[Freesurfer] Symposium on Parkinson’s disease, early triggers - MRI, PET, inflammation, genetics

[Alexandru Hanganu]

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 Dear Colleagues,

University of Montreal, Department of Neuroscience is organizing a
Symposium on Parkinson’s disease

May 3, 2019, in Montreal, Canada.

Key Speakers:
Roger Barker, Francesca Cicchetti, Antonio Strafella, Janelle
Drouin-Ouellet, Thomas M. Durcan, Ashley S. Harms, Kenneth Marek, Diana
Matheoud, Anurag Tandon, Malu G. Tansey, Michela Deleidi, Louis-Éric
Trudeau, Andrew D. Siderowf, Richard Youle.

This Symposium aims to outline to current results and research directions
in the early triggers and biomarkers of Parkinson’s disease, from an MRI,
PET, inflammation, morphopathology and genetics perspectives.

Early registration deadline: 1st March 2019.

more details at:
http://fourwav.es/neurosciences21-22mai2019
On behalf of the organizing committee,
Alexandru Hanganu
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Re: [Freesurfer] aparc+aseg fails to load in freeview

[Bruce Fischl]

Hi Lisa

it's possible. Look at the ?h.inflated.nofix surfaces and see if there is 
something dramatically wrong, like the skull or cerebellum being attached 
to one of the hemispheres.


cheers
Bruce
On Fri, 22 Feb 2019, Taylor, Lisa Marie wrote:


   External Email - Use Caution

Hi,

I saw that error too, but I am quite the novice when it comes to the technical 
aspects so I was not sure what that meant. I think I understand more now though.

I looked at the nifti raw file and the scan looks pretty good, better than the 
one I am working on right now. I did open what I could in freeview (the 
brainmask, WM, and T1), and I am noticing that the ventricles are quite large. 
Could this be posing the problem, you think? If so, can the image be salvaged?

Thanks again for your help and input!

Lisa



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Tim Schäfer 
[ts...@rcmd.org]
Sent: Friday, February 22, 2019 2:18 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] aparc+aseg fails to load in freeview

   External Email - Use Caution

Hm, I'm not an expert, but the log says 'XL defect detected...'.

I've seen this error on 2 or 3 subjects I tried to process (out of several 
hundreds). Usually it happened only when the source images looked very bad even 
by a quick visual inspection (excessive ringing, very bad contrast, etc). I 
ended up just discarding them.

Did you have a look at the raw files (DICOMs)? Do they look OK?

Tim


On February 22, 2019 at 11:03 PM "Taylor, Lisa Marie"  wrote:


External Email - Use Caution


Hi there,

I am fairly new at this but have been using freesurfer/freeview for the past 
two months to edit MRI images.

There is a particular file I am trying to open that fails to load the 
aparc+aseg volume. I've downloaded from the source and tried to run it through 
freesurfer again with the same error (it took nearly double the time to process 
than a typical file). I am not exactly sure how to figure out what/where the 
issue is coming from. Would you be able to help?

I am using OSX Yosemite.

I have attached the recon-all.log file to this email.

Thank you for your understanding and help in this issue.

Lisa



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Re: [Freesurfer] aparc+aseg fails to load in freeview

[Taylor, Lisa Marie]

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Hi,

I saw that error too, but I am quite the novice when it comes to the technical 
aspects so I was not sure what that meant. I think I understand more now though.

I looked at the nifti raw file and the scan looks pretty good, better than the 
one I am working on right now. I did open what I could in freeview (the 
brainmask, WM, and T1), and I am noticing that the ventricles are quite large. 
Could this be posing the problem, you think? If so, can the image be salvaged?

Thanks again for your help and input!

Lisa



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Tim Schäfer 
[ts...@rcmd.org]
Sent: Friday, February 22, 2019 2:18 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] aparc+aseg fails to load in freeview

External Email - Use Caution

Hm, I'm not an expert, but the log says 'XL defect detected...'.

 I've seen this error on 2 or 3 subjects I tried to process (out of several 
hundreds). Usually it happened only when the source images looked very bad even 
by a quick visual inspection (excessive ringing, very bad contrast, etc). I 
ended up just discarding them.

Did you have a look at the raw files (DICOMs)? Do they look OK?

Tim

> On February 22, 2019 at 11:03 PM "Taylor, Lisa Marie"  
> wrote:
>
>
> External Email - Use Caution
>
>
> Hi there,
>
> I am fairly new at this but have been using freesurfer/freeview for the past 
> two months to edit MRI images.
>
> There is a particular file I am trying to open that fails to load the 
> aparc+aseg volume. I've downloaded from the source and tried to run it 
> through freesurfer again with the same error (it took nearly double the time 
> to process than a typical file). I am not exactly sure how to figure out 
> what/where the issue is coming from. Would you be able to help?
>
> I am using OSX Yosemite.
>
> I have attached the recon-all.log file to this email.
>
> Thank you for your understanding and help in this issue.
>
> Lisa
>
> 
>
> This message may contain confidential information and is for the sole use of 
> the intended recipient(s). If you are not the intended recipient, do not use, 
> distribute, or copy this e-mail. Please notify the UC Irvine Health – 
> Compliance and Privacy Office via email at hacomplia...@uci.edu or by phone 
> 888-456-7006 immediately if you have received this e-mail in error. E-mail 
> transmission cannot be guaranteed to be secure or error-free as information 
> could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, 
> or contain viruses. The sender therefore does not accept liability for any 
> errors or omissions in the contents of this message, which arise as a result 
> of e-mail transmission.
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[Freesurfer] mri_segstats and mris_anatomical_stats read out different # of rois

[Winkelbeiner, Stephanie A]

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Hi Freesurfers,

I'm trying to read out GM and WM values from parcels (ROIs) but get a different 
amount of ROIs for GM and WM.
I use the following commands (embedded in a loop),

for GM
mris_anatomical_stats -mgz \
-cortex label/lh.cortex.label \
-f stats/lh.250.aparc.pial.stats \
-b -a 250.aparc \
-c label/colortable.ctab \
$subject lh pial

and for WM
mri_segstats \
--seg mri/vol250.lh.nii.gz \
--ctab ../fsaverage/colortable.ctab \
--i $dtipath/$subj/dti_FA.nii.gz \
--excludeid 0 \
--empty \
--sum stats/${subj}_fa_lh.stats

where "../fsaverage/colortable.ctab" has 299 labels and "mri/vol250.lh.nii.gz" 
is the segmented image that was extended 2mm into the WM and registered to the 
DTI image.

Is it possible that these two commands read out different amounts of ROIs?
And is there a reason why the -c flag in mris_anatomical_stats doesn't save the 
colortable for each subject?

I would be very grateful for some help!
Thanks,
Stephanie



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Re: [Freesurfer] aparc+aseg fails to load in freeview

[Tim Schäfer]

External Email - Use Caution

Hm, I'm not an expert, but the log says 'XL defect detected...'.

 I've seen this error on 2 or 3 subjects I tried to process (out of several 
hundreds). Usually it happened only when the source images looked very bad even 
by a quick visual inspection (excessive ringing, very bad contrast, etc). I 
ended up just discarding them.

Did you have a look at the raw files (DICOMs)? Do they look OK?

Tim

> On February 22, 2019 at 11:03 PM "Taylor, Lisa Marie"  
> wrote:
> 
> 
> External Email - Use Caution
> 
> 
> Hi there,
> 
> I am fairly new at this but have been using freesurfer/freeview for the past 
> two months to edit MRI images.
> 
> There is a particular file I am trying to open that fails to load the 
> aparc+aseg volume. I've downloaded from the source and tried to run it 
> through freesurfer again with the same error (it took nearly double the time 
> to process than a typical file). I am not exactly sure how to figure out 
> what/where the issue is coming from. Would you be able to help?
> 
> I am using OSX Yosemite.
> 
> I have attached the recon-all.log file to this email.
> 
> Thank you for your understanding and help in this issue.
> 
> Lisa
> 
> 
> 
> This message may contain confidential information and is for the sole use of 
> the intended recipient(s). If you are not the intended recipient, do not use, 
> distribute, or copy this e-mail. Please notify the UC Irvine Health – 
> Compliance and Privacy Office via email at hacomplia...@uci.edu or by phone 
> 888-456-7006 immediately if you have received this e-mail in error. E-mail 
> transmission cannot be guaranteed to be secure or error-free as information 
> could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, 
> or contain viruses. The sender therefore does not accept liability for any 
> errors or omissions in the contents of this message, which arise as a result 
> of e-mail transmission.
> ___
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Re: [Freesurfer] registration and resampling in native space

[Francesca Strappini]

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What is the best procedure? I really have no idea, I've been tried so many
things but nothing worked...

Il giorno ven 22 feb 2019 alle ore 23:41 Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> ha scritto:

> You will need to either get the ROIs into the anatomical space or compute
> a new registration to the space of the ROIs from the functional template
>
> On 2/22/19 3:43 PM, Francesca Strappini wrote:
>
> External Email - Use Caution
> Thanks!
> The vox2ras matrices are not same.
>
> This is one region:
>
> francesca@shalimpc:~/Desktop/sub3/ROIs$ mri_info
> sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
> Volume information for sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
>   type: nii
> dimensions: 64 x 64 x 50
>voxel sizes: 3.00, 3.00, 3.00
>   type: FLOAT (3)
>fov: 192.000
>dof: 0
> xstart: -96.0, xend: 96.0
> ystart: -96.0, yend: 96.0
> zstart: -75.0, zend: 75.0
> TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
> degrees
>nframes: 1
>PhEncDir: UNKNOWN
>FieldStrength: 0.00
> ras xform present
> xform info: x_r =  -0.9988, y_r =   0.0235, z_r =   0.0427, c_r =
> -2.2923
>   : x_a =   0.0124, y_a =   0.9702, z_a =  -0.2420, c_a =
> 19.4768
>   : x_s =   0.0471, y_s =   0.2412, z_s =   0.9693, c_s =
> 25.1269
> Orientation   : LAS
> Primary Slice Direction: axial
>
> voxel to ras transform:
>-2.9964   0.0704   0.128188.1380
> 0.0373   2.9106  -0.7261   -56.7017
> 0.1414   0.7237   2.9080   -75.2534
> 0.   0.   0. 1.
>
> voxel-to-ras determinant -27
>
> ras to voxel transform:
>-0.3329   0.0041   0.015730.7614
> 0.0078   0.3234   0.080423.6988
> 0.0142  -0.0807   0.323118.4853
>-0.  -0.  -0. 1.
>
> Orig:
>
> francesca@shalimpc:/usr/local/freesurfer/subjects/sub3/mri$ mri_info
> orig.mgz
> Volume information for orig.mgz
>   type: MGH
> dimensions: 256 x 256 x 256
>voxel sizes: 1.00, 1.00, 1.00
>   type: UCHAR (0)
>fov: 256.000
>dof: 0
> xstart: -128.0, xend: 128.0
> ystart: -128.0, yend: 128.0
> zstart: -128.0, zend: 128.0
> TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
> 0.00 degrees
>nframes: 1
>PhEncDir: UNKNOWN
>FieldStrength: 0.00
> ras xform present
> xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
> -2.3092
>   : x_a =   0., y_a =   0., z_a =   1., c_a =
> 26.4827
>   : x_s =   0., y_s =  -1., z_s =   0., c_s =
> 19.0338
>
> talairach xfm :
> /usr/local/freesurfer/subjects/sub3/mri/transforms/talairach.xfm
> Orientation   : LIA
> Primary Slice Direction: coronal
>
> voxel to ras transform:
>-1.   0.   0.   125.6908
> 0.   0.   1.  -101.5173
> 0.  -1.   0.   147.0338
> 0.   0.   0. 1.
>
> voxel-to-ras determinant -1
>
> ras to voxel transform:
>-1.   0.   0.   125.6908
>-0.   0.  -1.   147.0338
>-0.   1.   0.   101.5173
>-0.  -0.  -0. 1.
>
> This is the raw T1 to which the regions are registered:
>
> Volume information for
> sub-03_ses-anatomy_anat_sub-03_ses-anatomy_T1w.nii.gz
>   type: nii
> dimensions: 256 x 256 x 192
>voxel sizes: 1.00, 1.00, 1.00
>   type: FLOAT (3)
>fov: 256.000
>dof: 0
> xstart: -128.0, xend: 128.0
> ystart: -128.0, yend: 128.0
> zstart: -96.0, zend: 96.0
> TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
> 0.00 degrees
>nframes: 1
>PhEncDir: UNKNOWN
>FieldStrength: 0.00
> ras xform present
> xform info: x_r =  -0.0069, y_r =  -0.0360, z_r =  -0.9993, c_r =
> -2.3092
>   : x_a =  -0.9823, y_a =   0.1874, z_a =  -0., c_a =
> 26.4827
>   : x_s =  -0.1873, y_s =  -0.9816, z_s =   0.0366, c_s =
> 19.0338
> Orientation   : PIL
> Primary Slice Direction: sagittal
>
> voxel to ras transform:
>-0.0069  -0.0360  -0.999399.1125
>-0.9823   0.1874  -0.   128.2306
>-0.1873  -0.9816   0.0366   165.1330
> 0.   0.   0. 1.
>
> voxel-to-ras determinant -1
>
> ras to voxel transform:
>-0.0069  -0.9823  -0.1873   157.5619
>-0.0360   0.1874  -0.9816   141.6386
>-0.9993   0.   0.036692.9949
>-0.  -0.  -0. 1.

