[Freesurfer] curvature

Dear FreeSurfer, In the stats files (e.g aparc) there are also statistics for the "integrated rectified mean curvature", "integrated rectified gaussian curvature", "folding index" and "intrinsic curvature index". To what kind of properties do these measures refer and which one is advised to be

Re: [Freesurfer] Adjusted or unadjusted CT values and interpretation of volume values in ocn.dat from group analysis

On 09/20/2017 01:54 PM, Elizabeth Bartlett wrote: > Hello Freesurfer experts, > > I have performed a group level analysis of volume and cortical > thickness using mri_glmfit and performed multiple comparisons > correction with mri_glmfit-sim. I used the contrast matrix 0 1 0 to > analyze 1

Re: [Freesurfer] lobes volume (WM and GM)

No, not for lobe volume. Have you seen the original wmparc paper? On 09/20/2017 04:53 PM, Gonzalo Rojas Costa wrote: > Hi Douglas: > >I am looking for papers that used the volume of each lobe computed > using freesurfer, but I couldn't found it... Do you know any?... > >Sincerely, > > >

Re: [Freesurfer] merge in a sigle label the results obetained in fs-fast

Try mri_mergelabels On 09/21/2017 07:47 AM, std...@virgilio.it wrote: > Hi list, > > I would to merge (separatelly pos and neg) in a sigle .label which > contain all the clusters which represent the seed-cortical > connectivity after fs-fast analysis. > I aim to avoid to extraxt manually

Re: [Freesurfer] Error in Qcache

No, sorry, we may be slowly phasing qdec out, so you can try to use the "command line" stream (mris_preproc, mris_fwhm, and mri_glmfit with visualization in FreeView) On 09/21/2017 02:57 AM, Emmanuel Nwosu wrote: > Hi All, > > I will want to know if this error on this link >

Re: [Freesurfer] recon-all question

You could run it with -label-V1 This is run at the end of recon-all and should only take a few min and would change the recon-all.log file. On 09/21/2017 01:57 PM, STACEY M SCHAEFER wrote: > > Hello, > > > I want to run recon-all again on scans that have already been > hand-edited, the

Re: [Freesurfer] Edits to aparc+aseg

we don't have a path for editing aparc+aseg. Are the areas unknown on the surface? On 09/21/2017 02:20 PM, Jake Rieke wrote: > Hi FreeSurfers, > > I have a group of subjects with manual edits to the aparc+aseg volume. > These edits were made to re-label unknown regions of cortex. I am >

[Freesurfer] Edits to aparc+aseg

Hi FreeSurfers, I have a group of subjects with manual edits to the aparc+aseg volume. These edits were made to re-label unknown regions of cortex. I am wondering what recon-all flags I could use to implement the changes and re-generate cortical stats based on these edits. Thanks in advance.

[Freesurfer] recon-all question

Hello, I want to run recon-all again on scans that have already been hand-edited, the appropriate recon-all flags ran, and resulting output checked and approved. The images look good, but when the hippocampal subfield routine was later run on the images, it crashed, leaving an error in the

Re: [Freesurfer] Longitudinal increase in thickness/volume

Hi Caleb, is this in a single subject or a group result? In a single subject almost anything is expected. E.g. small motion can cause thickness changes , so can hydration levels. Best, Martin Am 21.09.2017 um 16:53 schrieb Huang, Caleb (NIH/NINDS) [F]: Hello, I'm tracking atrophy in

[Freesurfer] nu_correct failure

Hello expert, I ran several subjects on FS v6 and they failed on the same stage (mri_nu_correct.mni and nu_correct). How can I solve this problem? I have attache the recon-all.log file for 2 subjects. Best, Paul recon-all.log Description: Binary data recon-all.log Description: Binary data

Re: [Freesurfer] Mris_volume

Hi Fereshte, Could you please clarify what you mean by "obtain the surface label"? Thanks, Emma - Emma Boyd Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging From:

Re: [Freesurfer] longitudinal freesurfer- different scanners

Yes, see also my answers from 08 and 11 of September on the list. Best, Martin Am 17.09.2017 um 19:42 schrieb Martijn Steenwijk: The longitudinal pipeline will not overcome (contrast) differences due to scanner differences. If you register the scans to eachother you will see that there

Re: [Freesurfer] Longitudinal processing -qcache ERROR

Hi Lisa, not sure where the problem comes from. But generally one would not do the qcache on the base. Qcache maps results to fsaverage and nobody should ever look at the base results except for debugging purposes. The base is the within-subject template and it is used to initialize the

[Freesurfer] Longitudinal increase in thickness/volume

Hello, I'm tracking atrophy in the precentral region. I've run the subjects through the longitudinal stream. Because of time constraints, I've mostly focused on editing the precentral regions as well as any significant errors outside of the region. I've observed increases in thickness of up

Re: [Freesurfer] Newborn MRI segmentation

The neonatal pipeline and its atlasesis not yet released. I am working on it, so hopefully you do not need to wait long. Lilla On Thu, 21 Sep 2017, Paula Diniz wrote: > Hi experts! > > I want to perform recon-all pipeline on newborn MRI data. > > How I can do this? Which atlas you

Re: [Freesurfer] Mris_volume

Hi Emma Are there any ways to obtain the surface label then? Thank you! On Wed, Sep 20, 2017 at 5:15 PM Boyd, Emma wrote: > Hi Fereshte, > > > mris_volume does not create any output files, that number you see in the > terminal is the total volume of a given closed

[Freesurfer] TRACULA trac-all prep error

Dear TRACULA users, I'm trying to preprocess a DTI subject in TRACULA which has an already reconed-all error-free T1. I followed the tutorial, but trac-all -prep exited with errors very fast. Please find attached the log and error files, and the dmrirc. Also bvals and bvecs (were obtained from

Re: [Freesurfer] Freeview aborts under centos6

Dear Andrew, So the sys admin has changed the libraries. however, it did not change anything. Freeview aborts without comment. Below the command you asked for the result. Any other ideas? What other info would you like to get? Sorry for that persisting problem! And thanks for your help!

Re: [Freesurfer] Fs 6

Hey John, as you can see on the FreeSurfer download page, you need either a linux or macOS system to run FreeSurfer natively (https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall). There are several ways to tackle your problem: 1. get a linux or macOS machine 2. run FreeSurfer within a

[Freesurfer] merge in a sigle label the results obetained in fs-fast

Hi list, I would to merge (separatelly pos and neg) in a sigle .label which contain all the clusters which represent the seed-cortical connectivity after fs-fast analysis.I aim to avoid to extraxt manually single label for cluster by tksurfer. Thanks,

[Freesurfer] Newborn MRI segmentation

Hi experts! I want to perform recon-all pipeline on newborn MRI data. How I can do this? Which atlas you recommend? Any news about infant pipeline? Thanks!! Paula Diniz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Error in Qcache

Hi All, I will want to know if this error on this link https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051464.html was resolved. I am having a similar problem while sampling to the fsaverage. Thanks Kind regards Emmanuel ___

[Freesurfer] Fs 6

dear FS experts, is there any tutorial to install FS 6 under windows 10? John ___ 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