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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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_toolshttps://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% #################################################