Re: [Freesurfer] LGI ERROR

Hi Greve, Thanks for your help. It is that I only use FWMH = 5 to do my study, it is decided by my data. Can I think it so? Sincerely, Zheng At 2017-12-14 00:06:39, "Douglas Greve" wrote: The FWHM used in the MC simulation is computed from the data itself. The final FWHM is a m

Re: [Freesurfer] mri_surf2surf on edited subjects

The number of vertices match between the lh.sphere.reg and lh.pial. All of the timestamps are the same as well. I just tried this with v5.3 as well and the problem is the same. Thank you for helping with this! -Matt Defenderfer Matthew K. Defenderfer B.S. | Graduate Research Assistant Gradua

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin, We've taken a look at the scans you uploaded, and unfortunately it won't be possible to run the standard recon-all on your subject. Recon-all is not designed to work on scans with such large lesions. If you are interested, there may be a way to generate a reasonable model of the r

Re: [Freesurfer] mri_surf2surf on edited subjects

Hi Matt can you run mris_euler_number on that subject's lh.sphere.reg and see if it has the same number of vertices as the lh.pial for example? Or check timestamps. If it was not recreated after your editing you will need to rerun part of recon-all cheers Bruce On Wed, 13 Dec 2017, Defend

[Freesurfer] mri_surf2surf on edited subjects

Hi all, I am trying to transfer a surface file from fsaverage_sym space to a recently edited individual subject's hemisphere. I previously ran recon-all on the subject and then edited the wm, brainmask, etc. to fix some defects I had found. Before the edits, I could transfer the surface and lo

Re: [Freesurfer] Dura classified as GM in brainmask

Hi Bruce, Thank you for your reply. I am using 5.3.0 version. Do I still only correct misclassified GM voxels in the brainmask? For the subjects with brain classified as cerebral cortex in the aseg file which is outside of the pial surface (but present in the brainmask) how do I correct this:

Re: [Freesurfer] ?h.DKTatlas100.gcs to annot

they would be in $FREESURFER_HOME/subjects/fsaverage/label On Wed, 13 Dec 2017, tony han wrote: Hi Bruce, Thanks. If there is one available, could you point me to the location of the files? I check $FREESURFER_HOME/average and can't find annot files for DKTatlas.  If I'm going to make o

Re: [Freesurfer] JRE error in fsfast/matlab

Yes it terminates prematurely. Best Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, December 13, 2017 5:50 PM To: freesurfer@nmr.mgh.harvard

[Freesurfer] Transforming invasive electrodes coordinates to a template brain

Dear freesurfer experts, I would like to present invasive electrodes from different subjects in the same template brain. I thought about doing a volumetric registration (all the electrodes are depth) using mri_cvs_register: mri_cvs_register --mov {subject} --template {template} --outdir $SUBJ

Re: [Freesurfer] ?h.DKTatlas100.gcs to annot

Hi Bruce, Thanks. If there is one available, could you point me to the location of the files? I check $FREESURFER_HOME/average and can't find annot files for DKTatlas. If I'm going to make one with one of the fsaverage subjects, there won't be any difference of the resultant annot file no mat

[Freesurfer] Voxel time-series within a specific functional ROI

I am working on an fMRI-adaptation experiment and was wondering how to extract voxel time-series within a specific functional ROI. I have created a functional ROI mask. This mask has only one time-point. According to this thread https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-October/0

Re: [Freesurfer] free surfer v5 & 6

Hi Gianluca, > I am working with data coming from two different versions of Freesurfer, v5.1 > and v6. > As measurements looks different (an excerpt below from aseg.stats files), I > am trying to see if that difference is statistically relevant. > Could you anticipate something with this respe

Re: [Freesurfer] PET partial volume correction:mri_gtmpvc error

Hi Doug, Thanks for your response. Actually, we do modify the aseg.mgz (Sorry, I didn't realized and I shouldn't have considered this a 'standard FS pipeline'). We work with Multiple Sclerosis patients and because of the size and number of lesions in some of them, the pial and WM surfaces tha

Re: [Freesurfer] Dura classified as GM in brainmask

Hi Ciara what version are you running? I think you only need to correct voxels that cause the white and/or pial surfaces to be incorrect, as we correct the aseg with them (at least I think we do in v6) cheers Bruce On Wed, 13 Dec 2017, FSL Analysis wrote: Hi again, I realize my last quest

Re: [Freesurfer] ?h.DKTatlas100.gcs to annot

Hi Tony I think we distribute one, but if not you should just be able to run mris_ca_label on the fsaverage subject to generate one. cheers Bruce On Wed, 13 Dec 2017, tony han wrote: Hi, Is it possible to get an annot file for ?h.DKTatlas100.gcs, not for individuals, but for fsaverage

