Re: [Freesurfer] dt_recon error

Hi Yuko, it will get the bvals and bvecs from a set of tables distributed with FS. But the dicom has to have some information in it that tells it which table to use. It looks like your dicom did not have this information (it is not in the info dump created from the dicom). So you'll have to cre

Re: [Freesurfer] dt_recon error

Hi Doug, Thank you for your reply. > If so, then it cannot extract the bvecs and bvals. If you supply them in a > file on the command line I don't quite understand how --b works with dt_recon. I did: dt_recon --i /Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm --s AGY11 -

Re: [Freesurfer] extracting time courses from fMRI

yes, that is the correct procedure. doug Hellyer, Peter wrote: > Hi All, > > I'm trying to extract time courses from functional data > > I started by registering my motion corrected functional data to my > segmentation using bbregister, then I used: > > mri_vol2surf --src Motioncorrectedfunctiona

[Freesurfer] extracting time courses from fMRI

Hi All, I'm trying to extract time courses from functional data I started by registering my motion corrected functional data to my segmentation using bbregister, then I used: mri_vol2surf --src Motioncorrectedfunctional.nii.gz --srcreg register.dat --out suface.mgz —hemi rh & mri_segstats --i

Re: [Freesurfer] tcl script question: labl_set_color

I think you can set the outline color of each label indepently by using it's index which is assigned in the order in which it is loaded I believe. So in our example below  labl_set_color 0 255 0 0, change the first "0" to a "1" for the second label. Also, I would have thought labl_select -1 woul

Re: [Freesurfer] tcl script question: labl_set_color

OK, right-clicking on the surface did in fact de-select the label (turning it all to a uniform color). Way to script a right-click? (I see left click...) Now that this is more or less working, I am looking to do something slightly different: i.e., combine the boundaries of one set of regions, on

Re: [Freesurfer] [FreeSurfer]: mkanalysis-sess

OK, I think I've fixed it. I've checked the fix into dev which should be live tomorrow. When you make the analysis, add -per-session to the cmd line. doug Douglas N Greve wrote: > Hi Tapsya, I've verified the problem and am working on a fix. > doug > > tap...@nmr.mgh.harvard.edu wrote: >> Hi Doug

Re: [Freesurfer] mri_surf2surf error - Return code 254

not and keep the topology (there is some decimation that is used in the EEG/MEG inverse stuff, but it's just to generate points, not faces) On Fri, 9 Dec 2011, Douglas N Greve wrote: > Bruce, do you have a command to reduce the number of vertices? > > John Griffiths wrote: >> >> >> Ok. Can't s

Re: [Freesurfer] mri_surf2surf error - Return code 254

it won't On Fri, 9 Dec 2011, John Griffiths wrote: Ok. Can't see any options in mris_smooth info reducing the number of vertices. How would I do that? Ta,             john On 9 December 2011 17:22, Douglas N Greve wrote: Yes, give it both --sval-xyz and --tval-xyz to indicate that t

Re: [Freesurfer] mri_surf2surf error - Return code 254

Bruce, do you have a command to reduce the number of vertices? John Griffiths wrote: > > > Ok. Can't see any options in mris_smooth info reducing the number of > vertices. How would I do that? > > Ta, >john > > > On 9 December 2011 17:22, Douglas N Greve

Re: [Freesurfer] Event-Related design and jitter in stimulus onset

By default, optseq uses an internal clock synchronize to the TR (so events can only start on the TR). This can be changed by setting dPSD (eg, to 1). This would allow the NULL events to be multiples of 1 instead of 2. The PSD is specified in seconds. doug SHAHIN NASR wrote: > optseq2 --ntp 132

Re: [Freesurfer] mri_glmfit search space = 0

What are these asc files? Is this the input that you are having qdec load? If so, then there is at least one subject that has a 0 value at each vertex. The other 187 subjects may be non-zero. doug KYLE ROLLINS HANSEN wrote: > Doug- > Thank you for your response. The data set did not change betw

Re: [Freesurfer] Event-Related design and jitter in stimulus onset

What is your command line? SHAHIN NASR wrote: > > Thanks Doug. > In my experiment, each trial (event) consists of 1 sec stimulus > presentation and 5 sec blank interval (TR=2). I have also added a > condition with just blank presentation which will be repeated as much > as other eve

Re: [Freesurfer] mri_surf2surf error - Return code 254

Ok. Can't see any options in mris_smooth info reducing the number of vertices. How would I do that? Ta, john On 9 December 2011 17:22, Douglas N Greve wrote: > Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is > a surface. We usually use mris_smooth to smoot

Re: [Freesurfer] Event-Related design and jitter in stimulus onset

Thanks Doug. In my experiment, each trial (event) consists of 1 sec stimulus presentation and 5 sec blank interval (TR=2). I have also added a condition with just blank presentation which will be repeated as much as other events. I have used optseq2 commands to generate the trial seque

Re: [Freesurfer] WM hypointensities included in left-cerebral (right-cerebral) white matter volume ?...

yes doug Gonzalo Rojas Costa wrote: > Hi: > > In aseg.stats the WM hypointensities is included in left-cerebral > (right-cerebral) white matter volume ?... > > Sincerely, > > > Gonzalo Rojas Costa > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.