Re: [Freesurfer] registration and resampling in native space

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

You will need to either get the ROIs into the anatomical space or compute a new 
registration to the space of the ROIs from the functional template

On 2/22/19 3:43 PM, Francesca Strappini wrote:

External Email - Use Caution

Thanks!
The vox2ras matrices are not same.

This is one region:

francesca@shalimpc:~/Desktop/sub3/ROIs$ mri_info 
sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
Volume information for sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
  type: nii
dimensions: 64 x 64 x 50
   voxel sizes: 3.00, 3.00, 3.00
  type: FLOAT (3)
   fov: 192.000
   dof: 0
xstart: -96.0, xend: 96.0
ystart: -96.0, yend: 96.0
zstart: -75.0, zend: 75.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -0.9988, y_r =   0.0235, z_r =   0.0427, c_r =-2.2923
  : x_a =   0.0124, y_a =   0.9702, z_a =  -0.2420, c_a =19.4768
  : x_s =   0.0471, y_s =   0.2412, z_s =   0.9693, c_s =25.1269
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
   -2.9964   0.0704   0.128188.1380
0.0373   2.9106  -0.7261   -56.7017
0.1414   0.7237   2.9080   -75.2534
0.   0.   0. 1.

voxel-to-ras determinant -27

ras to voxel transform:
   -0.3329   0.0041   0.015730.7614
0.0078   0.3234   0.080423.6988
0.0142  -0.0807   0.323118.4853
   -0.  -0.  -0. 1.

Orig:

francesca@shalimpc:/usr/local/freesurfer/subjects/sub3/mri$ mri_info orig.mgz
Volume information for orig.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =-2.3092
  : x_a =   0., y_a =   0., z_a =   1., c_a =26.4827
  : x_s =   0., y_s =  -1., z_s =   0., c_s =19.0338

talairach xfm : /usr/local/freesurfer/subjects/sub3/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0.   125.6908
0.   0.   1.  -101.5173
0.  -1.   0.   147.0338
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.   0.   0.   125.6908
   -0.   0.  -1.   147.0338
   -0.   1.   0.   101.5173
   -0.  -0.  -0. 1.

This is the raw T1 to which the regions are registered:

Volume information for sub-03_ses-anatomy_anat_sub-03_ses-anatomy_T1w.nii.gz
  type: nii
dimensions: 256 x 256 x 192
   voxel sizes: 1.00, 1.00, 1.00
  type: FLOAT (3)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -96.0, zend: 96.0
TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -0.0069, y_r =  -0.0360, z_r =  -0.9993, c_r =-2.3092
  : x_a =  -0.9823, y_a =   0.1874, z_a =  -0., c_a =26.4827
  : x_s =  -0.1873, y_s =  -0.9816, z_s =   0.0366, c_s =19.0338
Orientation   : PIL
Primary Slice Direction: sagittal

voxel to ras transform:
   -0.0069  -0.0360  -0.999399.1125
   -0.9823   0.1874  -0.   128.2306
   -0.1873  -0.9816   0.0366   165.1330
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -0.0069  -0.9823  -0.1873   157.5619
   -0.0360   0.1874  -0.9816   141.6386
   -0.9993   0.   0.036692.9949
   -0.  -0.  -0. 1.



Il giorno ven 22 feb 2019 alle ore 22:19 Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> ha scritto:
That looks right. Can you verify that the seg (sourcedata...) is in the 
conformed anatomical space? Use mri_info can compare the output (particularly 
the vox2ras matrix) against orig.mgz. If they are the same, you can try adding 
--invertmtx to the mri_label2vol command line.

On 2/22/19 2:24 PM, Francesca Strappini wrote:

External Email - Use Caution

Th

Re: [Freesurfer] Different paradigm files

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

While the name of the paradigm file must be the same across runs and subjects, 
the contents paradigm file can be different. That should be able to handle what 
you are doing

On 2/22/19 3:42 PM, Zhi Li wrote:

External Email - Use Caution

Hello FreeSurfer experts,

It seems that all the subjects adopt a single same paradigm file in FsFast, am 
I correct? So how to handle it if each subject has different paradigm files, 
e.g., different onset time and duration? I could do the first-level analysis in 
each individual data, however, I cannot concatenate data with 'isxconcat-sess' 
due to that there is not an analysis folder generated from a same paradigm 
file. Any suggestions?

Thanks and best regards,

Lizhi



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Re: [Freesurfer] registration and resampling in native space

[Francesca Strappini]

External Email - Use Caution

Thanks!
The vox2ras matrices are not same.

This is one region:

francesca@shalimpc:~/Desktop/sub3/ROIs$ mri_info
sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
Volume information for sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
  type: nii
dimensions: 64 x 64 x 50
   voxel sizes: 3.00, 3.00, 3.00
  type: FLOAT (3)
   fov: 192.000
   dof: 0
xstart: -96.0, xend: 96.0
ystart: -96.0, yend: 96.0
zstart: -75.0, zend: 75.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -0.9988, y_r =   0.0235, z_r =   0.0427, c_r =
-2.2923
  : x_a =   0.0124, y_a =   0.9702, z_a =  -0.2420, c_a =
19.4768
  : x_s =   0.0471, y_s =   0.2412, z_s =   0.9693, c_s =
25.1269
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
   -2.9964   0.0704   0.128188.1380
0.0373   2.9106  -0.7261   -56.7017
0.1414   0.7237   2.9080   -75.2534
0.   0.   0. 1.

voxel-to-ras determinant -27

ras to voxel transform:
   -0.3329   0.0041   0.015730.7614
0.0078   0.3234   0.080423.6988
0.0142  -0.0807   0.323118.4853
   -0.  -0.  -0. 1.

Orig:

francesca@shalimpc:/usr/local/freesurfer/subjects/sub3/mri$ mri_info
orig.mgz
Volume information for orig.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
0.00 degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
-2.3092
  : x_a =   0., y_a =   0., z_a =   1., c_a =
26.4827
  : x_s =   0., y_s =  -1., z_s =   0., c_s =
19.0338

talairach xfm :
/usr/local/freesurfer/subjects/sub3/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0.   125.6908
0.   0.   1.  -101.5173
0.  -1.   0.   147.0338
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.   0.   0.   125.6908
   -0.   0.  -1.   147.0338
   -0.   1.   0.   101.5173
   -0.  -0.  -0. 1.

This is the raw T1 to which the regions are registered:

Volume information for sub-03_ses-anatomy_anat_sub-03_ses-anatomy_T1w.nii.gz
  type: nii
dimensions: 256 x 256 x 192
   voxel sizes: 1.00, 1.00, 1.00
  type: FLOAT (3)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -96.0, zend: 96.0
TR: 2250.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
0.00 degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -0.0069, y_r =  -0.0360, z_r =  -0.9993, c_r =
-2.3092
  : x_a =  -0.9823, y_a =   0.1874, z_a =  -0., c_a =
26.4827
  : x_s =  -0.1873, y_s =  -0.9816, z_s =   0.0366, c_s =
19.0338
Orientation   : PIL
Primary Slice Direction: sagittal

voxel to ras transform:
   -0.0069  -0.0360  -0.999399.1125
   -0.9823   0.1874  -0.   128.2306
   -0.1873  -0.9816   0.0366   165.1330
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -0.0069  -0.9823  -0.1873   157.5619
   -0.0360   0.1874  -0.9816   141.6386
   -0.9993   0.   0.036692.9949
   -0.  -0.  -0. 1.



Il giorno ven 22 feb 2019 alle ore 22:19 Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> ha scritto:

> That looks right. Can you verify that the seg (sourcedata...) is in the
> conformed anatomical space? Use mri_info can compare the output
> (particularly the vox2ras matrix) against orig.mgz. If they are the same,
> you can try adding --invertmtx to the mri_label2vol command line.
>
> On 2/22/19 2:24 PM, Francesca Strappini wrote:
>
> External Email - Use Caution
> Thanks a lot, Doug!
> I run the preprocessing:
> preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session
> And the runs look well registered.
>
> Then I run mri_label2vol:
> mri_label2vol --seg
> /home

[Freesurfer] Different paradigm files

[Zhi Li]

External Email - Use Caution

Hello FreeSurfer experts,

It seems that all the subjects adopt a single same paradigm file in FsFast,
am I correct? So how to handle it if each subject has different paradigm
files, e.g., different onset time and duration? I could do the first-level
analysis in each individual data, however, I cannot concatenate data with
'isxconcat-sess' due to that there is not an analysis folder generated from
a same paradigm file. Any suggestions?

Thanks and best regards,

Lizhi
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Re: [Freesurfer] vlrmerge for visualization only?

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

It depends on what you eventually want to do with it. The warning was so that 
people would not go off and do, eg, correction for multiple comparisons or 
something where there was some assumption about consistency between the 
surface-based and volume-based results.

On 2/22/19 3:18 PM, Haroon Popal wrote:

External Email - Use Caution

Hello FreeSurfer Developers,

I have functional contrast maps from the HCP dataset. I converted these to 
fsaverage space and now have GIFTIs for the surface data and a NIFTI for the 
subcortical volume data. I would like to combine these into one file for an 
analysis where I will be predicting the intensity of individual voxels. I 
thought I would use vlrmerge to do this, but noticed that the documentation 
notes that vlrmerge should only be used for visualization purposes. I was 
wondering if you thought that doing my analysis on the vlrmerge output would be 
a bad idea, even though I am not doing any real computation on the merged 
volume maps.

If this is a bad idea, is there another method that I can use to combine the 
surface and subcortical volume data?

Thank you.

--
Haroon S. Popal
Ph.D. Student
Cognitive Neuroscience Laboratory
Department of Psychology | Temple University



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[Freesurfer] vlrmerge for visualization only?

[Haroon Popal]

External Email - Use Caution

Hello FreeSurfer Developers,

I have functional contrast maps from the HCP dataset. I converted these to
fsaverage space and now have GIFTIs for the surface data and a NIFTI for
the subcortical volume data. I would like to combine these into one file
for an analysis where I will be predicting the intensity of individual
voxels. I thought I would use vlrmerge to do this, but noticed that the
documentation notes that vlrmerge should only be used for
visualization purposes. I was wondering if you thought that doing my
analysis on the vlrmerge output would be a bad idea, even though I am not
doing any real computation on the merged volume maps.

If this is a bad idea, is there another method that I can use to combine
the surface and subcortical volume data?

Thank you.

-- 
Haroon S. Popal
Ph.D. Student
Cognitive Neuroscience Laboratory
Department of Psychology | Temple University
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Re: [Freesurfer] registration and resampling in native space

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

That looks right. Can you verify that the seg (sourcedata...) is in the 
conformed anatomical space? Use mri_info can compare the output (particularly 
the vox2ras matrix) against orig.mgz. If they are the same, you can try adding 
--invertmtx to the mri_label2vol command line.

On 2/22/19 2:24 PM, Francesca Strappini wrote:

External Email - Use Caution

Thanks a lot, Doug!
I run the preprocessing:
preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session
And the runs look well registered.

Then I run mri_label2vol:
mri_label2vol --seg 
/home/francesca/Desktop/sub3/ROIs/sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
 --reg register.dof6.lta --temp template.nii.gz --o 
sourcedata_sub-03_anat_sub-03_mask_RH_V1d_registered.nii.gz

The region is in the correct space but completely misaligned. The misalignment 
is even bigger than the unregistered region. Maybe I'm not running the function 
correctly.
This set of regions are in the same space of the functional data but registered 
to the raw T1.

Best
Francesca

Il giorno ven 22 feb 2019 alle ore 18:51 Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> ha scritto:
There should be a registration file called register.dof6.lta. Use that with 
mri_label2vol passing your segmentation in with --seg. Run with --help to get 
more info

On 2/21/19 11:54 AM, Francesca Strappini wrote:

External Email - Use Caution

Thanks a lot!
Running preproc-sess with the --per-session flag is exactly was I was looking 
for!
Now that my functional runs are correctly registered to a reference image (so, 
to each other) I need to register them to a dataset of ROIs that were created 
outside freesurfer. These regions are in volume space and have the same 
resolution and box size of the functional runs. They are registered to the T1 
that was used for the reconstruction of the surface. I've tried different 
functions for the registration but nothing really worked. I suppose I need a 
registration matrix that relates these regions to the reference image I used 
during the preprocessing and to apply this to each region. What's the best 
procedure?

