Then I saved it with save_mgh function and tried to load it with

freeview using the following

...

command line: freeview

-f~/Documents/recon_all_success/freesurfer/fsaverage5/surf/lh.pial:overlay=~/Documents/emb_output/mgh

...

_format/lh_emb_sub-002_compassion.mgz

I am getting the following error: " Did not find any volume info 2 [0]PETSC ERROR:

---

...

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,

probably memory access

...

out of range [0]PETSC ERROR: Try option -start_in_debugger or

-on_error_attach_debugger

...

[0]PETSC ERROR: or see

http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig... ERROR:

...

or try http://valgrind.org on linux or man libgmalloc on Apple to find

memory corruption

...

errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,

and run

...

[0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message

---

...

[0]PETSC ERROR: Signal received! [0]PETSC ERROR:

---

...

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15

17:29:26 CDT 2008 HG

...

revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:

---

...

[0]PETSC ERROR: Unknown Name on a linux-gnu named loic-HP-ZBook-17 by

loic Fri Jun 21 12:15:53

...

2019 [0]PETSC ERROR: Libraries linked

from/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/lin

...

ux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc

--with-fc=g77

...

--download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3

CXXOPTFLAGS=-O3 FOPTFLAGS=-O3

...

[0]PETSC ERROR:

---

...

[0]PETSC ERROR: User provided function() line 0 in unknown directory

unknown file

...

[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0"

Any idea of what could be wrong in my process?

Thanks

Sincerely,

Loïc

Le jeu. 20 juin 2019 à 19:39, Bruce Fischl fischl@nmr.mgh.harvard.edu

a écrit :

...

  Hi Loïc

  the .mgz file should having dimensions nvertices x 1 x 1 for

freeview to

...

  know it is a surface overlay I believe

  cheers
  Bruce



  On Thu, 20 Jun 2019, Loïc Daumail wrote:

  >
  >         External Email - Use Caution
  >
  > Hi Bruce,
  >
  > I am reaching out to you, as I am trying to load the surface

scalar values of

...

  diffusion embedding
  > for overlay on a pial surface in Freeview.
  >
  > I used save_mgh to save a scalar matrix containing surface

embedding values in

...

  an .mgz format.
  > However I can't load it in freeview, be either only half of the

matrix data (one

...

  hemisphere I
  > assume) or the whole matrix saved in the same file.
  >
  > Is there anything specific I need to do in order to be able to

visualize a

...

  scalar overlay on a
  > surface? Is .mgz a wrong format for scalar values? I also tried

with .nii.gz, or

...

  .mgh. I am not even
  > sure save_mgh can do all this...
  >
  > Thanks in advance,
  >
  > Sincerely,
  >
  > Loïc
  >
  >
  >
  > Le lun. 27 mai 2019 à 11:54, Loïc Daumail <

loic.daumail@gmail.com> a écrit :

...

  >       Hi Tim,
  >
  > Your link works perfectly, it's awesome!
  > Thanks a lot,
  >
  > Best,
  >
  > Loïc
  >
  > Le lun. 27 mai 2019 à 11:43, Loïc Daumail <

loic.daumail@gmail.com> a écrit :

...

  >       Hi Tim,
  >
  > 'mean_rest' is a diffusion embedding map, which contains scores

for every vertex

...

  on
  > fsaverage5 surface resolution.
  > 'surf.b' is the pial surface of both hemispheres of

fsaverage5... I also tried

...

  forjust
  > lh hemisphere, but it gives me the same result...
  >
  > Thanks for the link!
  >
  > Best,
  >
  > Loïc
  >
  > Le lun. 27 mai 2019 à 11:20, Tim Schäfer <ts+ml@rcmd.org> a

écrit :

...

  >               External Email - Use Caution
  >
  >       Hi Loïc,
  >
  >       that does not look correct, the data is definitely off.

I'm not sure where

...

  >       the variables `mean_rest` and `surf.b` come from in your

code, and I

...

  suspect
  >       that something is wrong with them.
  >
  >       In the meantime, I got interested in this myself and put

together some

...

  code
  >       that will load the Desikan data for both hemispheres and

display it in

...

  >       surfstat. Feel free to use it, there also is an example

screenshot of the

...

  >       results:
  >
  >
  >

https://github.com/dfsp-spirit/comp_neuro_science/tree/master/surfstat_desik...

...

  >
  >       Best,
  >
  >       Tim
  >
  >       --
  >       Dr. Tim Schäfer
  >       Postdoc Computational Neuroimaging
  >       Department of Child and Adolescent Psychiatry,

Psychosomatics and

...

  >       Psychotherapy
  >       University Hospital Frankfurt, Goethe University Frankfurt

am Main,

...

  Germany
  >
  >       > On May 27, 2019 at 11:01 AM Loïc Daumail <

loic.daumail@gmail.com> wrote:

...

  >       >
  >       >
  >       >         External Email - Use Caution
  >       >
  >       > Hi Tim,
  >       >
  >       > Thanks a lot for your help, indeed, this is exactly what

I needed!

...

  >       > I wrote this :
  >       > "
  >       > subjects_dir =

'/home/loic/Documents/recon_all_success/freesurfer/';

...

  >       > subject_id = 'sub-004';
  >       > hemi = 'lh';
  >       >
  >       > aparc_file_this_hemi = fullfile(subjects_dir,

subject_id, 'label',

...

  >       > sprintf("%s.aparc.annot", hemi));
  >       > [vertices, label, colortable] =

read_annotation(aparc_file_this_hemi);

...

  >       > fprintf("Read aparc parcellation file '%s' containing %d

regions.\n",

...

  >       > aparc_file_this_hemi, length(colortable.struct_names));
  >       > for sidx = 1:length(colortable.struct_names)
  >       >      region = colortable.struct_names{sidx};
  >       >      struct_code = colortable.table(sidx, 5);
  >       >      vertices_of_struct_roi = find(label == struct_code);
  >       >     fprintf("Found region '%s' with %d verts.\n", region,
  >       > length(vertices_of_struct_roi));
  >       > end
  >       > fig1 = figure();
  >       > SurfStatView(mean_rest, surf.b);
  >       > SurfStatColormap(colortable.table(:,1:3)/255);
  >       > "
  >       > However, the image I obtain seems a bit fuzzy...( see

attached)

...

  >       > Is it because of my data?
  >       >
  >       > Thanks in advance,
  >       >
  >       > Loïc
  >       >
  >       >
  >       > Le jeu. 23 mai 2019 à 17:20, Tim Schäfer <ts+ml@rcmd.org>

a écrit :

...

  >       >
  >       > >         External Email - Use Caution
  >       > >
  >       > > Afaik SurfStat is not maintained anymore and I think

it's been this

...

  way
  >       > > for quite a while now. Maybe someone else knows better?
  >       > >
  >       > > The website is at

http://www.math.mcgill.ca/keith/surfstat/ and it

...

  says
  >       > > 'Updated 26 September 2008'. I'm not sure whether

that's really true,

...

  >       but
  >       > > at least for the last 14 months (the only time frame I

know about),

...

  >       there
  >       > > have not been any changes to that website or any new

releases of

...

  >       SurfStat.
  >       > >
  >       > > Tim
  >       > >
  >       > > > On May 23, 2019 at 4:36 PM Bruce Fischl <

fischl@nmr.mgh.harvard.edu>

...

  >       > > wrote:
  >       > > >
  >       > > >
  >       > > > Hi Loic
  >       > > >
  >       > > > sorry, can you ask whoever maintains surfstat? Or

maybe someone else

...

  >       on
  >       > > the
  >       > > > list knows? I don't. You can label surfaces manually

with the dev

...

  >       > > version
  >       > > > of freeview if you want.
  >       > > >
  >       > > > cheers
  >       > > > Bruce
  >       > > >
  >       > > >
  >       > > > On Thu, 23 May 2019, Loïc
  >       > > > Daumail wrote:
  >       > > >
  >       > > > >
  >       > > > >         External Email - Use Caution
  >       > > > >
  >       > > > > Hi Bruce,
  >       > > > >
  >       > > > > I am coming back to this request as I was

wondering:

...

  >       > > > > would it be possible to load freesurfer surface

atlases in

...

  surfstat
  >       in
  >       > > order to label my surfaces?
  >       > > > > Is their format compatible? I saw surfstat only

accepts a limited

...

  >       > > array of formats...
  >       > > > >
  >       > > > > Thanks,
  >       > > > > Best,
  >       > > > >
  >       > > > > Loïc
  >       > > > >
  >       > > > > Le lun. 20 mai 2019 à 16:15, Bruce Fischl
  >       <fischl@nmr.mgh.harvard.edu>
  >       > > a écrit :
  >       > > > >       sure. All the fsaverages are in the same

space (they are

...

  >       subsets
  >       > > of
  >       > > > >       fsaverage)
  >       > > > >       On Mon, 20 May 2019, Loïc Daumail wrote:
  >       > > > >
  >       > > > >       >
  >       > > > >       >         External Email - Use Caution
  >       > > > >       >
  >       > > > >       > Hi Bruce,
  >       > > > >       >
  >       > > > >       > Thanks for your response. Is it also fine

for fsaverage5

...

