[Freesurfer] error: mean: DIM must be an integer and a valid dimension / selxavg3-sess with octave

Dear FreeSurfers, I just wanted to share a solution for an issue that can arise when running selxavg3-sess with octave instead of Matlab. In fast_selxavg3.m (which is called by selxavg3) there is a line (579 in my version) that computes the mean of an array by calling the mean function with the D

Re: [Freesurfer] surface based analysis (projfrac)

Thank you Doug, Exactly! I meant GM near the CC. When I used "projfrac=0.5 " there was no differnce between the groups at "cwp 0.05", and when I changed the "projfrac to 0" I got significant differnce between the groups in specific areas at "cwp 0.01". Kindly, how can this be explained? I highly

[Freesurfer] vertex-wise ROI analysis

Dear FreeSurfer experts, is it possible to do a vertex-wise analysis on ROIs? When I extract the values per subject for (e.g.) the superior temporal gyrus grom the aparc file it is a pretty big region to get only one value. I would like to analyze it on a vertex level so I can see where exactly

Re: [Freesurfer] vertex-wise ROI analysis

You can do a vertex-wise analysis in any region you like (e.g. cortex, superior temporal cortex, etc.) check the "--label" option of mri_glmfit. see also: https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo -joost

Re: [Freesurfer] vertex-wise ROI analysis

thank you! I will give that a try. - Ursprüngliche Mail - Von: "Joost Janssen" An: "ckuehn" , "freesurfer" Gesendet: Mittwoch, 11. Januar 2017 15:07:36 Betreff: Re: [Freesurfer] vertex-wise ROI analysis You can do a vertex-wise analysis in any region you like (e.g. cortex, superior temp

Re: [Freesurfer] reposition surface for pial surface

Hello Antonin, Apologies, I forgot to send them. This is the email and the vertex coordinates. For vertex, it shows N/A hence, not sure what value i need to enter in the vertex section of edit coordinates in the reposition surface tool. Thank you Best, Paul On Tue, Jan 10, 2017 at 4:54 PM, Antonin

Re: [Freesurfer] hippocampal subfields

Dear Ferdi, It is really hard for us to know why you‘re getting such a weird error (segfault of kvlAutoCrop) in a submitted job when you don’t get it in an interactive session … You will have to look into the peculiarities of the submission system to see what is changing from one setting to the

[Freesurfer] Error message

Dear FS teams: when I running FS, there is a message like this: Error:Cannot find CTF archive /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.ctf Is it a real Error message? Cause, it seems that the recon -all process successfully finished. thanks Lawrence ___

Re: [Freesurfer] Error message

Hi Lawrence can you send us the full command line and screen output of what you ran? thanks Bruce On Wed, 11 Jan 2017, shi yao wang wrote: Dear FS teams:  when I running FS, there is a message like this:  Error:Cannot find CTF archive /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimate

[Freesurfer] mris_expand command and flags

Hello freesurfer, I have several questions about mris_expand command. I know it can be used to expand or shrink a point on a surface by a fixed amount or distance. My questions are: 1) Can it be used to expand the pial surface? if yes, please can you confirm if this is the right script= mris_expan

Re: [Freesurfer] mris_expand command and flags

Hi Paul it's hard to answer your questions without knowing what you are trying to achieve cheers Bruce On Wed, 11 Jan 2017, miracle ozzoude wrote: Hello freesurfer,  I have several questions about mris_expand command. I know it can be used to expand or shrink a point on a surface by a fixed

Re: [Freesurfer] mris_expand command and flags

Thanks bruce for your response. I am trying to expand the pial surface (see attached image) in order to estimate the GM/WM boundary properly. I have successfully expanded the white matter but when i tried the mris_expand scripts for pial surface (mris_expand -thickness lh.pial 0.5 lh.newpial), the

Re: [Freesurfer] mris_expand command and flags

Dear Paul, I am quite surprised that you were successful to estimate correct GM/WM boundary using this tool. As far as I know and looking at the source code, this tool GLOBALLY moves the position of the specified surface to some amount, so it cannot be used to correct local errors. It is used e

