Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Tracula mri_convert error
by Janosch Linkersdörfer 25 Nov '14

25 Nov '14

Hi experts, I wanted to play with Tracula. Strangely, already the first preprocessing step, i.e., conversion to .nii.gz, fails. Apparently, mri_convert (falsely) recognizes my dicom files as MGH dicoms ("This looks like an MGH DTI volume"). Could this be the reason why it fails? Thanks, Janosch

2 1

Resample the surface mesh
by ting xu 24 Nov '14

24 Nov '14

Dear freesurfer experts, Is there any way to down resample the native surface mesh and register the functional volume data to the down resampled surface in freesurfer? Many thanks, Ting

4 6

Download of latest Tracula version not possible
by Janosch Linkersdörfer 24 Nov '14

24 Nov '14

Hi all, I am trying to download the latest version of Tracula from this site http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. This seems not to be possible at the moment. Are there server problems? Thanks, Janosch

1 0

can I apply freesurfer significant clusters as ROI in fMRI study?
by chenchunhuichina 24 Nov '14

24 Nov '14

Dear freesurfer experts, I searched on the wiki but can not figure out how to solve this problem: I found some significant clusters on graymatter thickness, how can I use it as a ROI in my functional MRI study? I have both structure and function data of the same subjects, so I can either do it in stardard space or native space one by one if possible. Any help is appriciated~ Best 2014-11-20 Chunhui Chen _________________ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875

3 2

pial mask
by Octavian Lie 24 Nov '14

24 Nov '14

Dear all, After running the recon-all on a subject, I needed to create a 'pial' surface to include the hippocampi, which are not included well in the pial reconstruction. So I generated a mask and used it to mask brain.mgz. 1. All well, except that in both the mask and the masked brain volume (readybrain.mgz, see below), the fill extends with a variable layer of about 1 voxel) above the pial red contour in some areas (see the top, leading me to believe that the red contours we use when editing are not the actual pial surfaces, but some interpolations of the actual calculated pial surface. If this is true, then there may be some editing errors when using these contours. Another explanation could be the resolution of the mris_fill. Please let me know which is the case, and how to fix it so that the mask closely follows the red contour. 2. I need to generate a surface from readybrain.mgz, preferably that can be registered to the sphere.reg and on which cortical parcellation (DK atlass) can be applied. Is there a way? If not, I would still like to know how to generate the surface of this volume. Thank you, Octavian Here is the code I used: cd /usr/local/fs5.3/freesurfer/subjects/subjid mris_fill -c -r 0.1 surf/rh.pial mri/rh.pial.filled.mgz && \ mris_fill -c -r 0.1 surf/lh.pial mri/lh.pial.filled.mgz && \ mri_concat --combine --i mri/rh.pial.filled.mgz --i mri/lh.pial.filled.mgz --o mri/pial.filled.mgz && \ cd ./mri && \ mri_binarize --i aseg.mgz --match 5 --match 9 --match 10 --match 14 --match 17 --match 18 --match 19\ --match 25 --match 31 --match 44 --match 48 --match 49 --match 53 --match 54 --match 55 --match 57\ --match 63 --match 86 --match 96 --match 97 --match 105 --match 106 --match 114 --match 115\ --match 195 --match 199 --match 203 --match 204 --match 205 --match 216 --match 222 --match 225\ --match 507 --match 557 --match 1200 --match 1201 --match 1205 --match 1206 --match 2200 --match 2201\ --match 2205 --match 2206 --o hippoamy.mask.mgz && \ fscalc pial.filled.mgz add hippoamy.mask.mgz -o epimask.mgz && \ mri_convert brain.mgz brain.float.mgz -odt float && \ mri_mask brain.float.mgz epimask.mgz readybrain.mgz

1 0

multiple comparisons correction for individual hemispheres (native space)
by Milde, Christopher 24 Nov '14

24 Nov '14

Dear Freesurfer experts, I performed fMRI analysis using FSFast resulting in uncorrected significance maps (fsig.nii.gz). For selxavg3-sess I did not use the -fwhm flag (I rerun selxavg3-sess with -fwhm at moment). How can I use simulations for native space hemispheres?. I tried to adapt mri_glmfit-sim but unfortunately it failed... Sincerely yours, Christopher

2 1

Group analysis
by Roberta Santoro 24 Nov '14

24 Nov '14

Dear all, I created an average subject from my dataset and I would like to use it to run a group analysis of thickness. I am using the command: recon-all -s subjid -qcache -target MyAverage When looking at the terminal, I noticed that the srcsurfreg and the trgsurfreg are both sphere.reg: shouldn’t one of the two be sphere.reg.MyAverage? Otherwise, how is the alignment achieved? Thanks for your help. Best, Roberta

2 1

mri_glmfit-sim sim-sign
by Jon Alan Wieser 24 Nov '14

24 Nov '14

hi please explain the differece between --sim-sign abs, neg, and pos

2 3

seed-based fcMRI analysis between thalamus and cortex
by stdp82＠virgilio.it 24 Nov '14

24 Nov '14

Dear all, is FS-FAST able to perform seed-based fcMRI analysis between thalamus and cortex (e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2852505/)? Thanks for your work, Stefano

2 1

tksurfer curvature and overlay displays
by Graham Wideman 24 Nov '14

24 Nov '14

Hi all, I'm having some issues (some possibly mine, some possibly tksurfer's) getting tksurfer (5.3c6) to display curvature the way I think it should be able to. I am using the bert sample data. The Curvature display --------------------- If I use the Show Curvature button in the UI control panel, I get the familiar gyrus=green; sulcus=red pattern applied to the displayed brain. The Configure Curvature Display is a bit of a shambles, and I think should be fixed. First, it is virtually impossible to set midpoint using the slider, because the values it pushes to the adjacent textbox are way too coarse. Typing values into the midpoint textbox works, in that it affects the balance of red and green in the display. However the textbox does not affect the position of the slider, suggesting that it actually does not work. That said, there's no actual adjustment of the threshold size. Indeed, it's not clear that there actually IS a threshold -- perhaps there isn't. Maybe "threshold midpoint" just sets the midpoint of the color range? And then there's a a textbox labeled "threshold slope". I'm pretty sure that's nonsensical phrase. What this box appears to do is set the ratio of color to curvature value. Ie: "Color intensity". Bottom line -- this dialog only partially fits the purpose at hand, and is so confusingly wording that ones attempts to use it are pretty much random. It may even be that some UI elements or functionality that was once there has gone missing accidentally? Finally, I wanted a colorbar for the curvature display, and so far as I can tell there isn't one. I can turn on a colorbar, but it's the one for overlays. Using a Curvature variable as an overlay ---------------------------------------- I next tried to read in the k1.crv variable as an overlay. This sort of works, but gives a very mottled display (except using "heat map" color scheme), I think because even in definite sulcus and gyrus regions, the curvature values straddle the border of the grey range of color, and I'm not sure how to adjust it sensibly. -- I couldn't figure out how to set the overall color range, that is to say the extremes of the colorbar. These seem stubbornly stuck at 5.0 and -5.0. In particular, the Theshhold Max setting doesn't seem to affect the extremes of the color range. -- I couldn't figure out how to eliminate the large grey range in the middle of the color range. I noted that the Threshhold Min setting can be used to make the grey range larger, but setting Min below 1.5 (for example, zero) does not eliminate the grey between 0 and +/-1.5. ------------------------ Anybody have any helpful clues on these items! Thanks! -- Graham

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