Freesurfer

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30135 discussions

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

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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

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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

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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

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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

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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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Tracula_critical issue
by Alshikho, Mohamad J. 24 Nov '14

24 Nov '14

Hi Anastasia, I started recently using Tracula to do tractography for my DTI data. I did the analysis exactly as mentioned in wiki. The problem is that when I am repeating the third step (trac-all -path -c ) for the same subjects to generate the statistics; Tracula is updating all the information mentioned in the file "pathstats.overal.txt" regarding the tract's volume and the tract's metrics values. Every time the output is different. I think we have a problem in the scripts or something like this? Attached are three "pathstats.overal.txt" files for the same subject after three consecutive runs for the "trac-all -path -c" (the same subject) Looking forward for your support Thanks

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Regarding recon-all
by Gunjan Gautam 24 Nov '14

24 Nov '14

Hi, I used recon-all with all and its taking a lot of time. My main concern is only to get the stripped brain. I tried with autorecon1 as well but its also taking not less than 15min and I need to deal with a huge data. Last stage of autorecon1 is skull stripping which takes the NU corrected input (as it FS works as a pipeline). Is there any way to directly get the "stripped brain" and its binary mask. I also need to ask, which file of the output (name with extension) is the "binary brain mask" ? Best regards, Gunjan

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Amygdala subfields
by stdp82＠virgilio.it 24 Nov '14

24 Nov '14

Dear all, is the amygdala subfields segmentation available or you are working on it? Thanks, Stefano

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Re: [Freesurfer] Repost: estimating lesion size on surface
by Timothy Meier 23 Nov '14

23 Nov '14

Hi Bruce, Sorry, I did a poor job of describing the problem. We are trying to do an analysis of subject specific abnormalities on the surface. Instead of a traditional analysis assuming that patients have homogenous abnormalities (for example cortical thinning in anterior cingulate) relative to a control group, we want to count the number of abnormalities over the entire surface in each subject. On the surface, abnormalities can be defined as average thickness in a small region that is >2 SD away from mean thickness in a control group in that same region. Following that, we can compare the average number of subject specific abnormalities between groups. This method has been used to identify white matter abnormalities in patient populations in which heterogenous abnormalities are expected, such as TBI patients. However, it requires an a priori decision about what constitutes an abnormality. In this case, we need to specify it in number of vertices. We have previously used 128 ul as our defined abnormality size in the volume. Our first thought was to use that as a starting point and translate the volume to surface area or number of vertices. Is there a reasonable way to approximate how many voxels get translated into surface space? And is there a reasonable way to approximate how much area each data point would have on the surface? One approach we are considering is to calculate the average gray matter volume, surface area, and number of vertices from the aparc.stats file. With this information we'd have an approximate relationship between volume, surface area, and # vertices. We are curious if this seems like a reasonable choice, or if you have any thoughts on how to go about this. Thanks a lot, Tim On Fri, Nov 21, 2014 at 11:00 AM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Repost: estimating lesion size on surface (Bruce Fischl) > 2. Odd thing about mris_convert? Position changed from > freesurfer format to .stl (ting xu) > 3. prefrontal cortex label (Anna Jonsson) > 4. Re: Odd thing about mris_convert? Position changed from > freesurfer format to .stl (Bruce Fischl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 Nov 2014 16:45:17 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Repost: estimating lesion size on surface > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.11.1411201644480.6947(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Tim > > can you elaborate what the issue is? If you have binary lesion maps inthe > volume, can't you just sample those onto the surface and measure surface > area directly? I think I am missing something > > Bruce > On Wed, 19 Nov 2014, Timothy > Meier wrote: > > > Hello, > > I just wanted to repost this to see if anyone had any thoughts on an > > appropriate 'lesion' size for a pothole analysis performed on the > surface. > > We want to compare the average number of small surface lesions (estimated > > from cortical thickness) across single subjects for a control group > relative > > to our patient group. > > > > We have done similar analyses in the volume for white matter, so one > thought > > was to use that same lesion size. However, that requires estimating a > > surface area from our previously used volume. > > > > Any thoughts on how to approach this, or thoughts on an appropriate > lesion > > size to use would be appreciated. > > > > Thanks, > > > > -Tim > > > >

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