Re: [Freesurfer] Orientation by direction cosines

[Bruce Fischl]

here's the code if it is any help:

 for (c = 0; c < 3; c++) ostr[c] = '\0';

  for (c = 0; c < 3; c++) {
sag = Mdc[0][c];  // LR axis
cor = Mdc[1][c];  // PA axis
ax = Mdc[2][c];   // IS axis
// printf("c = %d, sag = %g, cor = %g, ax = %g\n",c,sag,cor,ax);
if (fabs(sag) > fabs(cor) && fabs(sag) > fabs(ax)) {
  if (sag > 0)
ostr[c] = 'R';
  else
ostr[c] = 'L';
  continue;
}
if (fabs(cor) > fabs(ax)) {
  if (cor > 0)
ostr[c] = 'A';
  else
ostr[c] = 'P';
  continue;
}
if (ax > 0)
  ostr[c] = 'S';
else
  ostr[c] = 'I';
  }
  return(ostr);

On Sat, 
26 Jan 2019, Ritesh Mahajan 
wrote:



   External Email - Use Caution

Hi Bruce, Thanks for your response.

It would be really helpful if you explain how does it interpret from matrix.

Thanks,
Ritesh Mahajan

- Original Message -
From: "Greve, Douglas N.,Ph.D." 
To: "freesurfer" 
Sent: Friday, January 25, 2019 10:26:47 PM
Subject: Re: [Freesurfer] Orientation by direction cosines

mri_info will do it. If you just want the orientation string, you can
add  --orientation. Or do you still want the interpretation of the matrix?

On 1/25/19 10:10 AM, Bruce Fischl wrote:

Hi Ritesh

I think that mri_info will try to figure this out and tell you (in the
"Orientation" output).

cheers
Bruce


On Fri, 25 Jan 2019, Ritesh Mahajan wrote:


External Email - Use Caution

Hello Team,

Can any one please explain how we come to know whether it is RAI or RAS or any 
other orientation through direction cosines:

Below is the direction cosine: I saw some non zero and negative values in non 
diagonal values of matrix. What does this signify ?

0.9993770-0.0352819
-0.00916448  0.965676-0.259588
0.0340709  0.25975   0.965075

Suppose it is Head First Supine. Any help will be really appreciated.

Thanks,
Ritesh Mahajan

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[Freesurfer] dispaly retinotopy result

[starxifd]

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Hi, FS experts!I used a retinotopy paradigm with four stationary wedges located at the horizontal and vertical meridians. (checkerboard flickering at 8Hz, 4 conditions, 16 seconds each * 4 repetitions:1. upper half of the vertical meridian2. right half of the horizontal meridian3. lower half of the vertical meridian4. left half of the horizontal meridianI used a standard block paradigm and four f-contrasts were set (1-vs-234, 2-vs-134, 3-vs-124 and 4-vs-123). I'm trying to draw ROIs of V1, V2 and V3, so I want to display all the contrast on one surface. Since the paradigm is not a typical rotating wedge paradigm, I failed to use the instruction from FS wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis) . I also tried the command: tksurfer-sess -s subjid -a meridian.lh -call.My question is:How to display all four contrasts in one time to identify the localization of V1, V2 and v3.-more info: FS version 6.0, osx systemAny advice and suggestions will be greatly appreciated!Thank you!best,star 



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Re: [Freesurfer] Orientation by direction cosines

[Ritesh Mahajan]

External Email - Use Caution

Hi Bruce, Thanks for your response.

It would be really helpful if you explain how does it interpret from matrix.

Thanks,
Ritesh Mahajan

- Original Message -
From: "Greve, Douglas N.,Ph.D." 
To: "freesurfer" 
Sent: Friday, January 25, 2019 10:26:47 PM
Subject: Re: [Freesurfer] Orientation by direction cosines

mri_info will do it. If you just want the orientation string, you can 
add  --orientation. Or do you still want the interpretation of the matrix?

On 1/25/19 10:10 AM, Bruce Fischl wrote:
> Hi Ritesh
>
> I think that mri_info will try to figure this out and tell you (in the
> "Orientation" output).
>
> cheers
> Bruce
>
>
> On Fri, 25 Jan 2019, Ritesh Mahajan wrote:
>
>> External Email - Use Caution
>>
>> Hello Team,
>>
>> Can any one please explain how we come to know whether it is RAI or RAS or 
>> any other orientation through direction cosines:
>>
>> Below is the direction cosine: I saw some non zero and negative values in 
>> non diagonal values of matrix. What does this signify ?
>>
>> 0.9993770-0.0352819
>> -0.00916448  0.965676-0.259588
>> 0.0340709  0.25975   0.965075
>>
>> Suppose it is Head First Supine. Any help will be really appreciated.
>>
>> Thanks,
>> Ritesh Mahajan
>>
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>>
>>
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Re: [Freesurfer] Functional connectivty walkthrough step 8 error

[Amrita Bedi]

External Email - Use Caution

Ok hopefully, the text is visible now.

bash-4.2$ mris_fwhm
USAGE: mris_fwhm
Smooths surface data and/or estimates FWHM
   --i input
   --subject subject (--s)
   --hemi hemi (--h), or --lh or --rh
   --surf surf 
   --label labelfile
   --cortex : used hemi.cortex.label
   --mask maskfile
   --X x.mat : matlab4 detrending matrix
   --detrend order : polynomial detrending (default 0, turned off with
output)
   --smooth-only : only smooth (implies --no-detrend)
   --no-detrend : turn of poly detrending
   --sqr : compute square of input before smoothing
   --sum sumfile
   --dat datfile (only contains fwhm)
   --ar1dat ar1datfile (contains ar1mean ar1std)
   --ar1 ar1vol : save spatial ar1 as an overlay
   --prune - remove any voxel that is zero in any subject (after any
inversion)
   --no-prune - do not prune (default)
   --out-mask outmask : save final mask

   --fwhm fwhm : apply before measuring
   --niters-only  : only report on niters for fwhm
   --o output

   --sd SUBJECTS_DIR
   --synth
   --synth-frames nframes : default is 10
   --threads nthreads

   --debug turn on debugging
   --checkopts don't run anything, just check options and exit
   --help  print out information on how to use this program
   --version   print out version and exit

$Id: mris_fwhm.c,v 1.40.2.4 2016/12/08 22:02:40 zkaufman Exp $



On Friday, January 25, 2019, Amrita Bedi  wrote:

> Sorry for the confusion. The Va doesn’t let us access our gmails so I’ll
> send an email with the text from my city mail email address.
>
> On Friday, January 25, 2019, Bruce Fischl 
> wrote:
>
>> Hi Amrita
>>
>> please don't take an image of the text and send us that. Just copy and
>> paste the text directly into the email. This is *much* more useful for us.
>>
>> cheers
>> Bruce
>>
>>
>> On Fri, 25 Jan 2019, Amrita Bedi wrote:
>>
>>
>>> External Email - Use Caution
>>>
>>>
>>> [0a440090-c896-4f22-8bd2-fe98f24c8013]
>>> On Friday, January 25, 2019, Amrita Bedi  wrote:
>>>   [IMAGE]
>>>Here you go.
>>>   On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. <
>>> dgr...@mgh.harvard.edu> wrote:
>>> Hi Amrita, can you just paste the text into the email?
>>> thanks
>>> doug
>>>
>>> On 1/25/19 10:51 AM, Amrita Bedi wrote:
>>>
>>>   External Email - Use Caution
>>>
>>>   Hi Dr Greve,
>>> Ran mris_fwhm and got the attached.
>>>
>>> On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <
>>> dgr...@mgh.harvard.edu> wrote:
>>>   Based on the output below, it looks like there are problems with
>>> running
>>>   one of the freesurfer binaries. Can you run mris_fwhm ? Just type
>>> the
>>>   command and return and see what happens.
>>>
>>>
>>>
>>>   /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
>>>   /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>>> on/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
>>>   --i
>>>   /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
>>>   --o
>>>   /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
>>>   --fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd
>>>   /share/VA_Imaging/Projects/salat/2389_TRT/abedi
>>>   /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
>>>   /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6:
>>> version
>>>   `GLIBCXX_3.4.11' not found (required by
>>>   /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)
>>>
>>>
>>>
>>>   On 1/23/19 10:11 AM, Amrita Bedi wrote:
>>>   >
>>>   > External Email - Use Caution
>>>   >
>>>   > Hi Dr Greve,
>>>   >
>>>   > Attached is the log file.
>>>   >
>>>   > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
>>>   > mailto:dgr...@mgh.harvard.edu>> wrote:
>>>   >
>>>   > Can you send the full terminal output and/or the log file?
>>>   >
>>>   > On 1/22/19 2:53 PM, Amrita Bedi wrote:
>>>   > >
>>>   > > External Email - Use Caution
>>>   > >
>>>   > > Hello Freesurfer developers,
>>>   > >
>>>   > > I was following the functional connectivity walkthrough
>>> for resting
>>>   > > stage BOLD data and I got the attached error when I ran
>>> step 8
>>>   > > (selxavg3-sess). Does anyone have any thoughts on how to
>>> trouble
>>>   > shoot
>>>   > > this?
>>>   > > Not sure if it’s of any use but I ran this using
>>> Freesurfer 6.0 on
>>>   > > Centos 7.4
>>>   > >
>>>   > > Thank You.
>>>   > >
>>>   > > Best
>>>   > > Amrita
>>>   > >
>>>   > > ___
>>>   > > Freesurfer mailing list
>>>   > > Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Functional connectivty walkthrough step 8 error

[Amrita Bedi]

External Email - Use Caution

Sorry for the confusion. The Va doesn’t let us access our gmails so I’ll
send an email with the text from my city mail email address.