  >       > > surface or I need to switch
  >       > > > >       my data to
  >       > > > >       > fsaverage?
  >       > > > >       >
  >       > > > >       > Thanks,
  >       > > > >       >
  >       > > > >       > Sincerely,
  >       > > > >       >
  >       > > > >       > Loïc
  >       > > > >       >
  >       > > > >       > Le lun. 20 mai 2019 à 15:52, Bruce Fischl <
  >       > > fischl@nmr.mgh.harvard.edu> a écrit :
  >       > > > >       >       Hi Loic
  >       > > > >       >
  >       > > > >       >       if you are on the fsaverage surface

you can save the

...

  >       > > -log10(p) values
  >       > > > >       >       using save_mgh.m, then load them in

freeview and

...

  >       > > threshold them or
  >       > > > >       >       whatever
  >       > > > >       >
  >       > > > >       >       cheers
  >       > > > >       >       Bruce
  >       > > > >       >       On Mon, 20 May 2019, Loïc Daumail

wrote:

...

  >       > > > >       >
  >       > > > >       >       >
  >       > > > >       >       >         External Email - Use

Caution

...

  >       > > > >       >       >
  >       > > > >       >       > Also, one more thing:
  >       > > > >       >       >
  >       > > > >       >       > My data is on fsaverage5

resolution.

...

  >       > > > >       >       >
  >       > > > >       >       > Thanks in advance,
  >       > > > >       >       >
  >       > > > >       >       > Sincerely,
  >       > > > >       >       >
  >       > > > >       >       > Loïc
  >       > > > >       >       >
  >       > > > >       >       > Le lun. 20 mai 2019 à 09:49, Loïc

Daumail <

...

  >       > > loic.daumail@gmail.com> a écrit :
  >       > > > >       >       >       Dear Freesurfer community,
  >       > > > >       >       >
  >       > > > >       >       > I obtained score matrices of

surfaces after

...

  >       performing
  >       > > diffusion embedding map
  >       > > > >       on fMRI
  >       > > > >       >       data.
  >       > > > >       >       >
  >       > > > >       >       > I am now using the SurfStat

toolbox(Matlab) in

...

  order
  >       > > to obtain p-value maps to
  >       > > > >       compare
  >       > > > >       >       between
  >       > > > >       >       > two groups.
  >       > > > >       >       >
  >       > > > >       >       > After obtaining the p-value map, I

would like to

...

  >       label
  >       > > the surface in order to
  >       > > > >       >       identify the
  >       > > > >       >       > regions of significant difference

between both

...

  >       groups.
  >       > > > >       >       >
  >       > > > >       >       > Would it be possible to use

Freview in order to do

...

  >       it?
  >       > > > >       >       > If so, which format should I use

for my SurfStatP

...

  >       > > output p-value map?
  >       > > > >       >       > How would you do it, (tools to

convert into a

...

  >       specific
  >       > > format, surfaces and
  >       > > > >       atlas to
  >       > > > >       >       load on
  >       > > > >       >       > Freeview, which format for those

ones)?

...

  >       > > > >       >       > I would be very grateful if you

could detail a

...

  bit,
  >       as
  >       > > I am new to these
  >       > > > >       tools!
  >       > > > >       >       >
  >       > > > >       >       > Thanks in advance,
  >       > > > >       >       >
  >       > > > >       >       > Loïc Daumail
  >       > > > >       >       >
  >       > > > >       >       >
  >       > > > >       >

---

  >       > > > >       >       Freesurfer mailing list
  >       > > > >       >       Freesurfer@nmr.mgh.harvard.edu
  >       > > > >       >
  >       > >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >       > > > >       >
  >       > > > >       >
  >       > > > >

---

  >       > > > >       Freesurfer mailing list
  >       > > > >       Freesurfer@nmr.mgh.harvard.edu
  >       > > > >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >       > > > >
  >       > > > >
  >       > > > >_______________________________________________
  >       > > > Freesurfer mailing list
  >       > > > Freesurfer@nmr.mgh.harvard.edu
  >       > > >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >       > >
  >       > > --
  >       > > Dr. Tim Schäfer
  >       > > Postdoc Computational Neuroimaging
  >       > > Department of Child and Adolescent Psychiatry,

Psychosomatics and

...

  >       > > Psychotherapy
  >       > > University Hospital Frankfurt, Goethe University

Frankfurt am Main,

...

  >       Germany
  >       > >
  >       > > _______________________________________________
  >       > > Freesurfer mailing list
  >       > > Freesurfer@nmr.mgh.harvard.edu
  >       > >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >       > _______________________________________________
  >       > Freesurfer mailing list
  >       > Freesurfer@nmr.mgh.harvard.edu
  >       >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >
  >       _______________________________________________
  >       Freesurfer mailing list
  >       Freesurfer@nmr.mgh.harvard.edu
  >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

Hi Doug,

Thanks for your help!

However, using mri_convert, I still get the same message with tclsh. " mri_convert lh.thickness template.mgh /usr/share/modules/init/bash: line 36: /usr/bin/tclsh: No such file or directory /usr/share/modules/init/bash: line 58: export: _moduleraw: not a function /usr/share/modules/init/bash: line 60: export: module: not a function mri_convert.bin lh.thickness template.mgh $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from lh.thickness... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to template.mgh... " There is progess though, as here, we see that template.mgh seems not empty: " mri_info template.mgh Volume information for template.mgh type: MGH dimensions: 10242 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 10242.000 dof: 0 xstart: -5121.0, xend: 5121.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000

talairach xfm : Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 0.0000 0.0000 5121.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 -0.0000 -0.0000 5121.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 -0.0000 -0.0000 -0.0000 1.0000 " Also, using MRIread and MRIwrite, we can see that it's not empty neither:

" Volume information for lh_emb_comp_sub-002.mgz type: MGH dimensions: 1 x 10242 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 10242.000 dof: 1 xstart: -0.5, xend: 0.5 ystart: -5121.0, yend: 5121.0 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 5120.5000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -5120.5000

talairach xfm : Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 0.0000 0.0000 5121.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 -0.0000 -0.0000 5121.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 -0.0000 -0.0000 -0.0000 1.0000 "

But then, trying to load the overlay on the lh.pial still isn't possible, with endless "FreadFloat: fread failed"

Thanks in advance for your help,

Sincerely,

Loïc

Le lun. 24 juin 2019 à 14:21, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> a écrit :

It is probably using a tcsh shell to do the compression. Try using MRIwrite instead. You will have to create an mri structure. The easiest way to do that is to mri_convert lh.thickness template.mgh then read the template in to matlab template = MRIread('template.mgh'); template.vol = yourdata MRIwrite(template,'yourdata.mgz')

On 6/24/2019 11:54 AM, Loïc Daumail wrote:

    External Email - Use Caution

Hi Bruce and Doug,

To respond to your questions: I projected the BOLD data on the surface using mri_vol2surf function. Then obtained a .mgz file of size 10242 x 1 x 1 x 200.

Then I performed diffusion embedding (unsupervised dimensionality reduction technique) on this .mgz file, whose output was a .npy file. I then loaded this file into a matrix on python, which size was 1 x 18715 x 5. I then saved this file as a .mat file. Then loaded it on matlab, and kept only 1 x 18715 x 1 part of the matrix, and stored it into a zeros(1, 20484). Then kept only the part from (0:10242) and used save_mgh function to save this data into a .mgz file Looking at the info of my .mgz file created with save_mgh, I see that the file doesn't seem to include the data:

" mri_info lh_emb_sub-002_compassion.mgz Volume information for lh_emb_sub-002_compassion.mgz type: MGH dimensions: 1 x 16 x 1 voxel sizes: -nan, -nan, -nan type: FLOAT (3) fov: -nan dof: 1 xstart: -nan, xend: -nan ystart: -nan, yend: -nan zstart: -nan, zend: -nan TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -nan, y_r = -nan, z_r = -nan, c_r = -nan : x_a = -nan, y_a = -nan, z_a = -nan, c_a = -nan : x_s = -nan, y_s = -nan, z_s = -nan, c_s = -nan

talairach xfm : Orientation : III Primary Slice Direction: axial

voxel to ras transform: -nan -nan -nan -nan -nan -nan -nan -nan -nan -nan -nan -nan 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -nan

ras to voxel transform: mat = NULL! MatrixFree: NULL mat POINTER! " It seems that save_mgh function requires tclsh package, as when I ran save_mgh for the first time with this command line: save_mgh('freeview_overlay', ['/home/loic/Documents/emb_output/mgh_format/emb_' char(subjectsList(1)) '_' char(statesList(1)) '.MGZ'], M);

I was getting this message in return in the matlab window: " /usr/share/modules/init/bash: line 36: /usr/bin/tclsh: No such file or directory /usr/share/modules/init/bash: line 58: export: _moduleraw: not a function /usr/share/modules/init/bash: line 60: export: module: not a function " Checking into the '/usr/bin/tclsh' directory, the only package called/related to tclsh was 'tclsh8.6'. I thus changed the name from 'tclsh8.6' to 'tclsh'.

Then tried to save the matrix again with save_mgh function. Now I don't see the error message anymore. However I still get a .mgz file with nans, as seen in the previous mri_info message above.

Would any of you have an advice on how I could make this work, in order to visualize this .mgz file on the left hemisphere pial surface in Freeview?

Thanks in advance,

Sincerely,

Loïc

Le ven. 21 juin 2019 à 16:24, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit :

...

I don't think it matters but I would use eye instead of nan for M. But the critical issue is where you get your data and what dimensions it has cheers Bruce

On Fri, 21 Jun 2019, Loïc Daumail wrote:

...

