subject:"Re\: \[Freesurfer\] equivolumetric surfaces"

Re: [Freesurfer] equivolumetric surfaces

2021-03-20 Thread バキット・ムダシル

External Email - Use Caution

Sure, I will give it a try. Thanks Matt.

Mudathir



> On Mar 19, 2021, at 22:25, Glasser, Matthew  wrote:
> 
> External Email - Use Caution
> 
> 
> You can do this with Connectome Workbench command (wb_command -surface-layer 
> and wb_command -volume-to-surface-mapping).
>  
> Matt.
>  
> From:  > on behalf of バキット・ムダシル 
> mailto:m-bak...@fmu.ac.jp>>
> Reply-To: Freesurfer support list  >
> Date: Friday, March 19, 2021 at 2:21 AM
> To: "freesurfer@nmr.mgh.harvard.edu " 
> mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: [Freesurfer] equivolumetric surfaces
> External Email - Use Caution
> Dear freesurfer experts, 
>  
> I want to create an equivolumetric surfaces (using the tool from: MailScanner 
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
> be 
> https://secure-web.cisco.com/1O7fxeb8WB8OcnE6l4q1HALvLzu_CCGz5dWKgk0QgGYvKzrQ9S096mvJCiLTPlywS0MlK_wopxltBaPMu2QTllvkKmYTor-D_Lns3XuUXc6ob1PtIwIyi80g3z0vay_oCK8Dy66cCZRfl5NW4Zn2EqQjpLajNfUb5Q6t9QWHwch64Lfc1ZoLYqXH1aZwCRGm7CGLajgSsQ32qhNKbAXQ3n-3Y6V8tz4bZpPZJl-qkgDHRc691v92itvWYZ7MQ9GrYOmAJ5MrBmqxGdtLheJA2Hg/https%3A%2F%2Fgithub.com%2Fkwagstyl%2Fsurface_tools
>  
> )
>  and to sample the intensities of the T1wDividedByT2w volume at all the 
> depths. I created the surfaces and after running the mri_vol2surf command I 
> faced the error below. I don’t know why the path to the surface is not 
> correct. I tried it in different devices with different versions of 
> freesurfer but the results were the same. Any idea what I did wrong? Thanks
>  
> Mudathir
>  
> #
>  freesurfer-darwin-macOS-7.1.1-20200811-8b40551 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer/7.1.1
> FSFAST_HOME   /Applications/freesurfer/7.1.1/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/7.1.1/subjects
> MNI_DIR   /Applications/freesurfer/7.1.1/mni
> FSL_DIR   /usr/local/fsl
> mudathir% mri_vol2surf --src $SUBJECTS_DIR/spl_01/mri/T1wDividedByT2w.nii.gz 
> --out $SUBJECTS_DIR/spl_01/lh.equi_intensity_1.0.mgh --hemi lh --surf 
> $SUBJECTS_DIR/spl_01/surf/lh.equi1.0.pial --out_type mgh --regheader spl_01
> srcvol = 
> /Applications/freesurfer/7.1.1/subjects/spl_01/mri/T1wDividedByT2w.nii.gz
> srcreg unspecified
> srcregold = 0
> srcwarp unspecified
> surf = /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Computing registration from header.
>   Using /Applications/freesurfer/7.1.1/subjects/spl_01/mri/orig.mgz as target 
> reference.
>  original matrix ---
>  1.0   0.0   0.0   0.0;
>  0.0   0.0   1.0   0.0;
>  0.0  -1.0   0.0   0.35001;
>  0.0   0.0   0.0   1.0;
>  original matrix ---
> Reading surface 
> /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
> error: No such file or directory
> error: 
> MRISread(/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial):
>  could not open file
> error: No such file or directory
> error: mri_vol2surf: could not read surface 
> /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
> mudathirbakhit%
> #
>  
> 
>  
> 
>  
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
>

Re: [Freesurfer] equivolumetric surfaces

2021-03-20 Thread バキット・ムダシル

External Email - Use Caution

Thanks Bruce!

Mudathir






> On Mar 20, 2021, at 1:07, Fischl, Bruce  wrote:
> 
> HI Mudathir
>  
> Looks like mri_vol2surf doesn’t want the full path in the “surf” parameter – 
> just stuff after the “lh.”.
>  
> Cheers
> Bruce
>  
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  
>  > On Behalf Of ·
> Sent: Friday, March 19, 2021 2:21 AM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: [Freesurfer] equivolumetric surfaces
>  
> External Email - Use Caution
> 
> Dear freesurfer experts,
>  
> I want to create an equivolumetric surfaces (using the tool from: MailScanner 
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
> be 
> https://secure-web.cisco.com/1q5cs6Q_ZjnLHZkjjEuUs4b1u23XY86a8gNRMaeFgH_N3J6JICUha47j_o_aD2q7QRhSc13qe9vJaiojvYmyb2s5pdCeKakYIGzkOczT8cZdVK8jE0wOP21LYDW_YDEuSFfh1fQBc-LgPaaR8tNdoTZO1A78ULqlJm2J5uxFLwoVY0h2rjV9LdP_-hWBSZe5W7SYS5n7UOfR3IS2bIBc5OwPtyxpHqYK3q9HZ3e78zAODwAXNDKO03VMN1K08oRVuqNXu6CxlbWI624ePQ19RkQ/https%3A%2F%2Fgithub.com%2Fkwagstyl%2Fsurface_tools
>  
> )
>  and to sample the intensities of the T1wDividedByT2w volume at all the 
> depths. I created the surfaces and after running the mri_vol2surf command I 
> faced the error below. I don’t know why the path to the surface is not 
> correct. I tried it in different devices with different versions of 
> freesurfer but the results were the same. Any idea what I did wrong? Thanks
>  
> Mudathir
>  
> #
>  freesurfer-darwin-macOS-7.1.1-20200811-8b40551 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer/7.1.1
> FSFAST_HOME   /Applications/freesurfer/7.1.1/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/7.1.1/subjects
> MNI_DIR   /Applications/freesurfer/7.1.1/mni
> FSL_DIR   /usr/local/fsl
> mudathir% mri_vol2surf --src $SUBJECTS_DIR/spl_01/mri/T1wDividedByT2w.nii.gz 
> --out $SUBJECTS_DIR/spl_01/lh.equi_intensity_1.0.mgh --hemi lh --surf 
> $SUBJECTS_DIR/spl_01/surf/lh.equi1.0.pial --out_type mgh --regheader spl_01
> srcvol = 
> /Applications/freesurfer/7.1.1/subjects/spl_01/mri/T1wDividedByT2w.nii.gz
> srcreg unspecified
> srcregold = 0
> srcwarp unspecified
> surf = /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Computing registration from header.
>   Using /Applications/freesurfer/7.1.1/subjects/spl_01/mri/orig.mgz as target 
> reference.
>  original matrix ---
>  1.0   0.0   0.0   0.0;
>  0.0   0.0   1.0   0.0;
>  0.0  -1.0   0.0   0.35001;
>  0.0   0.0   0.0   1.0;
>  original matrix ---
> Reading surface 
> /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
> error: No such file or directory
> error: 
> MRISread(/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial):
>  could not open file
> error: No such file or directory
> error: mri_vol2surf: could not read surface 
> /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
> mudathirbakhit%
> #
>  
> 
>  
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://secure-web.cisco.com/1wyE7iIo8jRU8wMM3cXcUBkX7at_VamMEES9jKX3b2zpU8rFrvUvPH_DahgQ04WXMUVzYgwJa5rne_1B74UQGeV39OtKybRLE-9nqLecoZs4qU0v7Ew-Ju3rSkv-reh6RC8qQSHalfoKgS3atanhp3ugHMlzlEd8qC7iqtWkw_YrIUtOUxU-cdr-N_886BlhDaTXUZV3xdLwOVC0W-G-3OPPgqbgoQleCYIlIVKdogeJJmzWkOip3oNYwK-NK7o6ih9ruPSmdEro51Q4kPu5bMw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>  
>

Re: [Freesurfer] equivolumetric surfaces

2021-03-19 Thread Douglas N. Greve


Right, it just wants the surface name (eg, white, pial)

On 3/19/2021 12:07 PM, Fischl, Bruce wrote:


HI Mudathir

Looks like mri_vol2surf doesn’t want the full path in the “surf” 
parameter – just stuff after the “lh.”.


Cheers

Bruce

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *·

*Sent:* Friday, March 19, 2021 2:21 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] equivolumetric surfaces

*External Email - Use Caution *

Dear freesurfer experts,

I want to create an equivolumetric surfaces (using the tool from: 
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://github.com/kwagstyl/surface_tools 
) 
and to sample the intensities of the T1wDividedByT2w volume at all the 
depths. I created the surfaces and after running the mri_vol2surf 
command I faced the error below. I don’t know why the path to the 
surface is not correct. I tried it in different devices with different 
versions of freesurfer but the results were the same. Any idea what I 
did wrong? Thanks


Mudathir

#

 freesurfer-darwin-macOS-7.1.1-20200811-8b40551 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.1.1
FSFAST_HOME /Applications/freesurfer/7.1.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.1.1/subjects
MNI_DIR /Applications/freesurfer/7.1.1/mni
FSL_DIR           /usr/local/fsl
mudathir% mri_vol2surf 
--src $SUBJECTS_DIR/spl_01/mri/T1wDividedByT2w.nii.gz 
--out $SUBJECTS_DIR/spl_01/lh.equi_intensity_1.0.mgh --hemi lh 
--surf $SUBJECTS_DIR/spl_01/surf/lh.equi1.0.pial --out_type mgh 
--regheader spl_01
srcvol = 
/Applications/freesurfer/7.1.1/subjects/spl_01/mri/T1wDividedByT2w.nii.gz

srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /Applications/freesurfer/7.1.1/subjects/spl_01/mri/orig.mgz as 
target reference.

 original matrix ---
 1.0   0.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0  -1.0   0.0   0.35001;
 0.0   0.0   0.0   1.0;
 original matrix ---
Reading surface 
/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial

error: No such file or directory
error: 
MRISread(/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial): 
could not open file

error: No such file or directory
error: mri_vol2surf: could not read surface 
/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial

mudathirbakhit%

#


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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] equivolumetric surfaces

2021-03-19 Thread Fischl, Bruce

HI Mudathir

Looks like mri_vol2surf doesn’t want the full path in the “surf” parameter – 
just stuff after the “lh.”.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ·
Sent: Friday, March 19, 2021 2:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] equivolumetric surfaces


External Email - Use Caution
Dear freesurfer experts,

I want to create an equivolumetric surfaces (using the tool from: MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 
https://github.com/kwagstyl/surface_tools)
 and to sample the intensities of the T1wDividedByT2w volume at all the depths. 
I created the surfaces and after running the mri_vol2surf command I faced the 
error below. I don’t know why the path to the surface is not correct. I tried 
it in different devices with different versions of freesurfer but the results 
were the same. Any idea what I did wrong? Thanks

Mudathir

#
 freesurfer-darwin-macOS-7.1.1-20200811-8b40551 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.1.1
FSFAST_HOME   /Applications/freesurfer/7.1.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.1.1/subjects
MNI_DIR   /Applications/freesurfer/7.1.1/mni
FSL_DIR   /usr/local/fsl
mudathir% mri_vol2surf --src $SUBJECTS_DIR/spl_01/mri/T1wDividedByT2w.nii.gz 
--out $SUBJECTS_DIR/spl_01/lh.equi_intensity_1.0.mgh --hemi lh --surf 
$SUBJECTS_DIR/spl_01/surf/lh.equi1.0.pial --out_type mgh --regheader spl_01
srcvol = 
/Applications/freesurfer/7.1.1/subjects/spl_01/mri/T1wDividedByT2w.nii.gz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /Applications/freesurfer/7.1.1/subjects/spl_01/mri/orig.mgz as target 
reference.
 original matrix ---
 1.0   0.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0  -1.0   0.0   0.35001;
 0.0   0.0   0.0   1.0;
 original matrix ---
Reading surface 
/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
error: No such file or directory
error: 
MRISread(/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial):
 could not open file
error: No such file or directory
error: mri_vol2surf: could not read surface 
/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
mudathirbakhit%
#


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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] equivolumetric surfaces

2021-03-19 Thread Glasser, Matthew

External Email - Use Caution

You can do this with Connectome Workbench command (wb_command -surface-layer 
and wb_command -volume-to-surface-mapping).

Matt.

From:  on behalf of バキット・ムダシル 

Reply-To: Freesurfer support list 
Date: Friday, March 19, 2021 at 2:21 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] equivolumetric surfaces

External Email - Use Caution
Dear freesurfer experts,

I want to create an equivolumetric surfaces (using the tool from: MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 
https://github.com/kwagstyl/surface_tools)
 and to sample the intensities of the T1wDividedByT2w volume at all the depths. 
I created the surfaces and after running the mri_vol2surf command I faced the 
error below. I don’t know why the path to the surface is not correct. I tried 
it in different devices with different versions of freesurfer but the results 
were the same. Any idea what I did wrong? Thanks

Mudathir

#
 freesurfer-darwin-macOS-7.1.1-20200811-8b40551 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.1.1
FSFAST_HOME   /Applications/freesurfer/7.1.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.1.1/subjects
MNI_DIR   /Applications/freesurfer/7.1.1/mni
FSL_DIR   /usr/local/fsl
mudathir% mri_vol2surf --src $SUBJECTS_DIR/spl_01/mri/T1wDividedByT2w.nii.gz 
--out $SUBJECTS_DIR/spl_01/lh.equi_intensity_1.0.mgh --hemi lh --surf 
$SUBJECTS_DIR/spl_01/surf/lh.equi1.0.pial --out_type mgh --regheader spl_01
srcvol = 
/Applications/freesurfer/7.1.1/subjects/spl_01/mri/T1wDividedByT2w.nii.gz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /Applications/freesurfer/7.1.1/subjects/spl_01/mri/orig.mgz as target 
reference.
 original matrix ---
 1.0   0.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0  -1.0   0.0   0.35001;
 0.0   0.0   0.0   1.0;
 original matrix ---
Reading surface 
/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
error: No such file or directory
error: 
MRISread(/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial):
 could not open file
error: No such file or directory
error: mri_vol2surf: could not read surface 
/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
mudathirbakhit%
#




The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] equivolumetric surfaces

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