On Friday, January 25, 2019, Bruce Fischl 
wrote:

> Hi Amrita
>
> please don't take an image of the text and send us that. Just copy and
> paste the text directly into the email. This is *much* more useful for us.
>
> cheers
> Bruce
>
>
> On Fri, 25 Jan 2019, Amrita Bedi wrote:
>
>
>> External Email - Use Caution
>>
>>
>> [0a440090-c896-4f22-8bd2-fe98f24c8013]
>> On Friday, January 25, 2019, Amrita Bedi  wrote:
>>   [IMAGE]
>>Here you go.
>>   On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>> Hi Amrita, can you just paste the text into the email?
>> thanks
>> doug
>>
>> On 1/25/19 10:51 AM, Amrita Bedi wrote:
>>
>>   External Email - Use Caution
>>
>>   Hi Dr Greve,
>> Ran mris_fwhm and got the attached.
>>
>> On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>>   Based on the output below, it looks like there are problems with
>> running
>>   one of the freesurfer binaries. Can you run mris_fwhm ? Just type
>> the
>>   command and return and see what happens.
>>
>>
>>
>>   /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
>>   /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>> on/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
>>   --i
>>   /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
>>   --o
>>   /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
>>   --fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd
>>   /share/VA_Imaging/Projects/salat/2389_TRT/abedi
>>   /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
>>   /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6:
>> version
>>   `GLIBCXX_3.4.11' not found (required by
>>   /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)
>>
>>
>>
>>   On 1/23/19 10:11 AM, Amrita Bedi wrote:
>>   >
>>   > External Email - Use Caution
>>   >
>>   > Hi Dr Greve,
>>   >
>>   > Attached is the log file.
>>   >
>>   > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
>>   > mailto:dgr...@mgh.harvard.edu>> wrote:
>>   >
>>   > Can you send the full terminal output and/or the log file?
>>   >
>>   > On 1/22/19 2:53 PM, Amrita Bedi wrote:
>>   > >
>>   > > External Email - Use Caution
>>   > >
>>   > > Hello Freesurfer developers,
>>   > >
>>   > > I was following the functional connectivity walkthrough for
>> resting
>>   > > stage BOLD data and I got the attached error when I ran
>> step 8
>>   > > (selxavg3-sess). Does anyone have any thoughts on how to
>> trouble
>>   > shoot
>>   > > this?
>>   > > Not sure if it’s of any use but I ran this using Freesurfer
>> 6.0 on
>>   > > Centos 7.4
>>   > >
>>   > > Thank You.
>>   > >
>>   > > Best
>>   > > Amrita
>>   > >
>>   > > ___
>>   > > Freesurfer mailing list
>>   > > Freesurfer@nmr.mgh.harvard.edu
>>   > 
>>   > > https://mail.nmr.mgh.harvard.e
>> du/mailman/listinfo/freesurfer
>>   > > >
>>   >
>>   >
>>   > ___
>>   > Freesurfer mailing list
>>   > Freesurfer@nmr.mgh.harvard.edu > harvard.edu>
>>   > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>   > > >
>>   >
>>   >
>>   > ___
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>>   > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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>>
>>
>>
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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Douglas,

Please find comments inline below.

best,
Matthieu

> Le 25 janv. 2019 à 18:01, Greve, Douglas N.,Ph.D.  a 
> écrit :
> 
> 
> 
> On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:
>> External Email - Use Caution
>> 
>> Dear Douglas,
>> 
>> Could you precise me:
>> 1) Is the intensity rescaling of PET image included in the mri_gtmpvc 
>> command based on reference region in gtmseg.mgz file rather than aseg.mgz ?
> It depends. If you are using pons, then that is not part of the aseg and is 
> generated as part of the creation of gtmseg. But most of the rest of gtmseg 
> is derived from the aseg and surfaces.
>> 2) Is this rescaling applied before PVE correction or after (i.e. based on 
>> PVE corrected reference region’s mean intensity) ?
> After

Thank you for this clarification. But do you use mean PET signal inside the 
reference region after the PVE correction, since in the particular case of pons 
there is no PVE correction applied to white matter ?

Do you see any objection whether intensity normalization was done before PVE 
correction based on the mean PET signal inside the reference region ?

>> 
>> Many thanks in advance for helping.
>> 
>> Best,
>> Matthieu
>> 
>>> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. >> > a écrit :
>>> 
>>> 
>>> 
>>> On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
 External Email - Use Caution
 
 
 I used the following command to obtain only rescaled voxel-wise PET image 
 (with no PVC):
 mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe 
 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc
 
 If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise 
 PET image (without PVC). Could I obtain the rescaled voxel-wise PET image 
 (without PVC) just by dividing each voxel of the native PET image by the 
 mean of the reference region ?
>>> Yes
 
 Best,
 Matt
 
 Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. 
 mailto:dgr...@mgh.harvard.edu>> a écrit :
 I'm not sure what you mean. If you are turning off PVC, why are you 
 computing RBV and MGX? What is your command line? What do you mean that 
 these options don't seem to work?
 
 On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
> External Email - Use Caution
> 
> Hi Douglas,
> 
> Thanks for helping.
> 
> To have an only rescaled voxel-wise PET image, these options seem to work 
> only when -rbv method is used and not -mgx.
> 
> Do you know why ?
> 
> Best,
> Matthieu 
> 
> 
> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> a écrit :
> You will need to set --psf 0 and --no-tfe to fully turn off PVC. 
> 
> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
>> External Email - Use Caution
>> 
>> Hi Douglas,
>> 
>> Could you help me on this point ?
>> 
>> Best,
>> Matthieu
>> 
>> 
>> Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
>> mailto:matthieuvanhou...@gmail.com>> a 
>> écrit :
>> Dear Douglas,
>> 
>> Is it possible to use mri_gtmpvc command in order to intensity normalize 
>> PET images without applying PVE correction by setting --psf to 0 ?
>> 
>> Best,
>> Matthieu
>> 
>> 
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>> 
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> 
> 
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> 
 ___
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
 
 
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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Greve, Douglas N.,Ph.D.]

On 1/25/19 7:57 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Dear Douglas,

Could you precise me:
1) Is the intensity rescaling of PET image included in the mri_gtmpvc command 
based on reference region in gtmseg.mgz file rather than aseg.mgz ?
It depends. If you are using pons, then that is not part of the aseg and is 
generated as part of the creation of gtmseg. But most of the rest of gtmseg is 
derived from the aseg and surfaces.
2) Is this rescaling applied before PVE correction or after (i.e. based on PVE 
corrected reference region’s mean intensity) ?
After

Many thanks in advance for helping.

Best,
Matthieu

Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :



On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

I used the following command to obtain only rescaled voxel-wise PET image (with 
no PVC):
mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg 
gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc

If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET 
image (without PVC). Could I obtain the rescaled voxel-wise PET image (without 
PVC) just by dividing each voxel of the native PET image by the mean of the 
reference region ?
Yes

Best,
Matt

Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
I'm not sure what you mean. If you are turning off PVC, why are you computing 
RBV and MGX? What is your command line? What do you mean that these options 
don't seem to work?

On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Thanks for helping.

To have an only rescaled voxel-wise PET image, these options seem to work only 
when -rbv method is used and not -mgx.

Do you know why ?

Best,
Matthieu


Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
You will need to set --psf 0 and --no-tfe to fully turn off PVC.

On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:

External Email - Use Caution

Hi Douglas,

Could you help me on this point ?

Best,
Matthieu


Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
mailto:matthieuvanhou...@gmail.com>> a écrit :
Dear Douglas,

Is it possible to use mri_gtmpvc command in order to intensity normalize PET 
images without applying PVE correction by setting --psf to 0 ?

Best,
Matthieu



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Re: [Freesurfer] Functional connectivty walkthrough step 8 error

[Bruce Fischl]

Hi Amrita

please don't take an image of the text and send us that. Just copy and 
paste the text directly into the email. This is *much* more useful for us.


cheers
Bruce


On Fri, 25 Jan 2019, Amrita Bedi wrote:



External Email - Use Caution


[0a440090-c896-4f22-8bd2-fe98f24c8013]
On Friday, January 25, 2019, Amrita Bedi  wrote:
  [IMAGE]
   Here you go. 
  On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. 
 wrote:
Hi Amrita, can you just paste the text into the email?
thanks
doug

On 1/25/19 10:51 AM, Amrita Bedi wrote:

  External Email - Use Caution

  Hi Dr Greve, 
Ran mris_fwhm and got the attached.

On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D.  
wrote:
  Based on the output below, it looks like there are problems with running
  one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
  command and return and see what happens.



  /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
  
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
  --i
  
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
  --o
  
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
  --fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd
  /share/VA_Imaging/Projects/salat/2389_TRT/abedi
  /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
  /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
  `GLIBCXX_3.4.11' not found (required by
  /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)



  On 1/23/19 10:11 AM, Amrita Bedi wrote:
  >
  > External Email - Use Caution
  >
  > Hi Dr Greve,
  >
  > Attached is the log file.
  >
  > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
  > mailto:dgr...@mgh.harvard.edu>> wrote:
  >
  >     Can you send the full terminal output and/or the log file?
  >
  >     On 1/22/19 2:53 PM, Amrita Bedi wrote:
  >     >
  >     > External Email - Use Caution
  >     >
  >     > Hello Freesurfer developers,
  >     >
  >     > I was following the functional connectivity walkthrough for 
resting
  >     > stage BOLD data and I got the attached error when I ran step 8
  >     > (selxavg3-sess). Does anyone have any thoughts on how to trouble
  >     shoot
  >     > this?
  >     > Not sure if it’s of any use but I ran this using Freesurfer 6.0 on
  >     > Centos 7.4
  >     >
  >     > Thank You.
  >     >
  >     > Best
  >     > Amrita
  >     >
  >     > ___
  >     > Freesurfer mailing list
  >     > Freesurfer@nmr.mgh.harvard.edu
  >     
  >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >     
  >
  >
  >     ___
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  >     Freesurfer@nmr.mgh.harvard.edu 

  >     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  >     
  >
  >
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Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

[Greve, Douglas N.,Ph.D.]

Those are the commands. Can you send the command lines you used and a fuller 
description of exactly how it is not working?

On 1/25/19 10:56 AM, Boris Rauchmann wrote:

External Email - Use Caution
Dear FreeSurfer Developers,

I´m trying to extract the cortical thickness of individuals from a study cohort 
based on an hammersmith n30r83 atlas segmentation. I have this atlas only in as 
a volumetric file. I already run recon-all on all subjects. I tried 
mri_vol2surf and then mris_seg2annot but without success so far. What commands 
would you recommend me to run?

Thanks,
Boris



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Re: [Freesurfer] Functional connectivty walkthrough step 8 error

[Amrita Bedi]

External Email - Use Caution

Pasted the text in the email but not sure if you can view it

On Friday, January 25, 2019, Amrita Bedi  wrote:

>
>
> On Friday, January 25, 2019, Amrita Bedi  wrote:
>
>>
>>
>> Here you go.
>> On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>>
>>> Hi Amrita, can you just paste the text into the email?
>>> thanks
>>> doug
>>>
>>> On 1/25/19 10:51 AM, Amrita Bedi wrote:
>>>
>>> External Email - Use Caution
>>> Hi Dr Greve,
>>>
>>> Ran mris_fwhm and got the attached.
>>>
>>> On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <
>>> dgr...@mgh.harvard.edu> wrote:
>>>
 Based on the output below, it looks like there are problems with
 running
 one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
 command and return and see what happens.



 /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
 /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
 on/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
 --i
 /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
 on/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
 --o
 /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
 on/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
 --fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd
 /share/VA_Imaging/Projects/salat/2389_TRT/abedi
 /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
 /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
 `GLIBCXX_3.4.11' not found (required by
 /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)



 On 1/23/19 10:11 AM, Amrita Bedi wrote:
 >
 > External Email - Use Caution
 >
 > Hi Dr Greve,
 >
 > Attached is the log file.
 >
 > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
 > mailto:dgr...@mgh.harvard.edu>> wrote:
 >
 > Can you send the full terminal output and/or the log file?
 >
 > On 1/22/19 2:53 PM, Amrita Bedi wrote:
 > >
 > > External Email - Use Caution
 > >
 > > Hello Freesurfer developers,
 > >
 > > I was following the functional connectivity walkthrough for
 resting
 > > stage BOLD data and I got the attached error when I ran step 8
 > > (selxavg3-sess). Does anyone have any thoughts on how to trouble
 > shoot
 > > this?
 > > Not sure if it’s of any use but I ran this using Freesurfer 6.0
 on
 > > Centos 7.4
 > >
 > > Thank You.
 > >
 > > Best
 > > Amrita
 > >
 > > ___
 > > 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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 > 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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>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
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Re: [Freesurfer] Functional connectivty walkthrough step 8 error

[Greve, Douglas N.,Ph.D.]

