Re: [Freesurfer] PROBLEMS WITH SEGMENTATION

Hi Bruce, thank a lot for your attention. I'll post to you the DICOM header so you will found all the information. We have a GE, Signa 3.0 T with a phased array coil at 8 channel and I haven't any access to other coil. Follow the DICOM header Format: 'DICOM'

[Freesurfer] Longitudinal -uselongbasectrlvol

Dear all, I'm encountering the following error in the otherwise excellent longitudinal scheme when adding the -uselongbasectrlvol flag: Command: recon-all -long ${s}_tp1 ${s} -all -uselongbasectrlvol -- # #...@# Intensity Normalization Wed Apr 14 18:12

Re: [Freesurfer] mris_make_face_parcellation

Hi We were able to extract the vertex number (and MNI coordinates) for the finer parcellation as well as for the aparc.a2005s parcellation by using mri_annotation2label. Now we have a .label file for each parcellation where all vertices number (and their coordinates) that belong to a parcellati

Re: [Freesurfer] mris_make_face_parcellation

Hi Diana, the vertex # should be the same in all parcellation, so you just need to lookup a different label for the same index. Note that you can load the annotations into matlab using read_annotation.m if you want. cheers, Bruce On Thu, 15 Apr 2010, Diana Wotruba wrote: > Hi > We were able t

Re: [Freesurfer] Longitudinal -uselongbasectrlvol

to fix this, you will need to edit recon-all (with a text editor). search for this line: -mask $longbasedir/mri/brain.mgz and put a \ at the end of it. n. On Thu, 2010-04-15 at 11:01 +0200, Lars Tjelta Westlye wrote: > Dear all, > > I'm encountering the following error in the other

[Freesurfer] selxavg3-sess error "design is ill-conditioned"

Hello, I'm trying to run selxavg3-sess for an analysis with TER < TR, and it errors with "design is ill-conditioned". I searched the mailing list archive, and the only past problem of this sort that I found was associated with a faulty tpef file, which I am not using. The details: There is only o

[Freesurfer] Problem with mri_surf2surf

Dear FS experts I tried to run mri_surf2surf on parcellations produced by mris_divide_parcellation but there is the following problem: [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi% mri_surf2surf --srcsubject fsaverage_divide_parc --sval-annot /Application/freesurfer

Re: [Freesurfer] selxavg3-sess error "design is ill-conditioned"

Did you optimize the stimulus schedule with the idea that you would do sub-TR FIR estimation? Eg, you would have had to have run optseq2 with this in mind. If not, then you probably cannot do an FIR analysis. Instead, assume a shape (eg, -gammafit 2.25 1.25) doug Ben Letham wrote: > Hello, > >

Re: [Freesurfer] Problem with mri_surf2surf

It says "no such file or directory". Does it exist? doug Jürgen Hänggi wrote: > Dear FS experts > > I tried to run mri_surf2surf on parcellations produced by > mris_divide_parcellation but there is the following problem: > > [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaen

Re: [Freesurfer] selxavg3-sess error "design is ill-conditioned"

Yes, the paradigm came from optseq2 with a PSD window 0 19.2 0.4. Looking more into the details, it seems that the design is pretty ill-conditioned, cond(Xn'*Xn) is 6.2e5, and the cut-off in fast_selxavg3.m is 1e4. Like I said, the design came from optseq2 and the cost/efficiency is the same as o

Re: [Freesurfer] selxavg3-sess error "design is ill-conditioned"

try it with a prestim of 0 Ben Letham wrote: > Yes, the paradigm came from optseq2 with a PSD window 0 19.2 0.4. > > Looking more into the details, it seems that the design is pretty > ill-conditioned, cond(Xn'*Xn) is 6.2e5, and the cut-off in > fast_selxavg3.m is 1e4. > > Like I said, the design

[Freesurfer] Saving time in longitudinal processing

Dear list, I am about to start processing a largish longitudinal dataset and wondered whether I could save some processing time in the following ways: 1) I have seen written in a few places that only norm.mgz is used from the cross-sectional stream during base template creation at the next stage.