Re: [Freesurfer] Event-Related design and jitter in stimulus onset

Hi Shahin, there are several ways to answer this question. If you are going to analyze assuming a shape to the HRF, then the actual delay between stimuli is technically not important (though 4s will be good to avoid attenuation in the following stimulus). If you're using an FIR model of the HRF

Re: [Freesurfer] run preproc-sess with -nomc

Hi Evelina, why do you want to run it without MC? I'm not sure it will run that way. When you run it with -noreg, it causes it not to run the registration. For the preprocessing you have set up, it requires that the registration be run at some point because it needs it to map the fmri to the su

Re: [Freesurfer] downsampling white matter surface and converting to .tri

Yea, or leave out the --trgsubject all together or spec fsaverage3 as the target. doug Bruce Fischl wrote: > I'll leave this for Doug, but it may be that the target subject has to > be fsaverage (which is the only one that is actually an icosahedron) > > cheers > Bruce > On Thu, 8 Dec 2011, John

Re: [Freesurfer] Contrasts in GLM

Both of those will essentially test the same thing, just with a different sign. FS always computes two-tailed tests and reports both tails, so the sign is only a matter of convention. Assuming the Patient class is first in the FSGD and you want volunteers > patients to show up as yellow, then y

Re: [Freesurfer] mri_glmfit search space = 0

Sorry, hit the send before I was ready. I was also going to point out that mri_glmfit will zero-out a voxel unless it finds that all inputs are non-zero (pruning). It looks like it could not find any voxels that met this criterion. doug Douglas N Greve wrote: > Did the data set change between t

Re: [Freesurfer] mri_glmfit search space = 0

Did the data set change between the two analyses? The KingLab wrote: > Hello Doug- > In going through the threads for freesurfer, I found the following which also > describes the issue I am having. However, the error arises for me while > running a collection of brains through qdec, so I have no

[Freesurfer] Probabilistic V1 labels to volume

Hi There was a post recently on the mailing list about exporting Probabilistic V1 labels to a volume. I have applied the probabilistic mapping of an individual subject and now have the "lh.v1.prob.label" I would like to convert this label as a volume, and the function mri_label2vol is a litt

Re: [Freesurfer] mri_glmfit-sim error with v5.0

Can you tar up your glmdir and drop it to me? doug Yuko Yotsumoto wrote: > Thank you Doug, > >> Hi Yuko, I think you must have an older version of glmfit-sim some how. >> I've put a newer version here: > > I replaced the /bin/mri_glmfit-sim, but got the same error. > > [ERROR 1] > In line 292: >

Re: [Freesurfer] dt_recon error

Hi Yuko, your dicom file might be from a different versioned scanner than dt_recon is used to seeing. If so, then it cannot extract the bvecs and bvals. If you supply them in a file on the command line, it should run properly. doug Yuko Yotsumoto wrote: > Hello, > > I'm having a problem with dt

Re: [Freesurfer] mri_surf2surf error - Return code 254

Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is a surface. We usually use mris_smooth to smooth surfaces; I'm not sure whether this use of mri_surf2surf will work properly. doug Bruce Fischl wrote: > Hi John > > Doug can say for sure, but I think you want to give it th

Re: [Freesurfer] [FreeSurfer]: mkanalysis-sess

Hi Tapsya, I've verified the problem and am working on a fix. doug tap...@nmr.mgh.harvard.edu wrote: > Hi Doug, > > It seems that there are still problems related to using -per-session. > Preproc-sess now finishes apparently fine (correct file names are > generated, i.e., fmc.*) but the analyses a

[Freesurfer] WM hypointensities included in left-cerebral (right-cerebral) white matter volume ?...

Hi: In aseg.stats the WM hypointensities is included in left-cerebral (right-cerebral) white matter volume ?... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/list

Re: [Freesurfer] Problem with .stats files for aparcstats2table

Hi Krish! Thanks for the reply, I was actually able to solve the problem with a general stats2table script provided here by Jamaan Alghamdi: http://www.easyneuroimaging.com/2011/03/using-bash-script-to-convert-freesurfer_17.html Best, Rob > > > Hi Tenny > > That's troubling! What does it

Re: [Freesurfer] surfaces and gifti

Hi Nick, I did one pass at supporting a "both" prefix for both hemis combined. Can you make the output "both.pial.gii" and let's adopt that convention? thanks Bruce On Fri, 9 Dec 2011, Nick Schmansky wrote: > this should work: > > mris_convert --combinesurfs ./lh.pial ./rh.pial ./pial.gii > >

Re: [Freesurfer] surfaces and gifti

this should work: mris_convert --combinesurfs ./lh.pial ./rh.pial ./pial.gii notice the output name has ./ in it, to override an old freesurfer-ism of appending a default hemi. also note that .gz is not necessary as gzip is the freesurfer default for gifti. however, freesurfers implementation d