I don't see anything.

On 1/25/19 11:56 AM, Amrita Bedi wrote:

External Email - Use Caution

[X]

Here you go.
On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Hi Amrita, can you just paste the text into the email?
thanks
doug

On 1/25/19 10:51 AM, Amrita Bedi wrote:

External Email - Use Caution

Hi Dr Greve,

Ran mris_fwhm and got the attached.

On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Based on the output below, it looks like there are problems with running
one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
command and return and see what happens.



/home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
--i
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
--o
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
--fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd
/share/VA_Imaging/Projects/salat/2389_TRT/abedi
/home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
/home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
`GLIBCXX_3.4.11' not found (required by
/home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)



On 1/23/19 10:11 AM, Amrita Bedi wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve,
>
> Attached is the log file.
>
> On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu> 
> >> wrote:
>
> Can you send the full terminal output and/or the log file?
>
> On 1/22/19 2:53 PM, Amrita Bedi wrote:
> >
> > External Email - Use Caution
> >
> > Hello Freesurfer developers,
> >
> > I was following the functional connectivity walkthrough for resting
> > stage BOLD data and I got the attached error when I ran step 8
> > (selxavg3-sess). Does anyone have any thoughts on how to trouble
> shoot
> > this?
> > Not sure if it’s of any use but I ran this using Freesurfer 6.0 on
> > Centos 7.4
> >
> > Thank You.
> >
> > Best
> > Amrita
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu 
> >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Functional connectivty walkthrough step 8 error

[Amrita Bedi]

External Email - Use Caution

On Friday, January 25, 2019, Amrita Bedi  wrote:

>
>
> Here you go.
> On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Hi Amrita, can you just paste the text into the email?
>> thanks
>> doug
>>
>> On 1/25/19 10:51 AM, Amrita Bedi wrote:
>>
>> External Email - Use Caution
>> Hi Dr Greve,
>>
>> Ran mris_fwhm and got the attached.
>>
>> On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>>
>>> Based on the output below, it looks like there are problems with running
>>> one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
>>> command and return and see what happens.
>>>
>>>
>>>
>>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>>> on/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
>>> --i
>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
>>> --o
>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
>>> --fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd
>>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi
>>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
>>> /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
>>> `GLIBCXX_3.4.11' not found (required by
>>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)
>>>
>>>
>>>
>>> On 1/23/19 10:11 AM, Amrita Bedi wrote:
>>> >
>>> > External Email - Use Caution
>>> >
>>> > Hi Dr Greve,
>>> >
>>> > Attached is the log file.
>>> >
>>> > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
>>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>>> >
>>> > Can you send the full terminal output and/or the log file?
>>> >
>>> > On 1/22/19 2:53 PM, Amrita Bedi wrote:
>>> > >
>>> > > External Email - Use Caution
>>> > >
>>> > > Hello Freesurfer developers,
>>> > >
>>> > > I was following the functional connectivity walkthrough for
>>> resting
>>> > > stage BOLD data and I got the attached error when I ran step 8
>>> > > (selxavg3-sess). Does anyone have any thoughts on how to trouble
>>> > shoot
>>> > > this?
>>> > > Not sure if it’s of any use but I ran this using Freesurfer 6.0
>>> on
>>> > > Centos 7.4
>>> > >
>>> > > Thank You.
>>> > >
>>> > > Best
>>> > > Amrita
>>> > >
>>> > > ___
>>> > > Freesurfer mailing list
>>> > > Freesurfer@nmr.mgh.harvard.edu
>>> > 
>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> > 
>>> >
>>> >
>>> > ___
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>>> > Freesurfer@nmr.mgh.harvard.edu >> vard.edu>
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> > 
>>> >
>>> >
>>> > ___
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>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
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>>
>>
>>
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Re: [Freesurfer] Orientation by direction cosines

[Greve, Douglas N.,Ph.D.]

mri_info will do it. If you just want the orientation string, you can 
add  --orientation. Or do you still want the interpretation of the matrix?

On 1/25/19 10:10 AM, Bruce Fischl wrote:
> Hi Ritesh
>
> I think that mri_info will try to figure this out and tell you (in the
> "Orientation" output).
>
> cheers
> Bruce
>
>
> On Fri, 25 Jan 2019, Ritesh Mahajan wrote:
>
>> External Email - Use Caution
>>
>> Hello Team,
>>
>> Can any one please explain how we come to know whether it is RAI or RAS or 
>> any other orientation through direction cosines:
>>
>> Below is the direction cosine: I saw some non zero and negative values in 
>> non diagonal values of matrix. What does this signify ?
>>
>> 0.9993770-0.0352819
>> -0.00916448  0.965676-0.259588
>> 0.0340709  0.25975   0.965075
>>
>> Suppose it is Head First Supine. Any help will be really appreciated.
>>
>> Thanks,
>> Ritesh Mahajan
>>
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>>
>>
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Re: [Freesurfer] Functional connectivty walkthrough step 8 error

[Amrita Bedi]

External Email - Use Caution

Here you go.
On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. 
wrote:

> Hi Amrita, can you just paste the text into the email?
> thanks
> doug
>
> On 1/25/19 10:51 AM, Amrita Bedi wrote:
>
> External Email - Use Caution
> Hi Dr Greve,
>
> Ran mris_fwhm and got the attached.
>
> On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Based on the output below, it looks like there are problems with running
>> one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
>> command and return and see what happens.
>>
>>
>>
>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>> on/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
>> --i
>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
>> --o
>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
>> on/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
>> --fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd
>> /share/VA_Imaging/Projects/salat/2389_TRT/abedi
>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
>> /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
>> `GLIBCXX_3.4.11' not found (required by
>> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)
>>
>>
>>
>> On 1/23/19 10:11 AM, Amrita Bedi wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hi Dr Greve,
>> >
>> > Attached is the log file.
>> >
>> > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>> >
>> > Can you send the full terminal output and/or the log file?
>> >
>> > On 1/22/19 2:53 PM, Amrita Bedi wrote:
>> > >
>> > > External Email - Use Caution
>> > >
>> > > Hello Freesurfer developers,
>> > >
>> > > I was following the functional connectivity walkthrough for
>> resting
>> > > stage BOLD data and I got the attached error when I ran step 8
>> > > (selxavg3-sess). Does anyone have any thoughts on how to trouble
>> > shoot
>> > > this?
>> > > Not sure if it’s of any use but I ran this using Freesurfer 6.0 on
>> > > Centos 7.4
>> > >
>> > > Thank You.
>> > >
>> > > Best
>> > > Amrita
>> > >
>> > > ___
>> > > 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 > vard.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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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] FSFAST poor registration

[Keri Woods]

External Email - Use Caution

Good thing it's not the software :) Also makes it easier for me to fix. In
my script there was one tiny mistake - the anatomical image for one subject
was repeated each time instead of using the files for different subjects. I
ran recon-all 100+ times on the same subject!! Checking the registration
was definitely worthwhile. Thanks again for the help, it made me look at
the problem in a different.

On Fri, Jan 25, 2019 at 6:34 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Yes, that file is the only thing linking the functional to the anatomical.
> It's too bad you messed up the files, but I'm relieved it was not my
> software:).
>
> On 1/25/19 5:09 AM, Keri Woods wrote:
>
> External Email - Use Caution
> Hi Douglas
>
> Thanks very much for getting back to me. I created new separate
> directories and re-processed one of the problem subjects individually, and
> the registration worked well. So the problem is that the anatomical and
> functional images come from different subjects. But I've checked and the
> subjectname files are correct. That's the only thing linking the anatomical
> and functional images? Thanks very much, you've helped me a lot. Now I just
> have to go and see where I mixed up the files!
>
> Thanks again,
> Keri
>
> On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Can you tar up the anatomical and functional analyses and send them to
>> me through our filedrop?
>>
>> https://gate.nmr.mgh.harvard.edu/filedrop2/
>>
>> when it asks for an email of the recipient, use gr...@nmr.mgh.harvard.edu
>>
>>
>> On 1/23/19 5:57 AM, Keri Woods wrote:
>> >
>> > External Email - Use Caution
>> >
>> > I meant some are nearly perfect.
>> >
>> > On Wed, Jan 23, 2019 at 11:49 AM Keri Woods > > > wrote:
>> >
>> > Hi Douglas
>> >
>> > Thanks for the response.
>> >
>> > No, some of the registrations are fine. Some are close, but not
>> > perfect, while others are very bad.
>> >
>> > I've checked the subjectname file for some subjects with poor
>> > registration (eg 20_101), and they are correct.
>> >
>> > Thanks,
>> > Keri
>> >
>> > On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>> >
>> > Are you saying that all of them have bad registrations? Some
>> > of them
>> > (eg, 20_1, 20_10) look like they should be good. Others (eg,
>> > 20_101)
>> > look like they could be bad. For the bad ones, are you totally
>> > sure that
>> > the subjetname file has the correct name of the subject?
>> >
>> > On 1/21/19 3:19 AM, Keri Woods wrote:
>> > >
>> > > External Email - Use Caution
>> > >
>> > > Hi Douglas
>> > >
>> > > Thank you for your reply.
>> > >
>> > > I'm using
>> > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
>> > >
>> > > I am using whole brain data. The functional and structural
>> > images were
>> > > acquired in different sessions on the same day, I don't know
>> > if that
>> > > complicated things? Each subject has 2 runs of the same task.
>> > >
>> > > This is what I get after running the command in the format of
>> > > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold
>> > -per-run -bbr-sum
>> > >
>> > > 20_1   013 0.5155
>> > > 20_1   014 0.5090
>> > > 20_10  013 0.5247
>> > > 20_10  014 0.5229
>> > > 20_100 038 0.8420
>> > > 20_100 040 0.8443
>> > > 20_101 008 0.9052
>> > > 20_101 010 0.9289
>> > > 20_102 058 0.6924
>> > > 20_102 059 0.6902
>> > > 20_103 045 0.9778
>> > > 20_103 046 0.9931
>> > > 20_104 010 0.9324
>> > > 20_104 012 0.9413
>> > > 20_105 013 0.8754
>> > > 20_105 014 0.8937
>> > > 20_106 047 0.4433
>> > > 20_106 048 0.4377
>> > > 20_107 008 0.9178
>> > > 20_107 010 0.9238
>> > > 20_11  013 0.7631
>> > > 20_11  014 0.7615
>> > > 20_110 048 0.7687
>> > > 20_110 049 0.7549
>> > > 20_112 013 0.8821
>> > > 20_112 014 0.9161
>> > > 20_113 052 0.7689
>> > > 20_113 053 0.7757
>> > > 20_116 046 1.0072
>> > > 20_116 047 1.0256
>> > > 20_117 008 0.7742
>> > > 20_117 010 0.7826
>> > > 20_119 013 0.7929
>> > > 20_119 014 0.7854
>> > > 20_120 048 0.5090
>> > > 20_120 049 0.4973
>> > > 20_126 047 0.8285
>> > > 20_126 048 0.8281
>> > > 20_128 046 0.9580
>> >   

Re: [Freesurfer] Functional connectivty walkthrough step 8 error

[Greve, Douglas N.,Ph.D.]

