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
<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
<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
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