Best
Francesca


Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> ha scritto:
Yes,  if you run it with the --targ as orig.mgz for the given subject,
then it will sample each run into the anatomical space (this can create
enourmous data data files!). Alternatively, you can run preproc-sess
with the --per-session flag and it will align all the runs to a single
template but otherwise keep everything in the functional space

On 2/20/19 11:53 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> I'll try to find some visual way to show what I mean, but it's really
> something mild and probably negligible.
> Do you know if is it possible with mri_vol2vol to give to all the runs
> that belong to the same subject the same system coordinates? So that
> each voxel across runs will have the same coordinates. I noticed that
> the transformation matrix is written in the header but it's not really
> applied to the data. Thank you!
>
>
> Best
> Francesca
>
>
> On Mon, Feb 18, 2019, 12:57 AM Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu> 
> >> wrote:
>
> Hi Francesca
>
> can you send us an image that shows why you think it can be improved?
>
> cheers
> Bruce
> On
> Mon, 18 Feb 2019, Francesca Strappini wrote:
>
> >
> > External Email - Use Caution
> >
> > Thank you!Now the registration is better but still not perfect.
> Is there a way to improve it?
> >
> > Best
> >
> > Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu> 
> >> ha
> > scritto:
> >   Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2
> weighted? If so,
> >   you should use --t2 instead of --t1 in bbregister
> >
> >   On 2/14/19 2:18 PM, Francesca Strappini wrote:
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Hi Doug,
> >   >
> >   > Could you advise me about how to correctly run mri_vol2vol?
> >   > The functional data did not get perfectly registered to
> the anatomy so
> >   > I'm afraid I'm not running it correctly.
> >   >
> >   > Thanks!
> >   >
> >   >
> >   > Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl
> >   > mailto:fis...@nmr.mgh.harvard.edu>
> >
> 
>  ha
> >   > scritto:
> >   >
> >   > Hi Francesca

Re: [Freesurfer] downsampling orig.mgz

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

You do not need to downsample the orig.mgz in this case

On 2/22/19 1:19 PM, Ey Dude wrote:

External Email - Use Caution

Hi all,

I would like to downsample my fsnative mesh by a factor of 0.1 and sample my 
BOLD data to surface space in a next step. I have successfully downsampled my 
surf files using mris_decimate and mri_surf2surf. However, I am still not able 
to run mri_vol2surf as it is asking for the orig.mgz file which is not 
downsampled yet and which I do not know how to downsample. Do I have to use 
mri_convert to do so? Would I have to set 0.1 0.1 0.1 as my downsamling factor?

Thank you so much for your help!
Ella



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Re: [Freesurfer] petsurfer Kinetic Modeling (MRTM1, MRTM2)

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

On 2/22/19 1:47 PM, john Anderson wrote:

External Email - Use Caution

Hi Dr Greve,

Yes, in my lab we normalize DPA713 tracer to whole brain mean using the command 
fslmaths something like
fslmaths pet.nii -mask mask  -inm 1 pet_normalized_whole_brain.nii.gz

For kinetic modeling.. kindly I would like to be sure that I got it right.
I am doing kinetic modeling for two groups of subjects patients and controls.
I am following PET surfer tutorial. In the case of patients and healthy 
controls comparison I can use MRTM1 and MRTM2 correct?
I don't know about DPA713. Generally, there will be a lot of studies done to 
verify the kinetic models that can be used. MRTM2 makes more assumptions than 
MRTM1, so it is not applicable to everything.

Also for the flag "--km-hb" are the IDs that I need to feed to this flag 
represent regions of high binding affinity in patients or healthy controls or 
it doesn't matter just regions known to have high binding. For example some 
tracers show regions of high binding affinity on healthy scans as well as 
patients scans.
Again, you should look through the literature and see what people have done to 
verify MRTM2 for your tracer.



On 2/22/19 11:43 AM, john Anderson wrote:

External Email - Use Caution

Dear Dr Greve,

Thank you so much for the response! Indeed, I used MRTM2 for HB pathological 
regions and the results were very confusing Based on your response bellow, 
I understand that for pathological regions I can feed "bp.nii.gz" files from 
"MRTM1" not "MRTM2" to a surface based analyses. Is this correct?

You can actually use either MRTM1 or MRTM2 for further analysis, but I think 
the way I have it documented, you would use MRTM2.



Also for the flag "--km-ref", I have interest in doing whole brain 
normalization (i.e. all ROIs in wmparc.mgz) in this case do I need to feed all 
the numbers relevant to all ROIs in gtmseg.ctab. Is there any way to let 
--km-ref know that I want to do whole brain normalization without feeding a 
very long list of numbers?

No, I don't think so. Sorry, I never considered this case. Are you sure that is 
what you want to do?



Thank you so much for help

John



On 2/22/19 7:58 AM, john Anderson wrote:

External Email - Use Caution

Hi Dr Greve,

I would like to use petsurfet to do kinetic modeling (KM), the pipeline is 
straightforward and easy to use. Thank you so much! I would appreciate any 
clarifications relevant to my questions bellow:

1) I understand that the flag "--km-ref" define the reference region for 
normalizing PET signal. in the linear below the reference region is cerebellum 
cortex. If we need to normalize to occipital just we change the numbers based 
on labels in aparc+aseg atlas?

Yes.

--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale


2) --km-hb define the high binding regions. Are these regions represent the 
regions that are pathologically involved where we expect it to have higher PET 
signal OR it represent the regions where PET tracer has the maximum binding in 
general regardless of pathology? I mean every tracer have high level in 
specific regions in the brain is this what the flag is referring too?

I have not dealt with pathological cases with MRTM2. I would avoid using them 
for the HB region as their kinetics may be different than healthy tissue.



Thanks for any clarification,

John




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Re: [Freesurfer] registration and resampling in native space

[Francesca Strappini]

External Email - Use Caution

Thanks a lot, Doug!
I run the preprocessing:
preproc-sess -surface sub3 lhrh -fwhm 0 -s sub3 -fsd bold -per-session
And the runs look well registered.

Then I run mri_label2vol:
mri_label2vol --seg
/home/francesca/Desktop/sub3/ROIs/sourcedata_sub-03_anat_sub-03_mask_RH_V1d.nii.gz
--reg register.dof6.lta --temp template.nii.gz --o
sourcedata_sub-03_anat_sub-03_mask_RH_V1d_registered.nii.gz

The region is in the correct space but completely misaligned. The
misalignment is even bigger than the unregistered region. Maybe I'm not
running the function correctly.
This set of regions are in the same space of the functional data but
registered to the raw T1.

Best
Francesca

Il giorno ven 22 feb 2019 alle ore 18:51 Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> ha scritto:

> There should be a registration file called register.dof6.lta. Use that
> with mri_label2vol passing your segmentation in with --seg. Run with --help
> to get more info
>
> On 2/21/19 11:54 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
> Thanks a lot!
> Running preproc-sess with the --per-session flag is exactly was I was
> looking for!
> Now that my functional runs are correctly registered to a reference image
> (so, to each other) I need to register them to a dataset of ROIs that were
> created outside freesurfer. These regions are in volume space and have the
> same resolution and box size of the functional runs. They are registered to
> the T1 that was used for the reconstruction of the surface. I've tried
> different functions for the registration but nothing really worked. I
> suppose I need a registration matrix that relates these regions to the
> reference image I used during the preprocessing and to apply this to each
> region. What's the best procedure?
>
> Best
> Francesca
>
>
> Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> ha scritto:
>
>> Yes,  if you run it with the --targ as orig.mgz for the given subject,
>> then it will sample each run into the anatomical space (this can create
>> enourmous data data files!). Alternatively, you can run preproc-sess
>> with the --per-session flag and it will align all the runs to a single
>> template but otherwise keep everything in the functional space
>>
>> On 2/20/19 11:53 AM, Francesca Strappini wrote:
>> >
>> > External Email - Use Caution
>> >
>> > I'll try to find some visual way to show what I mean, but it's really
>> > something mild and probably negligible.
>> > Do you know if is it possible with mri_vol2vol to give to all the runs
>> > that belong to the same subject the same system coordinates? So that
>> > each voxel across runs will have the same coordinates. I noticed that
>> > the transformation matrix is written in the header but it's not really
>> > applied to the data. Thank you!
>> >
>> >
>> > Best
>> > Francesca
>> >
>> >
>> > On Mon, Feb 18, 2019, 12:57 AM Bruce Fischl
>> > mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>> >
>> > Hi Francesca
>> >
>> > can you send us an image that shows why you think it can be
>> improved?
>> >
>> > cheers
>> > Bruce
>> > On
>> > Mon, 18 Feb 2019, Francesca Strappini wrote:
>> >
>> > >
>> > > External Email - Use Caution
>> > >
>> > > Thank you!Now the registration is better but still not perfect.
>> > Is there a way to improve it?
>> > >
>> > > Best
>> > >
>> > > Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>> ha
>> > > scritto:
>> > >   Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2
>> > weighted? If so,
>> > >   you should use --t2 instead of --t1 in bbregister
>> > >
>> > >   On 2/14/19 2:18 PM, Francesca Strappini wrote:
>> > >   >
>> > >   > External Email - Use Caution
>> > >   >
>> > >   > Hi Doug,
>> > >   >
>> > >   > Could you advise me about how to correctly run
>> mri_vol2vol?
>> > >   > The functional data did not get perfectly registered to
>> > the anatomy so
>> > >   > I'm afraid I'm not running it correctly.
>> > >   >
>> > >   > Thanks!
>> > >   >
>> > >   >
>> > >   > Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl
>> > >   > > > 
>> > > > >> ha
>> > >   > scritto:
>> > >   >
>> > >   > Hi Francesca
>> > >   >
>> > >   > sorry, I defer to Doug on the details of mri_vol2vol.
>> > >   >
>> > >   > cheers
>> > >   > Bruce
>> > >   >
>> > >   > On Tue, 12 Feb 2019,
>> > >   > Francesca Strappini wrote:
>> > >   >
>> > >   > >
>> > >   > > E

Re: [Freesurfer] petsurfer Kinetic Modeling (MRTM1, MRTM2)

[john Anderson]

External Email - Use Caution

Hi Dr Greve,

Yes, in my lab we normalize DPA713 tracer to whole brain mean using the command 
fslmaths something like
fslmaths pet.nii -mask mask  -inm 1 pet_normalized_whole_brain.nii.gz

For kinetic modeling.. kindly I would like to be sure that I got it right.
I am doing kinetic modeling for two groups of subjects patients and controls.
I am following PET surfer tutorial. In the case of patients and healthy 
controls comparison I can use MRTM1 and MRTM2 correct?

Also for the flag "--km-hb" are the IDs that I need to feed to this flag 
represent regions of high binding affinity in patients or healthy controls or 
it doesn't matter just regions known to have high binding. For example some 
tracers show regions of high binding affinity on healthy scans as well as 
patients scans.

On 2/22/19 11:43 AM, john Anderson wrote:

External Email - Use Caution

Dear Dr Greve,

Thank you so much for the response! Indeed, I used MRTM2 for HB pathological 
regions and the results were very confusing Based on your response bellow, 
I understand that for pathological regions I can feed "bp.nii.gz" files from 
"MRTM1" not "MRTM2" to a surface based analyses. Is this correct?

You can actually use either MRTM1 or MRTM2 for further analysis, but I think 
the way I have it documented, you would use MRTM2.

Also for the flag "--km-ref", I have interest in doing whole brain 
normalization (i.e. all ROIs in wmparc.mgz) in this case do I need to feed all 
the numbers relevant to all ROIs in gtmseg.ctab. Is there any way to let 
--km-ref know that I want to do whole brain normalization without feeding a 
very long list of numbers?

No, I don't think so. Sorry, I never considered this case. Are you sure that is 
what you want to do?

Thank you so much for help

John

On 2/22/19 7:58 AM, john Anderson wrote:

External Email - Use Caution

Hi Dr Greve,

I would like to use petsurfet to do kinetic modeling (KM), the pipeline is 
straightforward and easy to use. Thank you so much! I would appreciate any 
clarifications relevant to my questions bellow:

1) I understand that the flag "--km-ref" define the reference region for 
normalizing PET signal. in the linear below the reference region is cerebellum 
cortex. If we need to normalize to occipital just we change the numbers based 
on labels in aparc+aseg atlas?

Yes.

--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale

2) --km-hb define the high binding regions. Are these regions represent the 
regions that are pathologically involved where we expect it to have higher PET 
signal OR it represent the regions where PET tracer has the maximum binding in 
general regardless of pathology? I mean every tracer have high level in 
specific regions in the brain is this what the flag is referring too?

I have not dealt with pathological cases with MRTM2. I would avoid using them 
for the HB region as their kinetics may be different than healthy tissue.

Thanks for any clarification,

John

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Re: [Freesurfer] recon-all -hires

[Nasiriavanaki, Zahra]

Hi Doug


Thank you very much for your reply.

Actually the recon finished today without any error. It just took so long to be 
done for only one subject (almost two days!)!

I checked the registration and It looks ok.

I will try -conf2hires for my other subject that -hires didn't work on it.


Thanks

Mona


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: Friday, February 22, 2019 1:07:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all -hires

sometimes the -hires flag does not work very well. For the subjects where it 
does complete, do the surfaces look ok? You can also use recon-all.v6.hires 
with the -conf2hires option (available in fs6 on our network).

On 2/21/19 2:36 PM, Nasiriavanaki, Zahra wrote:

Hi Bruce


Thank you very much for  your reply.

Here is my command:

recon-all -all -s ${subj} -i  ./${subj}/anat/016/mT1v2.nii -expert  
./scripts/expertopts/expert.opts -hires -mail zn025 -parallel

I also attached my .log file.


