Freesurfer May 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

Re: [Freesurfer] Difficulties in processing cortical thickness with 2 atrophic brains
by Bruce Fischl 06 May '12

06 May '12

thanks. So there looks to be a pretty dramatic failure in the aseg which is the root of man of your problems. If you upload one of your datasets I'll take a look Bruce On Mon, 7 May 2012, Zixuan Yang wrote: > Sorry Bruce! Please find the attachment here. > > Many thanks! > Kind regards, > > Zixuan > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Friday, 4 May 2012 10:28 PM > To: Zixuan Yang > Subject: RE: [Freesurfer] Difficulties in processing cortical thickness with 2 atrophic brains > > Hi Zixuan > > there was no attachment. Also, can you cc the list so others can answer? > > thanks > Bruce > On > Fri, 4 May 2012, Zixuan Yang wrote: > >> >> Hi Bruce, >> >> >> >> Please find the attached aseg images of participant A and B. Many thanks!!! >> >> >> >> Kind regards, >> >> Zixuan >> >> >> >> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >> Sent: Friday, 4 May 2012 12:40 PM >> To: Zixuan Yang >> Cc: freesurfer(a)nmr.mgh.harvard.edu; mailman-owner(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Difficulties in processing cortical thickness with >> 2 atrophic brains >> >> >> >> What do the asegs look like? >> >> >> On May 2, 2012, at 8:18 PM, Zixuan Yang <zixuan.yang1(a)student.unsw.edu.au> >> wrote: >> >> Dear Freesurfer experts, >> >> >> >> I am processing some atrophic brains with Freesurfer. However >> considerable part of 2 participants? brains (WM+GM) is not >> recognized (especially for participant B, the posterior part is >> not processed at all). I have checked the Talairach registration >> of both, only the borderlines of the posterior brain regions >> are not exactly accurate. Then I have tried to add thousands of >> control points and run the <recon-all ?autorecon2-cp ?ssubject name> >> but that doesn?t help. >> >> >> >> Please find the attached slides of 2 participants. Could you >> please give me some suggestions for better processing or further >> editing? Many thanks!! >> >> >> >> Kind regards, >> >> Zixuan >> >> >> >> -- >> >> Zixuan YANG >> >> >> >> Ph.D student >> UNSW School of Psychiatry >> NPI - Euroa Centre, Prince of Wales Hospital Barker Street, >> RANDWICK NSW >> 2031 Australia >> Tel: 0405256313 >> >> Email: zixuan.yang1(a)unsw.edu.au >> >> >> >> <Participant A and B for cortical thickness.docx> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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. >> >> >> >

1 0

tracula
by carolina.mr 05 May '12

05 May '12

2 1

load multiple overlays with different colors
by keepmoon 05 May '12

05 May '12

Dear all, I search my question before I post it. I did find similar questions, but didn't find answer. I want to overlay two files with different colors. For example, one is sig1.mgh from cortical thickness, the other is sig2.mgh from area. I want to use tksurfer overlaying them with three colors: red is significant regions of thickness; blue is significant regions of area; green is overlap significant regions of thickness and area. I tried to use the following command: tksurfer fsaverage lh inflated -annot aparc.annot -fthresh 2 -overlay sig1.mgh -overlay sig2.mgh It just can display sig1.mgh or sig2.mgh, but can't display two together. In addition, I don't know how to control overlap and other regions color. Anyone knows how to do this? Any help will be appreciated! Thanks in advance! Kathy

4 10

copy of pbsubmit
by Knut J Bjuland 05 May '12

05 May '12

Hi I am trying to setup a local pc as cluster to debug trac-all. Is it possible to get a copy of pbsubmit? I think I could use it as wrapper fro qsub on my pc. Best regards Knut J

