External Email - Use Caution

Sure, I will give it a try. Thanks Matt.

Mudathir

On Mar 19, 2021, at 22:25, Glasser, Matthew glasserm@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of バキット・ムダシル <m-bakhit@fmu.ac.jp mailto:m-bakhit@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_CCGz5dWKgk0QgGYvKzr... 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. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1k7QAw-VSwbF2pqS5PKy3SrAruFlUJ2FkRUNZzMnrVYdxwQ... https://secure-web.cisco.com/1k7QAw-VSwbF2pqS5PKy3SrAruFlUJ2FkRUNZzMnrVYdxwQEqzEZHSds1MpbZs0s07orw8RxVpsxmBPEltMjBmfeB3EWNzvLGKbb9jcO_W8dEhQUSVBcS0eEOmSoPYFPioPZY9i0HCdfRAQaUPKF6Tb60VNTSWNoRK-otVx6H1zX8lz86hHDiFzgus6FRRDDVrPVkGdlQ4m1OH0po9cpH36NDwTK8xY_GAMvKFmAgNpjwNaarIHWHWGXnIoftIaFejQssaelbcdgj_Gz4i7P-pA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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-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_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