Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

using wm edits and control points at the same run
by james pardon 06 Jul '14

06 Jul '14

Hi, In a subject that I need to edit both wm.mgz and add some control points, I'm wondering what is the correct recon-all options so that all changes are applied in on additional run? I noticed that I could overwrite changes made by one or the other if I run them in tandem (and not simultaneously). Thanks James

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webiste is down
by Arman Eshaghi 05 Jul '14

05 Jul '14

Just a heads up that the Freesurfer website is down as of 6:36 am EST 5 July Arman

2 1

mri_convert WARNING: files are not found to be different and cannot be sorted and cannot fit in 256^3 mm^3 volume.
by Knut J Bjuland 05 Jul '14

05 Jul '14

Dear FreeSurfers, I have imported several dicom files with recon-all -i -subjid id. All files were imported correctly, apart from one subjects. When I try to convert it direcelty with mri_convert -ot mgz dicom/9999/1.dcm -s 9999 I get this error message. WARNING: files are not found to be different and cannot be sorted File1: ../../../../dicom/9999/162.dcm File2: ../../../../dicom/9999/2.dcm When I process the subject with recon-all -s 9999 -all. I got this message. WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (240.00 mm, 240.00 mm, 384.00 mm), which cannot fit in 256^3 mm^3 volumes. The resulting volume will have 384 slices. If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu) Can you please advise me how to import the dicom files? Should I convert them to nifti. Will this affect the end results compared to the other subjects that were imported correctly? Knut J

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Edit Recommendations
by Erik Kastman 05 Jul '14

05 Jul '14

Hi all, I’ve searched the edit tutorials for examples of the surface recon problem in the attached screenshots, but couldn’t find anything close. The problem is a jagged pial surface in only one plane - it seems to occur where gyri are very close together and doesn’t look like a problem in the other two planes. Any recommendations on how to fix this? Or is it not something to worry about? Thanks in advance, Erik Kastman

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Tracula ERROR: fMRIframe: frame >= nframes
by Jun Shinozaki 04 Jul '14

04 Jul '14

Dear All, I am trying to run a single subject in TRACULA (trac-all -prep -c dmrirc), but exited with ERRORS. ERROR: fMRIframe: frame >= nframes The attached file is a log file. Can anyone help me? Thank you in advance. Regards, Jun Shinozaki.

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Re: [Freesurfer] Base Misalignment during Longitudinal Image Processing
by Martin Reuter 04 Jul '14

04 Jul '14

Hi xuan, You can try freesurfer 5.3 for the base creation and see if that fixes it. If not, send me the two norm.mgz of the cross time points and I take a look. Thanks, martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: XUAN AMELIA TRAN <tranx(a)ucla.edu> Date:07/04/2014 4:00 AM (GMT+01:00) To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Base Misalignment during Longitudinal Image Processing Hi there, I used inputs from two time points that have been processed with Freesurfer 5.0.0 cross-sectional pipeline. I used the following command to create the base template (using Freesurfer 5.0.0): recon-all -base <templateid> -tp <tp1id> -tp <tp2id> -all The job log said the run was successful. However when inspected with freeview, the norm.mgz for base output shows misalignment (see image attached). Does anyone know how to fix this problem? Thank you! Xuan

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Base Misalignment during Longitudinal Image Processing
by XUAN AMELIA TRAN 03 Jul '14

03 Jul '14

Hi there, I used inputs from two time points that have been processed with Freesurfer 5.0.0 cross-sectional pipeline. I used the following command to create the base template (using Freesurfer 5.0.0): recon-all -base <templateid> -tp <tp1id> -tp <tp2id> -all The job log said the run was successful. However when inspected with freeview, the norm.mgz for base output shows misalignment (see image attached). Does anyone know how to fix this problem? Thank you! Xuan

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Voxels included in wm.mgz but not in white matter surface
by james pardon 03 Jul '14

03 Jul '14

Hi, I'm working on some subjects with gray matter lesions, where usually these lesions happen at the boundary of GM and WM (mostly patients with MS). The problem is that Freesurfer can not follow the cortex past this areas. I have tried to use control points, white matter edits and even editing the problematic regions on orig.mgz volume with neighboring voxels and re running recon-all. My results have improved substantially, however I still have a problem where after white matter edit, and adding some new voxels to wm.mgz, the wm surface (and overlying pial surface) does not respect the wm.mgz. In the attached screenshot for example, I can see some areas that are part of wm.mgz (in red) but not included in WM surface. I was wondering whether anyone can give a hint on what recon-all steps I might need to re-run? Thanks James

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talairach fixes
by Elissa McIntosh 03 Jul '14

03 Jul '14

Hello freesurfer experts, I have two questions. First, I've come across some of my subjects who have crooked alignment on the horizontal view, but have seemingly good talairach results. Does it matter that the alignment is crooked as long as talairach is good? My second question is how off does a talairach have to be to merit a manual fix? I've attached an image of someone whose talairach is slightly off making the green line go outside the brain more than it usually does. But I don't know if I'll do more harm by adjusting it slightly. On a related note, does it matter that the green line seems to go outside the brain in the moveable image? Where the green line extends beyond I've had to make manual edits in most of my subjects. Thank you!

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aseg.mgz and brainmask.mgz misalignment
by Mark Plantz 03 Jul '14

03 Jul '14

Hello freesurfers, I recently ran recon-all on a subject and noticed that aseg.auto_noCCseg.mgz and brainmask.mgz are not aligned properly. Not only is the overlap incorrect, but it appears that the slice #'s do not correlate with eachother. For instance, slice 120 of aseg.auto is not the same region as slice 120 of brainmask.mgz. I attached a screenshot to help illustrate the problem. Any ideas how to fix this problem manually? Thank you! - MP

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