Hi Amrita, can you just paste the text into the email?
thanks
doug

On 1/25/19 10:51 AM, Amrita Bedi wrote:

External Email - Use Caution

Hi Dr Greve,

Ran mris_fwhm and got the attached.

On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Based on the output below, it looks like there are problems with running
one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
command and return and see what happens.



/home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
--i
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
--o
/share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_recon/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
--fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd
/share/VA_Imaging/Projects/salat/2389_TRT/abedi
/home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
/home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
`GLIBCXX_3.4.11' not found (required by
/home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)



On 1/23/19 10:11 AM, Amrita Bedi wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve,
>
> Attached is the log file.
>
> On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu> 
> >> wrote:
>
> Can you send the full terminal output and/or the log file?
>
> On 1/22/19 2:53 PM, Amrita Bedi wrote:
> >
> > External Email - Use Caution
> >
> > Hello Freesurfer developers,
> >
> > I was following the functional connectivity walkthrough for resting
> > stage BOLD data and I got the attached error when I ran step 8
> > (selxavg3-sess). Does anyone have any thoughts on how to trouble
> shoot
> > this?
> > Not sure if it’s of any use but I ran this using Freesurfer 6.0 on
> > Centos 7.4
> >
> > Thank You.
> >
> > Best
> > Amrita
> >
> > ___
> > 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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Re: [Freesurfer] Surface to volume conversion

[Bruce Fischl]

Hi Emma

can you run mri_info on the .mgh and .nii.gz volumes and send us the 
output? Is the sig.mgh a surface overlay? If so, you can't visualize it 
directly, you have to overlay it on a surface (in either .mgh or .nii.gz 
foramt)


cheers
Bruce


On Fri, 25 Jan 2019, Bunting, Emma wrote:

   External Email - Use Caution 


Hi!

I’m trying to convert my sig.mgh output from GLM into a .nii file using 
mri_convert, and when I load the resulting volume in freeview this is what I 
see.

The command I’m using is:
mri_convert —in-type mgh —out_type nii.gz —out_orientation RAS /(root to 
sig.mgh file)/sig.mgh /(root to output file)/sig.nii.gz,

Is there something I should be doing differently?

Many thanks,

Emma

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Re: [Freesurfer] FSFAST poor registration

[Greve, Douglas N.,Ph.D.]

Yes, that file is the only thing linking the functional to the anatomical. It's 
too bad you messed up the files, but I'm relieved it was not my software:).

On 1/25/19 5:09 AM, Keri Woods wrote:

External Email - Use Caution

Hi Douglas

Thanks very much for getting back to me. I created new separate directories and 
re-processed one of the problem subjects individually, and the registration 
worked well. So the problem is that the anatomical and functional images come 
from different subjects. But I've checked and the subjectname files are 
correct. That's the only thing linking the anatomical and functional images? 
Thanks very much, you've helped me a lot. Now I just have to go and see where I 
mixed up the files!

Thanks again,
Keri

On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Can you tar up the anatomical and functional analyses and send them to
me through our filedrop?

https://gate.nmr.mgh.harvard.edu/filedrop2/

when it asks for an email of the recipient, use 
gr...@nmr.mgh.harvard.edu


On 1/23/19 5:57 AM, Keri Woods wrote:
>
> External Email - Use Caution
>
> I meant some are nearly perfect.
>
> On Wed, Jan 23, 2019 at 11:49 AM Keri Woods 
> mailto:keri.wo...@gmail.com>
> >> wrote:
>
> Hi Douglas
>
> Thanks for the response.
>
> No, some of the registrations are fine. Some are close, but not
> perfect, while others are very bad.
>
> I've checked the subjectname file for some subjects with poor
> registration (eg 20_101), and they are correct.
>
> Thanks,
> Keri
>
> On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu> 
> >> wrote:
>
> Are you saying that all of them have bad registrations? Some
> of them
> (eg, 20_1, 20_10) look like they should be good. Others (eg,
> 20_101)
> look like they could be bad. For the bad ones, are you totally
> sure that
> the subjetname file has the correct name of the subject?
>
> On 1/21/19 3:19 AM, Keri Woods wrote:
> >
> > External Email - Use Caution
> >
> > Hi Douglas
> >
> > Thank you for your reply.
> >
> > I'm using
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
> >
> > I am using whole brain data. The functional and structural
> images were
> > acquired in different sessions on the same day, I don't know
> if that
> > complicated things? Each subject has 2 runs of the same task.
> >
> > This is what I get after running the command in the format of
> > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold
> -per-run -bbr-sum
> >
> > 20_1   013 0.5155
> > 20_1   014 0.5090
> > 20_10  013 0.5247
> > 20_10  014 0.5229
> > 20_100 038 0.8420
> > 20_100 040 0.8443
> > 20_101 008 0.9052
> > 20_101 010 0.9289
> > 20_102 058 0.6924
> > 20_102 059 0.6902
> > 20_103 045 0.9778
> > 20_103 046 0.9931
> > 20_104 010 0.9324
> > 20_104 012 0.9413
> > 20_105 013 0.8754
> > 20_105 014 0.8937
> > 20_106 047 0.4433
> > 20_106 048 0.4377
> > 20_107 008 0.9178
> > 20_107 010 0.9238
> > 20_11  013 0.7631
> > 20_11  014 0.7615
> > 20_110 048 0.7687
> > 20_110 049 0.7549
> > 20_112 013 0.8821
> > 20_112 014 0.9161
> > 20_113 052 0.7689
> > 20_113 053 0.7757
> > 20_116 046 1.0072
> > 20_116 047 1.0256
> > 20_117 008 0.7742
> > 20_117 010 0.7826
> > 20_119 013 0.7929
> > 20_119 014 0.7854
> > 20_120 048 0.5090
> > 20_120 049 0.4973
> > 20_126 047 0.8285
> > 20_126 048 0.8281
> > 20_128 046 0.9580
> > 20_128 047 0.9314
> > 20_130 047 0.9439
> > 20_130 048 0.9425
> > 20_132 047 0.8550
> > 20_132 048 0.8558
> > 20_134_1   013 0.5716
> > 20_134_1   015 0.5744
> > 20_135 011 0.8357
> > 20_135 012 0.8401
> > 20_136 044 0.9995
> > 20_136 045 0.9604
> > 20_137 047 0.7922
> > 20_137 048 0.7990
> > 20_142 047 0.5282
> > 20_142 048 0.5278
> > 20_144 013 0.8755
> > 20_144 014 0.8838
> > 20_146 047 0.7997
> > 20_146 048 0.7895
> > 20_149 049 0.9251
> > 20_149 050 

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

[Hoopes, Andrew]

I believe this python2 issue has been fixed in the dev version found here 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/long_mris_slopes

best,
Andrew


On 1/25/19, 10:08 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Bruce Fischl"  wrote:

Hi Falk

thanks for catching the typo. I fixed it - nice to have an easy thing to 
fix for a change :)

Bruce


On Fri, 25 Jan 2019, falk.luesebr...@med.ovgu.de wrote:

> 
> External Email - Use Caution
> 
> Dear Juergen,
> 
>  
> 
> Thanks for your quick reply! Actually the spelling error is in the error 
message. Taken from
> http://martinos.org/~mreuter/long/long_mris_slopes
> 
>  
> 
> # extensive error checks
> 
> #if options.fsgd is None and
> 
> if options.qdec is None:
> 
> #print 'ERROR: Specify --fsgd or --qedc'
> 
> parser.print_help()
> 
> print '\nERROR: Specify --qedc (and other required arguments)\n'
> 
> sys.exit(1)
> 
>  
> 
> #if options.fsgd is not None and options.qdec is not None:
> 
> #print 'ERROR: Specify either --fsgd or --qedc, not both'
> 
> #sys.exit(1)
> 
>  
> 
> At least Martin is consistent with his typo. :D
> 
>  
> 
> Best,
> 
> Falk
> 
>  
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Juergen Haenggi
> Gesendet: Freitag, 25. Januar 2019 10:35
> An: Freesurfer Mailinglist 
> Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem 
for linux (WSL) using ubuntu 18.04.1 LTS
> 
>  
> 
> External Email - Use Caution
> 
> Dear Falk
> 
>  
> 
> I have no idea, but recognised that the error refers to --qedc and not to 
--qdec.
> 
> maybe there is a spelling error somewhere that is related to your problem.
> 
>  
> 
> HTH
> 
> Cheers
> 
> Jürgen
> 
> 
-
> 
> University of Zurich
> 
> Dr. Jürgen Hänggi, Ph.D.
> 
> Department of Psychology
> 
> Division Neuropsychology
> 
> Binzmuehlestrasse 14, PO Box 25 
> 
> 8050 Zurich, Switzerland
> 
>  
> 
> 0041 44 635 73 97 (phone office)
> 
> 0041 76 445 86 84 (phone mobile)   
> 
> 0041 44 635 74 09 (fax office)
> 
> BIN 4.D.04 (office room number) 
> 
>  
> 
> j.haen...@psychologie.uzh.ch (email)
> 
> http://www.psychologie.uzh.ch/neuropsy/ (website)
> 
> http://www.juergenhaenggi.ch (private website)   
> 
>  
> 
> This email (and any attachment/s) contains confidential and/or privileged
> 
> information. If you are not the intended recipient (or have received this
> 
> email in error) please notify the sender immediately and destroy this
> 
> email. Any unauthorised copying, disclosure or distribution of the
> 
> material in this email is strictly forbidden.
> 
> 
-
> 
>  
> 
>  
> 
> 
>
>   On 25 Jan 2019, at 10:26, falk.luesebr...@med.ovgu.de wrote:
> 
>  
> 
> External Email - Use Caution
> 
>  
> 
> Dear all,
> 
>  
> 
> Has anyone run the longitudinal pipeline successfully using the WSL? I’m 
running it with Ubuntu 18.04.1 LTS
> and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.
> 
>  
> 
> I’m trying to process my first longitudinal data set following the 
instructions of the tutorial as close as
> possible. The data has been processed without issues and now I want to do 
the statistical analysis. When I
> run:
> 
> long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh 
--do-avg --do-rate --do-pc1 --do-spc
> --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR
> 
>  
> 
> I get the following error:
> 
> File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448
> 
> print '\nERROR: Specify --qedc (and other required arguments)\n'
> 
>^
> 
> SyntaxError: invalid syntax
> 
>  
> 
> I get comparable errors for any other long_* command I try to run, e.g. 
long_qdec_table with or without any
> arguments gives:
> 
> File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119
> 
>print '\nERROR: Specify --qedc'
> 
>   

[Freesurfer] cortical thickness calculation based on hammersmith segmentation

[Boris Rauchmann]

External Email - Use Caution

 <>Dear FreeSurfer Developers,

 

I´m trying to extract the cortical thickness of individuals from a study cohort 
based on an hammersmith n30r83 atlas segmentation. I have this atlas only in as 
a volumetric file. I already run recon-all on all subjects. I tried 
mri_vol2surf and then mris_seg2annot but without success so far. What commands 
would you recommend me to run?

