Freesurfer October 2015

freesurfer@nmr.mgh.harvard.edu

142 participants
214 discussions

Re: [Freesurfer] Sulcal depth units (Simon Vandekar)
by Simon Vandekar 22 Jan '16

22 Jan '16

Hi Bruce, The units are not standardized because the standard deviation across the surface does not equal 1. >From line 227 in mris_inflate.c it says that the sulc file is demeaned before it is written out: MRISzeroMeanCurvature(mris) ; /* make sulc zero mean */ However I am still unclear on what the units are. They are too small to be millimeters. Given other published measurements of sulcal depth I think they might be in centimeters, but can you confirm? Thanks again, Simon >Hi Simon > >I just took a look at the code and I believe that we make it 0 median >(not mean) and unit standard deviation. The curvatures can get quite large >in regions where the vertex spacing is small and the median is robust to >this. > >cheers >Bruce > > >On Sat, 24 Oct 2015, Simon Vandekar wrote: > >> Hi Bruce, >> >> I think that unnormalized sulcal depth would be useful. However, I am also curious what the units are in the standard output, because they appear to not be z-score standardized in each hemisphere. >> >> Thanks again, >> Simon >> >> >>> H I Simon >>> Do you need the unnormalized sulc? It would be pretty easy to put something in to generate it >>> Bruce >>> >>>> On Oct 22, 2015, at 3:23 PM, Simon Vandekar <simonv(a)mail.med.upenn.edu> wrote: >>>> >>>> Hi Bruce, >>>> >>>> I chose a random subject from the ADNI dataset and computed the mean and variance for the left and right hemispheres separately. It looks like the mean is close to 0, however the variance is not 1. Do you think it is possible that the surfaces are demeaned, but the units are still something meaningful (i.e. not unitless)? >>>> >>>> >>>> sulc = read.table('rh.sulc.asc', header=FALSE, col.names=c('v', 'x', 'y', 'z', 'sulc')) >>>>> mean(sulc$sulc) >>>> [1] -1.236923e-08 >>>> >>>>> var(sulc$sulc) >>>> [1] 0.3276958 >>>> >>>>> quantile(sulc$sulc) >>>> 0% 25% 50% 75% 100% >>>> -1.72503 -0.42128 -0.03963 0.40072 1.80980 >>>> >>>> >>>> Thanks again, >>>> Simon >>>> >>>> >>>> >>>> >>>> >>>> Hi Simon >>>> >>>> they are originally mm, but I believe we z-score normalize them so that >>>> the sulc file is 0 mean and unit variance. >>>> >>>> cheers >>>> Bruce >>>> On Wed, 21 Oct 2015, Simon >>>> Vandekar wrote: >>>> >>>>> Dear Freesurfer experts, >>>>> >>>>> >>>>> I am reading the manuscript "Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System" by Fischl, Sereno, and Dale (1999) where the estimation of sulcal depth is described on page 199, however from the description I am still unsure of the exact units of sulcal depth. >>>>> Are the units for sulcal depth in mm or are they in arbitrary units? >>>>> >>>>> Thanks in advance, >>>>> Simon

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some questions about optseq
by charujing123 15 Jan '16

15 Jan '16

Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20 charujing123

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how to display individual Desikan parcels?
by Mihaela Stefan 05 Jan '16

05 Jan '16

Hello Freesurfers, I would like to be able to display just a few parcels from the Desikan atlas on the fsaverage inflated surface. For example, I would like to display only the superiorfrontal and the posteriorcingulate. I tried to recreate the parcels myself by drawing labels, but they don't look pretty (see the attachment). I traced the labels in qdec (based on the Annotation/Opacity tab) and then I mapped them to fsaverage and visualized them with freeview. There's probably a better way to do that but I couldn't figure it out. Can anyone help me with this? Thanks! Mihaela

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TRACULA question- pathstats not loading
by Golan, Noa 15 Dec '15

