Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

asegstats2table output meaning
by miracle ozzoude 21 Aug '17

21 Aug '17

Hello FreeSurfer, Where can I find the meaning of all of the outputs provided by asegstats and how some of the outputs are calculated (e.g. Total Gray matter etc.)? Thanks. Best, Paul

3 5

Resample to cropped FOV in anatomical space
by Michael Waskom 21 Aug '17

21 Aug '17

Hi Doug, I'd like to use the registration matrix from bbregister to transform functional data into a cropped FOV that corresponds with the anatomy. I thought that bbregister outputs a ras2ras transform, so if I could crop the anatomical volume with a correct header vox2ras, things should be fine. Is my thinking here wrong? Here is roughly what I have done: 1. Generate a registration matrix to the full anatomy bbregister --s subj --mov func.nii --reg reg.dat --t2 2. Crop the anatomy: mri_convert brain.mgz brain.nii fslroi brain.nii brain_crop.nii 50 150 50 150 50 150 (I know this is an fsl tool but I couldn't find an option to do exactly this in mri_convert) 3. Check the output -- looks fine so far tkregister2 --mov brain-crop.nii --regheader --s subj --surfs --reg /dev/null 4. Resample the functional volume mri_vol2vol --mov func.nii --targ brain_crop.nii --reg reg.dat --o func_xfm.nii 5. Check the output tkregister2 --mov func_xfm.nii --regheader --s subj --surfs --reg /dev/null The resulting functional image is shifted superior about ~20cm What am I missing in my understanding of the bbregister and header transformation matrices? Thanks! Michael

2 3

mris_anatomical_stats output
by stdp82＠virgilio.it 21 Aug '17

21 Aug '17

Hi list,how can I save the outputs of mris_anatomical_stats in xls file?Thanks Stefano

2 1

mri_glmfit-sim annotations
by Van Der Deijl, Rosanne 21 Aug '17

21 Aug '17

Dear Freesurfer team, I was wondering how the annotations for the clusters that came out of mri_glmfit are picked. I am wondering because I have a cluster which visually seems to cover mostly the insula (and with a previous set of subjects this same cluster was annotated as the insula), but it is now annotated as the superiortemporal (which it indeed also partly covers). Is just the region in which the largest part of the cluster lies picked for annotation, or is it done p-value-wise or in some other way? Thank you in advance! Kind regards, Rose

2 1

Cortical gyrification findings
by Martin Juneja 21 Aug '17

21 Aug '17

Hello FS experts, I am correlating some of the behavioral measures with cortical thickness (CT) and cortical gyrification (CG) measures. - For CT-behavioral: I have some expected results after correcting for multiple comparisons using mri_glmfit-sim - For CG-behavioral: Again, I have some expected results (more expected that CT-behavioral results) - only 3 clusters (sig.mgh result) but none of those survived after correcting for multiple comparisons using PALM, I can't use mri_glmfit-sim because my design is non-orthogonal. I also learnt from FS discussion forum and literature that CG is already extremely smooth so it would require large area to survive multiple comparisons correction. I was wondering if I can report my CG results based on this argument. If yes, then any more suggestions/references which I can use as arguments to justify my CG findings, that would really help. Thanks.

2 1

mri_mcsim error
by Zhiliang Long 21 Aug '17

21 Aug '17

Dear FS experts: I am writting to ask for help about mri_mcsim. I would like to run mri_mcsim with only one FWHM (e.g. --fwhm 13) instead of FWHM=1:fwhm-max (the default is FWHM=1:30). Thus i tried: mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/mask --base mc-z --surface fsaverage lh --nreps 100 --mask mask.mgh --fwhm 13 However, i got errors: ERROR: Option 13 unknown. Is there any information that i missed ? Thanks in advance for any suggestions. Best Zhiliang Long

2 1

Problem opening freeview
by Micah Rhodes 21 Aug '17

21 Aug '17

Hello, I am having a problem opening up freeview in MobaXterm (a bash terminal) on my windows 7 machine. Although freesurfer is working, when I attempt to open freeview, it tells me that "XWin_Moba.exe has stopped working." Have you ever come across this issue? Thanks

1 0

Freeview in FreeSurfer 6.0
by Wu Jianxiao (Jadecci) 21 Aug '17

21 Aug '17

Dear FreeSurfer team, I was viewing MNI152 template from FSL in freeview using FreeSurfer 6.0, and somehow there was a shift between 1mm and 2mm template. The problem does not show in FreeSurfer 5.3. Is there an error with freeview in FS6 or did the command change? The command I used is as follow: freeview $FSL_DIR/data/standard/MNI152_?mm_brain.nii.gz Thank you! Wu Jianxiao Department of Physiology & Department of Electrical and Computer Engineering National University of Singapore

2 1

Custom intensities in aparc+aseg
by Martin Kavec 20 Aug '17

20 Aug '17

Dear all, I ran my subjects through recon-all successfully. I am in a need to have custom intensities for segmentation and parcellation in aparc+aseg. Say, 10 - ventricles, 20 - amygdala, 30 - putamen, ... I would appreciate advice on how I could achieve that. Thanks in advance, Martin

2 3

Freesurfer manual edit problems
by Chethana Kishore 19 Aug '17

19 Aug '17

sir/maam, i request your help in solving in a query of mine. while the manual edit is being done , and we use the "save the main volume" button to save the progress. but subsequently on opening the image to further our edits it appears as a very brightly intense image and difficulty in differentiating the grey/white matter leading it to be unuseable. can u please suggest how to solve this problem? Thanks and regards Chethana K

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