    External Email - Use Caution

Me again,

Also, here is how I save the matrix on matlab:

M = nan(4,4); save_mgh('freeview_overlay',

['/home/loic/Documents/emb_output/mgh_format/lh_emb_'

...

char(subjectsList(1)) '_' char(statesList(1)) '.mgz'], M);

Thanks,

Sincerely,

Loïc

Le ven. 21 juin 2019 à 12:25, Loïc Daumail loic.daumail@gmail.com a

écrit :

...

  Hi Bruce,

Thanks for your tip. Unfortunately, I am still running through an

error...

...

I have a matrix of 18715 elements regarding both hemispheres. The size of fsaverage5 is 20484 I believe, so I filled the remaining

elements with zeros, and

...

also tried with rand().

The other issue is that I am not so sure which part of the matrix is

for lh and the other one

...

for rh. Thus, I divided 18715/2 and took the 9357 first elements of the

18715 matrix. Then

...

filled it with zeros or random values to reach 10242.

Then I saved it with save_mgh function and tried to load it with

freeview using the following

...

command line: freeview

-f~/Documents/recon_all_success/freesurfer/fsaverage5/surf/lh.pial:overlay=~/Documents/emb_output/mgh

...

_format/lh_emb_sub-002_compassion.mgz

I am getting the following error: " Did not find any volume info 2 [0]PETSC ERROR:

---

...

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,

probably memory access

...

out of range [0]PETSC ERROR: Try option -start_in_debugger or

-on_error_attach_debugger

...

[0]PETSC ERROR: or see

http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig... ERROR:

...

or try http://valgrind.org on linux or man libgmalloc on Apple to find

memory corruption

...

errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,

and run

...

[0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message

---

...

[0]PETSC ERROR: Signal received! [0]PETSC ERROR:

---

...

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15

17:29:26 CDT 2008 HG

...

revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:

---

...

[0]PETSC ERROR: Unknown Name on a linux-gnu named loic-HP-ZBook-17 by

loic Fri Jun 21 12:15:53

...

2019 [0]PETSC ERROR: Libraries linked

from/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/lin

...

ux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc

--with-fc=g77

...

--download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3

CXXOPTFLAGS=-O3 FOPTFLAGS=-O3

...

[0]PETSC ERROR:

---

...

[0]PETSC ERROR: User provided function() line 0 in unknown directory

unknown file

...

[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0"

Any idea of what could be wrong in my process?

Thanks

Sincerely,

Loïc

Le jeu. 20 juin 2019 à 19:39, Bruce Fischl fischl@nmr.mgh.harvard.edu

a écrit :

...

  Hi Loïc

  the .mgz file should having dimensions nvertices x 1 x 1 for

freeview to

...

  know it is a surface overlay I believe

  cheers
  Bruce



  On Thu, 20 Jun 2019, Loïc Daumail wrote:

  >
  >         External Email - Use Caution
  >
  > Hi Bruce,
  >
  > I am reaching out to you, as I am trying to load the surface

scalar values of

...

  diffusion embedding
  > for overlay on a pial surface in Freeview.
  >
  > I used save_mgh to save a scalar matrix containing surface

embedding values in

...

  an .mgz format.
  > However I can't load it in freeview, be either only half of the

matrix data (one

...

  hemisphere I
  > assume) or the whole matrix saved in the same file.
  >
  > Is there anything specific I need to do in order to be able to

visualize a

...

  scalar overlay on a
  > surface? Is .mgz a wrong format for scalar values? I also tried

with .nii.gz, or

...

  .mgh. I am not even
  > sure save_mgh can do all this...
  >
  > Thanks in advance,
  >
  > Sincerely,
  >
  > Loïc
  >
  >
  >
  > Le lun. 27 mai 2019 à 11:54, Loïc Daumail <

loic.daumail@gmail.com> a écrit :

...

  >       Hi Tim,
  >
  > Your link works perfectly, it's awesome!
  > Thanks a lot,
  >
  > Best,
  >
  > Loïc
  >
  > Le lun. 27 mai 2019 à 11:43, Loïc Daumail <

loic.daumail@gmail.com> a écrit :

...

  >       Hi Tim,
  >
  > 'mean_rest' is a diffusion embedding map, which contains scores

for every vertex

...

  on
  > fsaverage5 surface resolution.
  > 'surf.b' is the pial surface of both hemispheres of

fsaverage5... I also tried

...

  forjust
  > lh hemisphere, but it gives me the same result...
  >
  > Thanks for the link!
  >
  > Best,
  >
  > Loïc
  >
  > Le lun. 27 mai 2019 à 11:20, Tim Schäfer <ts+ml@rcmd.org> a

écrit :

...

  >               External Email - Use Caution
  >
  >       Hi Loïc,
  >
  >       that does not look correct, the data is definitely off.

I'm not sure where

...

  >       the variables `mean_rest` and `surf.b` come from in your

code, and I

...

  suspect
  >       that something is wrong with them.
  >
  >       In the meantime, I got interested in this myself and put

together some

...

  code
  >       that will load the Desikan data for both hemispheres and

display it in

...

  >       surfstat. Feel free to use it, there also is an example

screenshot of the

...

  >       results:
  >
  >
  >

https://github.com/dfsp-spirit/comp_neuro_science/tree/master/surfstat_desik...

...

  >
  >       Best,
  >
  >       Tim
  >
  >       --
  >       Dr. Tim Schäfer
  >       Postdoc Computational Neuroimaging
  >       Department of Child and Adolescent Psychiatry,

Psychosomatics and

...

  >       Psychotherapy
  >       University Hospital Frankfurt, Goethe University

Frankfurt am Main,

...

  Germany
  >
  >       > On May 27, 2019 at 11:01 AM Loïc Daumail <

loic.daumail@gmail.com> wrote:

...

  >       >
  >       >
  >       >         External Email - Use Caution
  >       >
  >       > Hi Tim,
  >       >
  >       > Thanks a lot for your help, indeed, this is exactly

what I needed!

...

  >       > I wrote this :
  >       > "
  >       > subjects_dir =

'/home/loic/Documents/recon_all_success/freesurfer/';

...

  >       > subject_id = 'sub-004';
  >       > hemi = 'lh';
  >       >
  >       > aparc_file_this_hemi = fullfile(subjects_dir,

subject_id, 'label',

...

  >       > sprintf("%s.aparc.annot", hemi));
  >       > [vertices, label, colortable] =

read_annotation(aparc_file_this_hemi);

...

  >       > fprintf("Read aparc parcellation file '%s' containing

%d regions.\n",

...

  >       > aparc_file_this_hemi, length(colortable.struct_names));
  >       > for sidx = 1:length(colortable.struct_names)
  >       >      region = colortable.struct_names{sidx};
  >       >      struct_code = colortable.table(sidx, 5);
  >       >      vertices_of_struct_roi = find(label ==

struct_code);

...

  >       >     fprintf("Found region '%s' with %d verts.\n",

region,

...

  >       > length(vertices_of_struct_roi));
  >       > end
  >       > fig1 = figure();
  >       > SurfStatView(mean_rest, surf.b);
  >       > SurfStatColormap(colortable.table(:,1:3)/255);
  >       > "
  >       > However, the image I obtain seems a bit fuzzy...( see

attached)

...

  >       > Is it because of my data?
  >       >
  >       > Thanks in advance,
  >       >
  >       > Loïc
  >       >
  >       >
  >       > Le jeu. 23 mai 2019 à 17:20, Tim Schäfer <

ts+ml@rcmd.org> a écrit :

...

  >       >
  >       > >         External Email - Use Caution
  >       > >
  >       > > Afaik SurfStat is not maintained anymore and I think

it's been this

...

  way
  >       > > for quite a while now. Maybe someone else knows

better?

...

  >       > >
  >       > > The website is at

http://www.math.mcgill.ca/keith/surfstat/ and it

...

  says
  >       > > 'Updated 26 September 2008'. I'm not sure whether

that's really true,

...

  >       but
  >       > > at least for the last 14 months (the only time frame

I know about),

...

  >       there
  >       > > have not been any changes to that website or any new

releases of

...

  >       SurfStat.
  >       > >
  >       > > Tim
  >       > >
  >       > > > On May 23, 2019 at 4:36 PM Bruce Fischl <

fischl@nmr.mgh.harvard.edu>

...

  >       > > wrote:
  >       > > >
  >       > > >
  >       > > > Hi Loic
  >       > > >
  >       > > > sorry, can you ask whoever maintains surfstat? Or

maybe someone else

...

  >       on
  >       > > the
  >       > > > list knows? I don't. You can label surfaces

manually with the dev

...

  >       > > version
  >       > > > of freeview if you want.
  >       > > >
  >       > > > cheers
  >       > > > Bruce
  >       > > >
  >       > > >
  >       > > > On Thu, 23 May 2019, Loïc
  >       > > > Daumail wrote:
  >       > > >
  >       > > > >
  >       > > > >         External Email - Use Caution
  >       > > > >
  >       > > > > Hi Bruce,
  >       > > > >
  >       > > > > I am coming back to this request as I was

wondering:

...

  >       > > > > would it be possible to load freesurfer surface

atlases in

...

  surfstat
  >       in
  >       > > order to label my surfaces?
  >       > > > > Is their format compatible? I saw surfstat only

accepts a limited

...

  >       > > array of formats...
  >       > > > >
  >       > > > > Thanks,
  >       > > > > Best,
  >       > > > >
  >       > > > > Loïc
  >       > > > >
  >       > > > > Le lun. 20 mai 2019 à 16:15, Bruce Fischl
  >       <fischl@nmr.mgh.harvard.edu>
  >       > > a écrit :
  >       > > > >       sure. All the fsaverages are in the same

space (they are

...

