Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

do I need to re-ROI the segmentation after recon-all
by shi yao wang 12 Sep '17

12 Sep '17

Dear FS experts: After I finishing recon-all, do I need to check the segmentation and re-roi some of region? thanks Lawrence Emory University

2 1

(no subject)
by yl88＠nyu.edu 12 Sep '17

12 Sep '17

Hi all, I have finished the command “recon -all” without error. But I get an error that says: “Received X error! Error code :158 Request code : 148 Minor code: 2 Error text :’GLXBadLargeRequest’” I am using the command “tksurfer sub lh inflated”. Then clicking the File->Label->load label.-> and choosing document of “the lh.apare.a2009.annot”. I don’t know why I got this error so would you be able to explain why this is the case and how I can go about resolving this problem? Best, Yvonne

2 1

automatic quality control in freesurfer
by shi yao wang 12 Sep '17

12 Sep '17

Dear FS experts: Just wondering if there were any automatic method to perform quality control especially for segmentation. thanks Lawrence

1 0

Talairach registration error
by Ariana Vajdi 11 Sep '17

11 Sep '17

Hello, Hope this message finds you well. I was beginning to run recon-all on a dataset and was encountering a problem with the talairach registration. I've encountered this error before here and there, but I've been receiving the same error for every scan that I've been trying to run, and I'm not sure why. It's also the first time I've used NIFTI files as the input - not sure if that's a contributing factor. I've also tried the -use-mritotal flag without any luck. These are the errors I receive: WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. I would appreciate your help. Thank you! Warmly, Ariana

2 4

Finding Duplicate Subjects in a Database
by Sherrill, John T 11 Sep '17

11 Sep '17

I am trying to find the best way to identify likely duplicate subjects with in a database of about 550 subjects. Some subjects where duel-consented for studies and had multiple scans over a relatively short period of time. What is the best way to tease these out? John Sherrill jtsherrill(a)uams.edu john_sherrill(a)me.com (870) 761-0580 ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

2 5

mammillary bodies
by Jacobs H (NP) 11 Sep '17

11 Sep '17

Hello all! I am looking for a automatic or semi-automatic segmentation tool for the mammillary bodies. Any suggestions? Many thanks! Heidi

1 0

Longitunal analysis with FS-FAST
by stdp82＠virgilio.it 11 Sep '17

11 Sep '17

Hi list,I would like to perform longitudinal analysis with FS-FAST, fMRI data.Please could you list, in summary, the processes that I should done?ThanksRegardsStefano

2 1

Cortical thickness
by Esteban, Eva(GE Healthcare) 11 Sep '17

11 Sep '17

Hello everyone, I am trying to compare the difference in cortical thickness between two subjects by overlaying the surfaces (lh.thickness and r rh.thickness) but -diff doesn't seem to be doing the work. Does anyone know of any other commands which could be useful for this? Thank you! Eva

2 2

Transfer files from Windows
by Fereshte 10 Sep '17

10 Sep '17

Dear FreeSurfer experts I've tried using FreeSurfer on windows with VirtualBox. I need to transfer some files on my windows to use in FreeSurfer. I've seen the same question in the frum but not appropriate answer and i couldn't find any helpful instructions on net either. I'd appreciate your help with it. Regards

3 4

PETsurf non linear registration
by Victor Montal Blancafort 08 Sep '17

08 Sep '17

Dear Freesurfer experts, I have been working with the PETsurf pipeline. I was wondering if there is any chance to use a non-linear registration (i.e ANTS) in order to compute the %tissue per voxel in native space. Currently, I am using your pipeline to process DWI data. Due to some EPI artifacts during the acquisition, I would like to use a deformation algorithm to get rid off those artifacts that would generate false values when projecting to surface (i.e misalignment between DTI and T1 in (shrinked) frontal areas, will cause erroneous (outliers) values. If this is not possible, could you please explain in detail how the mri_gtmpvc algorithm works to compute the % tissue fraction of each voxel (to implement it)? Correct me if I'm wrong: 1) Downsample the DWI to a 3x3x3 grip (any command for that)? 2) Normalize to the high-res MRI. 3) Using the aparc+aseg?, compute the % of each ROI in that voxel (again, command?). 4) Assign in the native space, the % of ROI at each voxel. 5) Compute the tissue prob as the sum of all ROIs for a certain tissue type in that voxel. BONUS: mri_vol2surf doesn't allow either non-linear registration? Any insight will be really appreciate!! Victor Montal

2 1

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