Thanks

MOna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Bruce Fischl 

Sent: Thursday, February 21, 2019 2:23:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all -hires

Hi MOna


what was your full command line? And can you send us the recon-all.log
file?

cheers
Bruce
On Thu, 21 Feb 2019, Nasiriavanaki, Zahra wrote:

>
> Dear Freesurfer experts
>
>
> I was running recon-all command with hires flag for our high resolution fMRI 
> data, but it has been in a
> constant status since yesterday.
>
> I copied the last few lines that are currently in my terminal. I had the same 
> issue with another
> subject before, and I had to terminate the recon-all and run it without 
> -hires.
>
> Could you please let me know how I can solve this issue?
>
>
> Thanks
>
> Mona
>
>
>
> #@# Fix Topology Copy rh Wed Feb 20 19:50:00 EST 2019
> /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts
>
>  cp ../surf/rh.orig.nofix ../surf/rh.orig
>
>
>  cp ../surf/rh.inflated.nofix ../surf/rh.inflated
>
> #@# Fix Topology lh Wed Feb 20 19:50:03 EST 2019
>
>  mris_fix_topology 
> -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
> lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T lh
>
> #@# Fix Topology rh Wed Feb 20 19:50:03 EST 2019
>
>  mris_fix_topology 
> -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
> rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T rh
>
> Waiting for PID 8994 of (8994 8997) to complete...
>
>
>
>
>



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[Freesurfer] downsampling orig.mgz

[Ey Dude]

External Email - Use CautionHi all,

 

I would like to downsample my fsnative mesh by a factor of 0.1 and sample my BOLD data to surface space in a next step. I have successfully downsampled my surf files using mris_decimate and mri_surf2surf. However, I am still not able to run mri_vol2surf as it is asking for the orig.mgz file which is not downsampled yet and which I do not know how to downsample. Do I have to use mri_convert to do so? Would I have to set 0.1 0.1 0.1 as my downsamling factor?

 

Thank you so much for your help!

Ella
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Re: [Freesurfer] ?h.white does not exist

[Weber, Wade A]

External Email - Use Caution

Ahh.  That makes sense, now.  I will do that, then.  Thank you!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Greve, Douglas N.,Ph.D.
Sent: Friday, February 22, 2019 12:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] ?h.white does not exist

you can do -autorecon2 -autorecon3 and it should work. The T2pial is done in 
the middle of  autorecon3. If you don't spec autorecon3, then it will skip the 
initial part of autorecon3, and that is what is causing the error
On 2/22/19 1:05 PM, Bruce Fischl wrote:
no, you need to run autorecon2 first
On Fri, 22 Feb 2019, Weber, Wade A wrote:


   External Email - Use Caution

I can, but how will autorecon3 run without finishing autorecon2?

-Original Message-
From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:58 AM
To: Freesurfer support list 

Subject: Re: [Freesurfer] ?h.white does not exist

Hi Wade

I don't think you can just skip autorecon3. Can you try running it first and 
see if that fixes your problems?

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A
wrote:


   External Email - Use Caution

Hi Bruce,

I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I 
have to do some Pial edits.  So I just skip autorecon3 to save time.  After I 
finish the edits, I re-run from -autorecon-pial and check again. Then I run 
autorecon3.

Wade


-Original Message-
From: 
freesurfer-boun...@nmr.mgh.harvard.edu

 On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:38 AM
To: Freesurfer support list 

Subject: Re: [Freesurfer] ?h.white does not exist

Hi Wade

from the recon-all.log it looks like you never ran autorecon3. Is
there a reason for this? Usually we run all the way through autorecon3
before running the T2pial stuff

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A wrote:



External Email - Use Caution

Hi all,



I’m trying to run –autorecon2 on 3 subjects (I already ran
–autorecon1 on them with no errors.) and I’m getting an error after
the –final_surfs part saying that lh.white does not exits (and it
doesn’t, I checked for it).  I have run about 10 other subjects, and they all 
ran fine and contain ?h.white files.  I saw 2 other strings in the archive with 
this same issue, but there was no resolution to them.
This error just started happening, and I didn’t change anything.  Here’s the 
command I’ve been using:



recon-all –subjid  -T2  -T2pial
-autorecon2



Here’s the error output:



MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/a
n
alysis_files/ANG_1034/surf/lh.wh
ite): could not open file



I’m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
on a virtual machine running Red Hat Enterprise Linux Workstation 7.6



I’ve attached the recon-all.log file



Thanks!









Wade A. Weber, MS

Psychiatry Research Program Coordinator



Dell Medical School | The University of Texas at Austin

o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu





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Re: [Freesurfer] ?h.white does not exist

[Weber, Wade A]

External Email - Use Caution

But that's the problem.  Autorecon2 won't finish because it's looking for 
lh.white, and it's not being made.  I tried to run just "recon-all -white" to 
see if that would create it, and it still didn't.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 12:06 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ?h.white does not exist

no, you need to run autorecon2 first
On Fri, 22 Feb 2019, Weber, Wade A
wrote:

>External Email - Use Caution
>
> I can, but how will autorecon3 run without finishing autorecon2?
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Bruce Fischl
> Sent: Friday, February 22, 2019 11:58 AM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] ?h.white does not exist
>
> Hi Wade
>
> I don't think you can just skip autorecon3. Can you try running it first and 
> see if that fixes your problems?
>
> cheers
> Bruce
> On Fri, 22 Feb 2019, Weber, Wade A
> wrote:
>
>>External Email - Use Caution
>>
>> Hi Bruce,
>>
>> I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I 
>> have to do some Pial edits.  So I just skip autorecon3 to save time.  After 
>> I finish the edits, I re-run from -autorecon-pial and check again. Then I 
>> run autorecon3.
>>
>> Wade
>>
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>  On Behalf Of Bruce Fischl
>> Sent: Friday, February 22, 2019 11:38 AM
>> To: Freesurfer support list 
>> Subject: Re: [Freesurfer] ?h.white does not exist
>>
>> Hi Wade
>>
>> from the recon-all.log it looks like you never ran autorecon3. Is 
>> there a reason for this? Usually we run all the way through 
>> autorecon3 before running the T2pial stuff
>>
>> cheers
>> Bruce
>> On Fri, 22 Feb 2019, Weber, Wade A wrote:
>>
>>>
>>> External Email - Use Caution
>>>
>>> Hi all,
>>>
>>>  
>>>
>>> I’m trying to run –autorecon2 on 3 subjects (I already ran
>>> –autorecon1 on them with no errors.) and I’m getting an error after 
>>> the –final_surfs part saying that lh.white does not exits (and it 
>>> doesn’t, I checked for it).  I have run about 10 other subjects, and they 
>>> all ran fine and contain ?h.white files.  I saw 2 other strings in the 
>>> archive with this same issue, but there was no resolution to them.
>>> This error just started happening, and I didn’t change anything.  Here’s 
>>> the command I’ve been using:
>>>
>>>  
>>>
>>> recon-all –subjid  -T2  -T2pial
>>> -autorecon2
>>>
>>>  
>>>
>>> Here’s the error output:
>>>
>>>  
>>>
>>> MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/
>>> a
>>> n
>>> alysis_files/ANG_1034/surf/lh.wh
>>> ite): could not open file
>>>
>>>  
>>>
>>> I’m running 
>>> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>>> on a virtual machine running Red Hat Enterprise Linux Workstation 
>>> 7.6
>>>
>>>  
>>>
>>> I’ve attached the recon-all.log file
>>>
>>>  
>>>
>>> Thanks!
>>>
>>>  
>>>
>>>  
>>>
>>> 
>>>
>>>  
>>>
>>> Wade A. Weber, MS
>>>
>>> Psychiatry Research Program Coordinator
>>>
>>>  
>>>
>>> Dell Medical School | The University of Texas at Austin
>>>
>>> o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu
>>>
>>>  
>>>
>>>
>>>
>>
>> ___
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>>
>>
>>
>
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>
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Re: [Freesurfer] ?h.white does not exist

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

you can do -autorecon2 -autorecon3 and it should work. The T2pial is done in 
the middle of  autorecon3. If you don't spec autorecon3, then it will skip the 
initial part of autorecon3, and that is what is causing the error

On 2/22/19 1:05 PM, Bruce Fischl wrote:
no, you need to run autorecon2 first
On Fri, 22 Feb 2019, Weber, Wade A wrote:

   External Email - Use Caution

I can, but how will autorecon3 run without finishing autorecon2?

-Original Message-
From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:58 AM
To: Freesurfer support list 

Subject: Re: [Freesurfer] ?h.white does not exist

Hi Wade

I don't think you can just skip autorecon3. Can you try running it first and 
see if that fixes your problems?

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A
wrote:

   External Email - Use Caution

Hi Bruce,

I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I 
have to do some Pial edits.  So I just skip autorecon3 to save time.  After I 
finish the edits, I re-run from -autorecon-pial and check again. Then I run 
autorecon3.

Wade


-Original Message-
From: 
freesurfer-boun...@nmr.mgh.harvard.edu

 On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:38 AM
To: Freesurfer support list 

Subject: Re: [Freesurfer] ?h.white does not exist

Hi Wade

from the recon-all.log it looks like you never ran autorecon3. Is
there a reason for this? Usually we run all the way through autorecon3
before running the T2pial stuff

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A wrote:


External Email - Use Caution

Hi all,



I’m trying to run –autorecon2 on 3 subjects (I already ran
–autorecon1 on them with no errors.) and I’m getting an error after
the –final_surfs part saying that lh.white does not exits (and it
doesn’t, I checked for it).  I have run about 10 other subjects, and they all 
ran fine and contain ?h.white files.  I saw 2 other strings in the archive with 
this same issue, but there was no resolution to them.
This error just started happening, and I didn’t change anything.  Here’s the 
command I’ve been using:



recon-all –subjid  -T2  -T2pial
-autorecon2



Here’s the error output:



MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/a
n
alysis_files/ANG_1034/surf/lh.wh
ite): could not open file



I’m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
on a virtual machine running Red Hat Enterprise Linux Workstation 7.6



I’ve attached the recon-all.log file



Thanks!









Wade A. Weber, MS

Psychiatry Research Program Coordinator



Dell Medical School | The University of Texas at Austin

o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu






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Re: [Freesurfer] recon-all -hires

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

sometimes the -hires flag does not work very well. For the subjects where it 
does complete, do the surfaces look ok? You can also use recon-all.v6.hires 
with the -conf2hires option (available in fs6 on our network).

On 2/21/19 2:36 PM, Nasiriavanaki, Zahra wrote:

Hi Bruce


Thank you very much for  your reply.

Here is my command:

recon-all -all -s ${subj} -i  ./${subj}/anat/016/mT1v2.nii -expert  
./scripts/expertopts/expert.opts -hires -mail zn025 -parallel

I also attached my .log file.


Thanks

MOna



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Bruce Fischl 

Sent: Thursday, February 21, 2019 2:23:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all -hires

Hi MOna


what was your full command line? And can you send us the recon-all.log
file?

cheers
Bruce
On Thu, 21 Feb 2019, Nasiriavanaki, Zahra wrote:

>
> Dear Freesurfer experts
>
>
> I was running recon-all command with hires flag for our high resolution fMRI 
> data, but it has been in a
> constant status since yesterday.
>
> I copied the last few lines that are currently in my terminal. I had the same 
> issue with another
> subject before, and I had to terminate the recon-all and run it without 
> -hires.
>
> Could you please let me know how I can solve this issue?
>
>
> Thanks
>
> Mona
>
>
>
> #@# Fix Topology Copy rh Wed Feb 20 19:50:00 EST 2019
> /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts
>
>  cp ../surf/rh.orig.nofix ../surf/rh.orig
>
>
>  cp ../surf/rh.inflated.nofix ../surf/rh.inflated
>
> #@# Fix Topology lh Wed Feb 20 19:50:03 EST 2019
>
>  mris_fix_topology 
> -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
> lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T lh
>
> #@# Fix Topology rh Wed Feb 20 19:50:03 EST 2019
>
>  mris_fix_topology 
> -rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
> rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T rh
>
> Waiting for PID 8994 of (8994 8997) to complete...
>
>
>
>
>



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Re: [Freesurfer] ?h.white does not exist

[Bruce Fischl]

no, you need to run autorecon2 first
On Fri, 22 Feb 2019, Weber, Wade A 
wrote:



   External Email - Use Caution

I can, but how will autorecon3 run without finishing autorecon2?

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:58 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ?h.white does not exist

Hi Wade

I don't think you can just skip autorecon3. Can you try running it first and 
see if that fixes your problems?

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A
wrote:


   External Email - Use Caution

Hi Bruce,

I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I 
have to do some Pial edits.  So I just skip autorecon3 to save time.  After I 
finish the edits, I re-run from -autorecon-pial and check again. Then I run 
autorecon3.

Wade


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
 On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:38 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ?h.white does not exist

Hi Wade

from the recon-all.log it looks like you never ran autorecon3. Is
there a reason for this? Usually we run all the way through autorecon3
before running the T2pial stuff

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A wrote:



External Email - Use Caution

Hi all,

 

I’m trying to run –autorecon2 on 3 subjects (I already ran
–autorecon1 on them with no errors.) and I’m getting an error after
the –final_surfs part saying that lh.white does not exits (and it
doesn’t, I checked for it).  I have run about 10 other subjects, and they all 
ran fine and contain ?h.white files.  I saw 2 other strings in the archive with 
this same issue, but there was no resolution to them.
This error just started happening, and I didn’t change anything.  Here’s the 
command I’ve been using:

 

recon-all –subjid  -T2  -T2pial
-autorecon2

 

Here’s the error output:

 

MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/a
n
alysis_files/ANG_1034/surf/lh.wh
ite): could not open file

 

I’m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
on a virtual machine running Red Hat Enterprise Linux Workstation 7.6

 

I’ve attached the recon-all.log file

 

Thanks!