  >       subsets
  >       > > of
  >       > > > >       fsaverage)
  >       > > > >       On Mon, 20 May 2019, Loïc Daumail wrote:
  >       > > > >
  >       > > > >       >
  >       > > > >       >         External Email - Use Caution
  >       > > > >       >
  >       > > > >       > Hi Bruce,
  >       > > > >       >
  >       > > > >       > Thanks for your response. Is it also fine

for fsaverage5

...

  >       > > surface or I need to switch
  >       > > > >       my data to
  >       > > > >       > fsaverage?
  >       > > > >       >
  >       > > > >       > Thanks,
  >       > > > >       >
  >       > > > >       > Sincerely,
  >       > > > >       >
  >       > > > >       > Loïc
  >       > > > >       >
  >       > > > >       > Le lun. 20 mai 2019 à 15:52, Bruce Fischl

<

...

  >       > > fischl@nmr.mgh.harvard.edu> a écrit :
  >       > > > >       >       Hi Loic
  >       > > > >       >
  >       > > > >       >       if you are on the fsaverage surface

you can save the

...

  >       > > -log10(p) values
  >       > > > >       >       using save_mgh.m, then load them in

freeview and

...

  >       > > threshold them or
  >       > > > >       >       whatever
  >       > > > >       >
  >       > > > >       >       cheers
  >       > > > >       >       Bruce
  >       > > > >       >       On Mon, 20 May 2019, Loïc Daumail

wrote:

...

  >       > > > >       >
  >       > > > >       >       >
  >       > > > >       >       >         External Email - Use

Caution

...

  >       > > > >       >       >
  >       > > > >       >       > Also, one more thing:
  >       > > > >       >       >
  >       > > > >       >       > My data is on fsaverage5

resolution.

...

  >       > > > >       >       >
  >       > > > >       >       > Thanks in advance,
  >       > > > >       >       >
  >       > > > >       >       > Sincerely,
  >       > > > >       >       >
  >       > > > >       >       > Loïc
  >       > > > >       >       >
  >       > > > >       >       > Le lun. 20 mai 2019 à 09:49, Loïc

Daumail <

...

  >       > > loic.daumail@gmail.com> a écrit :
  >       > > > >       >       >       Dear Freesurfer community,
  >       > > > >       >       >
  >       > > > >       >       > I obtained score matrices of

surfaces after

...

  >       performing
  >       > > diffusion embedding map
  >       > > > >       on fMRI
  >       > > > >       >       data.
  >       > > > >       >       >
  >       > > > >       >       > I am now using the SurfStat

toolbox(Matlab) in

...

  order
  >       > > to obtain p-value maps to
  >       > > > >       compare
  >       > > > >       >       between
  >       > > > >       >       > two groups.
  >       > > > >       >       >
  >       > > > >       >       > After obtaining the p-value map,

I would like to

...

  >       label
  >       > > the surface in order to
  >       > > > >       >       identify the
  >       > > > >       >       > regions of significant difference

between both

...

  >       groups.
  >       > > > >       >       >
  >       > > > >       >       > Would it be possible to use

Freview in order to do

...

  >       it?
  >       > > > >       >       > If so, which format should I use

for my SurfStatP

...

  >       > > output p-value map?
  >       > > > >       >       > How would you do it, (tools to

convert into a

...

  >       specific
  >       > > format, surfaces and
  >       > > > >       atlas to
  >       > > > >       >       load on
  >       > > > >       >       > Freeview, which format for those

ones)?

...

  >       > > > >       >       > I would be very grateful if you

could detail a

...

  bit,
  >       as
  >       > > I am new to these
  >       > > > >       tools!
  >       > > > >       >       >
  >       > > > >       >       > Thanks in advance,
  >       > > > >       >       >
  >       > > > >       >       > Loïc Daumail
  >       > > > >       >       >
  >       > > > >       >       >
  >       > > > >       >

---

  >       > > > >       >       Freesurfer mailing list
  >       > > > >       >       Freesurfer@nmr.mgh.harvard.edu
  >       > > > >       >
  >       > >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >       > > > >       >
  >       > > > >       >
  >       > > > >

---

  >       > > > >       Freesurfer mailing list
  >       > > > >       Freesurfer@nmr.mgh.harvard.edu
  >       > > > >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >       > > > >
  >       > > > >
  >       > > > >_______________________________________________
  >       > > > Freesurfer mailing list
  >       > > > Freesurfer@nmr.mgh.harvard.edu
  >       > > >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >       > >
  >       > > --
  >       > > Dr. Tim Schäfer
  >       > > Postdoc Computational Neuroimaging
  >       > > Department of Child and Adolescent Psychiatry,

Psychosomatics and

...

  >       > > Psychotherapy
  >       > > University Hospital Frankfurt, Goethe University

Frankfurt am Main,

...

  >       Germany
  >       > >
  >       > > _______________________________________________
  >       > > Freesurfer mailing list
  >       > > Freesurfer@nmr.mgh.harvard.edu
  >       > >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >       > _______________________________________________
  >       > Freesurfer mailing list
  >       > Freesurfer@nmr.mgh.harvard.edu
  >       >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >
  >       _______________________________________________
  >       Freesurfer mailing list
  >       Freesurfer@nmr.mgh.harvard.edu
  >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

Hi Freesurfer, Getting back the former request, I am still trying to load an overlay of my data onto a surface.. but it still doesn't work well. Here is the info of my overlay: " mri_info lh_emb_comp_sub-002.mgz Volume information for lh_emb_comp_sub-002.mgz type: MGH dimensions: 10242 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 10242.000 dof: 1 xstart: -5121.0, xend: 5121.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000

talairach xfm : Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 0.0000 0.0000 5121.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 -0.0000 -0.0000 5121.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 -0.0000 -0.0000 -0.0000 1.0000 " Here is what I get when loading on freeview:

" freeview -f ~/Documents/recon_all_success/freesurfer/sub-002/surf/lh.pial:overlay=lh_emb_comp_sub-002.mgz Number of vertices in overlay data does not match with surface. QClipboard: Unable to receive an event from the clipboard manager in a reasonable time " The data was normalized in MNI space. When I try to load it in FSLeyes, it works, but the overlay is completely absent, it seems that it's empty. On the FSLeyes GUI, it's written 'overlay out of bounds'... The endpoint of this process would be to define ROIs in specific regions, and Freeview is very handy with atlases. Any advice is welcome!

Thanks in advance,

Sincerely,

Loïc

Le lun. 24 juin 2019 à 17:01, Loïc Daumail loic.daumail@gmail.com a écrit :

I also tried saving the last file in 10242 x 1 x 1.. but nothing is coming neither.

Thanks,

Sincerely,

Loïc

Le lun. 24 juin 2019 à 16:50, Loïc Daumail loic.daumail@gmail.com a écrit :

...

Hi Doug,

Thanks for your help!

However, using mri_convert, I still get the same message with tclsh. " mri_convert lh.thickness template.mgh /usr/share/modules/init/bash: line 36: /usr/bin/tclsh: No such file or directory /usr/share/modules/init/bash: line 58: export: _moduleraw: not a function /usr/share/modules/init/bash: line 60: export: module: not a function mri_convert.bin lh.thickness template.mgh $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from lh.thickness... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to template.mgh... " There is progess though, as here, we see that template.mgh seems not empty: " mri_info template.mgh Volume information for template.mgh type: MGH dimensions: 10242 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 10242.000 dof: 0 xstart: -5121.0, xend: 5121.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000

talairach xfm : Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 0.0000 0.0000 5121.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 -0.0000 -0.0000 5121.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 -0.0000 -0.0000 -0.0000 1.0000 " Also, using MRIread and MRIwrite, we can see that it's not empty neither:

" Volume information for lh_emb_comp_sub-002.mgz type: MGH dimensions: 1 x 10242 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 10242.000 dof: 1 xstart: -0.5, xend: 0.5 ystart: -5121.0, yend: 5121.0 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 5120.5000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -5120.5000

talairach xfm : Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 0.0000 0.0000 5121.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 -0.0000 -0.0000 5121.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 -0.0000 -0.0000 -0.0000 1.0000 "

But then, trying to load the overlay on the lh.pial still isn't possible, with endless "FreadFloat: fread failed"

Thanks in advance for your help,

Sincerely,

Loïc

Le lun. 24 juin 2019 à 14:21, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> a écrit :

...

It is probably using a tcsh shell to do the compression. Try using MRIwrite instead. You will have to create an mri structure. The easiest way to do that is to mri_convert lh.thickness template.mgh then read the template in to matlab template = MRIread('template.mgh'); template.vol = yourdata MRIwrite(template,'yourdata.mgz')

On 6/24/2019 11:54 AM, Loïc Daumail wrote:

    External Email - Use Caution

Hi Bruce and Doug,

To respond to your questions: I projected the BOLD data on the surface using mri_vol2surf function. Then obtained a .mgz file of size 10242 x 1 x 1 x 200.

