[Freesurfer] SPM vol .nii to w file surface overlay

Dear Freesurfer users, I have tried to convert a volumetric SPM activity image from the form of a .nii file (created against the subjects T1.nii image) into a w file (paint file) to be overlaid on the inflated surface of the same subject's brain anatomy (created with Freesurfer recon-all), usin

Re: [Freesurfer] recon-all analyze 7.5 format

that would work, although you need to specify -all at the end. Note that using analyse is dangerous though! You won't know left from right. Bruce On Wed, 10 Feb 2010, SG KIM wrote: > Hi all, > > I've got .IMG and .HDR files in analyze 7.5 format, and ran > > recon-all -s subject -i file.img

Re: [Freesurfer] SPM vol .nii to w file surface overlay

Hi Nela, try registering them with bbregister, then making sure the registration is correct with tkregister2. cheers Bruce On Wed, 10 Feb 2010, Nela Cicmil wrote: > Dear Freesurfer users, > > I have tried to convert a volumetric SPM activity image from the form of a > .nii file (created again

[Freesurfer] projection depth using tksurfer or mri_vol2surf

Hi, I am rendering an analyze format img onto the fsaverage surface. I was wondering whether it is possible to specify the MAXIMAL depth of activation that is supposed to be projected onto the surface. Hereby I mean an ADDITIVE depth: The option --projdist (and also --projfrac) are not doing wh

Re: [Freesurfer] projection depth using tksurfer or mri_vol2surf

Hi Sepideh, do you mean pick the maximal activation over depths? The max is an unstable measure, and makes most subsequent statistical analyses invalid. cheers Bruce On Wed, 10 Feb 2010, Sepideh Sadaghiani wrote: > Hi, > > I am rendering an analyze format img onto the fsaverage surface. I wa

[Freesurfer] question abt mri_vol2surf - projfrac

Hello, I also had a question abt projfrac I have 3 x 3 x 3 mm voxel functional data - BOLD and ASL that I am trying to resample to fsaverage. Is the projfrac label applicable here at all ? In the help page it specifies only for thickness. If it is applicable, what value ? Thanks Ri _

[Freesurfer] ROI based on Talairach coordinate

Dear Freesurfer users and experts, This is my second attempt :( I am trying to construct a roi based on some talairach coordinate coming from a paper, but I completely fail to do it with matlab and neither manually with tksurfer. My first try was to use the transformation Talairach.xfm with matla

Re: [Freesurfer] question abt mri_vol2surf - projfrac

Hi Ri, yes, it tells you where to sample, so it is applicable. It may not make a huge difference for big voxels though. cheers, Bruce On Wed, 10 Feb 2010 rida...@mail.med.upenn.edu wrote: > Hello, > > I also had a question abt projfrac > > I have 3 x 3 x 3 mm voxel functional data - BOLD and A

Re: [Freesurfer] ROI based on Talairach coordinate

Hi Leila, you can use the tcl command select_talairach_point in tksurfer in the tcl window (with the % prompt), then make a label from that point and dilate it a few times. cheers, Bruce On Wed, 10 Feb 2010, Ben Hamida Cammoun Leila Faiza wrote: > Dear Freesurfer users and experts, > Thi

Re: [Freesurfer] tksurfer error

have you tried clicking the "redraw" button? On Wed, 10 Feb 2010, Daniel Ferreira Padilla wrote: > Dear Freesurfer users, > > > > I hope you could help me with that problem. I do the recon-all preprocessing > step and then I try tksurfer. But the following error comes up. Moreover > tksurfer wind

Re: [Freesurfer] tksurfer error

Yes, I click over the redraw button but it doesn’t work. It is strange but despite tksurfer window is empty, when I click on it, labels and values appear in tksurfer tools window. Any other idea? Thank you very much in advance -Mensaje original- De: Bruce Fischl [mailto:fis...@nmr.mgh.ha

Re: [Freesurfer] Freesurfer Digest, Vol 72, Issue 25

Hi Tamara, neuroecon is not ia64 but x86_64, that is you binaries will probanbly never run on this cluster no matter the permissions. You can just ask the neuroecon support people (help-...@caltech.edu) to install 4.5.0 under /share/apps. In addition to actually use freesurfer on this system (s

Re: [Freesurfer] tksurfer error

you can try some of the things suggested here: https://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems although those suggestions are targetted at the 'sliver' problem, where you get a display of only a tiny section of the brain. you dont seem to be getting any display. n. On Wed, 20

Re: [Freesurfer] Fw: manually specifying design matrix

Dear Doug Many thanks for your reply. Freesurfer does accept the design matrix you suggested. For the following design matrix 1.00.5000 1.0 -0.5000 01.0.5000 01. -0.5000 The contrast 0 0 1 is meaningful for effect of two po

[Freesurfer] DICOM Multiframe support

Hi! Is Freesurfer compatible with the DICOM MR multiframe files? Thanks in advance, -- Gabriel Castrillón Instituto de Alta Tecnología Médica de Antioquia - IATM http://www.iatm.com.co ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:/

Re: [Freesurfer] DICOM Multiframe support

Hi Gabriel, to do what? What kind of multi-frame files? We use them all the time locally (multi-echo mp-rage for anatomical analysis) cheers, Bruce On Wed, 10 Feb 2010, J. Gabriel Castrillón G. wrote: Hi! Is Freesurfer compatible with the DICOM MR multiframe files? Thanks in advance, __

Re: [Freesurfer] Skull Stripping extra dura & vasculature

Sheri, can you send the file to bruce via the file upload link: https://www.nmr.mgh.harvard.edu/facility/filedrop/uploadauth.html its too big to send as an attachment to the freesurfer list. n. On Tue, 2010-02-09 at 13:40 -0500, Bruce Fischl wrote: > Hi Sherri, > > it's hard to say without se