Re: [Freesurfer] Coordinates of particular volumes

I have tried to get the coordinates with following commands: *mri = MRIread('aseg.mgz');pos = find(mri.vol == 17);* *[i,j,k] = ind2sub(10213,pos);* However, I found that all values of 'j' are 1. is there something wrongs with my strategy? Best Regards, Aziz. On Mon, Sep 12, 2016 at 8:40 PM, Br

Re: [Freesurfer] Co-registering different source data

Hi Anna freeview now checks (in the dev version I believe) if the label has been sampled onto the surface and won't crash, but you need to use mri_label2label to sample it onto the surface before loading it onto the inflated surface in freeview cheers Bruce On Mon, 26 Sep 2016, Crawford, Ann

Re: [Freesurfer] Co-registering different source data

Hi, i created a test ROI which saves as a label. Every time I try to load it as a label on the surface (inflated), it crashed FreeView. I'm not sure why it won't load there. I noticed this happens with some other ore-made labels as well. What could be the cause of this? I also tried doing mri_

Re: [Freesurfer] Re Re: Question regarding mri_convert

what was different? And can you send us the rawavg.mgz for the two cases? On Mon, 26 Sep 2016, Tamara Tavares wrote: Thank you Bruce! Theoretically, I should get the same results if I pass my nii file through the recon-all command if I converted my dicom/IMA file into a nii using Slicer4 or th

Re: [Freesurfer] Co-registering different source data

Hi Anna scuba is very old and deprecated. Try using freeview instead cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote: > To create the volume ROI, I found something that said to use: > > scuba -v $filename > > to then make a new ROI. > > I got en error that I could not open scuba. Is this

[Freesurfer] Regional White Matter Hypointensity Volumes

Hello Freesurfers, I am interested in obtaining the regional volumes of white matter hypointensities. What volume would I use a reference for obtaining the 'regions' ? and what commands would I need to use to obtain these regional volumes ? ?If there isn't an appropriate white matter volume

[Freesurfer] Re Re: Question regarding mri_convert

Thank you Bruce! Theoretically, I should get the same results if I pass my nii file through the recon-all command if I converted my dicom/IMA file into a nii using Slicer4 or the mri convert command? I did this and I got different volumes. Thank you, Tamara ___

Re: [Freesurfer] Co-registering different source data

To create the volume ROI, I found something that said to use: scuba -v $filename to then make a new ROI. I got en error that I could not open scuba. Is this the correct way to go about this, or is there some other means that I should be doing not 'scuba'? Thank you, Anna _

Re: [Freesurfer] Sulcus depth

1. It is the signed dot product of the movement vector with the outwards pointing surface normal of the white matter surface during inflation. 2. Yes, because moving inwards for gyri the dot product is negative. 3. Yes, I think so, although I'm not sure I understand. 4. mris_anatomical_stats c

[Freesurfer] Sulcus depth

Dear FreeSurfer Team, I have questions about the sulcal depth. 1) I heard that the output/surf/?h.sulc is showing the sulcal depth. Is it correct that the sulcal depth measure unit is normalized z-score, mm? And is it correct that the (-) values of sulcal depth mean gyral region (green), and (+

Re: [Freesurfer] Co-registering different source data

yes, create a volume ROI and you can map it onto the surface using mri_vol2surf cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote: > For now, I am just trying to get any arbitrary ROI that I define. (I'm new to > this and am just trying to figure out how to get the basic process first.) >

Re: [Freesurfer] Co-registering different source data

For now, I am just trying to get any arbitrary ROI that I define. (I'm new to this and am just trying to figure out how to get the basic process first.) Eventually, I will want it related to another signal such as the EEG from an epilepsy subject for example. In that case, it would be the active

Re: [Freesurfer] Co-registering different source data

can you explain what the ROI is supposed to represent? If you can create it in the volume, you can use mri_vol2surf to map it onto the surface. cheers Bruce On Mon, 26 Sep 2016, Crawford, Anna wrote: > Hi, > > I am having trouble figuring out how to create my own ROI. I can visualize > the an

Re: [Freesurfer] Freesurfer Digest, Vol 151, Issue 30

Hi Ruopeng, When I try to open it, this is part of the error message that appears: freeview -v 2000_2/mri/T1.mgz 2000_2/mri/brainmask.mgz:colormap=heat:opacity=0.4 libGL error: No matching fbConfigs or visuals found libGL error: failed to load driver: swrast X Error: BadValue (integer paramet

Re: [Freesurfer] Software License for Industry

The FreeSurfer Software License Agreement does not contain any language explicitly or implicitly preventing commercial usage, however I will highlight the following text from the License Agreement: "Any commercialization of the Software is at the sole risk of the party or parties engaged in s

Re: [Freesurfer] Warping an ROI from one subject to another

Anyone have any thoughts on this? On 09/21/2016 04:18 PM, Joel Bruss wrote: > I have two subjects, subA and subB. subA has a binary ROI mask, native > space, that I'd like to place in subB's native space. Both subjects have > been run through all stages of recon, edited, etc. Is there a better o

[Freesurfer] Software License for Industry

Dear FS experts I have one concern regarding the license and the Freesurfer usage on industry. We are setting up a start-up specialized with the analysis of brain MRI and we are interested on using FreeSurfer package as our main neuroimaging tool, due to the large amount of utilities it provides.

Re: [Freesurfer] Co-registering different source data

Hi, I am having trouble figuring out how to create my own ROI. I can visualize the anatomical ROI created automatically. How do I create a new ROI? Thanks, Anna From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on beh

Re: [Freesurfer] Co-registering different source data

Hi Anna I'm not exactly sure what you mean, but if you register EEG electrodes to the white or pial surface, then you can visualize them on the inflated surface trivially. That is, you can create your ROI on any surface of the same hemisphere/subject and visualize it on any other cheers Bruce

[Freesurfer] Postdoctoral Positions -- Baby Brain Connectome

Postdoctoral research associate positions are available in the Department of Radiology and Biomedical Research Imaging Center (BRIC) at the University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current focuses are to better understand the dynamic development of brain structure, functio

[Freesurfer] Co-registering different source data

Hello, I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered ont

[Freesurfer] White matter editing using control points

Hi, I am having some trouble with white matter editing using control points. I am placing control points in white matter with intensity <110, and I find that it seems to have different effects in different slices/subjects, which makes it hard to develop a general standard for control point edi