Then I performed diffusion embedding (unsupervised dimensionality reduction technique) on this .mgz file, whose output was a .npy file. I then loaded this file into a matrix on python, which size was 1 x 18715 x 5. I then saved this file as a .mat file. Then loaded it on matlab, and kept only 1 x 18715 x 1 part of the matrix, and stored it into a zeros(1, 20484). Then kept only the part from (0:10242) and used save_mgh function to save this data into a .mgz file Looking at the info of my .mgz file created with save_mgh, I see that the file doesn't seem to include the data:

" mri_info lh_emb_sub-002_compassion.mgz Volume information for lh_emb_sub-002_compassion.mgz type: MGH dimensions: 1 x 16 x 1 voxel sizes: -nan, -nan, -nan type: FLOAT (3) fov: -nan dof: 1 xstart: -nan, xend: -nan ystart: -nan, yend: -nan zstart: -nan, zend: -nan TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -nan, y_r = -nan, z_r = -nan, c_r = -nan : x_a = -nan, y_a = -nan, z_a = -nan, c_a = -nan : x_s = -nan, y_s = -nan, z_s = -nan, c_s = -nan

talairach xfm : Orientation : III Primary Slice Direction: axial

voxel to ras transform: -nan -nan -nan -nan -nan -nan -nan -nan -nan -nan -nan -nan 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -nan

ras to voxel transform: mat = NULL! MatrixFree: NULL mat POINTER! " It seems that save_mgh function requires tclsh package, as when I ran save_mgh for the first time with this command line: save_mgh('freeview_overlay', ['/home/loic/Documents/emb_output/mgh_format/emb_' char(subjectsList(1)) '_' char(statesList(1)) '.MGZ'], M);

I was getting this message in return in the matlab window: " /usr/share/modules/init/bash: line 36: /usr/bin/tclsh: No such file or directory /usr/share/modules/init/bash: line 58: export: _moduleraw: not a function /usr/share/modules/init/bash: line 60: export: module: not a function " Checking into the '/usr/bin/tclsh' directory, the only package called/related to tclsh was 'tclsh8.6'. I thus changed the name from 'tclsh8.6' to 'tclsh'.

Then tried to save the matrix again with save_mgh function. Now I don't see the error message anymore. However I still get a .mgz file with nans, as seen in the previous mri_info message above.

Would any of you have an advice on how I could make this work, in order to visualize this .mgz file on the left hemisphere pial surface in Freeview?

Thanks in advance,

Sincerely,

Loïc

Le ven. 21 juin 2019 à 16:24, Bruce Fischl fischl@nmr.mgh.harvard.edu a écrit :

...

I don't think it matters but I would use eye instead of nan for M. But the critical issue is where you get your data and what dimensions it has cheers Bruce

On Fri, 21 Jun 2019, Loïc Daumail wrote:

...

    External Email - Use Caution

Me again,

Also, here is how I save the matrix on matlab:

M = nan(4,4); save_mgh('freeview_overlay',

['/home/loic/Documents/emb_output/mgh_format/lh_emb_'

...

char(subjectsList(1)) '_' char(statesList(1)) '.mgz'], M);

Thanks,

Sincerely,

Loïc

Le ven. 21 juin 2019 à 12:25, Loïc Daumail loic.daumail@gmail.com

a écrit :

...

  Hi Bruce,

Thanks for your tip. Unfortunately, I am still running through an

error...

...

I have a matrix of 18715 elements regarding both hemispheres. The size of fsaverage5 is 20484 I believe, so I filled the remaining

elements with zeros, and

...

also tried with rand().

The other issue is that I am not so sure which part of the matrix is

for lh and the other one

...

for rh. Thus, I divided 18715/2 and took the 9357 first elements of

the 18715 matrix. Then

...

filled it with zeros or random values to reach 10242.

Then I saved it with save_mgh function and tried to load it with

freeview using the following

...

command line: freeview

-f~/Documents/recon_all_success/freesurfer/fsaverage5/surf/lh.pial:overlay=~/Documents/emb_output/mgh

...

_format/lh_emb_sub-002_compassion.mgz

I am getting the following error: " Did not find any volume info 2 [0]PETSC ERROR:

---

...

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,

probably memory access

...

out of range [0]PETSC ERROR: Try option -start_in_debugger or

-on_error_attach_debugger

...

[0]PETSC ERROR: or see

http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig... ERROR:

...

or try http://valgrind.org on linux or man libgmalloc on Apple to

find memory corruption

...

errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile,

link, and run

...

[0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message

---

...

[0]PETSC ERROR: Signal received! [0]PETSC ERROR:

---

...

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15

17:29:26 CDT 2008 HG

...

revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR:

---

...

[0]PETSC ERROR: Unknown Name on a linux-gnu named loic-HP-ZBook-17 by

loic Fri Jun 21 12:15:53

...

2019 [0]PETSC ERROR: Libraries linked

from/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/lin

...

ux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc

--with-fc=g77

...

--download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3

CXXOPTFLAGS=-O3 FOPTFLAGS=-O3

...

[0]PETSC ERROR:

---

...

[0]PETSC ERROR: User provided function() line 0 in unknown directory

unknown file

...

[unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0"

Any idea of what could be wrong in my process?

Thanks

Sincerely,

Loïc

Le jeu. 20 juin 2019 à 19:39, Bruce Fischl <

fischl@nmr.mgh.harvard.edu> a écrit :

...

  Hi Loïc

  the .mgz file should having dimensions nvertices x 1 x 1 for

freeview to

...

  know it is a surface overlay I believe

  cheers
  Bruce



  On Thu, 20 Jun 2019, Loïc Daumail wrote:

  >
  >         External Email - Use Caution
  >
  > Hi Bruce,
  >
  > I am reaching out to you, as I am trying to load the surface

scalar values of

...

  diffusion embedding
  > for overlay on a pial surface in Freeview.
  >
  > I used save_mgh to save a scalar matrix containing surface

embedding values in

...

  an .mgz format.
  > However I can't load it in freeview, be either only half of

the matrix data (one

...

  hemisphere I
  > assume) or the whole matrix saved in the same file.
  >
  > Is there anything specific I need to do in order to be able

to visualize a

...

  scalar overlay on a
  > surface? Is .mgz a wrong format for scalar values? I also

tried with .nii.gz, or

...

  .mgh. I am not even
  > sure save_mgh can do all this...
  >
  > Thanks in advance,
  >
  > Sincerely,
  >
  > Loïc
  >
  >
  >
  > Le lun. 27 mai 2019 à 11:54, Loïc Daumail <

loic.daumail@gmail.com> a écrit :

...

  >       Hi Tim,
  >
  > Your link works perfectly, it's awesome!
  > Thanks a lot,
  >
  > Best,
  >
  > Loïc
  >
  > Le lun. 27 mai 2019 à 11:43, Loïc Daumail <

loic.daumail@gmail.com> a écrit :

...

  >       Hi Tim,
  >
  > 'mean_rest' is a diffusion embedding map, which contains

scores for every vertex

...

  on
  > fsaverage5 surface resolution.
  > 'surf.b' is the pial surface of both hemispheres of

fsaverage5... I also tried

...

  forjust
  > lh hemisphere, but it gives me the same result...
  >
  > Thanks for the link!
  >
  > Best,
  >
  > Loïc
  >
  > Le lun. 27 mai 2019 à 11:20, Tim Schäfer <ts+ml@rcmd.org> a

écrit :

...

  >               External Email - Use Caution
  >
  >       Hi Loïc,
  >
  >       that does not look correct, the data is definitely off.

I'm not sure where

...

  >       the variables `mean_rest` and `surf.b` come from in

your code, and I

...

  suspect
  >       that something is wrong with them.
  >
  >       In the meantime, I got interested in this myself and

put together some

...

  code
  >       that will load the Desikan data for both hemispheres

and display it in

...

  >       surfstat. Feel free to use it, there also is an example

screenshot of the

...

  >       results:
  >
  >
  >

https://github.com/dfsp-spirit/comp_neuro_science/tree/master/surfstat_desik...

...

  >
  >       Best,
  >
  >       Tim
  >
  >       --
  >       Dr. Tim Schäfer
  >       Postdoc Computational Neuroimaging
  >       Department of Child and Adolescent Psychiatry,

Psychosomatics and

...

  >       Psychotherapy
  >       University Hospital Frankfurt, Goethe University

Frankfurt am Main,

...

  Germany
  >
  >       > On May 27, 2019 at 11:01 AM Loïc Daumail <

loic.daumail@gmail.com> wrote:

...

  >       >
  >       >
  >       >         External Email - Use Caution
  >       >
  >       > Hi Tim,
  >       >
  >       > Thanks a lot for your help, indeed, this is exactly

what I needed!

...

  >       > I wrote this :
  >       > "
  >       > subjects_dir =

'/home/loic/Documents/recon_all_success/freesurfer/';

...

  >       > subject_id = 'sub-004';
  >       > hemi = 'lh';
  >       >
  >       > aparc_file_this_hemi = fullfile(subjects_dir,

subject_id, 'label',

...

  >       > sprintf("%s.aparc.annot", hemi));
  >       > [vertices, label, colortable] =

read_annotation(aparc_file_this_hemi);

...

  >       > fprintf("Read aparc parcellation file '%s' containing

%d regions.\n",

...

  >       > aparc_file_this_hemi,

length(colortable.struct_names));

...

  >       > for sidx = 1:length(colortable.struct_names)
  >       >      region = colortable.struct_names{sidx};
  >       >      struct_code = colortable.table(sidx, 5);
  >       >      vertices_of_struct_roi = find(label ==

struct_code);

...

  >       >     fprintf("Found region '%s' with %d verts.\n",

region,

...

