Dear Bruce We are trying to obtain a good contrast in 7T for thickness measurements using freesurfer by piloting different sequences, is there anyway we can process the T2*s in the pipeline?
On 08/07/2010 17:07, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: > Hi Lena, > > -notal-check will disable the error detection, not the tal itself, so > won't help in cases where the xform is truly wrong. The image you sent > looks PD/T2* weighted, which won't work for the talairaching we use (or for > many of our analysis steps).Do you have a T1-weighted image? > > cheers > Bruce > > > On Thu, 8 Jul 2010, Lena > Palaniyappan wrote: > >> >> The original image is attached - >> Even after notal-check, the recon exits with error >> mri_watershed Error: >> >> GLOBAL region of the brain empty ! >> \ (we have not included cerebellum fully in the slices: is this a problem?) >> Thanks for your help >> >> On 08/07/2010 16:05, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >>> well that certainly looks wrong. What does the original image look like? >>> On >>> Thu, 8 Jul 2010, Lena Palaniyappan wrote: >>> >>>> I am trying to reconstruct some 7T images but they repeatedly fail >>>> Talairach >>>> step >>>> The tkmedit displays normal coronal, sagittal positions for the target. >>>> If I use tkregister2 the moveable appears odd please see the attached >>>> >>>> The error message is >>>> >>>> >>>> #...@# Talairach Failure Detection Thu Jul 8 10:58:38 BST 2010 >>>> /Applications/freesurfer/subjects/7TMRIData/szanat05a/mri >>>> \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n >>>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >>>> ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) >>>> >>>> >>>> The talairach.xfm shows >>>> >>>> MNI Transform File >>>> % tkregister2 >>>> >>>> Transform_Type = Linear; >>>> Linear_Transform = >>>> 2.49591112 0.47519815 2.82347846 13.68270206 >>>> -3.58282375 2.34796309 -2.66250205 -5.44943428 >>>> -2.31779170 -0.83566302 0.94148278 7.01633883 ; >>>> >>>> What should I do next? >>>> Thanks >>>> Lena >>>> _______________________________________________________ >>>> Lena Palaniyappan >>>> Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of >>>> Nottingham) >>>> South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH >>>> >>>> >>>> This message has been checked for viruses but the contents of an attachment >>>> may still contain software viruses which could damage your computer system: >>>> you are advised to perform your own checks. Email communications with the >>>> University of Nottingham may be monitored as permitted by UK legislation. >>> >>> >>> 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. >> >> _______________________________________________________ >> Lena Palaniyappan >> Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of >> Nottingham) >> South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH >> >> >> _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
