Hi Angelique

like most well-behaved email list, each FS list email comes with a link that lets you unsubscribe yourself.

cheers Bruce On Fri, 22 Mar 2019, Van Ombergen Angelique wrote:

   External Email - Use Caution

Please unsubscribe me from the mailing list.

Best wishes, Angelique

...

On 22 Mar 2019, at 15:16, freesurfer-request@nmr.mgh.harvard.edu wrote:

Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu

You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."

Today's Topics:

1. Re: Build stamp missing in current dev release (Hoopes, Andrew)
2. VT images from pmod to freesurfer (Donatienne Van Weehaeghe)
3. Re: recon-all error (Daniel Callow)
4. Gray matter normalized intensity (Dorothy Sincasto)
5. Re: Gray matter normalized intensity (Glasser, Matthew)
6. Re: Gray matter normalized intensity (Bruce Fischl)
7. help ( Lance )
8. recon-all could not read surface file error (Daniel Callow)
9. Re: help (Bruce Fischl)
10. Re: recon-all could not read surface file error (Bruce Fischl)
11. Cerebellum within the pial surface (Matthieu VANHOUTTE)

---

Message: 1 Date: Thu, 21 Mar 2019 16:43:13 +0000 From: "Hoopes, Andrew" AHOOPES@mgh.harvard.edu Subject: Re: [Freesurfer] Build stamp missing in current dev release To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 5698A83B-BBA5-4EB7-A96F-CC515378666C@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"

Hi Baxter, this is a bug. Thanks for pointing it out, I'll fix it now. Andrew

?On 3/20/19, 2:43 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Baxter P. Rogers" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of baxter.rogers@vanderbilt.edu> wrote:

       External Email - Use Caution

This one: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux-... The build-stamp.txt file currently contains "freesurfer" with no version info. It used to be something like "freesurfer-linux-centos7_x86_64-dev-20181114-4f05c76" which is considerably more helpful :)

Thanks much, Baxter

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Message: 2 Date: Thu, 21 Mar 2019 12:49:54 -0400 From: Donatienne Van Weehaeghe donatiennevanweehaeghe@gmail.com Subject: [Freesurfer] VT images from pmod to freesurfer To: freesurfer@nmr.mgh.harvard.edu Message-ID: CA+W1dKxXS5FjNhYxerphn6RJcc5Jf0Sf_KjoBT6o74iEk4akQw@mail.gmail.com Content-Type: text/plain; charset="utf-8"

   External Email - Use Caution

Dear,

I encountered a problem when going from pmod to freesurfer.

I made Vt images in pmod using the logan plot, then I used the following commands to convert them to freesurfer space:

#flirt -noresample -in /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii -ref /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/T1-2mm_skullstripped.nii.gz -applyxfm -init /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUV.lrrev_lin_T1.mat -out /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii

#3dresample -master /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/occipital.nii.gz -inset /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii -prefix /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii

Then I did partial volume correction using this command:

#mri_gtmpvc --i /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii --reg Vt.reg.lta --psf 5 --seg /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz --default-seg-merge --auto-mask 5 0.01 --rbv --o /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg --no-rescale --threads 8

Then I did surface projection:

#mri_vol2surf --mov /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz --reg /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta --hemi lh --projfrac 0.5 --o /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/lh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz --cortex --trgsubject fsaverage

#mri_vol2surf --mov /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz --reg /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta --hemi rh --projfrac 0.5 --o /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz --cortex --trgsubject fsaverage

followed by smoothing, concatening and then a group comparison. However then I obtained the following error:

ERROR: cannot find /usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd

Kind regards

Donatienne