1 0

164k to fsaverage
by Sam Carpenter 04 May '12

04 May '12

Hi all. (apologies to those on both free surfer & caret list serves) I've having issues trying to convert some regions that are in .label.gii format. I'm trying to take them from Caret 164k mesh space into fsaverage space to be viewed on Free Surfer. I've successfully brought similar data the opposite direction, but for some reason I'm unable to go in the reverse. I've outlined my initial steps very briefly and go into further detail when I get to the areas where it appears that the (a) problem is. Steps: Load the spec file. The 'label.gii' can be loaded with the spec file, but it doesn’t really matter. I save this file as a .paint file first, so that it can be deformed, as in the Apply Deformation Map options there is no option for .label.gii only .paint. This could be a potential issue as the the packages I'm using are all originally in .gii format. I'm new to working with files in the .gii format. Does this file format present any issues with commands such as caret_command. I know I've had to do workarounds as the 'Apply Deformation Map' box does not appear to support .label.gii, .coord.gii, etc files. Am I wrong with this or is there a better way to deal with this issue? Apply the deformation map: 'fsaverage.L.registered-to-fs_LR.164k_fs_LR.deform_map' Here is where I think the problem is: The caret_command should be able to convert this into a series of .label files. The caret_command help box offers this: -file-convert -cp2fsl Convert a paint file into free surfer label files. No output name is needed since free surfer uses on file per paint ID with the name of the file being "paintID" label. Here is the command line I've been using: caret_command -file-convert -cp2fsl fs_L-to-fs_LR_Power_et_al_Neuron11.L.164k_fs_LR.paint Help-me-please.coord So, this command has been extracting the .label files. But when viewed in tksurfer, they are distorted. It seems to me that the issue is the .coord file. I've tried the .coord file that was with the spec file, but it was in original 164k mesh space. So I also tried to apply the same deformation map to the .coord after. In order to do this I saved the .coord.gii file as .coord file first, then applied the map . Still to no avail. I'm not sure what is the best .coord file to use, as I've tried multiple combinations of different .coord files and deform maps. Any help would be much appreciated. Thanks in advance. -Sam

1 0

question
by aurore curie 04 May '12

04 May '12

Hi I have a problem with one of my recon. It failed with error. If I check the brain mask.mgz and T1.mgz images on Tkmedit, I can see that the brain mask is mislocated: it includes the cerebellum and the neck but not the real brain. I don't understand how I can fix it. If someone can help me, I will really appreciate Thank you very much in advance for your answer Best regards Aurore

1 0

anisotropic input data
by EK Kim 04 May '12

04 May '12

Dear freesurfers, I wondered is it okay to analyze isotropic data which was converted to the anisotropic one. The original data has (0.390625, 0.390625, 1.5) mm size and (512, 512, 104) voxels. It obtained from 3T scanner. I know the Freesurfer recommend isotropic data (1,1,1)mm. Does it have any problem to use the data I just transformed? To do this, I rescaled the images and did bilinear interpolation to create an isotropic 8-bit version of images. Thanks for any help. EK

3 7

surfaceRAS to Talairach
by Jordan Poppenk 04 May '12

04 May '12

Dear FreeSurfer experts, How does one properly convert from surfaceRAS coords, as provided by fs_read_surf.m, to talairach coords? I have tried using freesurfer_surf2tal.m posted on the web by Darren Weber, supplying it with transform data from transforms/talairach.xfm, but the values returned often differ from those in tksurfer by as much as 20mm (and are clearly wrong). What I would like to do is match the coordinate system in tksurfer (which is clearly right). How does tksurfer do it? Cheers, Jordan

3 2

Postdoc - Neuroimaging of language
by Rutvik Desai 04 May '12

04 May '12

A post-doctoral research position is available in the laboratory of Dr. Rutvik Desai at the University of South Carolina. The lab focuses on cognitive neuroscience of language and semantic memory using fMRI, TMS, patient studies, and computational modeling. Excellent facilities for fMRI, TMS, tDCS, eye tracking, and EEG are available. The candidate will have an exciting opportunity to deepen and expand their skill set, and to pursue collaborative and self-directed projects. Candidates with a PhD in any of the cognitive sciences broadly defined (e.g., Psychology, Neuroscience, Computer Science, or a related field) are welcome to apply. A background in cognitive science of language and experience with fMRI experimental design, data collection, and data analysis is highly desirable. Candidates with expertise in connectionist modeling, machine learning, TMS, or EEG with a strong interest in fMRI will also be considered. Salary will be at NIH post-doctoral rates and commensurate with experience. Initial appointments will be for two years with opportunity for extension to three years. Applications should be addressed to Rutvik Desai (desairutvikATgmailDOTcom). Applications should include CV, brief statement of research interests, relevant publications, and names of three referees (who will be asked for a reference letter if necessary). The position starts in August, 2012, with some flexibility in the starting date. Applications will be assessed as they arrive. The University of South Carolina is an affirmative action, equal opportunity employer. Women and minorities are encouraged to apply. The University of South Carolina does not discriminate in educational or employment opportunities or decisions for qualified persons on the basis of race, color, religion, sex, national origin, age, disability, sexual orientation or veteran status.

1 0

TRACULA
by carolina.mr 04 May '12

04 May '12

1 0

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Freesurfer May 2012