Hi,
maybe you did not set the variable SUBJECTS_DIR to point to the subjects directory (probably /home/bmssa-server/freesurfer/subjects for your site).
Christina Rossmanith -- Dept. of Neurology University Hospital Mannheim University of Heidelberg
Am 07.02.2014 09:07, schrieb Muhammad Naveed Iqbal Qureshi:
Hi Douglas Greve,
Can you help me to run the following command properly
bmssa-server:/> set subj=/home/bmssa-server/freesurfer/subjects/CHR01 bmssa-server:/> mri_surf2vol --surfval {$subj}/surf/rh.thickness --hemi rh --fillribbon --template mri/orig.mgz --volregidentity {$subj} --outvol {$subj}_rh.ribbon.niigdiagno = -1 Using identity matrix for registration mghRead(mri/orig.mgz, -1): could not open file mri_surf2vol ERROR: reading mri/orig.mgz header bmssa-server:/> mghRead {$subj}/mri/orig.mgz
Thank you
*Best Regards,* *Muhammad Naveed Iqbal Qureshi* Pplease don't print this e-mail unless you really need to
From: freesurfer-request@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 120, Issue 8 To: freesurfer@nmr.mgh.harvard.edu Date: Thu, 6 Feb 2014 12:00:02 -0500
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Today's Topics:
- hippocampus misestimation (Adam Mezher)
- Re: hippocampus misestimation (Bruce Fischl)
- 3D thickness scale (Jonathan Holt)
- Re: 3D thickness scale (Louis Nicholas Vinke)
- Actual Thickness Values (Natasha Haris)
- Re: WM editing and longitudinal processing v5.3.0 (Derin J Cobia)
- Re: WM editing and longitudinal processing v5.3.0 (Bruce Fischl)
- Re: upgrading to freesurfer 5.3 (Anastasia Yendiki)
- Re: Tracula: from anatomical to diffusion space and FSL
probtracx (Anastasia Yendiki) 10. Re: Fwd: Tracula Error: bvecs and bvals don't have the same number of entries (Anastasia Yendiki) 11. Re: Fwd: trac-all -path error (Anastasia Yendiki) 12. Re: Tracula only outputs merged flt file (and missing bbr) (Anastasia Yendiki) 13. Re: Outputting all tracula statistics to table (Anastasia Yendiki) 14. Re: dmri_motion Error bvals (Anastasia Yendiki) 15. Cluster Summary (Natasha Haris) 16. Re: TRACULA error: pre-processing (Anastasia Yendiki) 17. Re: SLFP (Anastasia Yendiki) 18. Re: "trac-all -prior" giving "Segmentation fault (core dumped) (Anastasia Yendiki) 19. Re: TRACULA -stat (Anastasia Yendiki) 20. Re: Cluster Summary (Douglas Greve) 21. Re: upgrading to freesurfer 5.3 (Laura Christine Anderson) 22. Linear Mixed Effects Models (Eric Cunningham) 23. tracula and libnetcdf (Satrajit Ghosh) 24. Re: Linear Mixed Effects Models (jorge luis) 25. Re: tracula and libnetcdf (Satrajit Ghosh) 26. thickness visualization in SPM (Muhammad Naveed Iqbal Qureshi) 27. Re: thickness visualization in SPM (Douglas Greve) 28. Tracula shows some tracks with bbr and others with flt (Salil Soman) 29. Re: Tracula only outputs merged flt file (and missing bbr) (Salil Soman) 30. possible to render hippocampal subfield segmentations as 3D structures? (Salil Soman) 31. Rotation involved in recon-all (Ed Gronenschild) 32. Re: dmri_motion Error bvals (Liliana Maia) 33. A question on fsaverage (peng) 34. Fwd: A question on fsaverage (peng) 35. Re: Rotation involved in recon-all (Bruce Fischl) 36. Re: calculating spc on lobes annotation in longitudinal structural analysis (Jeremy Young) 37. Re: A question on fsaverage (Bruce Fischl) 38. Re: Rotation involved in recon-all (Ed Gronenschild) 39. Re: Rotation involved in recon-all (Harms, Michael) 40. Re: Rotation involved in recon-all (Ed Gronenschild) 41. Re: Rotation involved in recon-all (Harms, Michael) 42. Re: A question on fsaverage (peng) 43. basic math operations for volume labels? (Kami Koldewyn) 44. Re: basic math operations for volume labels? (Maritza Ebling) 45. FSFAST surface-based analysis to w-file (Caspar M. Schwiedrzik) 46. Re: Mean diffusivity (Rotem Saar) 47. Re: Actual Thickness Values (Douglas N Greve) 48. Re: Fwd: trac-all -path error (Jon Wieser)
Message: 1 Date: Wed, 5 Feb 2014 10:10:06 -0800 From: Adam Mezher adammezher@gmail.com Subject: [Freesurfer] hippocampus misestimation To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAO6KwZ6HXJqzOcAhY+ABUGJphBfr+q-j+u0gQmC_ccd=HsN5Aw@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Hi all,
I was curious to know if anyone has been able to use edits to correct hippocampal under- or over-estimation. I've experienced a number of
cases
in which about half of the left hippocampus is labeled as
ctx-lh-unknown or
Left-Cerebral-White-Matter (for reference, I'm using FreeSurfer
version 5.1
for these projects). If anyone has any suggestions to correct this
error,
it would be much appreciated.
Thank you, Adam
*Adam MezherStaff Research Associate IICenter for Imaging of Neurodegenerative DiseasesSan Francisco VA Medical Center4150
Clement St.
(114M)San Francisco, CA 94121Tel: 415-221-4810 Ext. 4629 Fax:
415-668-2864*