Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] color scale for longitudinal analysis using freeview
by Salil Soman 08 Jul '13

08 Jul '13

Dear experts, Could someone point me to the color key for the output of the longitudinal analysis as viewed in freebies (as generated by the freesurfer longitudinal analysis tutorial)? Thank you, Sal Salil Soman, MD, MS

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Exporting freesurfer images
by ye tian 08 Jul '13

08 Jul '13

Dear Freesurfers, Is there a way to export a large number of tkmedit images? I would like to show other people how certain areas evolve as I change coordinates, and I find myself capturing a lot of screenshots. Thank you very much! Sincerely, Ye

2 2

Painting voxels vs. adding control points
by ye tian 08 Jul '13

08 Jul '13

Dear freesurfers, I would like a second eye on my decision to edit wm.mgz. I think that the boundary between the gray and the white is unrealistic (e.g. Coronal.png). Furthermore, there is a discrepancy between -surfs and -surfs -aseg (e.g. attached coronal_aseg.png). If I indeed need to edit these slices, which way is more preferable, adding voxels or control points? Thank you very much! Sincerely, Ye

3 6

Exporting data from "Find Clusters and Goto Max"
by Sean Hatton 08 Jul '13

08 Jul '13

Hi all, Within QDEC, when I click on the "Find Clusters and Goto Max" button I can see the individual thickness values per datapoint. 1. I am co-vaying for age: would these values be raw thickness values or estimated margin means? 2. Considering I have 100s of subjects and several ROIs, how do I export these values for all subjects? I can click on each data point and copy the terminal readout or create an ROI, map label to subjects and export it out but both approaches are time consuming and prone to human error. Is there a way of using existing QDEC setup files to export all this data out more cleanly? Cheers, SEAN HATTON Brain & Mind Research Institute THE UNIVERSITY OF SYDNEY

2 1

Loading T1 maps onto inflated surfaces
by S Mian 08 Jul '13

08 Jul '13

Hi, I am new to FreeSurfer and I'm trying to figure out how to view T1 volumes on inflated surfaces in FreeSurfer. Any guidance would be appreciated! Thank you!

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Xhemi results
by amirhossein manzouri 08 Jul '13

08 Jul '13

Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? 2) If yes, shouldn't I see the similar mapping by overlaying this to lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh) 3) How do you interpret the result after analyzing within one group? ( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh) 4) Is there any way to look at the results through the brain per slice and also the whole brain? -- Best regards, Amirhossein Manzouri

1 0

Tumor segmentation...
by Dov Sadan 08 Jul '13

08 Jul '13

Hi all, I Have MRI scans (T1/T2/Flair) with (manually) segmented tumors and I would like 2 use Freesurfer to estimate the brain locations of those Tumors. (I.e. What area of the brain "affected" by these tumors) .. Of course thisis not for clinical use, but "research" -- Is this task possible with Freesurfer ? If so, how this can be done ? Thanks, Dov [Please excuse me for my English...:]

2 1

recon-all
by 小麦 08 Jul '13

08 Jul '13

Hi expert, When I excuted the recon-all,I got the result that the final result is without error but the process is with error.The recon-all.log is attached.I want to get the cortical thickness,so I want to know that is the process's error affect my final result? Thanks in advance, Bella

2 1

freesurfer skull strip removes brain except brainstem, and then has retesselation error
by Salil Soman 06 Jul '13

06 Jul '13

Hi, I have a study for which the original T1 looks good, was obtained identically to dozens of other studies that went through freesurfer without problem. For some reason this study keeps getting stripped down to a little more than its brainstem. Then the rest of the processing fails with an error of retesselation. Log files attached. Any suggestions on how I can properly process this data? Best wishes, Sal

2 1

T2pial refinement bbregister error
by Satrajit Ghosh 05 Jul '13

05 Jul '13

hi doug, bbregister was running into an error trying to do T2pial refinement sequence of commands and output here: https://gist.github.com/satra/5934639 and it looks like the absence of FSLDIR i didn't have FSL installed on this machine - i thought that freesurfer had it's own version of flirt. is FSL necessary? cheers, satra

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