  >       > length(vertices_of_struct_roi));
  >       > end
  >       > fig1 = figure();
  >       > SurfStatView(mean_rest, surf.b);
  >       > SurfStatColormap(colortable.table(:,1:3)/255);
  >       > "
  >       > However, the image I obtain seems a bit fuzzy...( see

attached)

...

  >       > Is it because of my data?
  >       >
  >       > Thanks in advance,
  >       >
  >       > Loïc
  >       >
  >       >
  >       > Le jeu. 23 mai 2019 à 17:20, Tim Schäfer <

ts+ml@rcmd.org> a écrit :

...

  >       >
  >       > >         External Email - Use Caution
  >       > >
  >       > > Afaik SurfStat is not maintained anymore and I

think it's been this

...

  way
  >       > > for quite a while now. Maybe someone else knows

better?

...

  >       > >
  >       > > The website is at

http://www.math.mcgill.ca/keith/surfstat/ and it

...

  says
  >       > > 'Updated 26 September 2008'. I'm not sure whether

that's really true,

...

  >       but
  >       > > at least for the last 14 months (the only time

frame I know about),

...

  >       there
  >       > > have not been any changes to that website or any

new releases of

...

  >       SurfStat.
  >       > >
  >       > > Tim
  >       > >
  >       > > > On May 23, 2019 at 4:36 PM Bruce Fischl <

fischl@nmr.mgh.harvard.edu>

...

  >       > > wrote:
  >       > > >
  >       > > >
  >       > > > Hi Loic
  >       > > >
  >       > > > sorry, can you ask whoever maintains surfstat? Or

maybe someone else

...

  >       on
  >       > > the
  >       > > > list knows? I don't. You can label surfaces

manually with the dev

...

  >       > > version
  >       > > > of freeview if you want.
  >       > > >
  >       > > > cheers
  >       > > > Bruce
  >       > > >
  >       > > >
  >       > > > On Thu, 23 May 2019, Loïc
  >       > > > Daumail wrote:
  >       > > >
  >       > > > >
  >       > > > >         External Email - Use Caution
  >       > > > >
  >       > > > > Hi Bruce,
  >       > > > >
  >       > > > > I am coming back to this request as I was

wondering:

...

  >       > > > > would it be possible to load freesurfer surface

atlases in

...

  surfstat
  >       in
  >       > > order to label my surfaces?
  >       > > > > Is their format compatible? I saw surfstat only

accepts a limited

...

  >       > > array of formats...
  >       > > > >
  >       > > > > Thanks,
  >       > > > > Best,
  >       > > > >
  >       > > > > Loïc
  >       > > > >
  >       > > > > Le lun. 20 mai 2019 à 16:15, Bruce Fischl
  >       <fischl@nmr.mgh.harvard.edu>
  >       > > a écrit :
  >       > > > >       sure. All the fsaverages are in the same

space (they are

...

  >       subsets
  >       > > of
  >       > > > >       fsaverage)
  >       > > > >       On Mon, 20 May 2019, Loïc Daumail wrote:
  >       > > > >
  >       > > > >       >
  >       > > > >       >         External Email - Use Caution
  >       > > > >       >
  >       > > > >       > Hi Bruce,
  >       > > > >       >
  >       > > > >       > Thanks for your response. Is it also

fine for fsaverage5

...

  >       > > surface or I need to switch
  >       > > > >       my data to
  >       > > > >       > fsaverage?
  >       > > > >       >
  >       > > > >       > Thanks,
  >       > > > >       >
  >       > > > >       > Sincerely,
  >       > > > >       >
  >       > > > >       > Loïc
  >       > > > >       >
  >       > > > >       > Le lun. 20 mai 2019 à 15:52, Bruce

Fischl <

...

  >       > > fischl@nmr.mgh.harvard.edu> a écrit :
  >       > > > >       >       Hi Loic
  >       > > > >       >
  >       > > > >       >       if you are on the fsaverage

surface you can save the

...

  >       > > -log10(p) values
  >       > > > >       >       using save_mgh.m, then load them

in freeview and

...

  >       > > threshold them or
  >       > > > >       >       whatever
  >       > > > >       >
  >       > > > >       >       cheers
  >       > > > >       >       Bruce
  >       > > > >       >       On Mon, 20 May 2019, Loïc Daumail

wrote:

...

  >       > > > >       >
  >       > > > >       >       >
  >       > > > >       >       >         External Email - Use

Caution

...

  >       > > > >       >       >
  >       > > > >       >       > Also, one more thing:
  >       > > > >       >       >
  >       > > > >       >       > My data is on fsaverage5

resolution.

...

  >       > > > >       >       >
  >       > > > >       >       > Thanks in advance,
  >       > > > >       >       >
  >       > > > >       >       > Sincerely,
  >       > > > >       >       >
  >       > > > >       >       > Loïc
  >       > > > >       >       >
  >       > > > >       >       > Le lun. 20 mai 2019 à 09:49,

Loïc Daumail <

...

  >       > > loic.daumail@gmail.com> a écrit :
  >       > > > >       >       >       Dear Freesurfer community,
  >       > > > >       >       >
  >       > > > >       >       > I obtained score matrices of

surfaces after

...

  >       performing
  >       > > diffusion embedding map
  >       > > > >       on fMRI
  >       > > > >       >       data.
  >       > > > >       >       >
  >       > > > >       >       > I am now using the SurfStat

toolbox(Matlab) in

...

  order
  >       > > to obtain p-value maps to
  >       > > > >       compare
  >       > > > >       >       between
  >       > > > >       >       > two groups.
  >       > > > >       >       >
  >       > > > >       >       > After obtaining the p-value

map, I would like to

...

  >       label
  >       > > the surface in order to
  >       > > > >       >       identify the
  >       > > > >       >       > regions of significant

difference between both

...

  >       groups.
  >       > > > >       >       >
  >       > > > >       >       > Would it be possible to use

Freview in order to do

...

  >       it?
  >       > > > >       >       > If so, which format should I

use for my SurfStatP

...

  >       > > output p-value map?
  >       > > > >       >       > How would you do it, (tools to

convert into a

...

  >       specific
  >       > > format, surfaces and
  >       > > > >       atlas to
  >       > > > >       >       load on
  >       > > > >       >       > Freeview, which format for

those ones)?

...

  >       > > > >       >       > I would be very grateful if you

could detail a

...

  bit,
  >       as
  >       > > I am new to these
  >       > > > >       tools!
  >       > > > >       >       >
  >       > > > >       >       > Thanks in advance,
  >       > > > >       >       >
  >       > > > >       >       > Loïc Daumail
  >       > > > >       >       >
  >       > > > >       >       >
  >       > > > >       >

---

  >       > > > >       >       Freesurfer mailing list
  >       > > > >       >       Freesurfer@nmr.mgh.harvard.edu
  >       > > > >       >
  >       > >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >       > > > >       >
  >       > > > >       >
  >       > > > >

---

  >       > > > >       Freesurfer mailing list
  >       > > > >       Freesurfer@nmr.mgh.harvard.edu
  >       > > > >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >       > > > >
  >       > > > >
  >       > > > >_______________________________________________
  >       > > > Freesurfer mailing list
  >       > > > Freesurfer@nmr.mgh.harvard.edu
  >       > > >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >       > >
  >       > > --
  >       > > Dr. Tim Schäfer
  >       > > Postdoc Computational Neuroimaging
  >       > > Department of Child and Adolescent Psychiatry,

Psychosomatics and

...

  >       > > Psychotherapy
  >       > > University Hospital Frankfurt, Goethe University

Frankfurt am Main,

...

  >       Germany
  >       > >
  >       > > _______________________________________________
  >       > > Freesurfer mailing list
  >       > > Freesurfer@nmr.mgh.harvard.edu
  >       > >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >       > _______________________________________________
  >       > Freesurfer mailing list
  >       > Freesurfer@nmr.mgh.harvard.edu
  >       >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >
  >       _______________________________________________
  >       Freesurfer mailing list
  >       Freesurfer@nmr.mgh.harvard.edu
  >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

  >
  >
  >_______________________________________________
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

Hi Tim,

Thanks a lot for the effort! Indeed, I self-created an mgh file from a matrix of 10242x1x1 elements. After a few adjustments, it perfectly works in order to view the data on Freeview. I overlayed the individuals' data on lh.pial of fsaverage5 (created during recon-all), as our diffusion embedding data has the same resolution.

Thanks everyone for all of your help!!

Sincerely,

Loïc

Le mer. 26 juin 2019 à 11:14, Tim Schäfer ts+ml@rcmd.org a écrit :

    External Email - Use Caution

I found it hard to read the quoted mails and to follow along, but if I'm not mistaken you are trying to overlay a self-created mgh file with dimension 10242x1x1 onto the pial surface of sub-002 at sub-002/surf/lh.pial.

How many vertices does sub-002/surf/lh.pial have? If the answer is not 10242, this is not gonna work.

In one of the earlier mails you mentioned fsaverage5. Could it it be that you really intend to overlay onto $FREESURFER_HOME/subjects/fsaverage5/surf/lh.pial?

Best,

Tim

...

On June 26, 2019 at 10:48 AM Loïc Daumail loic.daumail@gmail.com

wrote:

...

