External Email - Use Caution 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% > ################################################# > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 > > <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>
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