 

 



 

Wade A. Weber, MS

Psychiatry Research Program Coordinator

 

Dell Medical School | The University of Texas at Austin

o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu

 





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Re: [Freesurfer] CAT12 surfaces on tkregister2 and Freeview

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

what do you mean the surface is still messed up in freeview?

On 2/22/19 8:58 AM, Loucao, Ricardo wrote:

External Email - Use Caution

Thanks for the reply!
I tried the --vol-geom orig.mgz option but to no avail.

Small update: I inspected the metadata on the surface files using mris_info and 
discovered that the ctr property was different between the CAT generated 
surface and the pial surface that was produced from recon-all, while all the 
other transforms where the same.

So I figured the difference in the ctr should be compensated by a translation.

To do that, I first created a CAT2FS.fslmat transform of the form:

1 0 0 (CAT.ctr(1)-FS.ctr(1))
0 1 0 (CAT.ctr(3)-FS.ctr(3))
0 0 0 (CAT.ctr(2)-FS.ctr(2))
0 0 0 1

(NOTE: Im sure the order of the translation portion of the matrix has something 
to do with the orientation convention but I couldnt be bothered to dig deeper - 
I got this by trial and error)

and then converted it to LTA using lta_convert:

lta_convert --infsl CAT2FS.fslmat --outlta CAT2FS.lta --src orig.mgz --trg 
orig.mgz

and then applied this transformation using mris_transform:

mris_transform ?h.CAT CAT2FS.lta ?h.CATreg

sure enough when I load CATreg on tkregister2 I see everything perfectly 
aligned, but after doing mri_vol2surf the surface overlay is still messed up in 
Freeview. Any suggestions?

Thanks in advance for the help!

Ricardo





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Re: [Freesurfer] ?h.white does not exist

[Weber, Wade A]

External Email - Use Caution

I can, but how will autorecon3 run without finishing autorecon2?

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:58 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ?h.white does not exist

Hi Wade

I don't think you can just skip autorecon3. Can you try running it first and 
see if that fixes your problems?

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A
wrote:

>External Email - Use Caution
>
> Hi Bruce,
>
> I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I 
> have to do some Pial edits.  So I just skip autorecon3 to save time.  After I 
> finish the edits, I re-run from -autorecon-pial and check again. Then I run 
> autorecon3.
>
> Wade
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Bruce Fischl
> Sent: Friday, February 22, 2019 11:38 AM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] ?h.white does not exist
>
> Hi Wade
>
> from the recon-all.log it looks like you never ran autorecon3. Is 
> there a reason for this? Usually we run all the way through autorecon3 
> before running the T2pial stuff
>
> cheers
> Bruce
> On Fri, 22 Feb 2019, Weber, Wade A wrote:
>
>>
>> External Email - Use Caution
>>
>> Hi all,
>>
>>  
>>
>> I’m trying to run –autorecon2 on 3 subjects (I already ran 
>> –autorecon1 on them with no errors.) and I’m getting an error after 
>> the –final_surfs part saying that lh.white does not exits (and it 
>> doesn’t, I checked for it).  I have run about 10 other subjects, and they 
>> all ran fine and contain ?h.white files.  I saw 2 other strings in the 
>> archive with this same issue, but there was no resolution to them.
>> This error just started happening, and I didn’t change anything.  Here’s the 
>> command I’ve been using:
>>
>>  
>>
>> recon-all –subjid  -T2  -T2pial
>> -autorecon2
>>
>>  
>>
>> Here’s the error output:
>>
>>  
>>
>> MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/a
>> n
>> alysis_files/ANG_1034/surf/lh.wh
>> ite): could not open file
>>
>>  
>>
>> I’m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>> on a virtual machine running Red Hat Enterprise Linux Workstation 7.6
>>
>>  
>>
>> I’ve attached the recon-all.log file
>>
>>  
>>
>> Thanks!
>>
>>  
>>
>>  
>>
>> 
>>
>>  
>>
>> Wade A. Weber, MS
>>
>> Psychiatry Research Program Coordinator
>>
>>  
>>
>> Dell Medical School | The University of Texas at Austin
>>
>> o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu
>>
>>  
>>
>>
>>
>
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[Freesurfer] [All] postdoctoral position in PET imaging available at MGH / Martinos Center

[Bruce Fischl]

Postdoctoral position in integrated PET/MRI at Massachusetts General Hospital / 
Harvard Medical School

The Loggia and Hadjikhani Labs are inviting applications for a Post-Doctoral 
Research Fellow in the
Department of Radiology at Massachusetts General Hospital (A.A. Martinos Center 
for Biomedical Imaging)
and Harvard Medical School.

The candidate will use state-of-the-art integrated PET/MRI scanners to image 
neuroinflammation in the
central nervous systems of migraine patients, and the effect of 
nonpharmacological therapies. The
candidate will collaborate with Dr. Julie Price and several other members of 
the Martinos Center.

Requirements include a Ph.D. in Neuroscience, Physics, Chemistry, Engineering, 
or a related field, as
well as good command of written and oral English. Experience with Positron 
Emission Tomography is
preferred. Compensation is competitive and commensurate with experience.

If interested, please email Marco Loggia (ma...@nmr.mgh.harvard.edu) with your 
CV.

 




___

Marco L. Loggia, PhD
Assistant Professor of Radiology, Harvard Medical School 
Associate Director, Center for Integrative Pain NeuroImaging (CiPNI)

A. A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 Thirteenth Street, Room 2301
Charlestown, MA 02129
Phone: (617) 643-7267
Fax: (617) 726-7422 
Email: marco.log...@mgh.harvard.edu
Web: http://scholar.harvard.edu/loggia





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Re: [Freesurfer] ?h.white does not exist

[Bruce Fischl]

Hi Wade

I don't think you can just skip autorecon3. Can you try running it first 
and see if that fixes your problems?


cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A 
wrote:



   External Email - Use Caution

Hi Bruce,

I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I 
have to do some Pial edits.  So I just skip autorecon3 to save time.  After I 
finish the edits, I re-run from -autorecon-pial and check again. Then I run 
autorecon3.

Wade


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:38 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ?h.white does not exist

Hi Wade

from the recon-all.log it looks like you never ran autorecon3. Is there a 
reason for this? Usually we run all the way through autorecon3 before running 
the T2pial stuff

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A wrote:



External Email - Use Caution

Hi all,

 

I’m trying to run –autorecon2 on 3 subjects (I already ran –autorecon1
on them with no errors.) and I’m getting an error after the
–final_surfs part saying that lh.white does not exits (and it doesn’t,
I checked for it).  I have run about 10 other subjects, and they all ran fine 
and contain ?h.white files.  I saw 2 other strings in the archive with this 
same issue, but there was no resolution to them.
This error just started happening, and I didn’t change anything.  Here’s the 
command I’ve been using:

 

recon-all –subjid  -T2  -T2pial
-autorecon2

 

Here’s the error output:

 

MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/an
alysis_files/ANG_1034/surf/lh.wh
ite): could not open file

 

I’m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
on a virtual machine running Red Hat Enterprise Linux Workstation 7.6

 

I’ve attached the recon-all.log file

 

Thanks!

 

 



 

Wade A. Weber, MS

Psychiatry Research Program Coordinator

 

Dell Medical School | The University of Texas at Austin

o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu

 





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Re: [Freesurfer] Cortical thickness values extraction issue

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

You can make the bonferroni correction from of mri_glmfit-sim the same as qdec 
by not including --2spaces (the bonferroni correction in qdec is actually 1, 
not 0). Also, if you want to use such a low cluster forming threshold 
(1.3=p<.05), then you should use permutation and not MC (MC is not valid at 
such low thresholds).

On 2/22/19 7:49 AM, Giuliana Klencklen wrote:

External Email - Use Caution

Thanks Douglas, that makes sense. I have run mri_glmfit-sim and have that table 
file.
However, the cortical thickness values for each cluster displayed in that table 
can’t be used because the clusters (something.sig.cluster.mgh opened with 
tksurfer) do not match exactly (but are very similar to) those previously 
generated with QDEC. I do not understand the cause of this issue because all 
the stats I used, i.e., threshold, statistical correction, level of smooting, 
seem to be the same between both qdec and mri_glmfit-sim.

I send you here a typical example of the problematic clusters, as well as the 
summary for both qdec and mri_glmfit-sim. They appear similar except for the 
Bonferroni correction that is set at 2 for the mri_glmfit-sim while it is set 
at 0 for the qdec version? If it is the source of the current issue, how can I 
configure the Bonferroni correction? If not, do you have any idea how I can 
resolve the problem?

Many thanks in advance.

Regards,
Giuliana Klencklen
[QdecGroupComparison.jpg]

On Fri, Feb 15, 2019 at 5:24 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
This can happen if the label is small and/or you've used a lot of smoothing. It 
is better to do this kind of thing in fsaverage space rather than moving the 
labels back to the individual space. If you've run mri_glmfit-sim, then it 
should have created a table file  (something.y.ocn.dat). This file will have a 
row for each subject and a column for each cluster. The value will be the mean 
for that subject in that cluster.

On 2/15/19 6:23 AM, Giuliana Klencklen wrote:

External Email - Use Caution

Hi FS experts,

I did group-level, surface-based, vertex-wise analysis for baseline and 
longitudinal data. I used Qdec and do the same work with the fsgd version 
(mri_glmfit-sim command) to double-check the data.

I created label files with tksurfer for each of the clusters showing a 
significant between-group difference. Then, I used the following command stream 
to extract the cortical thickness values for each subject and cluster: 
mri_label2label, mris_anatomical_stats, and aparcstats2table.
E.g.,
mri_label2label --srcsubject fsaverage --srclabel 
/home/jagust/gklenck/Long_MRI/lh.ac-baseline-rostralmiddlefrontal.label 
--trgsubject ${s}_tp1 --trglabel 
${s}_tp1/label/lh.ac-baseline-rostralmiddlefrontal.label --hemi lh --regmethod 
surface

mris_anatomical_stats -l lh.ac-baseline-rostralmiddlefrontal.label -t 
lh.thickness -b -f ${s}_tp1/stats/lh.ac-baseline-rostralmiddlefrontal.stats 
${s}_tp1 lh

aparcstats2table --subjects ${s}_tp1 --hemi lh --parc 
ac-baseline-rostralmiddlefrontal --meas thickness --tablefile 
${out_dir}/lh.ac-baseline-rostralmiddlefrontal.aparc_stats.txt

Subsequently, when I conducted between-group comparisons for each cluster, a 
couple of clusters (7 out of 16) do not show a significant difference - which 
does not make sense. This problem seems to appear randomly.

Help to the FS archives, I tried to use mri_segstats command but was not able 
to find a correct combination of arguments. If this is the right track to solve 
this problem, what combination of arguments should I use? And if this is not, 
do you have any idea how I can solve this problem?

Many thanks in advance.

Regards,
Giuliana


--
Giuliana Klencklen, Ph.D.

Helen Wills Neuroscience Institute
University of California, Berkeley
118 Barker Hall
Berkeley, CA 94720-3190
510-395-0040
giuliana.klenck...@berkeley.edu



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--
Giuliana Klencklen, Ph.D.

Helen Wills Neuroscience Institute
University of California, Berkeley
118 Barker Hall
Berkeley, CA 94720-3190
510-395-0040
giuliana.klenck...@berkeley.edu



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Re: [Freesurfer] ?h.white does not exist

[Weber, Wade A]

External Email - Use Caution

Hi Bruce,

I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I 
have to do some Pial edits.  So I just skip autorecon3 to save time.  After I 
finish the edits, I re-run from -autorecon-pial and check again. Then I run 
autorecon3.

Wade


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:38 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ?h.white does not exist

Hi Wade

from the recon-all.log it looks like you never ran autorecon3. Is there a 
reason for this? Usually we run all the way through autorecon3 before running 
the T2pial stuff

cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A wrote:

> 
> External Email - Use Caution
> 
> Hi all,
> 
>  
> 
> I’m trying to run –autorecon2 on 3 subjects (I already ran –autorecon1 
> on them with no errors.) and I’m getting an error after the 
> –final_surfs part saying that lh.white does not exits (and it doesn’t, 
> I checked for it).  I have run about 10 other subjects, and they all ran fine 
> and contain ?h.white files.  I saw 2 other strings in the archive with this 
> same issue, but there was no resolution to them.
> This error just started happening, and I didn’t change anything.  Here’s the 
> command I’ve been using:
> 
>  
> 
> recon-all –subjid  -T2  -T2pial 
> -autorecon2
> 
>  
> 
> Here’s the error output:
> 
>  
> 
> MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/an
> alysis_files/ANG_1034/surf/lh.wh
> ite): could not open file
> 
>  
> 
> I’m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
> on a virtual machine running Red Hat Enterprise Linux Workstation 7.6
> 
>  
> 
> I’ve attached the recon-all.log file
> 
>  
> 
> Thanks!
> 
>  
> 
>  
> 
> 
> 
>  
> 
> Wade A. Weber, MS
> 
> Psychiatry Research Program Coordinator
> 
>  
> 
> Dell Medical School | The University of Texas at Austin
> 
> o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu
> 
>  
> 
> 
>

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Re: [Freesurfer] ?h.white does not exist

[Bruce Fischl]

Hi Wade

from the recon-all.log it looks like you never ran autorecon3. Is there a 
reason for this? Usually we run all the way through autorecon3 before 
running the T2pial stuff


cheers
Bruce
On Fri, 22 Feb 2019, Weber, Wade A wrote:



External Email - Use Caution

Hi all,

 

I’m trying to run –autorecon2 on 3 subjects (I already ran –autorecon1 on them 
with no errors.) and I’m
getting an error after the –final_surfs part saying that lh.white does not 
exits (and it doesn’t, I
checked for it).  I have run about 10 other subjects, and they all ran fine and 
contain ?h.white
files.  I saw 2 other strings in the archive with this same issue, but there 
was no resolution to them.
This error just started happening, and I didn’t change anything.  Here’s the 
command I’ve been using:

 

recon-all –subjid  -T2  -T2pial -autorecon2

 

Here’s the error output:

 

MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/analysis_files/ANG_1034/surf/lh.wh
ite): could not open file

 

I’m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c on a 
virtual machine running Red
Hat Enterprise Linux Workstation 7.6

 

I’ve attached the recon-all.log file

 

Thanks!

