Freesurfer August 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
152 discussions

registering a segmentation from one time-point to another
by Mehul Sampat 12 Aug '10

12 Aug '10

Hi Folks, I have two MR scans per subject. Lesions (white matter hypo-intensities) have been manually outlined for the first time-point. I would like to create a lesion mask for the 2nd time-point. But instead of starting from scratch, I would like to use the lesion-mask from the 1st time-point as a starting point for the lesion mask for time-point 2. for this task, I think I can use the following steps: Step 1) Register 1st time-point to the 2nd scan (using 2nd timepoint as reference) with flirt Step 2) Use mri_convert to apply the transformation matrix from flirt to the lesion mask and create a lesion mask for time-point 2. Step 3) make corrections to the lesion mask for time-point 2 if required. Would you suggest to do it in this manner or is an alternative approach recommended ? thanks Mehul ps: I thought of using the longitudinal freesurfer pipeline but i dont know how to compute the transformation matrix from time-point 1 to time-point 2 use the pipeline...

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Curvature of the Corpus Callosum in Schizophrenia
by Alan Francis 11 Aug '10

11 Aug '10

Hi All: Does a lower score on the curvature of the CC (as done by FreeSurfer) imply that the Corpus Callosum is more curved or is it the other way around? If I am not making any sense in my previous statement, a simpler question would be : What do the scores on the curvature index mean for the shape of the CC? thank you so much, A

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FSFAST Users Group Meetings
by Douglas N Greve 11 Aug '10

11 Aug '10

Hi All, I have scheduled a series of three meetings to talk about FSFAST, particularly the new version that is coming out with FreeSurfer 5.0 (due out "soon"). THIS IS NOT A HANDS-ON COURSE ON HOW TO USE FS-FAST!!! The purpose of these meetings is to give an overview of FSFAST, including the changes from version 4.5 to 5.0. So it is going to be mostly useful for people who already know some FSFAST. For others, it will serve as an introduction to FSFAST but you will not likely come out of a meeting knowing how to use FSFAST. I'm preparing on-line documentation and tutorials, and their might be a class in the future. These meetings will be held in 2204 (where the Brain Map lectures usually are) on the following dates and times: Mon Jul 12 3-4pm Tue Jul 27 3-4pm Wed Aug 11 4-5pm doug

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LGN and Heschl's gyrus in freesurfer
by ridatta＠mail.med.upenn.edu 11 Aug '10

11 Aug '10

Hello All, I have two questions - 1) Is there an LGN label or ROI in freesurfer ? 2) Is this implemented in freesurfer ? Mapping an intrinsic MR property of gray matter in auditory cortex of living humans: a possible marker for primary cortex and hemispheric differences. Sigalovsky IS, Fischl B, Melcher JR. If I am not wrong, this is similar to the Hinds and Fischl method of demarcating V1. So is this a separate step like the V1 demarcation or is it integrated in the recon-all pipe ? Please let me know. Thanks Ri

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using matlab loops for MRIwrite
by corinna bauer 11 Aug '10

11 Aug '10

Is there a way to use a loop with MRIwrite such that each subject's output has a different name? Thanks, Corinna

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orient_mri
by Prapti Gautam 11 Aug '10

11 Aug '10

Hi, I'm trying to use orient_mri to orient a volume that is displaying as an axial rather than a coronal volume. According to the instructions, I need to see 4 views and be able to rotate the loaded volume - but I only see one window.. do you know why this is ? there wasn't a error message as such , but the volume isn't being displayed as it should I think .. The command I use is : orient_mri -volume orig.mgz I'm using a linux ubuntu with freesurfer version 4.3 thanks, Prapti

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segmentation output from freesurfer version 4.0.2
by Keslerwest, Marilyn 10 Aug '10

10 Aug '10

Dear Freesurfer experts, We have aparc+aseg.mgz segmentation and other files from Freesurfer version 4.0.2 . We do not have the original images, and so cannot easily reprocess with a later version. I have looked at the release notes. I saw that version 4.0.2 has a problem with the estimated Total Intracranial Volume calculation and I have heard that there may be other issues. So I am wondering if you think it would be problematic to use these aparc+aseg.mgz files for overlay with the functional images for an ROI analysis. Thank you, - Marilyn ________________________________ This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

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Increasing Color Bar colors
by Jeff Sadino 10 Aug '10

10 Aug '10

Hello, I am interested in learning how to increase the number of colors that show up on the tksurfer color bar. Right now, I pretty much only get two or three colors at a time - blue, red, and yellow. I see pictures in publications that show the whole rainbow: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743662/?tool=pubmed also http://jsadino.awardspace.com/fs.html Can anyone please explain the process to me of how to get this increased color range on the tksurfer maps? Thank you very much, Jeff Sadino

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Cortical Thickness of a Volume-defined ROI
by efrat kliper 10 Aug '10

10 Aug '10

Dear FreeSurfer expert I am trying to create a mask for the right hemisphere frontal lobe cortex in order to calculate the mean cortical thickness for this specific ROI. I am using the following commands: To create a mask for the specific region: mri_binarize --i /mri/aparc+aseg --match 2028 --match 2027 --match 2003 --match 2024 --match 2018 --match 2020 --match 2019 --match 2014 --match 2032 --match 2002 --match 2026 --o /mri/rh_frontal_ctx.mgz But I am not sure what the next step is - I tried to follow this link: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness(Cortic… Thickness of a Volume-defined ROI) fslregister --s fsaverage --mov /mri/T1.mgz --reg T1_to_fsaverage.dat but I am not sure if that is the correct way, and also my ROI in the fsaverage subject volume is not perfectly matched to what I expect it to be - how can I fix that? They are very different. I also tried the mri_tessellate command to create surface by tessellating given input volume: mri_tessellate /data/Temp_efrat/subjects/TB_281_test/mri/rh_frontal_ctx_1.mgz -a 2028 2027 2003 2024 2018 2020 2019 2014 2032 2002 2026 frontal_ctx_test I get this massage: changing type of input volume to 8 bits/voxel... $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ slice 110: 431 vertices, 495 faces slice 120: 2986 vertices, 3215 faces slice 130: 6636 vertices, 7037 faces slice 140: 12817 vertices, 13506 faces slice 150: 22361 vertices, 23291 faces slice 160: 32454 vertices, 33549 faces slice 170: 44058 vertices, 45346 faces slice 180: 56174 vertices, 57633 faces slice 190: 67020 vertices, 68612 faces slice 200: 75820 vertices, 77402 faces slice 210: 78847 vertices, 80236 faces slice 220: 78900 vertices, 80278 faces slice 230: 78900 vertices, 80278 faces slice 240: 78900 vertices, 80278 faces slice 250: 78900 vertices, 80278 faces using the conformed surface RAS to save vertex points... writing 2028 using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; But I can not find the output file of that command. And then to calculate the thickness of the frontal cortex by using the mris_anatomical_stats TB_281_test rh -t frontal_ctx_test I am a little confused, I will be grateful if you can help me with that. Thanks a lot Efrat <Freesurfer(a)nmr.mgh.harvard.edu>

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Red Hat vs. CentOs
by dahlia＠nmr.mgh.harvard.edu 10 Aug '10

10 Aug '10

Hi, I'd like to make sure that a Dell desktop with pre-installed RHEL would work seamlessly with Freesurfer, equivalent to CentOS. Is this correct? Thanks, Dahlia.

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Freesurfer August 2010