    External Email - Use Caution

Hi Freesurfer, Getting back the former request, I am still trying to load an overlay of my data onto a surface.. but it still doesn't work well. Here is the info of my overlay: " mri_info lh_emb_comp_sub-002.mgz Volume information for lh_emb_comp_sub-002.mgz type: MGH dimensions: 10242 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 10242.000 dof: 1 xstart: -5121.0, xend: 5121.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000

talairach xfm : Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 0.0000 0.0000 5121.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 -0.0000 -0.0000 5121.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 -0.0000 -0.0000 -0.0000 1.0000 " Here is what I get when loading on freeview:

" freeview -f

~/Documents/recon_all_success/freesurfer/sub-002/surf/lh.pial:overlay=lh_emb_comp_sub-002.mgz

...

Number of vertices in overlay data does not match with surface. QClipboard: Unable to receive an event from the clipboard manager in a reasonable time " The data was normalized in MNI space. When I try to load it in FSLeyes, it works, but the overlay is completely absent, it seems that it's empty. On the FSLeyes GUI, it's written 'overlay out of bounds'... The endpoint of this process would be to define ROIs in specific regions, and Freeview is very handy with atlases. Any advice is welcome!

Thanks in advance,

Sincerely,

Loïc

Le lun. 24 juin 2019 à 17:01, Loïc Daumail loic.daumail@gmail.com a écrit :

...

I also tried saving the last file in 10242 x 1 x 1.. but nothing is

coming

...

...

neither.

Thanks,

Sincerely,

Loïc

Le lun. 24 juin 2019 à 16:50, Loïc Daumail loic.daumail@gmail.com a écrit :

...

Hi Doug,

Thanks for your help!

However, using mri_convert, I still get the same message with tclsh. " mri_convert lh.thickness template.mgh /usr/share/modules/init/bash: line 36: /usr/bin/tclsh: No such file or directory /usr/share/modules/init/bash: line 58: export: _moduleraw: not a

function

...

...

...

/usr/share/modules/init/bash: line 60: export: module: not a function mri_convert.bin lh.thickness template.mgh $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from lh.thickness... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to template.mgh... " There is progess though, as here, we see that template.mgh seems not empty: " mri_info template.mgh Volume information for template.mgh type: MGH dimensions: 10242 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 10242.000 dof: 0 xstart: -5121.0, xend: 5121.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:

0.00

...

...

...

degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000

talairach xfm : Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 0.0000 0.0000 5121.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 -0.0000 -0.0000 5121.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 -0.0000 -0.0000 -0.0000 1.0000 " Also, using MRIread and MRIwrite, we can see that it's not empty

neither:

...

...

...

" Volume information for lh_emb_comp_sub-002.mgz type: MGH dimensions: 1 x 10242 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 10242.000 dof: 1 xstart: -0.5, xend: 0.5 ystart: -5121.0, yend: 5121.0 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:

0.00

...

...

...

degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 5120.5000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -5120.5000

talairach xfm : Orientation : LIA Primary Slice Direction: coronal

voxel to ras transform: -1.0000 0.0000 0.0000 5121.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 -0.0000 -0.0000 5121.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 -0.0000 -0.0000 -0.0000 1.0000 "

But then, trying to load the overlay on the lh.pial still isn't

possible,

...

...

...

with endless "FreadFloat: fread failed"

Thanks in advance for your help,

Sincerely,

Loïc

Le lun. 24 juin 2019 à 14:21, Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> a écrit :

...

It is probably using a tcsh shell to do the compression. Try using MRIwrite instead. You will have to create an mri structure. The easiest way to do that is to mri_convert lh.thickness template.mgh then read the template in to matlab template = MRIread('template.mgh'); template.vol = yourdata MRIwrite(template,'yourdata.mgz')

On 6/24/2019 11:54 AM, Loïc Daumail wrote:

    External Email - Use Caution

Hi Bruce and Doug,

To respond to your questions: I projected the BOLD data on the surface using mri_vol2surf function. Then obtained a .mgz file of size 10242 x 1 x 1 x 200.

Then I performed diffusion embedding (unsupervised dimensionality reduction technique) on this .mgz file, whose output was a .npy file. I then loaded this file into a matrix on python, which size was 1 x 18715 x 5. I then saved this file as a .mat file. Then loaded it on matlab, and kept only 1 x 18715 x 1 part of the matrix, and stored it into a zeros(1, 20484). Then kept only the part from (0:10242) and used save_mgh function to save this data into a .mgz file Looking at the info of my .mgz file created with save_mgh, I see that the file doesn't seem to include the data:

" mri_info lh_emb_sub-002_compassion.mgz Volume information for lh_emb_sub-002_compassion.mgz type: MGH dimensions: 1 x 16 x 1 voxel sizes: -nan, -nan, -nan type: FLOAT (3) fov: -nan dof: 1 xstart: -nan, xend: -nan ystart: -nan, yend: -nan zstart: -nan, zend: -nan TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -nan, y_r = -nan, z_r = -nan, c_r = -nan : x_a = -nan, y_a = -nan, z_a = -nan, c_a = -nan : x_s = -nan, y_s = -nan, z_s = -nan, c_s = -nan

talairach xfm : Orientation : III Primary Slice Direction: axial

voxel to ras transform: -nan -nan -nan -nan -nan -nan -nan -nan -nan -nan -nan -nan 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -nan

ras to voxel transform: mat = NULL! MatrixFree: NULL mat POINTER! " It seems that save_mgh function requires tclsh package, as when I ran save_mgh for the first time with this command line: save_mgh('freeview_overlay', ['/home/loic/Documents/emb_output/mgh_format/emb_'

char(subjectsList(1))

...

...

...

...

'_' char(statesList(1)) '.MGZ'], M);

I was getting this message in return in the matlab window: " /usr/share/modules/init/bash: line 36: /usr/bin/tclsh: No such file

or

...

...

...

...

directory /usr/share/modules/init/bash: line 58: export: _moduleraw: not a

function

...

...

...

...

/usr/share/modules/init/bash: line 60: export: module: not a function " Checking into the '/usr/bin/tclsh' directory, the only package called/related to tclsh was 'tclsh8.6'. I thus changed the name from 'tclsh8.6' to 'tclsh'.

Then tried to save the matrix again with save_mgh function. Now I

don't

...

...

...

...

see the error message anymore. However I still get a .mgz file with nans, as seen in the previous mri_info message above.

Would any of you have an advice on how I could make this work, in

order

...

...

...

...

to visualize this .mgz file on the left hemisphere pial surface in

Freeview?

...

...

...

...

Thanks in advance,

Sincerely,

Loïc

Le ven. 21 juin 2019 à 16:24, Bruce Fischl <

fischl@nmr.mgh.harvard.edu>

...

...

...

...

a écrit :

...

I don't think it matters but I would use eye instead of nan for M.

But

...

...

...

...

...

the critical issue is where you get your data and what dimensions it has cheers Bruce

On Fri, 21 Jun 2019, Loïc Daumail wrote:

> > External Email - Use Caution > > Me again, > > Also, here is how I save the matrix on matlab: > > M = nan(4,4); > save_mgh('freeview_overlay', ['/home/loic/Documents/emb_output/mgh_format/lh_emb_' > char(subjectsList(1)) '_' char(statesList(1)) '.mgz'], M); > > Thanks, > > Sincerely, > > Loïc > > Le ven. 21 juin 2019 à 12:25, Loïc Daumail <

loic.daumail@gmail.com>

...

...

...

...

...

a écrit : > Hi Bruce, > > Thanks for your tip. Unfortunately, I am still running through an error... > I have a matrix of 18715 elements regarding both hemispheres. > The size of fsaverage5 is 20484 I believe, so I filled the

remaining

...

...

...

...

...

elements with zeros, and > also tried with rand(). > > The other issue is that I am not so sure which part of the matrix

is

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...

...

...

for lh and the other one > for rh. Thus, I divided 18715/2 and took the 9357 first elements

of

...

...

...

...

...

the 18715 matrix. Then > filled it with zeros or random values to reach 10242. > > Then I saved it with save_mgh function and tried to load it with freeview using the following > command line: > freeview

-f~/Documents/recon_all_success/freesurfer/fsaverage5/surf/lh.pial:overlay=~/Documents/emb_output/mgh

...

...

...

...

...

> _format/lh_emb_sub-002_compassion.mgz > > I am getting the following error: > " > Did not find any volume info > 2 [0]PETSC ERROR:

---

...

...

...

...

...

> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation

Violation,

...

...

...

...

...

probably memory access > out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see >

http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Sig...

...

...

...

...

...

ERROR: > or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption > errors > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run > [0]PETSC ERROR: to get more information on the crash.

> [0]PETSC ERROR: --------------------- Error Message

> [0]PETSC ERROR: Signal received! > [0]PETSC ERROR:

---

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> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG > revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > [0]PETSC ERROR: See docs/faq.html for hints about trouble

shooting.

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> [0]PETSC ERROR: See docs/index.html for manual pages. > [0]PETSC ERROR:

---

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> [0]PETSC ERROR: Unknown Name on a linux-gnu named

loic-HP-ZBook-17 by

...

...

...

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...

loic Fri Jun 21 12:15:53 > 2019 > [0]PETSC ERROR: Libraries linked

from/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/lin

...

...

...

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...

> ux-gnu-c-opt > [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 > [0]PETSC ERROR: Configure options --with-debugging=no

--with-cc=gcc

...

...

...

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...

--with-fc=g77 > --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1

--with-x=0

...

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> --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > [0]PETSC ERROR:

---

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...

> [0]PETSC ERROR: User provided function() line 0 in unknown

directory

...

