[Freesurfer] minor fsfast bug report

In the annot files generated by mri_glmfit-sim in 5.2.0 (e.g., cache.th20.pos.sig.ocn.annot), the names of the clusters take the form: cluster0 cluster-001 cluster-002 … but the last one is of the form cluster6 which is to say, no dash and no zero-padding. I assume they are meant to have a co

Re: [Freesurfer] FSFAST funcroi-sess problem

I followed the tutorial: mkanalysis-sess -fsd bold -analysis CPA.sm05.lh -surface fsaverage lh -fwhm 5 -event-related -paradigm CPA1.par -nconditions 20 -spmhrf 0 -TR 2 -refeventdur 20.265 -polyfit 2 -per-run -force -nuisreg nuisreg2.dat 7 -tpexclude tpexclude.dat On Jul 12, 2013, at

Re: [Freesurfer] Freesurfer surface circle of pre-defined size

Hi Sarah, I can image several ways to do this. If you can go onto the surface and find an index that you want to be the center, then you can create a label file with a single point. It would look something like this (see fsaverage/label/lh.cortex.label for example): --cut--

Re: [Freesurfer] integrating another atlas into Freesurfer

Hi Jeff, do you just want to map the annotations from fsaverage to your individual subject? If so, you can use mri_surf2surf, something like mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh \ --sval-annot $SUBJECTS_DIR/fsaverage/label/lh.aparc.annot \ --tval $S

Re: [Freesurfer] combining lh.annot and rh.annot files

Hi Jeff, what doyou mean? How would you visualize it? What would you do with it? Or do you mean you want to compare left and right? Or create aleft-right average? doug On 07/12/2013 08:07 PM, Jeff Eriksen wrote: > Is it possible to combine the lh and rh annotation files into a single > annotat

[Freesurfer] combining lh.annot and rh.annot files

Is it possible to combine the lh and rh annotation files into a single annotation file? How? -Jeff ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail i

Re: [Freesurfer] AC/PC positions and other questions

On 07/12/2013 07:18 PM, François Tadel wrote: > Dear freesurfers, > > I'm working on a function to import automatically the segmentation > folder into a Brainstorm database. I have a few questions: >- Is there a way to read/get the position of the anterior and > posterior commissures (AC/PC)?

Re: [Freesurfer] FSFAST funcroi-sess problem

Hi Joe, On 07/12/2013 06:51 PM, Joseph Dien wrote: > I'm using Freesurfer 5.3.0 > > (well, actually I ran the original analyses with 5.2.0 and then am > running this ROI follow-up with 5.2.0, could that be a problem? From > the release notes, it didn't look like it would be an issue) No, that

[Freesurfer] AC/PC positions and other questions

Dear freesurfers, I'm working on a function to import automatically the segmentation folder into a Brainstorm database. I have a few questions: - Is there a way to read/get the position of the anterior and posterior commissures (AC/PC)? - What file should I read to get the labels correspondi

[Freesurfer] FSFAST funcroi-sess problem

I'm using Freesurfer 5.3.0 (well, actually I ran the original analyses with 5.2.0 and then am running this ROI follow-up with 5.2.0, could that be a problem? From the release notes, it didn't look like it would be an issue) Anyway, I've run the following set of commands: funcroi-config -roi

[Freesurfer] integrating another atlas into Freesurfer

I have the Yeo resting-state fMRI atlases which I downloaded from http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011 They consist of 3 versions, fsaverage being of interest here. The fsaverage folder provided includes the typical FS folders corresponding a recon-all for the average bra

Re: [Freesurfer] Xhemi results

Thanks a lot! On Fri, Jul 12, 2013 at 6:58 PM, Douglas N Greve wrote: > It is the difference but it is on the tesselation of the left hemisphere. > If you want it on the right hemisphere, then you need to perform the > analysis on the right hemisphere. > doug > > > > On 07/12/2013 02:37 AM, amir

Re: [Freesurfer] Inflated surface smooth but white matter surface has holes

Hi Ye almost certainly not. Try running mris_euler_number - it will tell you the topology of the surface (which is the same for inflated/white/pial/...) cheers Bruce On Fri, 12 Jul 2013, ye tian wrote: Dear Freesurfers, My inflated surface looks smooth in tksurfer, but white matter surface h

[Freesurfer] Inflated surface smooth but white matter surface has holes

Dear Freesurfers, My inflated surface looks smooth in tksurfer, but white matter surface has holes in it. Is this an indication of topological defects? Thank you very much! Sincerely, Ye ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:

Re: [Freesurfer] large SD of aparc in one group

Laura, what is the coefficient of variation? Ie, the stddev/mean doug On 07/11/2013 08:54 AM, L. Koenders wrote: > Dear FreeSurfer experts, > > We have a question regarding the aparc output from the stats files, and > hopefulle you can help us. > We have 4 independent groups, of about 30 subject

Re: [Freesurfer] Non-grey matter classified as grey matter

Thanks a lot! On Fri, Jul 12, 2013 at 4:15 PM, Bruce Fischl wrote: > Hi Amir > > I'm not sure I understand the question. You need to acquire them on each > subject them same way you acquire your MPRAGE/T1-weighted image. Andre van > der Kouwe (ccd) has some sequences you can use on his website i

[Freesurfer] Freesurfer faster with CUDA or I7 3770k ?

Dear list, We are buying a computer dedicated mostly to Freesurfer. Initially we thought an I7 3770k a bit overclocked (about 4.5ghz) should be a good choice. However, I noticed that Freesurfer seem better tuned to use CUDA. Many of the messages I read are from 2010 so I am not sure whether this i

Re: [Freesurfer] Non-grey matter classified as grey matter

Hi Amir I'm not sure I understand the question. You need to acquire them on each subject them same way you acquire your MPRAGE/T1-weighted image. Andre van der Kouwe (ccd) has some sequences you can use on his website if you want guidance on parameters and such. cheers Bruce On Fri, 12 Jul

[Freesurfer] Adjust lighting in Freeview

Hi all, Is there a way to ajust the camera lighting / add lights in Freeview? Currently the lighthing is such that the surface with normal pointing upwards are illuminated well, but the surface with normal pointing downwards not that good. Thanks for replies in advance, Martijn __

Re: [Freesurfer] Pearsons r / adj. r squared

That helps! Great, thanks! On Thu, Jul 11, 2013 at 11:39 PM, Douglas N Greve wrote: > > I've attached a matlab script which should do it. > doug > > > On 07/11/2013 04:28 PM, Martijn Steenwijk wrote: > >> Dear all, >> >> Is there a way in freesurfer to compute surface wise pearsons r (for >> s

Re: [Freesurfer] Non-grey matter classified as grey matter

Dear Bruce, Would you please explain how and where to acquire FLAIR or T2 images to solve the problem? BR/Amir On Thu, Jul 11, 2013 at 9:47 PM, ye tian wrote: > Dear Bruce and Doug, > > Thank you very much! > > PS: I searched through my data folder and didn't find T2 images. There > goes all my