Re: [Freesurfer] Question about the outputs of recon-all

Hi, Douglas Thanks for your reply. So, as you stated, the fsaverage is already in the MNI space? Because my fMRI data are in the MNI space (after normalization) and I want to extract the region with significant different cortical thickness as seed to calculate functional connectivity. Best,

[Freesurfer] mris_preproc -iv option

Dear Freesurfer team, How does mris_preproc map volume data onto the surface when using the -iv option? Is an average between the white and pial boundaries taken, or are only the voxels taken into account that intersect with one of the two surfaces (and if yes, with which surface)?

Re: [Freesurfer] Resending my questions: Issues with first attempt in viewing Tracula output

Dear Anastasia, I send (uploaded) the files on Monday. Could you please confirm that they arrived. Thank you so very much for looking into it. Leora. Leora Amira, PhD Columbia University NYS Psychiatric Institute Division of Child and Adolescent Psychiatry 1051 Riverside Drive New York, NY 10032

Re: [Freesurfer] pial-outer-smoothed misalignment

Would it be possible to send me the surface and the volume that do not align in freeview? Thanks, Ruopeng On 08/13/2015 11:46 AM, Roan LaPlante wrote: Hello, I am trying to use mris_compute_lgi to create the smoothed pial surface with no gyri, and then use this surface for a different

[Freesurfer] Loading .w surface overlay in Freeview

Dear all, I am wondering if there is a facility for loading .w overlay files in Freeview? In the surface section of the GUI, the overlay tab is for volumetric files (.mgz, .nii, etc.). In the command line, the overlay option fails - for example: freeview -f

Re: [Freesurfer] cannot find qdec file

do you mean the one without the blank line at the end? I've attached that for you. Cheers, Clara - Ursprüngliche Mail - Von: Douglas N Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 13. August 2015 18:12:40 Betreff: Re: [Freesurfer] cannot find

Re: [Freesurfer] Resending my questions: Issues with first attempt in viewing Tracula output

I am glad I checked. Yes, I did use your email. I will tray to upload it again into the link you sent and I will email you to let you know when I had done that. Leora Amira, PhD Columbia University NYS Psychiatric Institute Division of Child and Adolescent Psychiatry 1051 Riverside Drive New

[Freesurfer] Caret Human_Macaque.PALS_B12 to freesurfer

Dear ladies and possibly gentlemen as well, I have got a rather nasty question. I would like to import the following caret file Human_Macaque.PALS_B12.RIGHT-DEPTH_Expansion.73730.surface_shape into free surfer and bring it into fs average space. In a next step I would like to import the

Re: [Freesurfer] Caret Human_Macaque.PALS_B12 to freesurfer

Hi Jan have you asked the HCP/Wash U group? I bet that they would know. Maybe Mike Harms or Matt Glasser can chime in? Bruce On Thu, 13 Aug 2015, Jan Willem Koten wrote: Dear ladies and possibly gentlemen as well,   I have got a rather nasty question. I would like to import the

Re: [Freesurfer] Exporting the Hippocampus

Hi Chester the voxel coords reflect positioning in the scanner and so there is a lot of variability in them depending on landmarking, head size, etc... cheers Bruce On Thu, 13 Aug 2015, Chester Dolph wrote: I used mri_binarize to get a mask of the hippocampus from aseg.mgz and then used

Re: [Freesurfer] Loading .w surface overlay in Freeview

can you use vol2surf to generate a .mgz/.mgh file instead? We have deprecated the use of .w files On Thu, 13 Aug 2015, Ivan Alvarez wrote: Dear all, I am wondering if there is a facility for loading .w overlay files in Freeview? In the surface section of the GUI, the overlay tab is for

Re: [Freesurfer] Exporting the Hippocampus

Hi Bruce, Thanks for the response. For ROI such as the hippocampus, is there a standard/accepted technique for voxelwise analysis? For instance, taking the meatiest slice of each subject (the slice with most nonzero voxels) and using that as the center slice. Then perform voxel base

Re: [Freesurfer] Exporting the Hippocampus

I used mri_binarize to get a mask of the hippocampus from aseg.mgz and then used mri_mask to mask the norm.mgz to get a volume of intensities. After this process, I noticed that hippocampus do not seem aligned in terms of the z (axial) axis. Of note, the hippocampus center of mass seem to

Re: [Freesurfer] Caret Human_Macaque.PALS_B12 to freesurfer

I agree this would be best asked on the Caret list to begin with (as far as conversion from Caret formats to FreeSurfer formats), however I don’t provide Caret support either having not used it in years (I can be more helpful with Connectome Workbench stuff). Donna on the Caret list can perhaps

Re: [Freesurfer] Caret Human_Macaque.PALS_B12 to freesurfer

Hi Matt thanks for the answer. I thought maybe someone in HCP had already imported this PALS file into FreeSurfer. cheers Bruce On Thu, 13 Aug 2015, Matt Glasser wrote: I agree this would be best asked on the Caret list to begin with (as far as conversion from Caret formats to

Re: [Freesurfer] cannot find qdec file

I'm not sure what to tell you. When I use the new file I don't get an error. When I use the old one I do. Can you run mris_preproc --debug --qdec-long long.qdec.table.dat and send me the result? On 08/13/2015 01:01 PM, Clara Kühn wrote: do you mean the one without the blank line at the end?

Re: [Freesurfer] cannot find qdec file

Can you send the new qdec table file? On 08/05/2015 04:05 AM, Clara Kühn wrote: no worries! sadly, though, deleting the empty line wasn't the answer to the problem :( Cheers, Clara - Ursprüngliche Mail - Von: Douglas N Greve gr...@nmr.mgh.harvard.edu An:

Re: [Freesurfer] Resending my questions: Issues with first attempt in viewing Tracula output

Sorry, didn't get anything! Did you use me as the recipient (ayendiki)? On Thu, 13 Aug 2015, Leora Amira wrote: Dear Anastasia, I send (uploaded) the files on Monday. Could you please confirm that they arrived. Thank you so very much for looking into it. Leora. Leora Amira, PhD Columbia