Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Parallel processing
by Brendan Robert Ansell 14 Jul '10

14 Jul '10

Hi FreeSurfer users, is it possible to run FreeSurfer on parallel processors? We would like to run mri_glmfit-sim in parallel to reduce the run time. Have you any experience running FreeSurfer in parallel, or would it be relatively easy to reconfigure? Any thoughts would be greatly appreciated. Thanks in advance, Brendan Ansell Melbourne University

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fieldsign-?h
by dave ma 14 Jul '10

14 Jul '10

Dear FS, after running retinotopy analysis over different subjects i d like now to compare the impact of the activation among the different areas among the subjects. The information to analyse is to find in ..user/bold/retinotopy/fieldsign, the file structure used by Freesurfer. My question is after loading the different fieldsign-?h files and reading them in matlab i got vectors of different length which is the number of the vertices containings values -1,0,1...so far so good, now i wanted to konw how to register those vertices so i can have a common base for a comparison between the different files of the different subjects. I hope someone could help Cheers Dave _________________________________________________________________ http://redirect.gimas.net/?n=M1007xHM2 Räumen Sie Ihr Postfach auf - ganz einfach mit Hotmail!

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Creating table of segmentation volumes
by liang wang 13 Jul '10

13 Jul '10

Hi, I was starting to create a table of segmentation volumes corresponding to several given label (--segno 255 i.e., CC_Anterior). However, I found the volume values for a same strucutre were different between the two files *aseg.stats and wmparc.stats*. For example, for CC_Anterior, one subject was 745 mm^3 in the aseg.stats, but 729 mm^3 in the wmparc.stats. I am not sure why they are different and which file should be selected to represent the volumes. I am appreciated for any suggestions. Best, Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

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recon-all -all finished without error but didn't produce aseg.mgz files
by aekairys＠umich.edu 13 Jul '10

13 Jul '10

Hi all, I just ran recon-all -s (subject) -all for several subjects and it looked like they ran successfully, however when I went to check the data in tkmedit, I realized there were no aseg.mgz as wel as other vital files. The subject did not produce an error log. Any one else ever have this happen? Best, Anson K. University of Michigan

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volume of temporal lobe, frontal lobe, etc...
by Gonzalo Rojas 13 Jul '10

13 Jul '10

Hi: How can I automatically compute, the volume of each brain lobe (temporal lobe, occipital lobe, etc) ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Displaying significant difference with a threshold of cluster size
by liang wang 13 Jul '10

13 Jul '10

Hi, Using mri_glmfit, I found significant between-group difference in cortical thickness in some regions. However, there are a lot regions with very small vertices surviving the given threshold. What I need to do is displaying large clusters (e.g. having 20 vertices at least) assumed as "true" difference. I don't know how to make it by a selected threshold of cluster size . Any suggestions would be appreciated. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wanglbit(a)gmail.com

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question(s) about brain volume calculation
by Golchin, Nima 12 Jul '10

12 Jul '10

I was wondering how FreeSurfer calculates brain volume. Is volume calculated from the voxels included in brainmask.mgz, from the area inside the generated Pial surface, or from summing the aseg volume statistics? Also, to exclude ventricular volume, do you just subtract the segmented ventricle label volume? I ask because I was wondering what freesurfer errors I should be concerned about most when looking at whole brain volume (pial surface including eye/skull, overzealous segmentation labeling, etc). Also, how should I consider whole brain volume regarding the difficulties freesurfer has calculating the surface of the hippocampus. Thanks for your help. -Nima

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Making Average Subject
by nitenson＠nmr.mgh.harvard.edu 12 Jul '10

12 Jul '10

Hi, I'm a newcomer to Freesurfer and I'm having problems trying to create an average subject from a subset of our patients. I used the command "make_average_surface --fsgd y.fsgd" with y.fsgd basically being a copy of an old fsgd file with a few subjects deleted. The process ran for several hours (I had to let it run over the weekend) and seemed to be processing the 12 subjects that I wanted. However when I tried to open it today with "tksurfer 12AboveChanceAvg lh inflated", I get the following message: surfer: current subjects dir: /space/sake/3/users/inverse/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /autofs/homes/006/nitenson ERROR: could not read header info from T1 or orig in /space/sake/3/users/inverse/subjects/12AboveChanceAvg/mri I noticed that the mri folder in the new average I created only has one mgz file (mni305.cor.mgz) while the mri folder in fsaverage has many more. I am currently running make_average_subject --fsgd y.fsgd, but it seems that it's starting to produce the same results. What is the best way to create an average subject on which to study functional overlays? Thanks, Adam Nitenson Brain Genomic Lab

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affine matrix
by Xu, Jun 12 Jul '10

12 Jul '10

Hi, I was trying to create affine matrix from DICOM file and compared with the one created by mri_convert. For T1 image, if I use mri_convert >mri_convert -it dicom [in filename] -ot nii [out filename] The affine matrix (srow*) part get from load_nii_hdr.m command is Affine I: srow_x: [0 0 -1.2000 92.2031] srow_y: [-1 0 0 132.7965] srow_z: [0 -1 0 131.8291] which is the same affine matrix I got directly from DICOM file according to the description in nifti header doc. However, if I use >mri_convert -it dicom [in filename] -ot nii [out filename] -out_orientation PRS The affine matrix (srow*) part get from load_nii_hdr.m command is Affine II: srow_x: [1 0 0 -123.7969] srow_y: [0 -1 0 140.7965] srow_z: [0 0 1.2000 -92.1709] That I do not know how to create. I know the orientation is changed from PSR (T1 sag original) to RPS (specified in out_orientation). Could you tell me what I can do in order to obtain an affine matrix II from affine I? Thanks. Jun

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Linear regression
by Dankner, Nathan (NIH/NIMH) [F] 12 Jul '10

12 Jul '10

Hi All, I sent this last week and it may have slipped through the cracks. I have a dataset with two subject groups. I'm looking to see if there are different age effects on cortical thickness by diagnosis. Initially we did this by testing the interaction of two categorical variables, diagnosis and age (with a median split on age). We are now trying to look at this with age as a continuous variable, but QDEC seemingly does not allow you to look at interactions with continuous variables. Is there a way of doing this using the command line? I've looked at the Group Analysis tutorial, but haven't been able to satisfactorily answer this question. Any help would be appreciated. Thanks, Nathan

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