 

 



 

Wade A. Weber, MS

Psychiatry Research Program Coordinator

 

Dell Medical School | The University of Texas at Austin

o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu

 


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Re: [Freesurfer] Templates used for eTIV computation in recon-all

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

That 3T18yo atlas is added when you include the -3T option (which for some 
reason you did when you used -all but not -autorecon1). It is expected that 
they could give different eTIVs. In the example you give below, all but the 
FS5-autorecon1 were fairly close. Did you check the registrations?

On 2/15/19 11:52 AM, Ami Tsuchida wrote:

External Email - Use Caution

Dear experts,

We were comparing recon-all output of Freesurfer 5.3 and 6.0 in our database, 
and found that eTIV values can increase by up to 40% going from 5.3 to 6.0. 
However, closer inspection revealed that it was not due to the version per se, 
but how we call recon-all. We had computed one version with recon-all -all, and 
the other with recon-all -autorecon1, thinking that eTIV output from these two 
were identical. Some testing in two versions with two flags showed that in both 
versions, using -all flag automatically add

--atlas 3T18yoSchwartzReactN32_as_orig



in the talairach_avi command, while -autorecon1 does not. The talairach_avi.log 
indicates that the former set the target to 3T18yoSchwartzReactN32_as_orig, 
while the latter use the 711-2C_as_mni_average_305.



My first question is, is this some kind of bug or is it intentional?


We thought that the difference in the templates caused the change in the 
estimates, but it looks like that's not the only answer:
We still get very different eTIV values from -autorecon1 option in FS5.3 and 
6.0, even though the target images are the same. The results from -all option 
are more comparable.



Here is the eTIV from one subject we tested:


-FS5, autorecon1: 1318267


-FS6, autorecon1: 1561456


-FS5, -all: 1662005


-FS6, -all:1678336


Here I attached the shortened recon-all log files from two versions of 
Freesurfer, with with -all or -autorecon1, as well as eTIV output from the four 
variations we tested in one subject.
Could you help us resolve why we get the varying estimates?





Thank you!




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Re: [Freesurfer] commends of GLM for volume

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

See slide 47 here
https://fscph.nru.dk/slides/Emily/Copenhagen_Group_Analysis.pdf

On 2/19/19 6:07 PM, ?? wrote:

External Email - Use Caution

Yes, one more question where can I get the example of mri glimfit  for ROI 
analysis

---Original---
From: "Greve, Douglas 
N.,Ph.D."
Date: Tue, Feb 19, 2019 22:47 PM
To: 
"freesurfer@nmr.mgh.harvard.edu";
Subject: Re: [Freesurfer] commends of GLM for volume

You can get the volumes of structures, eg, hipocampal volume, for each
structure and subject using asegstats2table, then mri_glmfit can read in
that table. But it is an ROI analysis, not a voxel-wise analysis. Is
that what you want to do?

On 2/19/19 5:20 PM, ?? wrote:
>
> External Email - Use Caution
>
> Or I can not use mri to do the Glm for subcortical volume analysis ?
>
> ---Original---
> *From:* "Greve, Douglas 
> N.,Ph.D."
> *Date:* Tue, Feb 19, 2019 21:29 PM
> *To:* 
> "freesurfer@nmr.mgh.harvard.edu";
> *Subject:* Re: [Freesurfer] commends of GLM for volume
>
> IIs this an fMRI analysis? If so, you should use permutation for both
> surface and subcort. See
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLevelPerm
>
> On 2/19/19 6:00 AM, ?? wrote:
> >
> > External Email - Use Caution
> >
> > Hello Greve,
> > I am glad to tell you that after 3 hours, something did print more on
> > terminal. when I was doing the GLM follow the tutorial, it only
> > provided the example of the cortical thickness. And I did not know how
> > to transfer it into volume.
> > Here is my commends
> >
> > mris_preproc --fsgd FSGD/PDDvsHC.fsgd --cache-in
> > volmue.fwhm10.fsaverage --target fsaverage --hemi lh --out
> > lh.PDDvsHC.volume.10.mgh
> >
> > mri_glmfit --y lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C
> > Contras-HC-PDD.mtx --surf fsaverage lh --cortex --glmdir
> > lh.volume.PDDvsHC.glimdir --eres-save
> >
> > mri_glmfit-sim --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp
> > 999 --2spaces
> >
> > We I check the results, it still talked about the cortical thickness ,
> > so could you tell me how to change this commends to the volume of
> > subcortical. Or do you have the example which use GLM for comparing
> > the difference of subcortical volume between two groups.
> >
> > Thanks so much for your help
> >
> > Yours
> >
> > Zeng
> >
> > Here is the results
> >
> >
> > ClusterNoMax VtxMax Size(mm^2)MNIX MNIY MNIZCWPCWPLowCWPHi
> > NVtxsWghtVtx Annot
> >
> >
> > 16.960 86488 4544.63 15.7-77.36.70.000200.00.00040
> > 789115125.67pericalcarine
> >
> >
> > 23.529158070 3287.33 55.0-52.98.20.000200.00.00040
> > 679611225.54inferiorparietal
> >
> >
> > 32.630 67804 1909.67 43.3 45.8 -9.30.002200.001400.00300 2858
> > 4399.15parsorbitalis
> >
> > Here is the terminal output.
> >
> > $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
> >
> >
> > cwd /Volumes/NIU20/volumetric_FS/glm
> >
> >
> > cmdline mri_glmfit.bin --glmdir lh.PDDvsHC.volume.glmdir --y
> > lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C
> > Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage lh --eres-save
> >
> >
> > sysnameDarwin
> >
> >
> > hostname dyn3199-104.wlan.ic.ac.uk
> >
> >
> > machinex86_64
> >
> >
> > usercengzhou
> >
> >
> > FixVertexAreaFlag = 1
> >
> >
> > UseMaskWithSmoothing1
> >
> >
> > OneSampleGroupMean 0
> >
> >
> > y/Volumes/NIU20/volumetric_FS/glm/lh.PDDvsHC.volume.10.mgh
> >
> >
> > logyflag 0
> >
> >
> > usedti0
> >
> >
> > FSGD FSGD/PDDvsHC.fsgd
> >
> >
> >
> labelmask/Volumes/NIU20/volumetric_FS/glm/fsaverage/label/lh.cortex.label
> >
> >
> > maskinv 0
> >
> >
> > glmdir lh.PDDvsHC.volume.glmdir
> >
> >
> > IllCondOK 0
> >
> >
> > ReScaleX 1
> >
> >
> > DoFFx 0
> >
> >
> > ResidualFWHM 14.826153
> >
> >
> > SearchSpace 73852.172969
> >
> >
> > anattype surface
> >
> >
> >
> >
> > cd /Volumes/NIU20/volumetric_FS/glm
> >
> >
> > /Applications/freesurfer/bin/mri_glmfit-sim
> >
> >
> > --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 999 --2spaces
> >
> >
> >
> > $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
> >
> >
> > Mon Feb 18 15:52:07 GMT 2019
> >
> >
> > Darwin dyn3199-104.wlan.ic.ac.uk 14.5.0 Darwin Kernel Version 14.5.0:
> > Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
> >
> >
> > cengzhou
> >
> >
> > setenv SUBJECTS_DIR /Volumes/NIU20/volumetric_FS/glm
> >
> >
> > FREESURFER_HOME /Applications/freesurfer
> >
> >
> >
> > Original mri_glmfit command line:
> >
> >
> > cmdline mri_glmfit.bin --glmdir rh.PDDvsHC.volume.glmdir --y
> > rh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C
> > Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage rh --eres-save
> >
> >
> >
> > DoSim = 0
> >
> >
> > UseCache = 1
> >
> >
> > DoPoll = 0
> >
> >
> > DoPBSubmit = 0
> >
> >
> > D

Re: [Freesurfer] petsurfer Kinetic Modeling (MRTM1, MRTM2)

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

On 2/22/19 11:43 AM, john Anderson wrote:

External Email - Use Caution

Dear Dr Greve,

Thank you so much for the response! Indeed, I used MRTM2 for HB pathological 
regions and the results were very confusing Based on your response bellow, 
I understand that for pathological regions I can feed "bp.nii.gz" files from 
"MRTM1" not "MRTM2" to a surface based analyses. Is this correct?
You can actually use either MRTM1 or MRTM2 for further analysis, but I think 
the way I have it documented, you would use MRTM2.

Also for the flag "--km-ref", I have interest in doing whole brain 
normalization (i.e. all ROIs in wmparc.mgz) in this case do I need to feed all 
the numbers relevant to all ROIs in gtmseg.ctab. Is there any way to let 
--km-ref know that I want to do whole brain normalization without feeding a 
very long list of numbers?
No, I don't think so. Sorry, I never considered this case. Are you sure that is 
what you want to do?

Thank you so much for help
John

On 2/22/19 7:58 AM, john Anderson wrote:

External Email - Use Caution

Hi Dr Greve,

I would like to use petsurfet to do kinetic modeling (KM), the pipeline is 
straightforward and easy to use. Thank you so much! I would appreciate any 
clarifications relevant to my questions bellow:

1) I understand that the flag "--km-ref" define the reference region for 
normalizing PET signal. in the linear below the reference region is cerebellum 
cortex. If we need to normalize to occipital just we change the numbers based 
on labels in aparc+aseg atlas?

Yes.

--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale


2) --km-hb define the high binding regions. Are these regions represent the 
regions that are pathologically involved where we expect it to have higher PET 
signal OR it represent the regions where PET tracer has the maximum binding in 
general regardless of pathology? I mean every tracer have high level in 
specific regions in the brain is this what the flag is referring too?

I have not dealt with pathological cases with MRTM2. I would avoid using them 
for the HB region as their kinetics may be different than healthy tissue.



Thanks for any clarification,

John




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Re: [Freesurfer] QDEC Longitudinal Analysis: Missing spc option from dropdown menu

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

qdec is not really being supported anymore. It is better if you use the command 
 line stream

On 2/21/19 6:22 PM, Arsenije Subotic wrote:

External Email - Use Caution

Dear Freesurfer experts,


I am having issues choosing the spc option for my QDEC two stage longitudinal 
analysis as it is not there. The spc files are all present in my participants 
files and the Qdecrc file is in the qdec subdirectory containing the line 
long.thickness-spc. Is there a way to bypass this problem somehow?


Thank you,

Arsenije


---

Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subot...@ucalgary.ca




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Re: [Freesurfer] registration and resampling in native space

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

There should be a registration file called register.dof6.lta. Use that with 
mri_label2vol passing your segmentation in with --seg. Run with --help to get 
more info

On 2/21/19 11:54 AM, Francesca Strappini wrote:

External Email - Use Caution

Thanks a lot!
Running preproc-sess with the --per-session flag is exactly was I was looking 
for!
Now that my functional runs are correctly registered to a reference image (so, 
to each other) I need to register them to a dataset of ROIs that were created 
outside freesurfer. These regions are in volume space and have the same 
resolution and box size of the functional runs. They are registered to the T1 
that was used for the reconstruction of the surface. I've tried different 
functions for the registration but nothing really worked. I suppose I need a 
registration matrix that relates these regions to the reference image I used 
during the preprocessing and to apply this to each region. What's the best 
procedure?

