Freesurfer

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19 participants
30088 discussions

Whole brain tractography using Freesurfer surfaces as seed and target
by Karen Marie Sandø Ambrosen 04 Nov '13

04 Nov '13

Hi Freesurfer experts, I am trying to perform whole brain tractography using FSL's Probtrackx2 with Freesurfer white surfaces as seed and pial surfaces as targets. To obtain a whole brain connectivity graph I need the streamlines between the hemispheres. This means that I need to remove the part of the medial wall between the hemispheres corresponding to corpus callosum and anterior and posterior commissures. One possible solution might be to use mri_surf2vol to transform the white surfaces to volumes and hereafter multiply by corpus callosum and anterior and posterior commissures to cut holes in the white surface. After removing the relevant parts the volume is transformed back to a surface which is used as input to the tractography. I don't know if this is the best way to do it or if there is a better way to automatically obtain the whole brain white/pial surface? Any thoughts and comments are highly appreciated. Best, Karen

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unilateral hippocampus segmentation fail
by Andreas Berger 04 Nov '13

04 Nov '13

Hi FreeSurfers, i came across a few subjects in which FreeSurfer 5.3 failed to properly label most of the hippocampus in one hemisphere. Specifically, it is the left hippocampus in all of the 5 cases in which this occured. The subjects are young, healthy, and without any anatomical peculiarities. Segmentation was fine in these subjects with FreeSurfer 5.1. Screenshots of one of these subjects are attached. regards, Andreas

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difference in atlas size
by Satrajit Ghosh 03 Nov '13

03 Nov '13

hi i noticed a big discrepancy in size between these two, but not among other lh and rh gcs files. > 28769857 May 13 17:21 rh.DKTatlas100.gcs > 6883965 May 13 17:21 lh.DKTatlas100.gcs are these the intended sizes? this is from the 5.3 centos6_x86_64 distro cheers, satra

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ERROR: could not find ribbon.mgz
by jana dinges 03 Nov '13

03 Nov '13

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Image acquisition in different head coils
by carolina.mr 02 Nov '13

02 Nov '13

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Dilated ventricles
by Victor Kovac 01 Nov '13

01 Nov '13

Dear Freesurfer experts, I have run recon-all and included the -bigventrcles flag on a number of brains with ventriculomegaly. This fixed the segmentation errors in a few cases; however, there are still brains with dilated ventricles for which recon-all is not providing accurate segmentation (see attached image). Are there any other tricks I can attempt to solve this issue? I was considering doing manual pial and white matter edits in conjunction with filling the ventricles by using the Edit Voxels Tool. Would this be advisable? Thank you! Victor

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funcroi calculating percent signal change
by Alexandra Tanner 01 Nov '13

01 Nov '13

Hi Doug and Freesurfers, I would like to calculate percent signal change within an anatomical ROI for a group of subjects in Freesurfer 5.0. We are not functionally constraining our ROI, however, we do want to calculate the percent signal change across the entire region in each of our conditions (the contrasts we are using are condition-vs-fixation). Below are examples of the commands I've run for one of our conditions: funcroi-config -analysis SIRP_Stable5 -label lh.7Network_6.PFC.label -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg funcroi-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/SIRP_lh_7Networks_6_PFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED -o /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/Anatomical_roicfg_103113/18ActiveFolate_12Placebo_PreAndPost_7Tpost/lh_7Networks_6_PFC_1vFix -c Cond1vFix Is it necessary to now generate the mean functional baseline offset value within the ROI in order to calculate percent signal change if our contrast is comparing condition-vs-fixation? Any clarification on when the offset value is needed would be greatly appreciated! Thanks, Alex

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preferred method for generating appropriate bvecs for tracula
by Salil Soman 01 Nov '13

01 Nov '13

Hi, I have dicoms that I turn to nifti using dcm2nii (with the default settings plus anonymization option turned on [-a y]). The bvec files it generates by default are 3 rows by n columns (where n is b0 number + directions). I am under the impression tracula requires this to be converted to a n row by 3 column file. 1) is this correct, 2) is there a preferred way to perform this transformation on linux systems? Thanks you, -Sal

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How to generate histograms of intensities in one anatomical region?
by 赵越 01 Nov '13

01 Nov '13

Hi All, I have T1-weighted MPRAGE images and I run recon-all to generate surfaces and labels in freesurfer. Then I would like to do statistical analysis in the regions I am interested in. For example, I would like to generate a histogram of intensities in frontal cortex or in occipital. I can display these regions in different color in freeview based on the look-up table but I don't know how to use them to generate histograms in freesurfer or create binary masks then I can do the analysis with these masks in matlab. I use freesurfer to do this because I see these beautiful color segmentations. It would be really painful to manually create regional masks for a group study. I am new to freesurfer and I really appreciate if someone can point out a direction. Thanks! Best,Yue

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offset in QDEC
by Hamza Alshuft 01 Nov '13

01 Nov '13

Dear Freesurfers and experts Can any one please tell me what the offset box next to the max. box (under Threshold) in QDEC GUI is for? When I change from e.g 0 to 1 or higher I get larger significant clusters. How and when is this feature used? I also notice this very question is on the archive list but not answered. Here is the quote "Hi Bruce, I'm referring to "offset" in qdec/Display threshold line, near Min/Mid/Max. For example, I'm noting that if set +1 as offset the red statistical area is more larger. Stefano" Thanks Hamza This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. 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.

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