Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

Dear Doug, Kindly find attached a sample of my lh.aparc.stats file! Best regards, Amirhossein Manzouri On Mon, May 19, 2014 at 7:59 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Can you send me your lh.aparc.stats file? doug On 05/14/2014 01:41 PM, amirhossein manzouri wrote:

Re: [Freesurfer] mris_anatomical_stats lgi error

Hi, Do I need to run laleb2label and label2annot to get once again the BA.thresh? Or is it enough to just extract the stats? I already extracted the aseg stats and one of the subjects came out with slightly different values this time, while the other presented the same values. Was this

[Freesurfer] ASL Image Exception: # 22 ERRORS

Hi. I'm trying to run an ASL analysis on my data. I have pcASL control-tag data that for the most part are getting run through the analysis without problems. However, there seems to be some difficulties with the calibration. I'm running the command as root in csh: oxford_asl -i

Re: [Freesurfer] mris_anatomical_stats lgi error

Hi Andreia I haven't been following this whole thread, but the matlab warning is not a problem cheers Bruce On Tue, 20 May 2014, _andre...@sapo.pt wrote: Hi, Do I need to run laleb2label and label2annot to get once again the BA.thresh? Or is it enough to just extract the stats? I

Re: [Freesurfer] mris_anatomical_stats lgi error

Hi Bruce, Thank you! Andreia Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Andreia I haven't been following this whole thread, but the matlab warning is not a problem cheers Bruce On Tue, 20 May 2014, _andre...@sapo.pt wrote: Hi, Do I need to run laleb2label and label2annot

Re: [Freesurfer] Referencing

They are both relevant, so it's hard to say, but I guess if you only get one I would suggest the first (earlier) one cheers Bruce On Mon, 19 May 2014, WaliD YassiN wrote: Hello, We would like to cite Freesurfer for using its subcortical segmentation, but we are limited in the number of

[Freesurfer] missing temporal lobes

Hello all, We are having trouble with the output after running recon-all -all -subjid subjectx on our scans. Registrations and skull striping look okay, but the white matter and pial surface segmentations leave outportions of the anterior temporal lobe. After adding control points to the

Re: [Freesurfer] mris_anatomical_stats lgi error

If you ran with -autorecon3, then you do not need to redo the labels. As for the aseg, it depends on what you ran and what edits you made. If you ran with -autorecon2 and you had added control points, then it would change slightly. You can ignore that matlab warning (it is only saying that

Re: [Freesurfer] ASL Image Exception: # 22 ERRORS

That is an FSL program, so you probably don't want advice from the FreeSurfer list! doug On 05/20/2014 05:29 AM, Athanasia Monika Mowinckel wrote: Hi. I'm trying to run an ASL analysis on my data. I have pcASL control-tag data that for the most part are getting run through the analysis

Re: [Freesurfer] normalization problem (versions 5.1 and 5.3)

Thanks for your response, Bruce. Since we would rather not re-run all 200+ subjects through version 5.3, would it be possible, for the sake of keeping things consistent, to add any flags to recon-all using version 5.1, to be able to include the remaining 35 subjects into our analysis? On Fri,

[Freesurfer] Monte Carlo Cluster Size Threshold

Hello Freesurfer Experts, I am looking for the threshold cluster size used in a Monte Carlo Simulation (ran in qdec) at p=0.05. I believe the attached pdf (used to be mc-z.abs.th13.pdf) contains this information but I am not sure about how it is annotated. Does MaxClustBin correspond to a

[Freesurfer] registering MRI structural data with MEG volume converted data

Hello Freesurfer Experts, We've used the following tcsh script to convert MEG surface data, morphed to fsaverage .w paint (every timestep) format, to volume data in NIFTI format: # Convert to .nii format (volume from surface data of dSPM) placing .nii files in NII_DIR # FREESURFER_HOME is

Re: [Freesurfer] registering MRI structural data with MEG volume converted data

Sorry, I don't understand what the issue/problem is doug On 05/20/2014 02:01 PM, Franklin Lovell Orndorff-Plunkett wrote: Hello Freesurfer Experts, We've used the following tcsh script to convert MEG surface data, morphed to fsaverage .w paint (every timestep) format, to volume data in

[Freesurfer] freeview vs tksurfer

Hi all, Two questions: First, does Freeview currently support flatmaps, or -patch support still in development? Second, I notice some different behavior between tksurfer and freeview *vis-a-vis *surface overlays. In tksurfer, we were able to plot volume overlays to surfaces by specifying a

Re: [Freesurfer] Monte Carlo Cluster Size Threshold

Just realized I didn't attach the pdf in the initial email. Sorry! On May 20, 2014, at 12:01 PM, Wegman, Clem J. wrote: Hello Freesurfer Experts, I am looking for the threshold cluster size used in a Monte Carlo Simulation (ran in qdec) at p=0.05. I believe the attached pdf (used to be

[Freesurfer] how to get scalp-cortex diff instead of white-pial diff?

Dear Freesurfer experts, I would like to get a map of scalp-cortex distance for every vertex on the pial surface (for use in predicting the effects of TMS). I believe there is no existing automated method for doing this. Are there any suggestions for how to calculate a scalp-cortex distance map?

Re: [Freesurfer] how to get scalp-cortex diff instead of white-pial diff?

Hi, Please see responses in text (also FS experts please fill in on the things I am unsure of). On Tue, May 20, 2014 at 5:09 PM, Christopher Chatham chath...@gmail.com wrote: Dear Freesurfer experts, I would like to get a map of scalp-cortex distance for every vertex on the pial surface

Re: [Freesurfer] how to get scalp-cortex diff instead of white-pial diff?

I doubt that renaming is going to do what you want to do. I would follow Dan's suggestion about reading it into matlab. It will probably be slow, but you only need to do it once doug On 05/20/2014 05:42 PM, dgw wrote: Hi, Please see responses in text (also FS experts please fill in on the

Re: [Freesurfer] how to get scalp-cortex diff instead of white-pial diff?

Hi Christopher that won't work as we assume that the surfaces have the same topology (# of edges, vertices and triangles). You'll need to use a distance transform I expect, which shouldn't be too bad. Check out mris_distance_transform. You'll want to run it with the pial surface, then pick