[Freesurfer] Problems with segmentation
Hi freesurfers After checking recon-all -autorecon-all processing, I realized that a part of the duramadre has been not fully removed (please see attached file). Can anyone help me how to solve this please. Best regards. -- Leo Kay. <>___ 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] Philips DICOM format problem
Hi All I'm new in freesurfer. I have a question regards Philips DICOM format. I tried to convert from dicom to .mgz using mri_convert but i get the following error message: MRIresample(): error inverting matrix; determinant is nan, matrix is: -0.000 -0.000 nan nan; 0.000 0.000 nan nan; 0.000 -0.000 nan nan; 0.000 0.000 0.000 1.000; Have anyone experienced this before? Any help converting from philips dicom format? Best regards Leo. ___ 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] recon-all
Hi I have been trying to import my data and create a subject directory using the following command: recon-all -i -s replacing with the path where my T1 structural nifti is allocated, and -s with the name of the subject (susu), which is supposed to be the name of the directory too. But after running this command i receive this message: *recon-all /home/virtualuser/apps/freesurfer/subjects susu ERROR: Flag /home/virtualuser/apps/freesurfer/subjects unrecognized. /home/virtualuser/apps/freesurfer/subjects susu Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s exited with ERRORS at Thu Mar 17 14:49:33 EDT 2011*. Can anyone help me determining the problem. Thanks in advance Leo ___ 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] [Fressurfer] fMRI and anatomical T1
Hi all Can anyone help me overlaying fMRI activations from fsl on a anatomical T1 volume in freesurfer. Is there any previous format conversion to do before? Thanks in advance best regards, -- Leo Kay. ___ 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] Fwd: fMRI and anatomical T1 overlaid
Thanks Doug. After doing reg-feat2anat , I checked the registration and overlaid zstat file: tksurfer subjectid rh inflated -overlay featdir/rendered_thresh_zstat1.nii.gz I have attached an image of tksurfer interface . I'm not quite sure about what blue and red clusters mean. They are suposed to be activations, but I'm not watching the same in FSL-view. Could you give me a hand please? Am I using the right stat file? Thanks in advance best regards. -- Forwarded message -- From: Douglas N Greve Date: 2011/3/23 Subject: Re: [Freesurfer] [Fressurfer] fMRI and anatomical T1 To: leonardo kay Cc: freesurfer@nmr.mgh.harvard.edu There is a tutorial on this on our wiki. Basically, you need to run reg-feat2anat to get a registration file, then run tksurfer passing it the registration file and the stat volume as the overlay. doug leonardo kay wrote: > Hi all > > Can anyone help me overlaying fMRI activations from fsl on a anatomical T1 > volume in freesurfer. > Is there any previous format conversion to do before? > > Thanks in advance > best regards, > > -- > Leo Kay. > > > > ___ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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. -- Leo Kay. <>___ 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] (no subject)
Hi all Do anyone have experience doing parcellations using AXIAL T2 FLAIR acquisitions? What sequence do you recomend most for parcellation/labelling under freesurfer? Best regards, -- Leo Kay. ___ 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] Cortical Thickness
Hi Freesurfer experts. Do anyone know how to measure the cortical thickness of an specific brain area? I have been using mris_anatomical_stats but it only outputs the brain cortical thickness of the requested hemisphere. Best regards. -- Leo Kay. ___ 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] Creating a ROI mask
Hi freesurfer 's Can anyone help me how to create a ROI mask. I have read the Cortical Thickness of a Volume-defined ROI tutorial but it doesn't specify how to generate that ROI.nii file. How many points are needed? What brain image must be used as a reference? Any help will be greatly appreciated Best regards. -- Leo Kay. ___ 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] Subject information
Hi all Is there someway (command line) to get direct information on each subject acquisition parameters? Best regards. -- Leo Kay. ___ 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] make_average_subject error
Hi all Could anyone help me with this error: MRISreadAnnotationIntoArray: vertex index out of range: 1499028058 i=5A595959, in_array_size=133467 annot file: /home/virtualuser/apps/freesurfer/subjects/s1/surf/../label/lh.aparc.annot This appeared after trying to average my subject data. It says ' vertex index out of range '. All acquisitions were made using the same parameters so I don't know what this may mean. Thanks in advance -- Leo Kay. ___ 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.
