Hello FreeSurfer Developers,
We have attempted to run the standard recon-all pipeline on multiple MRI datasets, and seem to be encountering the same error. While the recon-all log does not indicate there are any errors (so far as we can tell as novices), when we look at the inflated surfaces, there is clearly some problem creating the inflated surface, in that the hemispheres appeared to be mirrored. For the purpose of simplicity, we will include the log and scan information for the most recent anatomical scan we have to run the recon-all pipeline on. I believe the attached screenshot (anterior coronal view) will make the issue more apparent.
1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform: Mac OS 10.12 3) recon-all.log: see attached 4) Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2 -parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner) 5) Scan information: Data Axes Tilt: Oblique (15.784 deg. from plumb) Data Axes Approximate Orientation: first (x) = Anterior-to-Posterior second (y) = Superior-to-Inferior third (z) = Right-to-Left [-orient ASR] R-to-L extent: -80.718 [R] -to- 94.282 [L] -step- 1.000 mm [176 voxels] A-to-P extent: -188.767 [A] -to- 58.233 [P] -step- 1.000 mm [248 voxels] I-to-S extent: -186.650 [I] -to- 68.350 [S] -step- 1.000 mm [256 voxels]
Any help would be tremendously appreciated!
Thanks,
David Saltzman
Lab Manager
Language and Brain Laboratory
Department of Speech, Language, & Hearing Sciences
University of Connecticut
Can you upload that subject to our filedrop? See below for link
On 01/30/2017 11:19 AM, Saltzman, David wrote:
Hello FreeSurfer Developers,
We have attempted to run the standard recon-all pipeline on multiple MRI datasets, and seem to be encountering the same error. While the recon-all log does not indicate there are any errors (so far as we can tell as novices), when we look at the inflated surfaces, there is clearly some problem creating the inflated surface, in that the hemispheres appeared to be mirrored. For the purpose of simplicity, we will include the log and scan information for the most recent anatomical scan we have to run the recon-all pipeline on. I believe the attached screenshot (anterior coronal view) will make the issue more apparent.
- FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
- Platform: Mac OS 10.12
- recon-all.log: see attached
- Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2
-parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner) 5) Scan information: Data Axes Tilt: Oblique (15.784 deg. from plumb) Data Axes Approximate Orientation: first (x) = Anterior-to-Posterior second (y) = Superior-to-Inferior third (z) = Right-to-Left [-orient ASR] R-to-L extent: -80.718 [R] -to- 94.282 [L] -step- 1.000 mm [176 voxels] A-to-P extent: -188.767 [A] -to- 58.233 [P] -step- 1.000 mm [248 voxels] I-to-S extent: -186.650 [I] -to- 68.350 [S] -step- 1.000 mm [256 voxels]
Any help would be tremendously appreciated!
Thanks,
David Saltzman
/Lab Manager/
Language and Brain Laboratory
Department of Speech, Language, & Hearing Sciences
University of Connecticut
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hopefully I did this correctly: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=49h8h1nu06w
Thanks!
David Saltzman
Lab Manager
Language and Brain Laboratory
Department of Speech, Language, & Hearing Sciences
University of Connecticut
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, January 30, 2017 11:55:47 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Issue with creating inflated surface - poor surface registration?
Can you upload that subject to our filedrop? See below for link
On 01/30/2017 11:19 AM, Saltzman, David wrote:
Hello FreeSurfer Developers,
We have attempted to run the standard recon-all pipeline on multiple MRI datasets, and seem to be encountering the same error. While the recon-all log does not indicate there are any errors (so far as we can tell as novices), when we look at the inflated surfaces, there is clearly some problem creating the inflated surface, in that the hemispheres appeared to be mirrored. For the purpose of simplicity, we will include the log and scan information for the most recent anatomical scan we have to run the recon-all pipeline on. I believe the attached screenshot (anterior coronal view) will make the issue more apparent.
- FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
- Platform: Mac OS 10.12
- recon-all.log: see attached
- Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2
-parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner) 5) Scan information: Data Axes Tilt: Oblique (15.784 deg. from plumb) Data Axes Approximate Orientation: first (x) = Anterior-to-Posterior second (y) = Superior-to-Inferior third (z) = Right-to-Left [-orient ASR] R-to-L extent: -80.718 [R] -to- 94.282 [L] -step- 1.000 mm [176 voxels] A-to-P extent: -188.767 [A] -to- 58.233 [P] -step- 1.000 mm [248 voxels] I-to-S extent: -186.650 [I] -to- 68.350 [S] -step- 1.000 mm [256 voxels]
Any help would be tremendously appreciated!
Thanks,
David Saltzman
/Lab Manager/
Language and Brain Laboratory
Department of Speech, Language, & Hearing Sciences
University of Connecticut
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
let me know if the problem is the visualization as Bruce suggests. If not, I'll take a look
On 01/30/2017 12:00 PM, Saltzman, David wrote:
Hopefully I did this correctly: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=49h8h1nu06w
Thanks!
David Saltzman
/Lab Manager/
Language and Brain Laboratory
Department of Speech, Language, & Hearing Sciences
University of Connecticut
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu *Sent:* Monday, January 30, 2017 11:55:47 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Fw: Issue with creating inflated surface - poor surface registration? Can you upload that subject to our filedrop? See below for link
On 01/30/2017 11:19 AM, Saltzman, David wrote:
Hello FreeSurfer Developers,
We have attempted to run the standard recon-all pipeline on multiple MRI datasets, and seem to be encountering the same error. While the recon-all log does not indicate there are any errors (so far as we can tell as novices), when we look at the inflated surfaces, there is clearly some problem creating the inflated surface, in that the hemispheres appeared to be mirrored. For the purpose of simplicity, we will include the log and scan information for the most recent anatomical scan we have to run the recon-all pipeline on. I believe the attached screenshot (anterior coronal view) will make the issue more apparent.
- FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
- Platform: Mac OS 10.12
- recon-all.log: see attached
- Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2
-parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner) 5) Scan information: Data Axes Tilt: Oblique (15.784 deg. from plumb) Data Axes Approximate Orientation: first (x) = Anterior-to-Posterior second (y) = Superior-to-Inferior third (z) = Right-to-Left [-orient ASR] R-to-L extent: -80.718 [R] -to- 94.282 [L] -step- 1.000 mm [176 voxels] A-to-P extent: -188.767 [A] -to- 58.233 [P] -step- 1.000 mm [248 voxels] I-to-S extent: -186.650 [I] -to- 68.350 [S] -step- 1.000 mm [256 voxels]
Any help would be tremendously appreciated!
Thanks,
David Saltzman
/Lab Manager/
Language and Brain Laboratory
Department of Speech, Language, & Hearing Sciences
University of Connecticut
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi David
I'm not sure that there is anything actually wrong, I think what you are seeing is just a visualization issue. The inflated surfaces will overlap when viewed together in freeview, since they are centered on each hemi and inflated. You can use the :offset=x,y,z modifier for the -f ?h.inflated to move them left/right so they don't overlap if you want.
cheers Bruce
On Mon, 30 Jan 2017, Saltzman, David wrote:
Hello FreeSurfer Developers,
We have attempted to run the standard recon-all pipeline on multiple MRI datasets, and seem to be encountering the same error. While the recon-all log does not indicate there are any errors (so far as we can tell as novices), when we look at the inflated surfaces, there is clearly some problem creating the inflated surface, in that the hemispheres appeared to be mirrored. For the purpose of simplicity, we will include the log and scan information for the most recent anatomical scan we have to run the recon-all pipeline on. I believe the attached screenshot (anterior coronal view) will make the issue more apparent.
- FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform:
Mac OS 10.12 3) recon-all.log: see attached 4) Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2 -parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner) 5) Scan information: Data Axes Tilt: Oblique (15.784 deg. from plumb) Data Axes Approximate Orientation: first (x) = Anterior-to-Posterior second (y) = Superior-to-Inferior third (z) = Right-to-Left [-orient ASR] R-to-L extent: -80.718 [R] -to- 94.282 [L] -step- 1.000 mm [176 voxels] A-to-P extent: -188.767 [A] -to- 58.233 [P] -step- 1.000 mm [248 voxels] I-to-S extent: -186.650 [I] -to- 68.350 [S] -step- 1.000 mm [256 voxels]
Any help would be tremendously appreciated!
Thanks,
David Saltzman
Lab Manager
Language and Brain Laboratory
Department of Speech, Language, & Hearing Sciences
University of Connecticut
We adjusted the offset and that was clearly the problem. Looks like it worked great. Thank you so much for clearing this up!
David Saltzman
Lab Manager
Language and Brain Laboratory
Department of Speech, Language, & Hearing Sciences
University of Connecticut
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Monday, January 30, 2017 12:01:15 PM To: Freesurfer support list Cc: Rothermich, Kathrin Subject: Re: [Freesurfer] Fw: Issue with creating inflated surface - poor surface registration?
Hi David
I'm not sure that there is anything actually wrong, I think what you are seeing is just a visualization issue. The inflated surfaces will overlap when viewed together in freeview, since they are centered on each hemi and inflated. You can use the :offset=x,y,z modifier for the -f ?h.inflated to move them left/right so they don't overlap if you want.
cheers Bruce
On Mon, 30 Jan 2017, Saltzman, David wrote:
Hello FreeSurfer Developers,
We have attempted to run the standard recon-all pipeline on multiple MRI datasets, and seem to be encountering the same error. While the recon-all log does not indicate there are any errors (so far as we can tell as novices), when we look at the inflated surfaces, there is clearly some problem creating the inflated surface, in that the hemispheres appeared to be mirrored. For the purpose of simplicity, we will include the log and scan information for the most recent anatomical scan we have to run the recon-all pipeline on. I believe the attached screenshot (anterior coronal view) will make the issue more apparent.
- FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform:
Mac OS 10.12 3) recon-all.log: see attached 4) Command run: recon-all -i "inputfile.nii" -subject subj1 -cortparc2 -parcstats2 -aparc2aseg -all -3T (scans were performed on a 3T scanner) 5) Scan information: Data Axes Tilt: Oblique (15.784 deg. from plumb) Data Axes Approximate Orientation: first (x) = Anterior-to-Posterior second (y) = Superior-to-Inferior third (z) = Right-to-Left [-orient ASR] R-to-L extent: -80.718 [R] -to- 94.282 [L] -step- 1.000 mm [176 voxels] A-to-P extent: -188.767 [A] -to- 58.233 [P] -step- 1.000 mm [248 voxels] I-to-S extent: -186.650 [I] -to- 68.350 [S] -step- 1.000 mm [256 voxels]
Any help would be tremendously appreciated!
Thanks,
David Saltzman
Lab Manager
Language and Brain Laboratory
Department of Speech, Language, & Hearing Sciences
University of Connecticut
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Saltzman, David