Re: [Freesurfer] Hippocampal Subfield and Amyg Nuclei ICV Correction

Hi Eugenio, Thank you so much for the helpful information! Best, Arkadiy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the pe

Re: [Freesurfer] Dura classified as GM in brainmask

Hi again, I realize my last question about the brainmask did not make sense. I meant to ask if I have to either manually delete all non-brain voxels around the eye area which is very time consuming per subject or just delete those misclassified as GM? ( I check this through the command: tkmedit su

Re: [Freesurfer] Hippocampal Subfield and Amyg Nuclei ICV Correction

Hi Arkadiy 1. Yes 2. If you’re correcting the subfields by hippocampal volume: a) the question is a different one (“which fraction of the hippo volume is attributed to each subfield”); and b) I wouldn’t correct by ICV, because the values are already fractions / normalized (see point a). Cheers,

Re: [Freesurfer] Creating functional ROI

I was wondering if there is other way than using matlab to do this. On Mon, Dec 11, 2017 at 9:07 PM, Ashley Cole wrote: > Thank you, Doug. This worked. > > Now I have two questions: > > 1- Is it possible for a given threshold in funcroi-config to have let say > 15 voxels on the surface but zero

Re: [Freesurfer] Dura classified as GM in brainmask

Hi again, I realize my last question about the brainmask did not make sense. I meant to ask if I have to either manually delete all non-brain voxels around the eye area which is very time consuming per subject or just delete those misclassified as GM? ( I check this through this command: tkmedit s

[Freesurfer] ?h.DKTatlas100.gcs to annot

Hi, Is it possible to get an annot file for ?h.DKTatlas100.gcs, not for individuals, but for fsaverage atlas? I want to plot the 'standard' parcellation, instead of individual ones, on the surface so that I can use as a general reference. Thanks! Tony

[Freesurfer] Hippocampal Subfield and Amyg Nuclei ICV Correction

Dear Experts, I have seen this question pop up a few times in the forum, but have not seen a clear response, so I was wondering if someone might be able to clarify or offer their opinion. 1. Do the hippocampal subfields and amygdala nuclei need to be corrected for ICV (either by including

Re: [Freesurfer] LGI ERROR

The FWHM used in the MC simulation is computed from the data itself. The final FWHM is a mixture of the applied FWHM and smoothness inherent in the data. LGI has a lot of inherent smoothness, so the final FWHM is very large. The MC sim table only goes up to 30mm, after that it generates an erro

Re: [Freesurfer] cortical thickness smoothing

On 12/13/17 8:03 AM, John Anderson wrote: Dear Dr Greve thank you so much for the advice. Kindly, I have one addition question and I highly appreciate your feedback! Smoothing on surface is very interesting and it is really more accurate than applying the Gaussian smoothing directly on volum

Re: [Freesurfer] JRE error in fsfast/matlab

By default the graphics are turned off when running selxavg-sess. I often see that error message, but it never ends up causing the program to terminate. Is your process terminating prematurely? On 12/13/17 10:24 AM, Yagmur Ozdemir 19 wrote: Hello FreeSurfer experts, I have been running into

[Freesurfer] JRE error in fsfast/matlab

Hello FreeSurfer experts, I have been running into a matlab-related problem that I was wondering if anyone came across. I am using Matlab2017b with Freesurfer 6.0. Whenever I run selxavg-sess command, the matlab tries to find the OpenGL re

Re: [Freesurfer] cortical thickness smoothing

Dear Dr Greve thank you so much for the advice. Kindly, I have one addition question and I highly appreciate your feedback! Smoothing on surface is very interesting and it is really more accurate than applying the Gaussian smoothing directly on volumetric images. I don't see any aggressive shift

[Freesurfer] extract surface area for singe vertex

Dear Freesurfer experts, I've run a longitudinal two stage model of 2 time points to look at the rate of change in surface area and whether my two groups change differently. I find a superior parietal cluster in the right hemisphere. So far I've already run the mri_glmfit-sim to get the values

[Freesurfer] [Re] medial wall label in Freesurfer 6

Hi Andrew, Thanks very much! I have tried the new version of make_average_surface and it works fine. I am very gratefull. Best, M del Mar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/f

[Freesurfer] Research engineer in Neuroimaging wanted

Dear Freesurfer list, the 'Institut de Neuroscience de la Timone ' (INT), Marseille, France, is looking for a research engineer for a duration of one year. The candidate will bring a scientific support to MR neuroimaging research. If satisfactory, the contract will lead