Re: [Freesurfer] Sig.mgh to annotation

How do you define the clusters? You can use mri_surfcluster to define clusters, and it can output annotations. You can also use mris_label2annot if you have clusters defined as labels. doug Jürgen Hänggi wrote: > Dear FS experts > > We would like to transform the sig.mgh file to an annotation

Re: [Freesurfer] FS 5.1

Hi Derin we are tracking down some issues with it and hope to have it out within a month cheers Bruce On Thu, 20 Jan 2011, Derin Cobia wrote: > All, > > Just curious about the current estimated timeline for version 5.1, trying to > schedule some projects around it. Thanks! > > -Derin > > > >

[Freesurfer] Job postings

*POSTDOCTORAL POSITION* *IMAGING HUMAN AUDITORY CORTEX*** The Human Cognitive Neurophysiology Laboratory (www.ebire.org/hcnlab ) affiliated with UC Davis and the Department of Veterans Affairs Northern California is searching for a postdoctoral fellow to study h

Re: [Freesurfer] mkanalysis-sess in Stable 5

This should work mkanalysis-sess -analysis fmcsm5_functionals_Stable5 -TR 2 -paradigm paradigm -event-related -native -fwhm 5 -mcextreg -nconditions 9 -fir 4 24 I would also run the preprocessing from scratch. doug Adam Nitenson wrote: > Hi Freesurfers, > > I'm trying to update our anal

Re: [Freesurfer] Beginner Question on registration process

I don't know of another way to map control points. By MRI space I assume that you mean the scanner RAS space? Eg, the space defined by the nifti qform? I think this matrix will be L = inv(T)*Q where Q is the scanner vox2ras of the orig volume and T is the tkregister vox2ras of the orig volume.

Re: [Freesurfer] FS 5.1

Hi Derin, since I gave the initial estimate of end of last year, I feel I should answer. At that point we planed to include only the new longitudinal stream. The new longitudinal stream with single voxel space has been tested and is included since early November. However with this release we hav

Re: [Freesurfer] Beginner Question on registration process

Hi Gabriele, not sure if there is an easy way (probably Doug knows). But if there isn't, I wrote a tool mri_map_cpdat to map control points from one space to another. A control points dat file is a txt file containing coordinates. The tool will be available in 5.1 where it is used to transfer manu

[Freesurfer] FS 5.1

All, Just curious about the current estimated timeline for version 5.1, trying to schedule some projects around it. Thanks! -Derin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf

Re: [Freesurfer] How to make a surface overlay? - repost

glad it worked out On Thu, 20 Jan 2011, Ed Gronenschild wrote: > Hi Bruce, > > I managed to do what I wanted: by linking the > ?.aparc.annot file with ?thickness file and > FreeSurferColorLUT.txt I get a list of > thickness value, segID and structure name. > > Now I can change each thickness into

Re: [Freesurfer] How to make a surface overlay? - repost

Hi Bruce, I managed to do what I wanted: by linking the ?.aparc.annot file with ?thickness file and FreeSurferColorLUT.txt I get a list of thickness value, segID and structure name. Now I can change each thickness into whatever value I want and save it as a curve file which I can then overlay on

[Freesurfer] Beginner Question on registration process

Hi all, I'm a new freesurfer user and I've a small question for you all. Which the faster and reliable way to map a list of points into the freesurfer geometrical space? I've already read the pdf/ppt but there's no suggestion in there about which command should be used (if any). I've read about m

Re: [Freesurfer] error message in mri_concat: fp==0

stacksize 10240 kbytes, sorry! -- yours, Dr. Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom

Re: [Freesurfer] error message in mri_concat: fp==0

cputime,filesize,datasize,memoryuse,vmemoryuse: unlimited stacksize 10240 bytes coredumpsize 0 kbytes descriptors 1024 memorylocked 32 kbytes maxproc 137216 yours, LMR On 20/01/2011, Bruce Fischl wrote: > I see. Maybe there are too many open file descriptors? If you type 'limit' > what does it t

Re: [Freesurfer] error message in mri_concat: fp==0

I see. Maybe there are too many open file descriptors? If you type 'limit' what does it tell you? On Thu, 20 Jan 2011, Lars M. Rimol wrote: > Hi Bruce, > > Yes I can create files. I was trying to run a script with almost 500 > mgh files that I wanted to concatenate. I figured there was somethin

Re: [Freesurfer] error message in mri_concat: fp==0

Hi Bruce, Yes I can create files. I was trying to run a script with almost 500 mgh files that I wanted to concatenate. I figured there was something wrong with the script because I could run command lines to concatenate 10-20 files from that list in the terminal (all 500 files was too much to copy

Re: [Freesurfer] Different sequences in one evaluation

Thanks for the speedy replies, I think that in case of a 3D acquisition, the bigger the volume the better the SNR (until a certain point, of course), and in this case the volume is bigger with 9,9%. The parameters of the MPRAGE are: TR/TE/TI: 1900/3.41/900 ms; FA: 9°; FOV: 210x240 mm2; 224x256 m

Re: [Freesurfer] error message in mri_concat: fp==0

Hi Lars do you have write permission? Is the partition full? Try: touch /home/lmr/test.mgh and see if that works cheers Bruce On Thu, 20 Jan 2011, Lars M. Rimol wrote: > Hi, > > I got this error message when attempting to use mri_concat. Number or > inputs, frames etc. seems ok, but when

[Freesurfer] error message in mri_concat: fp==0

Hi, I got this error message when attempting to use mri_concat. Number or inputs, frames etc. seems ok, but when it is about to write the output file, this happens: Writing to /home/lmr/test.mgh , -1): could not open file: fp==0 (I use v.4.5.0) Any suggestions? Thank you! yours, LMR -- yo

Re: [Freesurfer] Different sequences in one evaluation

Hi Gergely, I think this will be trouble. I'll cc Andre van der Kouwe, but for the 3D acquisitions, if you have a bigger field of view is has an effect on image SNR, so that will be a bias between your groups. cheers Bruce On Thu, 20 Jan 2011, Gergely Orsi wrote: > Hi Freesurfers, > > I have

Re: [Freesurfer] Different sequences in one evaluation

Hi Gergely, Was this collected on a Siemens scanner? If so, the Siemen's MPRAGE sequence is such that the "slices" form the "inner loop" of the acquisition -- that is "Number of slices" lines in k-space are acquired for each TR period. So, having a differing number of slices theoretically has an

[Freesurfer] Different sequences in one evaluation

Hi Freesurfers, I have a quick question: I have two groups, both measured on the same scanner, with the same sequence (3D MPRAGE), and with almost the same parameters. TR/TE/TI/BW/MATRIX/FOV/FOV-phase/Flip angle/Slice thickness/in-plane resolution... everything is the same, but the number of sli