15 Dec '15

Hi, I am currently analyzing DTI data and I am having issues with one file in particular. When I run the tracheal -path -c step, all of the files are generated except the pathstats text files. Any thoughts? Thanks! Noa

2 1

Tracula stats COR-.info does not exist
by Simon Jones 15 Dec '15

15 Dec '15

Dear Tracula developers, I posted a problem with tracula when I ran trac-all -stat -c dmrirc_ind_mni_cvs_all_stats.all I receive this error message Loading output reference volume from /home/spj24/app/freesurfer/subjects/cvs_avg35 corRead(): can't open file /home/spj24/app/freesurfer/subjects/cvs_avg35/COR-.info ERROR: Could not read /home/spj24/app/freesurfer/subjects/cvs_avg35 There is no file called COR-.info in the directory /home/spj24/app/freesurfer/subjects/cvs_avg35/ I have now changed the lines in the configuration file set doregcvs = 1 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # #set cvstemp = donald set cvstemp = cvs_avg35 set cvstempdir = $FREESURFER_HOME/subjects to set doregcvs = 1 set cvstemp = cvs_avg35/mri/brainmask.mgz set cvstempdir = $FREESURFER_HOME/subjects i.e. explicitly pointing to an image in the cvs_avg35 directory and the stats seem to complete without error. Is that the right thing to do? Thanks for your help, Simon

2 1

Tracula with multi-shell data?
by Henrik Sjöström 15 Dec '15

15 Dec '15

Hi! I have some questions regarding Tracula and multi-shell DWI. -Is it possible to activate the multi-shell model within bedpostx when running it through tracula? -does anyone have experience on running multi-shell data through Tracula (2 or 3 crossing fibers)? We are planning an experiment and discussing protocols consisting of around 32 directions with b=1000 and 64 directions at b=2500 so I'm looking for opinions on this with regard to Tracula processing. Thanks! Henrik Sjöström

2 1

Tracula Tracts density
by John Anderson 15 Dec '15

15 Dec '15

2 1

TRACULA visualisation differences
by Worker, Amanda 15 Dec '15

15 Dec '15

Hi all, I'm just visualising tracts that have been processed using TRACULA and I'm noticing some differences that seem slightly odd. For example, when I load the ILF for one subject, the pathway looks huge and takes up a very large portion of the brain. However, when I load the same tract along with all of the other tracts it looks like a well segmented region. I have checked my registration with the T1 and it looks good, so I'm not sure why there is a difference. Looking at the stats for this tract volumes range from 300-600 approx. This is a patient vs control study so I would expect some differences in volume, but this seems like a big difference from the example given on the wiki which is around 160. But the average MD and FA seem reasonable and consistent at around 0.0008 and 0.4. This is the same for many of the subjects - would you base your quality control on the visualisation of the single tracts or all of the tracts loaded together. Is there an obvious difference/ why would they load differently? I have attached some screenshots so that you can see what I mean. Thanks in advance. Amanda

2 1

3dClustSim and Gaussian filter width
by Emma Thompson 08 Dec '15

08 Dec '15

Dear Freesurfers, I am trying to use 3dclustsim in AFNI to determine the minimum number of voxel in a cluster to reach significance, my understanding is that in the command line the -fwhm s flag refers to the gaussian filter width and NOT the Gaussian Kernel, can anyone point me to how I might be able to obtain this for each hemisphere in freesurfer? I am using my own average brain that I created, but it would help to know how to do this for the fsaverage as well. Many thanks for your help! http://afni.nimh.nih.gov/pub../pub/dist/doc/program_help/3dClustSim.html

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bring volumes to fsaverage space
by Shani Ben Amitay 04 Dec '15

04 Dec '15

Dear freesurfers, I would like to know what will be the best way to bring volumes in the individual subject's space to the fsaverage space. Thanks, Shani

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Freesurfer October 2015