Re: [Freesurfer] Extraction of cortical thickness in native space

Thanks, Doug! I think we were probably going about this the wrong way. If I transform the ROI from MNI space back into native space, will the following commands give the proper cortical thickness extraction from native space? mri_vol2surf --mov roi_in_native_space.nii.gz --out

Re: [Freesurfer] mri_segstats - CTABWriteFileASCII; could not open file for writing

and does that file exist in /tmp? Is there space in /tmp? On 02/28/2018 01:33 PM, Yash Patel wrote: > Yes, I made sure I had permission to write into /tmp. > > On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve > > wrote: > > do

Re: [Freesurfer] mir_vol2surface registration file error

Hello, Thank you so much! I used the following command as you said and got an error : must specify a source registration file or --regheader mri_vol2surf --src negative_allsocial_avgnull.nii --src_type analyze --trgsubject fsaverage --hemi lh --o ./neg_allsocial.nii --projfrac 0.5 Best, Srishti

Re: [Freesurfer] Fwd: Freeview update on Mac

Hi Sarah, Drawing an ROI on a surface is a little bit complicated. You will need to have a surface and volume loaded first. Then you create or load a ROI as a volume ROI. On the control panel, there should be a "Map to surface" option, you can map the ROI to the loaded surface. Then you

[Freesurfer] Fwd: Freeview update on Mac

Great! Thank you so much, Andrew. I downloaded the updated Freeview. I am still wondering how to draw an ROI on the surface in Freeview. I don't have the options. Could you please let me know what command you are running to get the Freeview? I am having the updated version Jan 2018. Thanks,

Re: [Freesurfer] Resolution limits of FLAIR/T2w for effective pial refinement

I would add that my guess is the FLAIR is helpful up to about 1.25-1.5mm thickest dimension cheers Bruce On Wed, 28 Feb 2018, Glasser, Matthew wrote: > The trouble with highly anisotropic resolutions is that your resolution is > only as good as your worst axis for the convoluted cerebral

Re: [Freesurfer] mri_segstats - CTABWriteFileASCII; could not open file for writing

Thanks for the advice. I did have permission to write into /tmp; however the HPC wouldn't allow it through the mri_segstats command line. The issue was resolved by making a directory in the tmp manually, and then mri_segstats works normally. Thanks, Yash On Wed, Feb 28, 2018 at 1:33 PM, Yash

Re: [Freesurfer] Resolution limits of FLAIR/T2w for effective pial refinement

The trouble with highly anisotropic resolutions is that your resolution is only as good as your worst axis for the convoluted cerebral cortex. 0.8mm or better would be optimal given a minimum cortical thickness of 1.6mm. You can always try with what you have and see if it is net beneficial or

[Freesurfer] Resolution limits of FLAIR/T2w for effective pial refinement

Hi all, I wonder if people have any data (or anecdotes - I'm not picky) with regard to how high of resolution T2w or FLAIR images need to be in order to be useful for FreeSurfer's pial refinement. I've seen a couple threads suggesting the optimal is ~1mm isotropic, and that thick slice (1x1x5

Re: [Freesurfer] mri_segstats - CTABWriteFileASCII; could not open file for writing

Yes, I made sure I had permission to write into /tmp. On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve wrote: > do you have write permission to /tmp ? > > > On 02/27/2018 03:25 PM, Yash Patel wrote: > > Hello FreeSurfer experts, > > > > I am attempting to run

Re: [Freesurfer] Images fail to convert

can you tar or zip the data in /Volumes/PPDrive/Alliance/Source/Cases2Resubmit/MissingFSoutput_20180222/CVCD03060383 and send it to me on our filedrop (see below) On 02/27/2018 04:28 PM, Cheryl McCreary wrote: > > Dear Experts, > > I am trying to process a some T1 data through FreeSurfer 5.3.0,

Re: [Freesurfer] mri_segstats - CTABWriteFileASCII; could not open file for writing

do you have write permission to /tmp ? On 02/27/2018 03:25 PM, Yash Patel wrote: > Hello FreeSurfer experts, > > I am attempting to run "mri_segstats --annot [subjectid] lh aparc > --sum [outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035" > > Whenever I try, I receive the following

Re: [Freesurfer] missing '*h.pial*' files, cannot find fseverage folder.

what version of FS are you using? On 02/27/2018 01:29 PM, shilin18 wrote: > > *Hi all, very nice to find a place to ask all the fs giants a question.* > > *I run recon-all …-all -localGI, which always return this at the end. > Can anyone help me find out what I need to do to evade this error?

Re: [Freesurfer] Question of fs-fast

It  would not work by default. I think it could be made to work, but it would take a lot of work On 02/28/2018 11:12 AM, std...@virgilio.it wrote: > > Hi list, > > I wonder to know whether the FS-FAST tool is applicable on High Res > Hippo fMRI images (175x60x175mm; 0.39x2x0.39mm). > > In

[Freesurfer] Question of fs-fast

Hi list, I wonder to know whether the FS-FAST tool is applicable on High Res Hippo fMRI images (175x60x175mm; 0.39x2x0.39mm). In particular do you think that it could be possible to map the FC of a subfiled with the rest of the hippocampus? If yes, have you particular advises on this issue.

Re: [Freesurfer] demean age in CT analysis in QDEC?

what is your contrast of interest? If you are interested in the age slopes, then you don't need to demean. If you want to use age as a nuisance variable, then you should first test for an interaction between age and group using the DODS model. If there is no interaction, then switch to a DOSS

Re: [Freesurfer] mir_vol2surface registration file error

you need to add --trgsubject fsaverage to your mri_vol2surf command line On 2/27/18 12:23 PM, srishti goel wrote: Hello, We are trying to project a volume map onto a surface. Our network based volume map is a .vmp file and our surface is a nifti file. We were able to convert the volume maps

Re: [Freesurfer] Extraction of cortical thickness in native space

You are currently using 6 dofs (rigid registration). If you use --dof 12, it will get better. Having said that, nothing will make it that good since this is a volume-based affine registration. On 2/28/18 10:04 AM, Albrecht, Daniel S. wrote: Hi Doug, Sorry for the lack of information. We

[Freesurfer] 1st International Workshop on Predictive Processing (WoPP)

Dear All, We invite you to the " 1st International Workshop on Predictive Processing (WoPP) " organized by Basque Center on Cognition, Brain and Language (BCBL) that will be held in one of most beautiful cities in europe, San Sebastian, Spain from 20 - 22 June 2018 , at Palacio Miramar in