Use mris_apply_reg, eg, mris_apply_reg --src lh.thickness --streg lh.white lh.white.downsampled --o lh.thickness.downsampled.mgz
There is a slight issue in that the output will be an mgz file and lh.thickness is in our old "curv" format. You can use mri_surf2surf to convert it to curv (which is needed by mri_vol2surf)
On 2/24/19 8:38 AM, Ella Hanns wrote:
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Thanks for the quick reply! When trying to run mri_vol2surf on my BOLD data, Freesurfer gives me an error because the thickness file does not match my other surf files. I have downsampled all other surf files using mris_decimate. However, I do not seem to be able to downsample the thickness file using mri_surf2surf (as it is missing a proper thickness file for reference) or mris_decimate. I would like to keep my data in native space, so it is not an option to resample the surface onto fsaverage. What is the best way to go here? Is there another way to downsample the thickness file? Cheers, Ella *Gesendet:* Freitag, 22. Februar 2019 um 22:34 Uhr *Von:* freesurfer-request@nmr.mgh.harvard.edu *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* Freesurfer Digest, Vol 180, Issue 48 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
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Today's Topics:
- Re: ?h.white does not exist (Bruce Fischl)
- [All] postdoctoral position in PET imaging available at MGH /
Martinos Center (Bruce Fischl) 3. Re: ?h.white does not exist (Weber, Wade A) 4. Re: CAT12 surfaces on tkregister2 and Freeview (Greve, Douglas N.,Ph.D.) 5. Re: ?h.white does not exist (Bruce Fischl) 6. Re: recon-all -hires (Greve, Douglas N.,Ph.D.) 7. Re: ?h.white does not exist (Greve, Douglas N.,Ph.D.) 8. Re: ?h.white does not exist (Weber, Wade A) 9. Re: ?h.white does not exist (Weber, Wade A) 10. downsampling orig.mgz (Ey Dude) 11. Re: recon-all -hires (Nasiriavanaki, Zahra) 12. Re: petsurfer Kinetic Modeling (MRTM1, MRTM2) (john Anderson) 13. Re: registration and resampling in native space (Francesca Strappini) 14. Re: petsurfer Kinetic Modeling (MRTM1, MRTM2) (Greve, Douglas N.,Ph.D.) 15. Re: registration and resampling in native space (Greve, Douglas N.,Ph.D.) 16. vlrmerge for visualization only? (Haroon Popal) 17. Re: downsampling orig.mgz (Greve, Douglas N.,Ph.D.) 18. Re: vlrmerge for visualization only? (Greve, Douglas N.,Ph.D.) 19. Different paradigm files (Zhi Li) 20. Re: registration and resampling in native space (Francesca Strappini) 21. Re: Different paradigm files (Greve, Douglas N.,Ph.D.)
Message: 1 Date: Fri, 22 Feb 2019 12:57:59 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ?h.white does not exist To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1902221257350.12350@gate.nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
Hi Wade
I don't think you can just skip autorecon3. Can you try running it first and see if that fixes your problems?
cheers Bruce On Fri, 22 Feb 2019, Weber, Wade A wrote:
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Hi Bruce,
I'm using MPRAGEs that aren't as FreeSurfer friendly as they could
be, so I have to do some Pial edits. So I just skip autorecon3 to save time. After I finish the edits, I re-run from -autorecon-pial and check again. Then I run autorecon3.
Wade
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu
freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl
Sent: Friday, February 22, 2019 11:38 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ?h.white does not exist
Hi Wade
from the recon-all.log it looks like you never ran autorecon3. Is
there a reason for this? Usually we run all the way through autorecon3 before running the T2pial stuff
cheers Bruce On Fri, 22 Feb 2019, Weber, Wade A wrote:
????????External Email - Use Caution
Hi all,
?
I?m trying to run ?autorecon2 on 3 subjects (I already ran ?autorecon1 on them with no errors.) and I?m getting an error after the ?final_surfs part saying that lh.white does not exits (and it doesn?t, I checked for it).? I have run about 10 other subjects, and they
all ran fine and contain ?h.white files.? I saw 2 other strings in the archive with this same issue, but there was no resolution to them.
This error just started happening, and I didn?t change anything.?
Here?s the command I?ve been using:
?
recon-all ?subjid <my subject #> -T2 <name of t2.nii file> -T2pial -autorecon2
?
Here?s the error output:
?
MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/an alysis_files/ANG_1034/surf/lh.wh ite): could not open file
?
I?m running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c on a virtual machine running Red Hat Enterprise Linux Workstation 7.6
?
I?ve attached the recon-all.log file
?
Thanks!
?
?
?
Wade A. Weber, MS
Psychiatry Research Program Coordinator
?
Dell Medical School | The University of Texas at Austin
o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu
?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Message: 2 Date: Fri, 22 Feb 2019 12:58:41 -0500 (EST) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: [Freesurfer] [All] postdoctoral position in PET imaging available at MGH / Martinos Center To: freesurfer@nmr.mgh.harvard.edu Cc: Marco Loggia marco@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1902221258220.12350@gate.nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-15"
Postdoctoral position in integrated PET/MRI at Massachusetts General Hospital / Harvard Medical School
The Loggia and Hadjikhani Labs are inviting applications for a Post-Doctoral Research Fellow in the Department of Radiology at Massachusetts General Hospital (A.A. Martinos Center for Biomedical Imaging) and Harvard Medical School.
The candidate will use state-of-the-art integrated PET/MRI scanners to image neuroinflammation in the central nervous systems of migraine patients, and the effect of nonpharmacological therapies. The candidate will collaborate with Dr. Julie Price and several other members of the Martinos Center.
Requirements include a Ph.D. in Neuroscience, Physics, Chemistry, Engineering, or a related field, as well as good command of written and oral English. Experience with Positron Emission Tomography is preferred. Compensation is competitive and commensurate with experience.
If interested, please email Marco Loggia (marco@nmr.mgh.harvard.edu) with your CV.
?
Marco L. Loggia, PhD Assistant Professor of Radiology,?Harvard Medical School? Associate Director, Center for Integrative?Pain NeuroImaging (CiPNI)
A. A. Martinos Center for Biomedical?Imaging Massachusetts General Hospital 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422? Email: marco.loggia@mgh.harvard.edu Web: http://scholar.harvard.edu/loggia