External Email - Use Caution Sure, I will give it a try. Thanks Matt.
Mudathir > On Mar 19, 2021, at 22:25, Glasser, Matthew <glass...@wustl.edu> 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: <freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of バキット・ムダシル > <m-bak...@fmu.ac.jp <mailto:m-bak...@fmu.ac.jp>> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Friday, March 19, 2021 at 2:21 AM > To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" > <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 > > <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% > ################################################# > > > > > > 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. 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