Best
Francesca


Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> ha scritto:
Yes,  if you run it with the --targ as orig.mgz for the given subject,
then it will sample each run into the anatomical space (this can create
enourmous data data files!). Alternatively, you can run preproc-sess
with the --per-session flag and it will align all the runs to a single
template but otherwise keep everything in the functional space

On 2/20/19 11:53 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> I'll try to find some visual way to show what I mean, but it's really
> something mild and probably negligible.
> Do you know if is it possible with mri_vol2vol to give to all the runs
> that belong to the same subject the same system coordinates? So that
> each voxel across runs will have the same coordinates. I noticed that
> the transformation matrix is written in the header but it's not really
> applied to the data. Thank you!
>
>
> Best
> Francesca
>
>
> On Mon, Feb 18, 2019, 12:57 AM Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu> 
> >> wrote:
>
> Hi Francesca
>
> can you send us an image that shows why you think it can be improved?
>
> cheers
> Bruce
> On
> Mon, 18 Feb 2019, Francesca Strappini wrote:
>
> >
> > External Email - Use Caution
> >
> > Thank you!Now the registration is better but still not perfect.
> Is there a way to improve it?
> >
> > Best
> >
> > Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu> 
> >> ha
> > scritto:
> >   Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2
> weighted? If so,
> >   you should use --t2 instead of --t1 in bbregister
> >
> >   On 2/14/19 2:18 PM, Francesca Strappini wrote:
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Hi Doug,
> >   >
> >   > Could you advise me about how to correctly run mri_vol2vol?
> >   > The functional data did not get perfectly registered to
> the anatomy so
> >   > I'm afraid I'm not running it correctly.
> >   >
> >   > Thanks!
> >   >
> >   >
> >   > Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl
> >   > mailto:fis...@nmr.mgh.harvard.edu>
> >
> 
>  ha
> >   > scritto:
> >   >
> >   > Hi Francesca
> >   >
> >   > sorry, I defer to Doug on the details of mri_vol2vol.
> >   >
> >   > cheers
> >   > Bruce
> >   >
> >   > On Tue, 12 Feb 2019,
> >   > Francesca Strappini wrote:
> >   >
> >   > >
> >   > > External Email - Use Caution
> >   > >
> >   > > Thank you for the reply!
> >   > > I run:
> >   > > mri_vol2vol --reg register.dat --mov
> func_data.nii.gz --targ
> >   > > /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o
> >   > func_data_registered2T1.nii.gz --no-resample
> >   > >
> >   > > Then I checked the registration and it seems that
> the original
> >   > run is better aligned to the T1 than
> >   > > the registered one. Maybe am I not running
> mri_vol2vol correctly?
> >   > >
> >   > > Thanks!
> >   > > Best
> >   > >
> >   > >
> >   > > Il giorno mar 12 feb 2019 alle ore 02:19 Bruce Fischl
> >  

Re: [Freesurfer] dt_recon registration check

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

See here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration_freeview

On 2/21/19 3:01 PM, Daniel Davidson Callow wrote:

External Email - Use Caution

Hello,

I have run through dt_recon and want to use anatomically based segmentations 
(aseg) to create ROIs for the diffusion-weighted data using mri_vol2vol.

I ran

mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ 
$subj_dir/diffusion_recons/${subj}.${cond}/mri/aparc+aseg.mgz --inv --interp 
nearest --o $subj_dir/dtrecon/${subj}.${cond}./aparc+aseg2diff.nii.gz --reg 
$subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg

Which worked.

I now want to quality check and make sure the ROIs I make from the aseg2diff 
segmentation is accurately aligned in diffusion space (such as making sure the 
hippocampal ROIs for aseg are actually going to overlay the hippocampal region 
of the diffusion data). My question is what is the best way to quality check 
for quality registration between the diffusion and anatomical data?

Best,
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
dcal...@umd.edu
443-254-6298




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Re: [Freesurfer] PETSurfer: Needs for gtmseg

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

It should have corrected surface.

On 2/22/19 3:26 AM, Matthieu VANHOUTTE wrote:
>  External Email - Use Caution
>
> Dear FS's experts,
>
> In the perspective of correcting generated surfaces errors or defects,
> does the gtmseg command need corrected surfaces or could it be launch
> independently before having these corrected surfaces ?
>
> Best,
>
> Matthieu
>
>
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Re: [Freesurfer] Registering from subjects to a common volume

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

that looks right to me

On 2/22/19 6:25 AM, Tim Schäfer wrote:
>  External Email - Use Caution
>
> Nevermind, I think I got it to work:
>
> mri_vol2vol --mov subject_x_samples.mgz --s subject_x --targ 
> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o 
> subject_x_samples_in_mni305.mgz --no-save-reg --interp nearest
>
> If anybody could confirm that this makes sense, I'd still be grateful. ;)
>
>> On February 22, 2019 at 11:27 AM Tim Schäfer  wrote:
>>
>>
>>  External Email - Use Caution
>>
>> Dear list,
>>
>> I would like to register volume data from several subjects to a common 
>> volume, e.g., the volume of the fsaverage subject.
>>
>> The volume data contains some marked voxels and is in the same space as the 
>> orig.mgz of the respective subject. I would like to find/see the positions 
>> of the voxels in a volume like 
>> $FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz.
>>
>> This would require a non-linear, inter-subject registration I guess. How can 
>> I do this in FreeSurfer? Most likely I can somehow use mri_vol2vol to 
>> achieve this, but I don't see how. Is the talairach transform what I want?
>>
>> -- 
>> Tim
>>
>> ___
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>>


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Re: [Freesurfer] petsurfer Kinetic Modeling (MRTM1, MRTM2)

[john Anderson]

External Email - Use Caution

Dear Dr Greve,

Thank you so much for the response! Indeed, I used MRTM2 for HB pathological 
regions and the results were very confusing Based on your response bellow, 
I understand that for pathological regions I can feed "bp.nii.gz" files from 
"MRTM1" not "MRTM2" to a surface based analyses. Is this correct?

Also for the flag "--km-ref", I have interest in doing whole brain 
normalization (i.e. all ROIs in wmparc.mgz) in this case do I need to feed all 
the numbers relevant to all ROIs in gtmseg.ctab. Is there any way to let 
--km-ref know that I want to do whole brain normalization without feeding a 
very long list of numbers?

Thank you so much for help
John

On 2/22/19 7:58 AM, john Anderson wrote:

External Email - Use Caution

Hi Dr Greve,

I would like to use petsurfet to do kinetic modeling (KM), the pipeline is 
straightforward and easy to use. Thank you so much! I would appreciate any 
clarifications relevant to my questions bellow:

1) I understand that the flag "--km-ref" define the reference region for 
normalizing PET signal. in the linear below the reference region is cerebellum 
cortex. If we need to normalize to occipital just we change the numbers based 
on labels in aparc+aseg atlas?

Yes.

--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale

2) --km-hb define the high binding regions. Are these regions represent the 
regions that are pathologically involved where we expect it to have higher PET 
signal OR it represent the regions where PET tracer has the maximum binding in 
general regardless of pathology? I mean every tracer have high level in 
specific regions in the brain is this what the flag is referring too?

I have not dealt with pathological cases with MRTM2. I would avoid using them 
for the HB region as their kinetics may be different than healthy tissue.

Thanks for any clarification,

John___
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Re: [Freesurfer] petsurfer Kinetic Modeling (MRTM1, MRTM2)

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

On 2/22/19 7:58 AM, john Anderson wrote:

External Email - Use Caution

Hi Dr Greve,
I would like to use petsurfet to do kinetic modeling (KM), the pipeline is 
straightforward and easy to use. Thank you so much! I would appreciate any 
clarifications relevant to my questions bellow:
1) I understand that the flag "--km-ref" define the reference region for 
normalizing PET signal. in the linear below the reference region is cerebellum 
cortex. If we need to normalize to occipital just we change the numbers based 
on labels in aparc+aseg atlas?
Yes.

--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale


2) --km-hb define the high binding regions. Are these regions represent the 
regions that are pathologically involved where we expect it to have higher PET 
signal OR it represent the regions where PET tracer has the maximum binding in 
general regardless of pathology? I mean every tracer have high level in 
specific regions in the brain is this what the flag is referring too?
I have not dealt with pathological cases with MRTM2. I would avoid using them 
for the HB region as their kinetics may be different than healthy tissue.

Thanks for any clarification,
John



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Re: [Freesurfer] Recon-all XL defect detected...

[Matthieu VANHOUTTE]

   External Email - Use Caution


Hi Bruce,

Did you have time to tale a look at ?

Best,

Matthieu

On 19/02/2019 16:39, Bruce Fischl wrote:

will do
On Tue, 19 Feb 2019, Matthieu VANHOUTTE wrote:



External Email - Use Caution

Hi Bruce,

I don't see major thing that could be wrong.

I uploaded on the FileDrop the subject directory compressed. Could 
you have a look at it and tell me

what you think ?

Best,
Matthieu

On 18/02/2019 15:56, Bruce Fischl wrote:
  Hi Matthieu

  have you looked at the lh.inflated.nofix to see if anything 
major is wrong? The code
  doesn't exit when it detects an XL defect - it just warns you 
and doesn't search as
  thoroughly for solutions (which would take forever). It sounds 
like the 0 faces error is
  your problem, but they are likely related. Take a look at the 
inflated.nofix and see if
  you can identify the XL defect. It is probably near the back of 
the brain since it is

  one of the first defects encountered.

  cheers
  Bruce




   On Mon, 18 Feb 2019, Matthieu VANHOUTTE wrote:


    External Email - Use Caution

    Dear Freesurfer's experts,

    I have run recon-all on one subject and it stopped with a 
"XL defect

    detected..."  (please see below
    the log):

    #@# Fix Topology lh Sat Feb 16 08:22:31 CET 2019

     mris_fix_topology -rusage
/FS6.0.1/awellv3s013/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere
    qsphere.nofix -ga -seed 1234 awellv3s013 lh

    reading spherical homeomorphism from 'qsphere.nofix'
    using genetic algorithm with optimized parameters
    setting seed for random number genererator to 1234

*
    Topology Correction Parameters
    retessellation mode:   genetic search
    number of patches/generation : 10
    number of generations :    10
    surface mri loglikelihood coefficient : 1.0
    volume mri loglikelihood coefficient :  10.0
    normal dot loglikelihood coefficient :  1.0
    quadratic curvature loglikelihood coefficient : 1.0
    volume resolution : 2
    eliminate vertices during search :  1
    initial patch selection :   1
    select all defect vertices :    0
    ordering dependant retessellation:  0
    use precomputed edge table :    0
    smooth retessellated patch :    2
    match retessellated patch : 1
    verbose mode :  0

*
    INFO: assuming .mgz format
    $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 
zkaufman Exp $
      $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman 
Exp $
    before topology correction, eno=-112 (nv=135382, 
nf=270988, ne=406482, g=57)
    using quasi-homeomorphic spherical map to tessellate 
cortical surface...


    Correction of the Topology
    Finding true center and radius of Spherical Surface...done
    Surface centered at (0,0,0) with radius 100.0 in 10 
iterations

    marking ambiguous vertices...
    39303 ambiguous faces found in tessellation
    segmenting defects...
    22 defects found, arbitrating ambiguous regions...
    analyzing neighboring defects...
      -merging segment 16 into 2
    21 defects to be corrected
    0 vertices coincident
    reading input surface 
FS6.0.1/awellv3s013/surf/lh.qsphere.nofix...

    reading brain volume from brain...
    reading wm segmentation from wm...
    Computing Initial Surface Statistics
      -face   loglikelihood: -9.1744  (-4.5872)
      -vertex loglikelihood: -6.3047  (-3.1523)
      -normal dot loglikelihood: -3.6091  (-3.6091)
      -quad curv  loglikelihood: -5.8524  (-2.9262)
      Total Loglikelihood : -24.9405

    CORRECTING DEFECT 0 (vertices=41, convex hull=76, v0=1825)
    After retessellation of defect 0 (v0=1825), euler #=-4
    (114791,342427,227632) : difference with
    theory (-18) = -14

    CORRECTING DEFECT 1 (vertices=22, convex hull=53, v0=6219)
    After retessellation of defect 1 (v0=6219), euler #=-3
    (114805,342485,227677) : difference with
    theory (-17) = -14

    CORRECTING DEFECT 2 (vertices=19736, convex hull=2755, 
v0=16117)

    normal vector of length zero at vertex 115020 with 0 faces
    vertex 115020 has 0 face
    XL d

Re: [Freesurfer] How to get gray matter tissue via freesurfer?

[Bruce Fischl]

can you clarify what you mean by "gray matter segmentation"? We provide 
both a binary segmentation of gray matter (in the aseg.mgz) as well as 
various gyral/sulcal parcellations (in e.g. the aparc+aseg.mgz)


cheers
Bruce


On Fri, 22 Feb 2019, 潘祖江 wrote:



External Email - Use Caution

Hi all,
I have came across a problem.

As we know, by using recon-all command we can get white matter segmentation,
but what I need to use is gray matter segmentation, so what could I do to get 
ideal
segmentation?

Hope to get response from someone who concerns.

Thanks.


--


潘祖江 Zujiang Pan

清华大学 计算机科学与技术 

Department of Computer Science and Technology

Tsinghua University, 100084

+86 15600487317

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Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label

[Bruce Fischl]

Hi Yi Leng

no, I guess the thing to do for now is use the labels, which appear 
reasonable, and not the .annot


cheers
Bruce
On Fri, 22 Feb 2019, Yi Leng Fung wrote:



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Hello Bruce, 

I am just checking in as I am curious if there has been any update available 
regarding the entorhinal
and perirhinal annot/labelling? I hope I haven't missed anything. 

Thank you! 

Yi Leng 

On Sun, Feb 10, 2019, 16:32 Yi Leng Fung  wrote:

Hello Bruce,

I have uploaded a tarred and gzipped subject onto the ftp site. Do let me know 
if there is
anything else I could help with.