Re: [Freesurfer] mris_expand command and flags

Hello Antonin, GM/WM boundary = thickness. correct me if i am wrong. Shouldn't expanding/shrinking the ?h.white or ?h.pial surface to the correct size and shape help with that? I have moved the position of the ?h.white to capture most of the WM using mris_expand but i haven't been successfully with

Re: [Freesurfer] createMorph & applyMorph: unexpected results

Hi Stefano, If you have the final_CVSmorph_toSynthF.m3z file you can use mri_vol2vol dirctly to apply it to another volume. Look for examples in mri_cvs_register --help. We are moving away from using the tm3d file format. Lilla On Wed, 11 Jan 2017, Stefano Zappalà wrote: Hello FreeSurfe

Re: [Freesurfer] autorecon1 crash (with nu_correct).

I'm seeing it for multiple subjects, same issue. I can't get passed the autorecon1 steps. Any thoughts? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mai

Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream

Hi Dr. Reuter. Thank you again for your help. I ran the following command: "mri_robust_register --mov rawavg_1.mgz --dst rawavg_2.mgz --lta v1to2.lta --affine --satit" on the two rawavg.mgz images; one from each time point from the cross-sectional outputs. I have attached the information from the

Re: [Freesurfer] mris_expand command and flags

Dear Paul, mris_expand can be used only in the hypothetical cases, where in all brain systematically the surface is shifted to equal amount from the position which is anatomically relevant. Therefore it cannot be used to correct for local errors. To ilustrate the use of this tool, see the scre

Re: [Freesurfer] autorecon1 crash (with nu_correct).

please include previous correspondence. we get a lot of emails here and can't remember the context of each one. thanks On 01/11/2017 03:17 PM, Jamie Hanson wrote: > > I'm seeing it for multiple subjects, same issue. I can't get passed > the autorecon1 steps. Any thoughts? -- Douglas N. Greve

[Freesurfer] Binary Mask Overlay

Hi FreeSurfer Team, I used QDEC to do a group analysis and from that I generated a surface-based mask using the command "mri_binarize --i sig.mgh --min 3 --o mask.mgz" Ultimately, I would like to overlay this mask on an individual subject (other than the fsaverage "lh.inflated" surface). Usin

Re: [Freesurfer] autorecon1 crash (with nu_correct).

Apologies my email must have clipped it out. I pasted it below. === Hello Freesurfer List, I was running into issues processing subjects, with errors just getting through the autorecon1 step of the pipeline. My terminal outputs the following: /home/jamielh/Volumes/Hanson/Pardini_Pro

Re: [Freesurfer] autorecon1 crash (with nu_correct).

Is it happening on all subjects or just some of them? On 01/11/2017 03:45 PM, Jamie Hanson wrote: > Apologies my email must have clipped it out. > I pasted it below. > > > > === > > Hello Freesurfer List, > > I was running into issues processing subjects, with errors just > getting through t

Re: [Freesurfer] autorecon1 crash (with nu_correct).

> Is it happening on all subjects or just some of them? all of them... > > > On 01/11/2017 03:45 PM, Jamie Hanson wrote: > >> Apologies my email must have clipped it out. >> I pasted it below. >> >> >> >> === >> >> Hello Freesurfer List, >> >> I was running into issues processing subject

Re: [Freesurfer] autorecon1 crash (with nu_correct).

I'm suspecting that there is an error or incompatibility in the MNI software (where we get nu_correct). Unforutnately, the person who would handle this (Zeke) is away until next Wed. Can it wait until then? On 01/11/2017 04:58 PM, Jamie Hanson wrote: > > Is it happening on all subjects or

Re: [Freesurfer] autorecon1 crash (with nu_correct).

Totally fine. I will try to check in then. On Wed, Jan 11, 2017 at 5:15 PM, Douglas N Greve wrote: > I'm suspecting that there is an error or incompatibility in the MNI > software (where we get nu_correct). Unforutnately, the person who would > handle this (Zeke) is away until next Wed. Can it

Re: [Freesurfer] autorecon1 crash (with nu_correct).

Hello Zeke, I included the terminal output error for the stable version of Freesurfer, but get the same error with the dev version. Here's an example, pasted below: Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696bbc1 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20170103-696b