 

Thanks,

Boris___
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[Freesurfer] Functional connectivty walkthrough step 8 error

[Amrita Bedi]

External Email - Use Caution

Hi Dr Greve,

Ran mris_fwhm and got the attached.

On Thursday, January 24, 2019, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Based on the output below, it looks like there are problems with running
> one of the freesurfer binaries. Can you run mris_fwhm ? Just type the
> command and return and see what happens.
>
>
>
> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm --mask
> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
> on/Bold1/fc.lpccseed.surf.lh/mask.nii.gz
> --i
> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
> on/Bold1/fc.lpccseed.surf.lh/rho1mn.nii.gz
> --o
> /share/VA_Imaging/Projects/salat/2389_TRT/abedi/TRT_0008_rec
> on/Bold1/fc.lpccseed.surf.lh/rho1mn.sm.nii.gz
> --fwhm 20.00 --smooth-only --s fsaverage --hemi lh --sd
> /share/VA_Imaging/Projects/salat/2389_TRT/abedi
> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
> /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
> `GLIBCXX_3.4.11' not found (required by
> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)
>
>
>
> On 1/23/19 10:11 AM, Amrita Bedi wrote:
> >
> > External Email - Use Caution
> >
> > Hi Dr Greve,
> >
> > Attached is the log file.
> >
> > On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > Can you send the full terminal output and/or the log file?
> >
> > On 1/22/19 2:53 PM, Amrita Bedi wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hello Freesurfer developers,
> > >
> > > I was following the functional connectivity walkthrough for resting
> > > stage BOLD data and I got the attached error when I ran step 8
> > > (selxavg3-sess). Does anyone have any thoughts on how to trouble
> > shoot
> > > this?
> > > Not sure if it’s of any use but I ran this using Freesurfer 6.0 on
> > > Centos 7.4
> > >
> > > Thank You.
> > >
> > > Best
> > > Amrita
> > >
> > > ___
> > > 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  harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Error in running make_average_subject

[Korom, Marta]

External Email - Use Caution

Hello Bruce, Doug and Emanuel,

I tried what you suggested (ln -s orig.mgz norm.mgz), and I also downloaded
the development version and tried that, but neither procedures fixed
the problem.

In the meantime, my father-in-law took a week and fixed the script and now
it runs smoothly and finishes without error. The following code segment of
the make_average_subject file needed to be fixed:

*Erroneous code segment: *
…
if($DoSurfaces && $DoVolumes) then
  set cmd = (recon-all -s $average_subject -cortribbon -aparc2aseg)
  echo $cmd
  $cmd
  if($status) exit 1;
endif
…

*New, corrected code segment: *

if($DoSurfaces && $DoVolumes) then
  *#set cmd = (recon-all -s $average_subject -cortribbon -aparc2aseg)*
*  set cmd = (recon-all -s $average_subject -nuintensitycor -gcareg -canorm
-careg -calabel -cortribbon -aparc2aseg)*
  echo $cmd
  $cmd
  if($status) exit 1;
endif
…

The code that is highlighted with red and a hashtag is what caused the
script to exit with errors. The one below that (highlighted with green) is
the fixed line of code that finishes without errors.

The patched make_average_subject file is also attached. Feel free to use
it.

Best,
Marta (and my father-in-law)


On Tue, Jan 22, 2019 at 2:45 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> This has been fixed in our development version. I can give you a new
> script or you can try this:
> cd $SUBJECTS_DIR/*avgsubjectPRUEBAESTASI!
> ln -s orig.mgz norm.mgz
> Then re-run make_average_subject
>
>
>
>
> *
> On 12/14/18 1:43 PM, Emanuel Alvaredo wrote:
> >
> > External Email - Use Caution
> >
> > Thanks Greve. The output is attached  now.
> >
> >
> > Emanuel
> >
> >
> > On Fri, Dec 14, 2018 at 1:01 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> >  can you include the full terminal output?
> >
> > On 12/13/18 7:45 AM, Emanuel Alvaredo wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Hello Bruce, thanks for your anwer. Sure. The command is
> >>
> >> *make_average_subject --out avgsubjectPRUEBAESTASI! --subjects
> >> Bartley_Recon Baez_Recon Bonilla_Recon*
> >>
> >> The output is in the attached file
> >>
> >> Thanks!
> >>
> >> Emanuel
> >>
> >>
> >> On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl
> >> mailto:fis...@nmr.mgh.harvard.edu>>
> >> wrote:
> >>
> >> Hi Emanuel,
> >>
> >> can you include the full command line and output?
> >>
> >> cheers
> >> Bruce
> >> On Wed, 12 Dec 2018,
> >> Emanuel Alvaredo wrote:
> >>
> >> >
> >> > External Email - Use Caution
> >> >
> >> > Thanks for your answer Douglas. I replaced the
> >> make_average_surface  file with the new one but  I
> >> > have the same message error.
> >> > ASeg Vox2RAS: ---
> >> > -1.0   0.0   0.0   128.0;
> >> >  0.0   0.0   1.0  -128.0;
> >> >  0.0  -1.0   0.0   128.0;
> >> >  0.0   0.0   0.0   1.0;
> >> > mghRead(mri/norm.mgz, -1): could not open file
> >> > -
> >> >
> >> > Labeling Slice
> >> > relabeling unlikely voxels in interior of white matter
> >> > mri/norm.mgz: could not load norm volume from (null)
> >> >
> >> > Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP
> >> Tue Oct 2 17:16:02 UTC 2018 x86_64 x86_64
> >> > x86_64 GNU/Linux
> >> >
> >> > Thanks
> >> >
> >> > Emanuel
> >> >
> >> >
> >> > On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D.
> >> mailto:dgr...@mgh.harvard.edu>> wrote:
> >> >   Sorry, the disk that held that patch failed and we
> >> did not have a backup so not
> >> >   everything was restored. I just put this file there:
> >> >
> >> >
> >>
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface
> >> >
> >> >   Copy it to $FREESURFER_HOME/bin. Let me know how it goes
> >> >
> >> >
> >> >   On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:
> >> >
> >> >   External Email - Use Caution
> >> >
> >> >   Thanks Bruce. The following is the command.
> >> >
> >> >  make_average_subject --out avgsubjectPRUEBAESTASIEmac
> >> --subjects  subject1
> >> > subject2 subject3
> >> >
> >> >
> >> > And I made a mistake in may last mail. I use the word path
> >> instead of patch
> >> >
> >> > I have found this page with a patch for de issue
> >> >
> >> >
> >>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
> >> >
> >> > 

Re: [Freesurfer] move statistical map onto the cerebellum surface

[Bruce Fischl]

Hi John

--projfrac assumes that we know the thickness at each point, which is 
probably not true in your case, unless you have models of the top and 
bottom of the cerebellar cortex. You can use projdist instead, which takes 
a distance in mm (0 would mean you are sampling at the gray/white 
boundary). Unless your data is very high resolution though you probably 
won't be able to sample from a specific layer with any confidence. We do 
have data around on the thickness of the various cerebellar layers if that 
would be useful to you.


cheers
Bruce

On Fri, 25 Jan 2019, john Anderson wrote:



External Email - Use Caution

Hi Dr Greve, yes  indeed I used the flag "projfrac" and I missed including it 
in my command bellow. I greatly
apologize!

My I kindly ask, if "projfrac" is not used then at which layer of the 
cerebellum the projection will take place, is
it 0.5? Also, is there any method that can help to use "projfrac".
I apologies if my questions are overwhelming. I am just trying to learn how to 
it correctly. Thanks



It should only do that if you have specified a projection fraction. Is that 
your full command line? Can you send
the full terminal output?

 

On 1/24/19 4:56 PM, john Anderson wrote:

> 

> External Email - Use Caution

> 

> Hi Dr Greve, I appreciate your guidance very much.

> 

> I followed your suggestion. I put lh.cerebellum in fsaverage and I ran

> mri_vol2surf.

> as follows:

> mri_vol2surf --mov grf.th1.3.pos.sig.cluster.mgh --hemi lh --surf

> cerebellum --mni152reg --o grf_onto_cerebellum.nii.gz

> 

> Now I am getting this error

> 

> ERROR: number of vertices in /FSV6.0/fsaverage/surf/lh.thickness does

> not match surface (163842,34247)

> 

> Any suggestions are appreciated ;-)

> John

> ‐‐‐ Original Message ‐‐‐

On Thursday, January 24, 2019 4:56 PM, john Anderson 
 wrote:

  Hi Dr Greve, I appreciate your guidance very much.

  I followed your suggestion. I put lh.cerebellum in fsaverage and I ran 
mri_vol2surf.
as follows:
mri_vol2surf --mov grf.th1.3.pos.sig.cluster.mgh --hemi lh --surf cerebellum 
--mni152reg --o
grf_onto_cerebellum.nii.gz

Now I am getting this error

ERROR: number of vertices in /FSV6.0/fsaverage/surf/lh.thickness does not match 
surface (163842,34247)

Any suggestions are appreciated ;-)
John





You will have to put the cerebellar surface in fsaverage/surf/lh.cerebellum Note use 
"lh" even if it is the
entire cerebellum as FS commands generally require a hemisphere.

The run mri_vol2surf specifying --hemi lh --surf cerebellum

 

On 1/23/19 10:04 AM, john Anderson wrote:

> 

> External Email - Use Caution

> 

> Dear FS experts,

> I ran surface based PET analysis on subcortical regions. Then

> corrected the results for multiple comparisons using  the method --grf

> in the command mri_glmfit-sim.

> 

> I can visualize the output of multiple comparisons (i.e. the file

> grf.th1.3.pos.sig.cluster.mgh) on volume using tkmedit, this

> statistical map shows difference between the groups in the

> cerebellum Instead of visualizing the results on volume, I want to

> move this file to the cerebellum surface. I already created the

> cerebellum surfaces from aseg.mgz file in fsaverage using the command

> mris_tesselate.

> 

> How can I move the the file grf.th1.3.pos.sig.cluster.mgh from volume

> space and map it on the cerebellum surface?

> 

> I tried mri_vol2surf but this command requires the flag --hemi as a

> result it will map the file "grf.th1.3.pos.sig.cluster.mgh" on

> cerebral hemispheres (lh or rh) but not the cerebellum..

> How can I map the file "grf.th1.3.pos.sig.cluster.mgh" on the

> cerebellum surface?

> 

> Thanks for any suggestions,

> John

> 

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Re: [Freesurfer] Orientation by direction cosines

[Bruce Fischl]

Hi Ritesh

I think that mri_info will try to figure this out and tell you (in the 
"Orientation" output).

cheers
Bruce


On Fri, 25 Jan 2019, Ritesh Mahajan wrote:

>External Email - Use Caution
>
> Hello Team,
>
> Can any one please explain how we come to know whether it is RAI or RAS or 
> any other orientation through direction cosines:
>
> Below is the direction cosine: I saw some non zero and negative values in non 
> diagonal values of matrix. What does this signify ?
>
> 0.9993770-0.0352819
> -0.00916448  0.965676-0.259588
> 0.0340709  0.25975   0.965075
>
> Suppose it is Head First Supine. Any help will be really appreciated.
>
> Thanks,
> Ritesh Mahajan
>
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Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

[Bruce Fischl]

Hi Falk

thanks for catching the typo. I fixed it - nice to have an easy thing to 
fix for a change :)


Bruce


On Fri, 25 Jan 2019, falk.luesebr...@med.ovgu.de wrote:



External Email - Use Caution

Dear Juergen,

 

Thanks for your quick reply! Actually the spelling error is in the error 
message. Taken from
http://martinos.org/~mreuter/long/long_mris_slopes

 

# extensive error checks

#    if options.fsgd is None and

if options.qdec is None:

#    print 'ERROR: Specify --fsgd or --qedc'

    parser.print_help()

    print '\nERROR: Specify --qedc (and other required arguments)\n'

    sys.exit(1)

 

#    if options.fsgd is not None and options.qdec is not None:

#    print 'ERROR: Specify either --fsgd or --qedc, not both'

#    sys.exit(1)

 

At least Martin is consistent with his typo. :D

 

Best,

Falk

 

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Juergen Haenggi
Gesendet: Freitag, 25. Januar 2019 10:35
An: Freesurfer Mailinglist 
Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for 
linux (WSL) using ubuntu 18.04.1 LTS

 

External Email - Use Caution

Dear Falk

 

I have no idea, but recognised that the error refers to --qedc and not to 
--qdec.

maybe there is a spelling error somewhere that is related to your problem.

 

HTH

Cheers

Jürgen

-

University of Zurich

Dr. Jürgen Hänggi, Ph.D.

Department of Psychology

Division Neuropsychology

Binzmuehlestrasse 14, PO Box 25 

8050 Zurich, Switzerland

 

0041 44 635 73 97 (phone office)

0041 76 445 86 84 (phone mobile)       

0041 44 635 74 09 (fax office)

BIN 4.D.04 (office room number)                     

 

j.haen...@psychologie.uzh.ch (email)

http://www.psychologie.uzh.ch/neuropsy/ (website)

http://www.juergenhaenggi.ch (private website)   

 

This email (and any attachment/s) contains confidential and/or privileged

information. If you are not the intended recipient (or have received this

email in error) please notify the sender immediately and destroy this

email. Any unauthorised copying, disclosure or distribution of the

material in this email is strictly forbidden.

-

 

 



  On 25 Jan 2019, at 10:26, falk.luesebr...@med.ovgu.de wrote:

 

External Email - Use Caution

 

Dear all,

 

Has anyone run the longitudinal pipeline successfully using the WSL? I’m 
running it with Ubuntu 18.04.1 LTS
and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.

 

I’m trying to process my first longitudinal data set following the instructions 
of the tutorial as close as
possible. The data has been processed without issues and now I want to do the 
statistical analysis. When I
run:

long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh 
--do-avg --do-rate --do-pc1 --do-spc
--do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR

 

I get the following error:

File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448

    print '\nERROR: Specify --qedc (and other required arguments)\n'

   ^

SyntaxError: invalid syntax

 

I get comparable errors for any other long_* command I try to run, e.g. 
long_qdec_table with or without any
arguments gives:

File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119

   print '\nERROR: Specify --qedc'

  ^

SyntaxError: Missing parentheses in call to 'print'. Did you mean 
print('\nERROR: Specify --qedc')?

 

Does anyone have a clue where this error originates from using either WSL or 
Ubuntu 18.04?  

 

Best,

Falk

...

 



Universitätsklinik für Neurologie



Otto-von-Guericke-Universität Magdeburg
Medizinische Fakultät
Leipziger Str. 44
39120 Magdeburg

 

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de
http://www.kneu.ovgu.de/kneu.html

 

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Re: [Freesurfer] mri_convert

[Bruce Fischl]

Hi Nazain

I can't replicate this problem. Can you verify that the aseg.mgz is 
correct? If it is, maybe email me those 3 files as well as the complete 
output of mri_convert?


cheers
Bruce
On Fri, 25 Jan 2019, N Saf wrote:



External Email - Use Caution

Dear Bruce,
I had a problem with bringing aseg.mgz into my subject space and you recommend 
this command before:

mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.resliced.mgz

which perfectly worked for me but now when I want to try it in
 new version6 it does not work and the aseg.resliced file contains just 
corpus callosum!, I don't know which I do wrong because it worked before and still 
work with the analysis which I done with last version. would you please 


help me to figure it out?thank you very much for your help.

best regards,

Nazain

PS:the link of previous mail:https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50794.html 





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Re: [Freesurfer] How to extract cortical features of a ROI

[Bruce Fischl]

Hi Kan

if you draw a volumetric label you first need to sample it to the surface 
of that subject (mri_label2label --sample). If all you want are stats from 
the subject there is no need to map it to fsaverage - that is only 
necessary if you want to use a group coordinate system.


cheers
Bruce



On Fri, 25 Jan 2019, 
310913949 wrote:




External Email - Use Caution


Dear Freesurfer Experts,
       I want to extract cortical features of a ROI that I drawn manually on  
the rawavg.mgz in Freesurfer, but i
don't know how to do that. I think maybe first the  lesion mask should be 
registered to the  standard templates
fsaverage, but I don't know what the command line is , could  you tell me?  And 
secondly, I should use
mri_label2label to map the label to individual subject  and extract the 
cortical features of the ROI, am I right?
      I am looking forward to your reply!Thanks.

                                                  Best wishes!
                                                      Kan Deng

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Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

[Matthieu Vanhoutte]

External Email - Use Caution

Dear Douglas,

Could you precise me:
1) Is the intensity rescaling of PET image included in the mri_gtmpvc command 
based on reference region in gtmseg.mgz file rather than aseg.mgz ?
2) Is this rescaling applied before PVE correction or after (i.e. based on PVE 
corrected reference region’s mean intensity) ?

Many thanks in advance for helping.

Best,
Matthieu

> Le 7 janv. 2019 à 17:26, Greve, Douglas N.,Ph.D.  a 
> écrit :
> 
> 
> 
> On 1/7/19 11:18 AM, Matthieu Vanhoutte wrote:
>> External Email - Use Caution
>> 
>> 
>> I used the following command to obtain only rescaled voxel-wise PET image 
>> (with no PVC):
>> mri_gtmpvc --i PET.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe 
>> --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o  nopvc
>> 
>> If I omitted --rbv or --mgx option I didn't get the rescaled voxel-wise PET 
>> image (without PVC). Could I obtain the rescaled voxel-wise PET image 
>> (without PVC) just by dividing each voxel of the native PET image by the 
>> mean of the reference region ?
> Yes
>> 
>> Best,
>> Matt
>> 
>> Le lun. 7 janv. 2019 à 16:01, Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>> a écrit :
>> I'm not sure what you mean. If you are turning off PVC, why are you 
>> computing RBV and MGX? What is your command line? What do you mean that 
>> these options don't seem to work?
>> 
>> On 12/21/18 2:22 PM, Matthieu Vanhoutte wrote:
>>> External Email - Use Caution
>>> 
>>> Hi Douglas,
>>> 
>>> Thanks for helping.
>>> 
>>> To have an only rescaled voxel-wise PET image, these options seem to work 
>>> only when -rbv method is used and not -mgx.
>>> 
>>> Do you know why ?
>>> 
>>> Best,
>>> Matthieu 
>>> 
>>> 
>>> Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. 
>>> mailto:dgr...@mgh.harvard.edu>> a écrit :
>>> You will need to set --psf 0 and --no-tfe to fully turn off PVC. 
>>> 
>>> On 12/18/18 4:50 AM, Matthieu Vanhoutte wrote:
 External Email - Use Caution
 
 Hi Douglas,
 
 Could you help me on this point ?
 
 Best,
 Matthieu
 
 
 Le mer. 12 déc. 2018 à 10:50, Matthieu Vanhoutte 
 mailto:matthieuvanhou...@gmail.com>> a écrit 
 :
 Dear Douglas,
 
 Is it possible to use mri_gtmpvc command in order to intensity normalize 
 PET images without applying PVE correction by setting --psf to 0 ?
 
 Best,
 Matthieu
 
 
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>>> 
>>> 
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[Freesurfer] Vertex-wise area anlaysis

[Klaas Bahnsen]

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Dear Freesurfer Experts,

First of all: Thank you so much for your work and your fantastic product.

I turn to you with a short question, I hope it is not too unnecessary and can 
be answered quickly.
My interest lies in vertex wise longitudinal investigation of cortex surface 
area. The paper 'False positive rates in surface-based anatomical analysis' 
(Greve, Fischl 2018) briefly describes how Freesurfer calculates cortex surface 
areas: First the transfer to the target atlas with "Jacobian Correction" and 
second the division by eTIV (ICV) to include the factor of different head 
sizes. Finally, a smoothing should be applied. My question is where these data 
are stored in the Freesurfer data structure or where they are generated.  My 
understanding is that first recon-all stores this data per scan under 
SubjectID/surf/?h.area. These could then be picked up by mris_preproc and 
smoothed with mri_surf2surf. This smoothed file could then be used for example 
for a GLM model (mri_glmfit). Are the steps described in the paper covered with 
this workflow? Or must a special option be selected at some point, e.g. to 
perform the division by the eTIV.
I'm a bit unsure at the moment because I also found a collection of questions 
from previous courses on the FreeSurfer Wiki page. In course 2014 Copenhagen 
the question is asked which units are used in the output files which are 
calculated by mris_preproc. Part of the answer states that the data in 
?h.area.mgh on vertex level do not have much meaning, because they are 
dependent on the triangle mesh.

Hopefully you can help me and hopefully I won't steal you too much time with my 
question.

With kind regards,
Klaas Bahnsen




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Re: [Freesurfer] move statistical map onto the cerebellum surface

[john Anderson]

External Email - Use Caution

Hi Dr Greve, yes  indeed I used the flag "projfrac" and I missed including it 
in my command bellow. I greatly apologize!

My I kindly ask, if "projfrac" is not used then at which layer of the 
cerebellum the projection will take place, is it 0.5? Also, is there any method 
that can help to use "projfrac".
I apologies if my questions are overwhelming. I am just trying to learn how to 
it correctly. Thanks

It should only do that if you have specified a projection fraction. Is that 
your full command line? Can you send the full terminal output?

On 1/24/19 4:56 PM, john Anderson wrote:

>

> External Email - Use Caution

>

> Hi Dr Greve, I appreciate your guidance very much.

>

> I followed your suggestion. I put lh.cerebellum in fsaverage and I ran

> mri_vol2surf.

> as follows:

> mri_vol2surf --mov grf.th1.3.pos.sig.cluster.mgh --hemi lh --surf

> cerebellum --mni152reg --o grf_onto_cerebellum.nii.gz

>

> Now I am getting this error

>

> ERROR: number of vertices in /FSV6.0/fsaverage/surf/lh.thickness does

> not match surface (163842,34247)

>

> Any suggestions are appreciated ;-)

> John

> ‐‐‐ Original Message ‐‐‐

On Thursday, January 24, 2019 4:56 PM, john Anderson 
 wrote:

> Hi Dr Greve, I appreciate your guidance very much.
>
> I followed your suggestion. I put lh.cerebellum in fsaverage and I ran 
> mri_vol2surf.
> as follows:
> mri_vol2surf --mov grf.th1.3.pos.sig.cluster.mgh --hemi lh --surf cerebellum 
> --mni152reg --o grf_onto_cerebellum.nii.gz
>
> Now I am getting this error
>
> ERROR: number of vertices in /FSV6.0/fsaverage/surf/lh.thickness does not 
> match surface (163842,34247)
>
> Any suggestions are appreciated ;-)
> John
>
> You will have to put the cerebellar surface in fsaverage/surf/lh.cerebellum 
> Note use "lh" even if it is the entire cerebellum as FS commands generally 
> require a hemisphere.
>
> The run mri_vol2surf specifying --hemi lh --surf cerebellum
>
> On 1/23/19 10:04 AM, john Anderson wrote:
>
>>
>
>> External Email - Use Caution
>
>>
>
>> Dear FS experts,
>
>> I ran surface based PET analysis on subcortical regions. Then
>
>> corrected the results for multiple comparisons using  the method --grf
>
>> in the command mri_glmfit-sim.
>
>>
>
>> I can visualize the output of multiple comparisons (i.e. the file
>
>> grf.th1.3.pos.sig.cluster.mgh) on volume using tkmedit, this
>
>> statistical map shows difference between the groups in the
>
>> cerebellum Instead of visualizing the results on volume, I want to
>
>> move this file to the cerebellum surface. I already created the
>
>> cerebellum surfaces from aseg.mgz file in fsaverage using the command
>
>> mris_tesselate.
>
>>
>
>> How can I move the the file grf.th1.3.pos.sig.cluster.mgh from volume
>
>> space and map it on the cerebellum surface?
>
>>
>
>> I tried mri_vol2surf but this command requires the flag --hemi as a
>
>> result it will map the file "grf.th1.3.pos.sig.cluster.mgh" on
>
>> cerebral hemispheres (lh or rh) but not the cerebellum..
>
>> How can I map the file "grf.th1.3.pos.sig.cluster.mgh" on the
>
>> cerebellum surface?
>
>>
>
>> Thanks for any suggestions,
>
>> John
>
>>
>
>> ___
>
>> 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] Neuroscientist with focus on electrophysiology and imaging in Parkinson disease patients!

[Muthuraman Muthuraman]

External Email - Use Caution

*Doctoral Student*

*Neuroscientist with focus on electrophysiology and imaging in Parkinson
disease patients *

The *clinic of neurology, imaging and neurostimulation group
(http://imaging-neurostim.com ) University of
Mainz*, Germany, invites applications for a

*PhD Student  *

for a functional translational neuroscience (FTN) scholarship three year
position to work on electrophysiology and imaging in Parkinson disease (PD)
patients. A project with multimodality usage of modalities like
electroencephalography (EEG) and functional magnetic resonance imaging
(fMRI) to analyze network fingerprints in PD patients.

The successful applicant holds a Master’s degree (or equivalent) in a
relevant academic area such as *basic life sciences, neuropsychology,
applied* *mathematics or biomedical engineering or similar disciplines. *German
language proficiency is mandatory for communicating with the patients. The
working language at the institute is English. Experience with
electrophysiology and the analysis of brain signals is advantageous, but
not essential. The applicant’s merits are assessed on the basis of the
quality of Master’s level studies and thesis, previous experience with the
brain imaging, motivation and research interests.

The location for this research will mainly be the workgroups “*Section of
Movement Disorders, Neurostimulation and Neuroimaging*“ of Prof. Sergiu
Groppa at the Department of Neurology and “*Biomedical Statistics and
Multimodal Signal Processing Unit*” of Prof. Muthuraman Muthuraman, both at
the Focus Program Translational Neurosciences (http://www.ftn.uni-mainz.de/)
and Neuroimaging Centre Mainz (http://www.ftn.nic.uni-mainz.de/). Expected
close collaborations with national and international partners.

The application should include a statement of research interests, a
curriculum vitae (max. 4 pages) composed according to good scientific
practice, a certificate of Master’s degree, copy of the master’s thesis and
grades of Master’s level studies, the names and e-mail addresses of two
referees and a proof of proficiency in English.

The position will be open until filled. To apply for the position, please
send the above documents as pdfs until 15.02.2019 to* Prof. Sergiu Groppa*,
and *Prof. Muthuraman Muthuraman*, Department of Neurology, Section of
movement disorders and neurostimulation, University of Mainz,
Langenbeckstrasse 1, 55131 Mainz, Germany, or by Email to
*segroppa(at)uni-mainz.de
; mmuthura(at)uni-mainz.de *. For
additional information please contact* Muthuraman Muthuraman.  *
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[Freesurfer] Orientation by direction cosines

[Ritesh Mahajan]

External Email - Use Caution

Hello Team, 

Can any one please explain how we come to know whether it is RAI or RAS or any 
other orientation through direction cosines: 

Below is the direction cosine: I saw some non zero and negative values in non 
diagonal values of matrix. What does this signify ?

0.9993770-0.0352819
-0.00916448  0.965676-0.259588
0.0340709  0.25975   0.965075

Suppose it is Head First Supine. Any help will be really appreciated.

Thanks,
Ritesh Mahajan

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Re: [Freesurfer] FSFAST poor registration

[Keri Woods]

External Email - Use Caution

Hi Douglas

Thanks very much for getting back to me. I created new separate directories
and re-processed one of the problem subjects individually, and the
registration worked well. So the problem is that the anatomical and
functional images come from different subjects. But I've checked and the
subjectname files are correct. That's the only thing linking the anatomical
and functional images? Thanks very much, you've helped me a lot. Now I just
have to go and see where I mixed up the files!

Thanks again,
Keri

On Thu, Jan 24, 2019 at 10:32 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Can you tar up the anatomical and functional analyses and send them to
> me through our filedrop?
>
> https://gate.nmr.mgh.harvard.edu/filedrop2/
>
> when it asks for an email of the recipient, use gr...@nmr.mgh.harvard.edu
>
>
> On 1/23/19 5:57 AM, Keri Woods wrote:
> >
> > External Email - Use Caution
> >
> > I meant some are nearly perfect.
> >
> > On Wed, Jan 23, 2019 at 11:49 AM Keri Woods  > > wrote:
> >
> > Hi Douglas
> >
> > Thanks for the response.
> >
> > No, some of the registrations are fine. Some are close, but not
> > perfect, while others are very bad.
> >
> > I've checked the subjectname file for some subjects with poor
> > registration (eg 20_101), and they are correct.
> >
> > Thanks,
> > Keri
> >
> > On Tue, Jan 22, 2019 at 8:57 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > Are you saying that all of them have bad registrations? Some
> > of them
> > (eg, 20_1, 20_10) look like they should be good. Others (eg,
> > 20_101)
> > look like they could be bad. For the bad ones, are you totally
> > sure that
> > the subjetname file has the correct name of the subject?
> >
> > On 1/21/19 3:19 AM, Keri Woods wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hi Douglas
> > >
> > > Thank you for your reply.
> > >
> > > I'm using
> > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
> > >
> > > I am using whole brain data. The functional and structural
> > images were
> > > acquired in different sessions on the same day, I don't know
> > if that
> > > complicated things? Each subject has 2 runs of the same task.
> > >
> > > This is what I get after running the command in the format of
> > > tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold
> > -per-run -bbr-sum
> > >
> > > 20_1   013 0.5155
> > > 20_1   014 0.5090
> > > 20_10  013 0.5247
> > > 20_10  014 0.5229
> > > 20_100 038 0.8420
> > > 20_100 040 0.8443
> > > 20_101 008 0.9052
> > > 20_101 010 0.9289
> > > 20_102 058 0.6924
> > > 20_102 059 0.6902
> > > 20_103 045 0.9778
> > > 20_103 046 0.9931
> > > 20_104 010 0.9324
> > > 20_104 012 0.9413
> > > 20_105 013 0.8754
> > > 20_105 014 0.8937
> > > 20_106 047 0.4433
> > > 20_106 048 0.4377
> > > 20_107 008 0.9178
> > > 20_107 010 0.9238
> > > 20_11  013 0.7631
> > > 20_11  014 0.7615
> > > 20_110 048 0.7687
> > > 20_110 049 0.7549
> > > 20_112 013 0.8821
> > > 20_112 014 0.9161
> > > 20_113 052 0.7689
> > > 20_113 053 0.7757
> > > 20_116 046 1.0072
> > > 20_116 047 1.0256
> > > 20_117 008 0.7742
> > > 20_117 010 0.7826
> > > 20_119 013 0.7929
> > > 20_119 014 0.7854
> > > 20_120 048 0.5090
> > > 20_120 049 0.4973
> > > 20_126 047 0.8285
> > > 20_126 048 0.8281
> > > 20_128 046 0.9580
> > > 20_128 047 0.9314
> > > 20_130 047 0.9439
> > > 20_130 048 0.9425
> > > 20_132 047 0.8550
> > > 20_132 048 0.8558
> > > 20_134_1   013 0.5716
> > > 20_134_1   015 0.5744
> > > 20_135 011 0.8357
> > > 20_135 012 0.8401
> > > 20_136 044 0.9995
> > > 20_136 045 0.9604
> > > 20_137 047 0.7922
> > > 20_137 048 0.7990
> > > 20_142 047 0.5282
> > > 20_142 048 0.5278
> > > 20_144 013 0.8755
> > > 20_144 014 0.8838
> > > 20_146 047 0.7997
> > > 20_146 048 0.7895
> > > 20_149 049 0.9251
> > > 20_149 050 0.9408
> > > 20_151 048 0.5905
> > > 20_151 049 0.5519
> > > 20_152 048 0.9024
> >  

Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

[Lars.Dinkelbach]

External Email - Use Caution

Dear all,

I am getting the same problem on ubunto 18.04 without WSL. I would be glad for 
advice how to fix it.

Best,
Lars

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von 
"falk.luesebr...@med.ovgu.de [falk.luesebr...@med.ovgu.de]
Gesendet: Freitag, 25. Januar 2019 10:41
An: Freesurfer Mailinglist
Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for 
linux (WSL) using ubuntu 18.04.1 LTS


External Email - Use Caution
Dear Juergen,

Thanks for your quick reply! Actually the spelling error is in the error 
message. Taken from http://martinos.org/~mreuter/long/long_mris_slopes

# extensive error checks
#if options.fsgd is None and
if options.qdec is None:
#print 'ERROR: Specify --fsgd or --qedc'
parser.print_help()
print '\nERROR: Specify --qedc (and other required arguments)\n'
sys.exit(1)

#if options.fsgd is not None and options.qdec is not None:
#print 'ERROR: Specify either --fsgd or --qedc, not both'
#sys.exit(1)

At least Martin is consistent with his typo. :D

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Juergen Haenggi
Gesendet: Freitag, 25. Januar 2019 10:35
An: Freesurfer Mailinglist 
Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for 
linux (WSL) using ubuntu 18.04.1 LTS


External Email - Use Caution
Dear Falk

I have no idea, but recognised that the error refers to --qedc and not to 
--qdec.
maybe there is a spelling error somewhere that is related to your problem.