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unknown file > [unset]: aborting job: > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0" > > Any idea of what could be wrong in my process? > > Thanks > > Sincerely, > > Loïc > > > > Le jeu. 20 juin 2019 à 19:39, Bruce Fischl < fischl@nmr.mgh.harvard.edu> a écrit : > Hi Loïc > > the .mgz file should having dimensions nvertices x 1 x 1 for freeview to > know it is a surface overlay I believe > > cheers > Bruce > > > > On Thu, 20 Jun 2019, Loïc Daumail wrote: > > > > > External Email - Use Caution > > > > Hi Bruce, > > > > I am reaching out to you, as I am trying to load the

surface

...

...

...

...

...

scalar values of > diffusion embedding > > for overlay on a pial surface in Freeview. > > > > I used save_mgh to save a scalar matrix containing surface embedding values in > an .mgz format. > > However I can't load it in freeview, be either only half

of

...

...

...

...

...

the matrix data (one > hemisphere I > > assume) or the whole matrix saved in the same file. > > > > Is there anything specific I need to do in order to be

able

...

...

...

...

...

to visualize a > scalar overlay on a > > surface? Is .mgz a wrong format for scalar values? I also tried with .nii.gz, or > .mgh. I am not even > > sure save_mgh can do all this... > > > > Thanks in advance, > > > > Sincerely, > > > > Loïc > > > > > > > > Le lun. 27 mai 2019 à 11:54, Loïc Daumail < loic.daumail@gmail.com> a écrit : > > Hi Tim, > > > > Your link works perfectly, it's awesome! > > Thanks a lot, > > > > Best, > > > > Loïc > > > > Le lun. 27 mai 2019 à 11:43, Loïc Daumail < loic.daumail@gmail.com> a écrit : > > Hi Tim, > > > > 'mean_rest' is a diffusion embedding map, which contains scores for every vertex > on > > fsaverage5 surface resolution. > > 'surf.b' is the pial surface of both hemispheres of fsaverage5... I also tried > forjust > > lh hemisphere, but it gives me the same result... > > > > Thanks for the link! > > > > Best, > > > > Loïc > > > > Le lun. 27 mai 2019 à 11:20, Tim Schäfer ts+ml@rcmd.org

a

...

...

...

...

...

écrit : > > External Email - Use Caution > > > > Hi Loïc, > > > > that does not look correct, the data is definitely

off.

...

...

...

...

...

I'm not sure where > > the variables `mean_rest` and `surf.b` come from in your code, and I > suspect > > that something is wrong with them. > > > > In the meantime, I got interested in this myself and put together some > code > > that will load the Desikan data for both hemispheres and display it in > > surfstat. Feel free to use it, there also is an

example

...

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...

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...

screenshot of the > > results: > > > > > > >

https://github.com/dfsp-spirit/comp_neuro_science/tree/master/surfstat_desik...

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> > > > Best, > > > > Tim > > > > -- > > Dr. Tim Schäfer > > Postdoc Computational Neuroimaging > > Department of Child and Adolescent Psychiatry, Psychosomatics and > > Psychotherapy > > University Hospital Frankfurt, Goethe University Frankfurt am Main, > Germany > > > > > On May 27, 2019 at 11:01 AM Loïc Daumail < loic.daumail@gmail.com> wrote: > > > > > > > > > External Email - Use Caution > > > > > > Hi Tim, > > > > > > Thanks a lot for your help, indeed, this is

exactly

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what I needed! > > > I wrote this : > > > " > > > subjects_dir = '/home/loic/Documents/recon_all_success/freesurfer/'; > > > subject_id = 'sub-004'; > > > hemi = 'lh'; > > > > > > aparc_file_this_hemi = fullfile(subjects_dir, subject_id, 'label', > > > sprintf("%s.aparc.annot", hemi)); > > > [vertices, label, colortable] = read_annotation(aparc_file_this_hemi); > > > fprintf("Read aparc parcellation file '%s'

containing

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%d regions.\n", > > > aparc_file_this_hemi, length(colortable.struct_names)); > > > for sidx = 1:length(colortable.struct_names) > > > region = colortable.struct_names{sidx}; > > > struct_code = colortable.table(sidx, 5); > > > vertices_of_struct_roi = find(label == struct_code); > > > fprintf("Found region '%s' with %d verts.\n", region, > > > length(vertices_of_struct_roi)); > > > end > > > fig1 = figure(); > > > SurfStatView(mean_rest, surf.b); > > > SurfStatColormap(colortable.table(:,1:3)/255); > > > " > > > However, the image I obtain seems a bit fuzzy...(

see

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attached) > > > Is it because of my data? > > > > > > Thanks in advance, > > > > > > Loïc > > > > > > > > > Le jeu. 23 mai 2019 à 17:20, Tim Schäfer < ts+ml@rcmd.org> a écrit : > > > > > > > External Email - Use Caution > > > > > > > > Afaik SurfStat is not maintained anymore and I think it's been this > way > > > > for quite a while now. Maybe someone else knows better? > > > > > > > > The website is at http://www.math.mcgill.ca/keith/surfstat/ and it > says > > > > 'Updated 26 September 2008'. I'm not sure

whether

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that's really true, > > but > > > > at least for the last 14 months (the only time frame I know about), > > there > > > > have not been any changes to that website or any new releases of > > SurfStat. > > > > > > > > Tim > > > > > > > > > On May 23, 2019 at 4:36 PM Bruce Fischl < fischl@nmr.mgh.harvard.edu> > > > > wrote: > > > > > > > > > > > > > > > Hi Loic > > > > > > > > > > sorry, can you ask whoever maintains

surfstat? Or

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maybe someone else > > on > > > > the > > > > > list knows? I don't. You can label surfaces manually with the dev > > > > version > > > > > of freeview if you want. > > > > > > > > > > cheers > > > > > Bruce > > > > > > > > > > > > > > > On Thu, 23 May 2019, Loïc > > > > > Daumail wrote: > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > Hi Bruce, > > > > > > > > > > > > I am coming back to this request as I was wondering: > > > > > > would it be possible to load freesurfer

surface

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atlases in > surfstat > > in > > > > order to label my surfaces? > > > > > > Is their format compatible? I saw surfstat

only

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accepts a limited > > > > array of formats... > > > > > > > > > > > > Thanks, > > > > > > Best, > > > > > > > > > > > > Loïc > > > > > > > > > > > > Le lun. 20 mai 2019 à 16:15, Bruce Fischl > > fischl@nmr.mgh.harvard.edu > > > > a écrit : > > > > > > sure. All the fsaverages are in the

same

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space (they are > > subsets > > > > of > > > > > > fsaverage) > > > > > > On Mon, 20 May 2019, Loïc Daumail

wrote:

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> > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > Hi Bruce, > > > > > > > > > > > > > > Thanks for your response. Is it also fine for fsaverage5 > > > > surface or I need to switch > > > > > > my data to > > > > > > > fsaverage? > > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > > Sincerely, > > > > > > > > > > > > > > Loïc > > > > > > > > > > > > > > Le lun. 20 mai 2019 à 15:52, Bruce Fischl < > > > > fischl@nmr.mgh.harvard.edu> a écrit : > > > > > > > Hi Loic > > > > > > > > > > > > > > if you are on the fsaverage surface you can save the > > > > -log10(p) values > > > > > > > using save_mgh.m, then load

them

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in freeview and > > > > threshold them or > > > > > > > whatever > > > > > > > > > > > > > > cheers > > > > > > > Bruce > > > > > > > On Mon, 20 May 2019, Loïc

Daumail

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wrote: > > > > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > > > Also, one more thing: > > > > > > > > > > > > > > > > My data is on fsaverage5 resolution. > > > > > > > > > > > > > > > > Thanks in advance, > > > > > > > > > > > > > > > > Sincerely, > > > > > > > > > > > > > > > > Loïc > > > > > > > > > > > > > > > > Le lun. 20 mai 2019 à 09:49, Loïc Daumail < > > > > loic.daumail@gmail.com> a écrit : > > > > > > > > Dear Freesurfer

community,

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> > > > > > > > > > > > > > > > I obtained score matrices of surfaces after > > performing > > > > diffusion embedding map > > > > > > on fMRI > > > > > > > data. > > > > > > > > > > > > > > > > I am now using the SurfStat toolbox(Matlab) in > order > > > > to obtain p-value maps to > > > > > > compare > > > > > > > between > > > > > > > > two groups. > > > > > > > > > > > > > > > > After obtaining the p-value map, I would like to > > label > > > > the surface in order to > > > > > > > identify the > > > > > > > > regions of significant difference between both > > groups. > > > > > > > > > > > > > > > > Would it be possible to use Freview in order to do > > it? > > > > > > > > If so, which format should I use for my SurfStatP > > > > output p-value map? > > > > > > > > How would you do it, (tools

to

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convert into a > > specific > > > > format, surfaces and > > > > > > atlas to > > > > > > > load on > > > > > > > > Freeview, which format for those ones)? > > > > > > > > I would be very grateful if

you

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could detail a > bit, > > as > > > > I am new to these > > > > > > tools! > > > > > > > > > > > > > > > > Thanks in advance, > > > > > > > > > > > > > > > > Loïc Daumail > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > >

Freesurfer@nmr.mgh.harvard.edu

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> > > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > >

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> > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- > > > > Dr. Tim Schäfer > > > > Postdoc Computational Neuroimaging > > > > Department of Child and Adolescent Psychiatry, Psychosomatics and > > > > Psychotherapy > > > > University Hospital Frankfurt, Goethe University Frankfurt am Main, > > Germany > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu >

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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> > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://

mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer