Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

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

Difficulties in processing cortical thickness with 2 atrophic brains
by Zixuan Yang 03 May '12

03 May '12

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 -s subject 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<mailto:zixuan.yang1@unsw.edu.au>

2 1

recon-all error
by bowang21＠mail.ustc.edu.cn 03 May '12

03 May '12

Dear FreeSurfer experts, I have 20 subjects' data to analysis.And I started 20 terminals to process each subject's data.But they come across error one by one.By now there have been 17 subjects' processes stoped. By the way, I use virtualBOX whose RAM are 4G to process the data.I wander if there are some conflicts when proecess many datas in the meantime? In the adjunct,there are some errors reported by Freesurfer. Yours Bobo

2 1

Vertex wise analysis and area/pial area/volume interpretation
by Mahinda Yogarajah 03 May '12

03 May '12

Dear Experts, I had 2 questions with regard to vertex wise analysis using qdec. 1) How should one interpret the dependent variables area/pial area and volume when comparing 2 groups with qdec and a vertex wise (as opposed to ROI based) analysis - or are they uninterpretable in this context ? I read briefly about areal as an alternative measure - could someone explain the difference, and how thickness, volume and area related to one another ? 2) When running monte-carlo cluster wise multiple correction in qdec - if one finds a significant cluster is it ok to view them within qdec by highlighting the "mc-z ... " file in the analysis result box, and then changing the minimum threshold to whatever value one selected for the monte carlo simulation ? The reason I ask is that the text ouput given by the monte carlo cluster analysis gives different coorinates in the cluster table to that output given when one clicks on the "find clusters and go to max" button ... Thanks. Mahinda

3 5

asegstats2table problem
by Brain Apprentice 03 May '12

03 May '12

Hello Surfers, Command: asegstats2table --skip --delimiter comma --common-segs --stats=lh.BA.stats --meas volume --tablefile V5vo-BA-lh.csv --subjectsfile=a.txt I am trying to create a table of "lh.BA.stats" values where all subject are listed in a.txt. asegstats2table tries to work however there is nothing in the table but the subject-id's. Does anyone have any ideas what is going wrong? Thanks, B.A.

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