Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

Hi David, so edits are affecting the surfaces in cross, just not as much as you would like. We need to check if there is a problem there. For the longitudinal stream, edits in the base should affect surfaces in the base, which in turn will affect surfaces in the long. In long, surfaces would

Re: [Freesurfer] Volume to Surface mapping looks great for Vols created in FSL but not SPM

Hi Doug, Thanks for the email. It is in 3mm space, so I guess I should reslice. Can you please clarify the comment about fsaverage? Does the --mni152reg flag not apply to that subject? I'm not sure what you mean about the inclusion indicating ambiguity. Thanks again, Rita On Tue, Apr 4, 2017

Re: [Freesurfer] Volume to Surface mapping looks great for Vols created in FSL but not SPM

The --mni152reg flag is only appropriate if the mov file is in the 2mm mni152 space. The inclusion of fsaverage as the source subject indicates some ambiguity about this On 4/3/17 1:56 PM, Rita Elena Loiotile wrote: Hi, I'm trying to compare analyses that I've done entirely on the surface t

Re: [Freesurfer] Registration of both the brain and the "surf" files to the same template.

you can try mri_coreg with --dof 7 On 4/4/17 2:31 AM, Paolo wrote: For further clarity, we want to evaluate the geometric distortions to test how robust different sequences are to the local magnetic filed/susceptibility variations. So we want to keep the image as untouched as possible, but pos

Re: [Freesurfer] Comparing LME models

Great thanks Martin. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

Hi there, I have a similar problem not using longitudinal stream, just a routine recon-all analyses, this with several processed subjects, Here is my message sent several days ago. Thanks, Octavian. Dear Bruce, I just transferred subject r02.tar.gz. Again, wm.mgz edits (all deleted voxels, no a

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

Thanks for looking into this. I have uploaded another two subject folders as dsemanek3.zip, this time from a single time point for the same subject having been run through the cross stream of recon-all, the one with “test” appended at the end has had white matter edits on sagittal slices 126-142

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Re: [Freesurfer] ROI seed size

Hi Erik what are you using the seed for? A 3mm radius is a relatively small spot on the surface cheers Bruce On Mon, 3 Apr 2017, ERIK JAHNER wrote: What is the appropriate size for a surface based seed? I am referencing a study with volumetric based seeds with spheres with a radius of 3m

Re: [Freesurfer] Custom color maps

Hi Peter, We will need a lot more details to help. I suggest you look through the e-mail list a bit. I spent a lot of time helping a user or two with a similar issue. The key details are what are you trying to show (an annotation, a single label, or values)? hth d On Wed, Mar 29, 2017 at 11:15 A

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[Freesurfer] Generate stat file of ROI voxel sizes

Hello experts, We are looking to generate a stat file containing the number of voxels in a series of ROIs. We have a collection of about 300 different user-defined cortical ROI nifti volumes (not from aseg) and need to retrieve the number of voxels in each ROI for further analysis, but so far h

Re: [Freesurfer] Can anyone help with this error - trying to compare 2 scans in same person

Hi Brad, the base commands needs a space before -tp recon-all -base 005_IHD_1_base -tp 005_IHD_1 -tp 005_IHD_1_post -all check if the directory 005_IHD_1_base exists. Also check if this file exits: /usr/local/freesurfer/subjects/005_IHD_1_base/mri/transforms/talairach.auto.xfm Best, Martin

[Freesurfer] Can anyone help with this error - trying to compare 2 scans in same person

From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Brad Matushewski Sent: March 30, 2017 2:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Trying to compare 2 scans from same person, 6 months apart. First scan is 005_IHD_

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

So the way to debug this is to test if we can replicate the problem of WM edits not taking effect in a regular cross sectional stream. If true this means that there is a bug to the way WM edits are considered in FS6.0. It is unlikely that we missed that, but can happen. Probably something else

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

I used –uselongbasewmedits only as a test to see if I could get some condition under which the wm edits would be taken into account when the surfaces were generated. I did not use that flag for the data I uploaded. The wm edits to base did not influence the base wm surfaces or the cross wm surf

Re: [Freesurfer] wm edits not incorporated

Yes, I have this exact same problem. I have uploaded two rounds of data for review to the ftp service a week or so ago and I believe they are being reviewed. After several days of testing on my end with various permutations of flags and cross and long runs and intervention points I didn’t see a

Re: [Freesurfer] Creating an illustration on what Freesurfer has considered to be intracranial volume

Dear Erik, since I just worked on the details of this, please have a look at http://www.freesurfer.net/fswiki/eTIV to clarify that FreeSurfer does not use any segmentation to make the eTIV estimation on, but uses the talairach transfom to estimate the eTIV since the two have a linear relation

[Freesurfer] Creating an illustration on what Freesurfer has considered to be intracranial volume

Dear Freesurfer experts, I would like to create an image on tissue that Freesurfer has been included into the intracranial volume calculation. Is there anyway to summarize segmentations masks so I get one mask containing all tissue that has been included into the intracranial volume? best Erik __

Re: [Freesurfer] Comparing LME models

Hi Bronwyn, ok, now I understand. I am not sure which one to take, I guess it won't matter much. Why don't you try either way and see if you get the same result. Best, Martin On 03/30/2017 12:59 AM, Bronwyn Overs wrote: Hi Martin, Yes this is for a mass univariate approach. Re segmentatio

Re: [Freesurfer] A question regarding LUT/Freeview

Hi Amir, If you are trying to display labels as isosurface in 3D view, try input like this: 2028-2029,2032-2035 Best, Ruopeng > On Apr 4, 2017, at 4:43 AM, amir hosein wrote: > > Dear All, > > A quick question. > I Want to use Freeview to display a number of brain areas (that I have chose

Re: [Freesurfer] eTIV estimation on same subject over time

Hi Mel, when manually checking the talairach transform, make sure you are checking the one that is actually used for the eTIV computation (that changed over the years and versions). http://www.freesurfer.net/fswiki/eTIV so I think currently it is the talairach.xfm you can use lta_diff (maybe

Re: [Freesurfer] Fwd: recon-all error

Dear Patricia, see this thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51797.html Your working directory probably resides on the filesystem which does not support symbolic links. You probably could workaround this by editing your recon-all and replace line set cmd2 = (l

Re: [Freesurfer] correlation coefficient R

Hi Doug, Thanks! I realize now I didn't explain myself properly. I need one single R value for the correlation analysis I made, similarly to when I correlate two variables with Pearson's R in a statistical package. I have a referee asking me to put it on a table with the freesurfer results. Is t

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[Freesurfer] A question regarding LUT/Freeview

Dear All, A quick question. I Want to use Freeview to display a number of brain areas (that I have chosen for some purposes) on the brain. As I have studied in this forum, it is suggested that I should create a custom Look-Up-Table in which I only keep the labels that are my target and erase ot

[Freesurfer] eTIV estimation on same subject over time

Dear list, we are currently working with some longitudinal data where we would like to measure volume changes over time and compare the cross-sectional and longitudinal stream on. When we run the cross-sectional stream and just look at changes of eTIV within subjects over a period of 6 months