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Thanks Bruce!

Mudathir






> On Mar 20, 2021, at 1:07, Fischl, Bruce <bfis...@mgh.harvard.edu> 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 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
> <freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of ????·????
> Sent: Friday, March 19, 2021 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/1q5cs6Q_ZjnLHZkjjEuUs4b1u23XY86a8gNRMaeFgH_N3J6JICUha47j_o_aD2q7QRhSc13qe9vJaiojvYmyb2s5pdCeKakYIGzkOczT8cZdVK8jE0wOP21LYDW_YDEuSFfh1fQBc-LgPaaR8tNdoTZO1A78ULqlJm2J5uxFLwoVY0h2rjV9LdP_-hWBSZe5W7SYS5n7UOfR3IS2bIBc5OwPtyxpHqYK3q9HZ3e78zAODwAXNDKO03VMN1K08oRVuqNXu6CxlbWI624ePQ19RkQ/https%3A%2F%2Fgithub.com%2Fkwagstyl%2Fsurface_tools
>  
> <https://secure-web.cisco.com/1RxQBNBh7QLlgBP46WWIONAGLCrtuooPBalXpNMTOlsF1eoOQXja0KaogvHBx39bkqpnP1Qnz5FuZhT-DTLRXZLIQWp64WXTSgyrwspQMNHWCVzQPv1cqguMDF7AiGzYh01WxTW7m8FHiaJUhjGnV4OUOHBvBdP7TEBNSTE-wITBcBhQio6M-0BWoLcRMIE8ov3uosoZa-RneDMp9tALUDf97709r5pZLfXcySduo0v7WZYNjE9grdo_LK1JjVuAC/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 -----------
>  1.00000   0.00000   0.00000   0.00000;
>  0.00000   0.00000   1.00000   0.00000;
>  0.00000  -1.00000   0.00000   0.35001;
>  0.00000   0.00000   0.00000   1.00000;
> -------- 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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