Cheers,
Yi Leng


On Sat, Feb 9, 2019 at 2:25 AM Bruce Fischl  wrote:
  Hi Yi-Leng

  can you upload the worst subject to our ftp site (the entire gzipped and
  tarred subject dir please).

  cheers
  Bruce
  On Fri, 8 Feb 2019, Yi Leng Fung wrote:

  >
  > External Email - Use Caution
  >
  > [64b4f0f085b91c1f8130601d2cf65e8861fc5b7f.png?u=328927]
  > Hello Bruce, 
  >
  > On all four of our studies, the labels and the annot look similar in 
the sense that
  almost the entire
  > rh.perirhinal_exvivo.thresh.label was contained within the
  rh.entorhinal_exvivo.thresh.label (screenshot of the
  > right hemisphere with labels and annot attached for your reference). The
  resulting annot label shows an extremely
  > under-represented perirhinal on the right hemispheres. The left 
hemispheres did not
  show such a dramatic overlap.
  >
  > Cheers,
  > Yi-Leng
  >
  >
  > On Fri, Feb 8, 2019 at 3:44 PM Bruce Fischl 
 wrote:
  > Do the labels look better than the annot?
  >
  > On Feb 6, 2019, at 10:15 PM, Yi Leng Fung 
 wrote:
  >
  >       External Email - Use Caution
  >
  >       Hello FreeSurfer team,
  >
  > Thank you for providing the recon-all patch. We have applied this to 
four studies
  and have seen a
  > notable difference between in the representation of entorhinal over 
perirhinal on
  the right hemisphere
  > labelling on each analysis ran. The left hemisphere appears to have 
less overlap.
  >
  > I have attached a screenshot of both hemispheres to demonstrate. Would 
really
  appreciate any feedback.
  > Thanks!
  >
  > Cheers,
  > Yi-Leng
  >
  >
  > On Wed, Feb 6, 2019 at 3:11 AM Hoopes, Andrew  
wrote:
  >
  >       Hi Yi Leng, there’s a recon-all patch for 6.0 at
  >       
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/recon-all.
  You can
  >       update it with:
  >
  >        
  >
  >       cd ${FREESURFER_HOME}/bin
  >
  >       mv recon-all recon-all.backup
  >
  >       curl
  
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/recon-all -o
  >       recon-all
  >
  >       chmod +x recon-all
  >
  >        
  >
  >       Let us know if that works!
  >
  >        
  >
  >       thanks
  >
  >       Andrew
  >
  >        
  >
  >       From:  on behalf of Yi 
Leng Fung
  >       
  >       Reply-To: FS Help 
  >       Date: Monday, February 4, 2019 at 9:17 PM
  >       To: FS Help 
  >       Cc: Jean Augustinack 
  >       Subject: Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and
  >       ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
  >
  >  
  >
  > External Email - Use Caution
  >
  > Image removed by sender.
  >
  > Thank you!
  >
  >  
  >
  > Cheers,
  >
  > Yi Leng
  >
  >  
  >
  >  
  >
  > On Tue, Feb 5, 2019 at 1:05 PM Bruce Fischl 
 wrote:
  >
  >       thanks. It is almost certainly a bug in recon-all. I'm testing a 
fix
  >       tomorrow and hopefully we can have one out to you (and the rest 
of the
  >       list) by tomorrow.
  >
  >       Sorry!
  >       Bruce
  >       On Tue, 5 Feb 2019, Yi Leng Fung wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > [3a1715320c6fbab489126e656ad6e765d6e0a6ee.png?u=328927]
  >       > Hello Bruce,
  >       >
  >       > Yep, the exvivo entorhinal thresh label overlay on the 
perirhinal
  annotation. I
  >       have attached a screenshot of it
  >       > for your reference.
  >       >
  >       > Cheers,
  >       > Yi-Leng
  >       >
  >       >
  >       > On Tue, Feb 5, 2019 at 12:31 PM Bruce Fischl 

  wrote:
  >       >       Hi Yi-Leng
  >       >
  >       >       eek! Can you verify that the 
lh.entorhinal_exvivo.thresh.label is
  >       >       correct? Does it overlay on the perirhinal annotation?
  >       >
  > 

Re: [Freesurfer] Alignment to ACPC

[Bruce Fischl]

Hi Sadia

we don't align to AC-PC, but we do compute a talairach transformation in 
$SUBJECTS_DIR/$subjects/mri/transforms/talairach.xfm that should do so. You 
can apply it using mri_convert or mri_vol2vol.


cheers
Bruce

On 
Fri, 22 Feb 2019, Sadia Sheikh wrote:




External Email - Use Caution

Hello Freesurfer experts
Freesurfer preprocessed data by(recon-all) are ACPC aligned?
If not how can I align my files to ACPC? I read the documents but I am still 
very confused about the
alignment and coordinate system in freesurfer.

Thanks in advance

Regards
Sadia
Research Student

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Re: [Freesurfer] CAT12 surfaces on tkregister2 and Freeview

[Loucao, Ricardo]

External Email - Use Caution

Thanks for the reply!
I tried the --vol-geom orig.mgz option but to no avail.

Small update: I inspected the metadata on the surface files using mris_info and 
discovered that the ctr property was different between the CAT generated 
surface and the pial surface that was produced from recon-all, while all the 
other transforms where the same.

So I figured the difference in the ctr should be compensated by a translation.

To do that, I first created a CAT2FS.fslmat transform of the form:

1 0 0 (CAT.ctr(1)-FS.ctr(1))
0 1 0 (CAT.ctr(3)-FS.ctr(3))
0 0 0 (CAT.ctr(2)-FS.ctr(2))
0 0 0 1

(NOTE: Im sure the order of the translation portion of the matrix has something 
to do with the orientation convention but I couldnt be bothered to dig deeper - 
I got this by trial and error)

and then converted it to LTA using lta_convert:

lta_convert --infsl CAT2FS.fslmat --outlta CAT2FS.lta --src orig.mgz --trg 
orig.mgz

and then applied this transformation using mris_transform:

mris_transform ?h.CAT CAT2FS.lta ?h.CATreg

sure enough when I load CATreg on tkregister2 I see everything perfectly 
aligned, but after doing mri_vol2surf the surface overlay is still messed up in 
Freeview. Any suggestions?

Thanks in advance for the help!

Ricardo





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt



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[Freesurfer] petsurfer Kinetic Modeling (MRTM1, MRTM2)

[john Anderson]

External Email - Use Caution

Hi Dr Greve,
I would like to use petsurfet to do kinetic modeling (KM), the pipeline is 
straightforward and easy to use. Thank you so much! I would appreciate any 
clarifications relevant to my questions bellow:
1) I understand that the flag "--km-ref" define the reference region for 
normalizing PET signal. in the linear below the reference region is cerebellum 
cortex. If we need to normalize to occipital just we change the numbers based 
on labels in aparc+aseg atlas?

--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale

2) --km-hb define the high binding regions. Are these regions represent the 
regions that are pathologically involved where we expect it to have higher PET 
signal OR it represent the regions where PET tracer has the maximum binding in 
general regardless of pathology? I mean every tracer have high level in 
specific regions in the brain is this what the flag is referring too?

Thanks for any clarification,
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Re: [Freesurfer] Registering from subjects to a common volume

[Tim Schäfer]

External Email - Use Caution

Nevermind, I think I got it to work:

mri_vol2vol --mov subject_x_samples.mgz --s subject_x --targ 
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o 
subject_x_samples_in_mni305.mgz --no-save-reg --interp nearest

If anybody could confirm that this makes sense, I'd still be grateful. ;)

> On February 22, 2019 at 11:27 AM Tim Schäfer  wrote:
> 
> 
> External Email - Use Caution
> 
> Dear list,
> 
> I would like to register volume data from several subjects to a common 
> volume, e.g., the volume of the fsaverage subject. 
> 
> The volume data contains some marked voxels and is in the same space as the 
> orig.mgz of the respective subject. I would like to find/see the positions of 
> the voxels in a volume like $FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz.
> 
> This would require a non-linear, inter-subject registration I guess. How can 
> I do this in FreeSurfer? Most likely I can somehow use mri_vol2vol to achieve 
> this, but I don't see how. Is the talairach transform what I want?
> 
> -- 
> Tim
> 
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>

-- 
Tim

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[Freesurfer] Registering from subjects to a common volume

[Tim Schäfer]

External Email - Use Caution

Dear list,

I would like to register volume data from several subjects to a common volume, 
e.g., the volume of the fsaverage subject. 

The volume data contains some marked voxels and is in the same space as the 
orig.mgz of the respective subject. I would like to find/see the positions of 
the voxels in a volume like $FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz.

This would require a non-linear, inter-subject registration I guess. How can I 
do this in FreeSurfer? Most likely I can somehow use mri_vol2vol to achieve 
this, but I don't see how. Is the talairach transform what I want?

-- 
Tim

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[Freesurfer] How to get gray matter tissue via freesurfer?

[潘祖江]

External Email - Use Caution

Hi all,


I have came across a problem.


As we know, by using recon-all command we can get white matter segmentation,
but what I need to use is gray matter segmentation, so what could I do to get 
ideal
segmentation?


Hope to get response from someone who concerns.


Thanks.


--



潘祖江 Zujiang Pan


清华大学 计算机科学与技术 

Department of Computer Science and Technology

Tsinghua University, 100084

+86 15600487317___
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[Freesurfer] PETSurfer: Needs for gtmseg

[Matthieu VANHOUTTE]

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Dear FS's experts,

In the perspective of correcting generated surfaces errors or defects, 
does the gtmseg command need corrected surfaces or could it be launch 
independently before having these corrected surfaces ?

Best,

Matthieu


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Re: [Freesurfer] Special image protocol

[mustafa amin]

External Email - Use Caution

Thank you for the information

Mustafa M. Amin
Consultant Psychiatrist in Biological Psychiatry
Department of Psychiatry
Faculty of Medicine
Universitas Sumatera Utara

> On 22 Feb 2019, at 00.10, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> I highly recommend the multiecho mprage at about 1mm.
> 
>> On 2/21/19 10:30 AM, Bruce Fischl wrote:
>> Hi Mustafa
>> 
>> FreeSurfer should work fine with many image protocols. If you have the
>> freedom to choose one, Andre van der Kouwe (ccd) can point you at the
>> sequence he developed for Siemens. If you are using a different scanner
>> give us the details and we can recommend something
>> 
>> cheers
>> Bruce
>> 
>> 
>> On Thu, 21 Feb
>> 2019, mustafa amin wrote:
>> 
>>>External Email - Use Caution
>>> 
>>> Dear member,
>>> 
>>> I am really new with this freesurfer, just need to ask 1 question. Is there 
>>> a special image protocol before running the MRI and then upload it to 
>>> freesurfer? Please share your thoughts. Thank you for your kind attention 
>>> and cooperation.
>>> 
>>> Yours faithfully,
>>> 
>>> Mustafa M. Amin
>>> Consultant Psychiatrist in Biological Psychiatry
>>> Department of Psychiatry
>>> Faculty of Medicine
>>> Universitas Sumatera Utara
>>> 
>>> 
>>> ___
>>> 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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Re: [Freesurfer] Issue posting to Freesurfer support

[Tim Schäfer]

External Email - Use Caution

Dear Daniel,

your emails do show up on the list, see 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/maillist.html

Here is your last email, for example:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61484.html

Best,

> On February 21, 2019 at 11:41 PM Daniel Callow  wrote:
> 
> 
> External Email - Use Caution
> 
> Hello,
> 
> I am signed up to post emails to Freesurfer support list <
> freesurfer@nmr.mgh.harvard.edu> which I have cced in this email. However,
> when I submit my questions they do not seem to show up or go to the
> listserv. Is there someone I could contact to help with this?
> 
> Best,
> *Daniel Callow*
> *PhD Student, Neuroscience and Cognitive Science*
> Exercise for Brain Health Lab
> University of Maryland, College Park
> *ddcc2...@gmail.com *
> 443-254-6298
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-- 
Tim

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Re: [Freesurfer] Special image protocol

[mustafa amin]

External Email - Use Caution

Hi Bruce

Thank you for letting me know about this, I’ll contact Andre if I need further 
explanation.

Cheers

Mustafa M. Amin
Consultant Psychiatrist in Biological Psychiatry
Department of Psychiatry
Faculty of Medicine
Universitas Sumatera Utara

> On 21 Feb 2019, at 22.30, Bruce Fischl  wrote:
> 
> Hi Mustafa
> 
> FreeSurfer should work fine with many image protocols. If you have the 
> freedom to choose one, Andre van der Kouwe (ccd) can point you at the 
> sequence he developed for Siemens. If you are using a different scanner 
> give us the details and we can recommend something
> 
> cheers
> Bruce
> 
> 
> On Thu, 21 Feb 
> 2019, mustafa amin wrote:
> 
>>   External Email - Use Caution
>> 
>> Dear member,
>> 
>> I am really new with this freesurfer, just need to ask 1 question. Is there 
>> a special image protocol before running the MRI and then upload it to 
>> freesurfer? Please share your thoughts. Thank you for your kind attention 
>> and cooperation.
>> 
>> Yours faithfully,
>> 
>> Mustafa M. Amin
>> Consultant Psychiatrist in Biological Psychiatry
>> Department of Psychiatry
>> Faculty of Medicine
>> Universitas Sumatera Utara
>> 
>> 
>> ___
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>> 
>> 
>> 
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