HTH
Cheers
Jürgen
-
University of Zurich
Dr. Jürgen Hänggi, Ph.D.
Department of Psychology
Division Neuropsychology
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland

0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)

j.haen...@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

This email (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
email in error) please notify the sender immediately and destroy this
email. Any unauthorised copying, disclosure or distribution of the
material in this email is strictly forbidden.
-




On 25 Jan 2019, at 10:26, 
falk.luesebr...@med.ovgu.de wrote:

External Email - Use Caution

Dear all,

Has anyone run the longitudinal pipeline successfully using the WSL? I’m 
running it with Ubuntu 18.04.1 LTS and 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.

I’m trying to process my first longitudinal data set following the instructions 
of the tutorial as close as possible. The data has been processed without 
issues and now I want to do the statistical analysis. When I run:
long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh 
--do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years 
--qcache fsaverage --sd $SUBJECTS_DIR

I get the following error:
File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448
print '\nERROR: Specify --qedc (and other required arguments)\n'
   ^
SyntaxError: invalid syntax

I get comparable errors for any other long_* command I try to run, e.g. 
long_qdec_table with or without any arguments gives:
File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119
   print '\nERROR: Specify --qedc'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean 
print('\nERROR: Specify --qedc')?

Does anyone have a clue where this error originates from using either WSL or 
Ubuntu 18.04?

Best,
Falk
...


Universitätsklinik für Neurologie



Otto-von-Guericke-Universität Magdeburg
Medizinische Fakultät
Leipziger Str. 44
39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de
http://www.kneu.ovgu.de/kneu.html

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Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

[falk.luesebr...@med.ovgu.de]

External Email - Use Caution

I was able to circumvent the error by switching from python3 to python2.

In python3 print was changed to a function making it necessary to put the 
arguments in brackets.

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von 
falk.luesebr...@med.ovgu.de
Gesendet: Freitag, 25. Januar 2019 10:42
An: Freesurfer Mailinglist 
Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for 
linux (WSL) using ubuntu 18.04.1 LTS


External Email - Use Caution
Dear Juergen,

Thanks for your quick reply! Actually the spelling error is in the error 
message. Taken from http://martinos.org/~mreuter/long/long_mris_slopes

# extensive error checks
#if options.fsgd is None and
if options.qdec is None:
#print 'ERROR: Specify --fsgd or --qedc'
parser.print_help()
print '\nERROR: Specify --qedc (and other required arguments)\n'
sys.exit(1)

#if options.fsgd is not None and options.qdec is not None:
#print 'ERROR: Specify either --fsgd or --qedc, not both'
#sys.exit(1)

At least Martin is consistent with his typo. :D

Best,
Falk

Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 Im Auftrag von Juergen Haenggi
Gesendet: Freitag, 25. Januar 2019 10:35
An: Freesurfer Mailinglist 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for 
linux (WSL) using ubuntu 18.04.1 LTS


External Email - Use Caution
Dear Falk

I have no idea, but recognised that the error refers to --qedc and not to 
--qdec.
maybe there is a spelling error somewhere that is related to your problem.

HTH
Cheers
Jürgen
-
University of Zurich
Dr. Jürgen Hänggi, Ph.D.
Department of Psychology
Division Neuropsychology
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland

0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)

j.haen...@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

This email (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
email in error) please notify the sender immediately and destroy this
email. Any unauthorised copying, disclosure or distribution of the
material in this email is strictly forbidden.
-



On 25 Jan 2019, at 10:26, 
falk.luesebr...@med.ovgu.de wrote:

External Email - Use Caution

Dear all,

Has anyone run the longitudinal pipeline successfully using the WSL? I’m 
running it with Ubuntu 18.04.1 LTS and 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.

I’m trying to process my first longitudinal data set following the instructions 
of the tutorial as close as possible. The data has been processed without 
issues and now I want to do the statistical analysis. When I run:
long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh 
--do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years 
--qcache fsaverage --sd $SUBJECTS_DIR

I get the following error:
File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448
print '\nERROR: Specify --qedc (and other required arguments)\n'
   ^
SyntaxError: invalid syntax

I get comparable errors for any other long_* command I try to run, e.g. 
long_qdec_table with or without any arguments gives:
File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119
   print '\nERROR: Specify --qedc'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean 
print('\nERROR: Specify --qedc')?

Does anyone have a clue where this error originates from using either WSL or 
Ubuntu 18.04?

Best,
Falk
...


Universitätsklinik für Neurologie


Otto-von-Guericke-Universität Magdeburg
Medizinische Fakultät
Leipziger Str. 44
39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de
http://www.kneu.ovgu.de/kneu.html

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Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

[falk.luesebr...@med.ovgu.de]

External Email - Use Caution

Dear Juergen,

Thanks for your quick reply! Actually the spelling error is in the error 
message. Taken from http://martinos.org/~mreuter/long/long_mris_slopes

# extensive error checks
#if options.fsgd is None and
if options.qdec is None:
#print 'ERROR: Specify --fsgd or --qedc'
parser.print_help()
print '\nERROR: Specify --qedc (and other required arguments)\n'
sys.exit(1)

#if options.fsgd is not None and options.qdec is not None:
#print 'ERROR: Specify either --fsgd or --qedc, not both'
#sys.exit(1)

At least Martin is consistent with his typo. :D

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Juergen Haenggi
Gesendet: Freitag, 25. Januar 2019 10:35
An: Freesurfer Mailinglist 
Betreff: Re: [Freesurfer] Longitudinal processing with windows subsystem for 
linux (WSL) using ubuntu 18.04.1 LTS


External Email - Use Caution
Dear Falk

I have no idea, but recognised that the error refers to --qedc and not to 
--qdec.
maybe there is a spelling error somewhere that is related to your problem.

HTH
Cheers
Jürgen
-
University of Zurich
Dr. Jürgen Hänggi, Ph.D.
Department of Psychology
Division Neuropsychology
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland

0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)

j.haen...@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

This email (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
email in error) please notify the sender immediately and destroy this
email. Any unauthorised copying, disclosure or distribution of the
material in this email is strictly forbidden.
-




On 25 Jan 2019, at 10:26, 
falk.luesebr...@med.ovgu.de wrote:

External Email - Use Caution

Dear all,

Has anyone run the longitudinal pipeline successfully using the WSL? I’m 
running it with Ubuntu 18.04.1 LTS and 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.

I’m trying to process my first longitudinal data set following the instructions 
of the tutorial as close as possible. The data has been processed without 
issues and now I want to do the statistical analysis. When I run:
long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh 
--do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years 
--qcache fsaverage --sd $SUBJECTS_DIR

I get the following error:
File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448
print '\nERROR: Specify --qedc (and other required arguments)\n'
   ^
SyntaxError: invalid syntax

I get comparable errors for any other long_* command I try to run, e.g. 
long_qdec_table with or without any arguments gives:
File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119
   print '\nERROR: Specify --qedc'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean 
print('\nERROR: Specify --qedc')?

Does anyone have a clue where this error originates from using either WSL or 
Ubuntu 18.04?

Best,
Falk
...


Universitätsklinik für Neurologie



Otto-von-Guericke-Universität Magdeburg
Medizinische Fakultät
Leipziger Str. 44
39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de
http://www.kneu.ovgu.de/kneu.html

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Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

[Juergen Haenggi]

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Dear Falk

I have no idea, but recognised that the error refers to --qedc and not to 
--qdec.
maybe there is a spelling error somewhere that is related to your problem.

HTH
Cheers
Jürgen

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Dr. Jürgen Hänggi, Ph.D.
Department of Psychology
Division Neuropsychology
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> On 25 Jan 2019, at 10:26, falk.luesebr...@med.ovgu.de wrote:
> 
> External Email - Use Caution
> 
> 
> Dear all,
>  
> Has anyone run the longitudinal pipeline successfully using the WSL? I’m 
> running it with Ubuntu 18.04.1 LTS and 
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.
>  
> I’m trying to process my first longitudinal data set following the 
> instructions of the tutorial as close as possible. The data has been 
> processed without issues and now I want to do the statistical analysis. When 
> I run:
> long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh 
> --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years 
> --qcache fsaverage --sd $SUBJECTS_DIR
>  
> I get the following error:
> File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448
> print '\nERROR: Specify --qedc (and other required arguments)\n'
>^
> SyntaxError: invalid syntax
>  
> I get comparable errors for any other long_* command I try to run, e.g. 
> long_qdec_table with or without any arguments gives:
> File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119
>print '\nERROR: Specify --qedc'
>   ^
> SyntaxError: Missing parentheses in call to 'print'. Did you mean 
> print('\nERROR: Specify --qedc')?
>  
> Does anyone have a clue where this error originates from using either WSL or 
> Ubuntu 18.04?  
>  
> Best,
> Falk
> ...
>  
> 
> Universitätsklinik für Neurologie
> 
> 
> Otto-von-Guericke-Universität Magdeburg
> Medizinische Fakultät
> Leipziger Str. 44
> 39120 Magdeburg
>  
> Telefon: +49-391-6117-512
> 
> falk.luesebr...@med.ovgu.de 
> http://www.kneu.ovgu.de/kneu.html 
>  
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[Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

[falk.luesebr...@med.ovgu.de]

External Email - Use Caution

Dear all,

Has anyone run the longitudinal pipeline successfully using the WSL? I'm 
running it with Ubuntu 18.04.1 LTS and 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c.

I'm trying to process my first longitudinal data set following the instructions 
of the tutorial as close as possible. The data has been processed without 
issues and now I want to do the statistical analysis. When I run:
long_mris_slopes --qdec ./long.qdec.table.dat --meas thickness --hemi lh 
--do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years 
--qcache fsaverage --sd $SUBJECTS_DIR

I get the following error:
File "/home/luesebri/Software/FreeSurfer/bin/long_mris_slopes", line 448
print '\nERROR: Specify --qedc (and other required arguments)\n'
   ^
SyntaxError: invalid syntax

I get comparable errors for any other long_* command I try to run, e.g. 
long_qdec_table with or without any arguments gives:
File "/home/luesebri/Software/FreeSurfer/bin/long_qdec_table", line 119
   print '\nERROR: Specify --qedc'
  ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean 
print('\nERROR: Specify --qedc')?

Does anyone have a clue where this error originates from using either WSL or 
Ubuntu 18.04?

Best,
Falk
...

[klinikum_logo_schmal_e-mail_blau]
Universitätsklinik für Neurologie


Otto-von-Guericke-Universität Magdeburg
Medizinische Fakultät
Leipziger Str. 44
39120 Magdeburg

Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de
http://www.kneu.ovgu.de/kneu.html

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[Freesurfer] mri_convert

[N Saf]

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Dear Bruce,
I had a problem with bringing aseg.mgz into my subject space and you
recommend this command before:

mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.resliced.mgz

which perfectly worked for me but now when I want to try it in
 new version6 it does not work and the aseg.resliced file contains just
corpus callosum!, I don't know which I do wrong because it worked
before and still
work with the analysis which I done with last version. would you please

help me to figure it out?thank you very much for your help.

best regards,

Nazain

PS:the link of previous
mail:https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50794.html
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