Dear Bruce,
Thank you for your help! This did the trick.
Kind regards,
Daan
--------- Message: 4 Date: Tue, 14 Mar 2017 10:58:13 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Faulty alignment to standard surface To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1703141054510.10321@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
HI Daan
wow, that is a pretty unusual folding pattern, which I'm sure is the source of the issue. Are you sure which one is the central sulcus? If so, draw it (I guess using tksurfer as the current version of freeview doesn't have extensive surface drawing tools yet), probably by just "custom filling" the sulc, then rerun mris_register using the flag:
mris_register --help | grep "-L" Usage: grep [OPTION]... PATTERN [FILE]... Try 'grep --help' for more information. tiamat [C2.3T.recon] mris_register --help | grep "-L" -L <labelfile atlas_gcsa_file label_name>
where label_name is the exact name of the central sulcus label in the gcsa file you use, and can be obtained by looking in our color lookup table file such as FreeSurferColorLUT.txt, or just running mris_info on the gcsa file you are using (they are all in $FREESURFER_HOME/average).
cheers Bruce
On Tue, 14 Mar 2017, Daan Wesselink wrote:
Dear Douglas,
Thank you for your response. The surface placement on the individual seems correct (see?https://ibb.co/f4aeAa ). However, if I load the annotation files, the labels are wrong. In this screenshot (https://ibb.co/cycFiv ), I've loaded the BA annotation outlines and BA3a in yellow on the left hemisphere. It seems to think the wrong fold is the central sulcus.
Thanks,
Daan?
Message: 7 Date: Sun, 12 Mar 2017 19:00:21 -0400 From: Douglas Greve <greve@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Faulty alignment to standard surface To: freesurfer@nmr.mgh.harvard.edu Message-ID: <7ab364ef-539f-fd65-4346-db68d915ca05@nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" not sure what you mean. Can you send a pic? Is the surface placement on the individual correct (ie, are the white and pial surfaces properly placed on the T1)? On 3/10/17 11:19 AM, Daan Wesselink wrote: > Dear experts, > > I've run the standard recon-all pipeline on a subject, for whom the > log does not report any errors and the white and pial surface follow > the structural nicely. However, the coregistration to the standard > surface has gone wrong: it seems like the central sulcus (e.g. labels > BA1, BA3a) is placed on top of the postcentral sulcus. > > Does someone know how to fix this problem and/or better identify the > step where it went wrong? > > Many thanks, > > Daan Wesselink > >
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On 14 March 2017 at 15:50, freesurfer-request@nmr.mgh.harvard.edu < freesurfer-request@nmr.mgh.harvard.edu> wrote:
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Today's Topics:
- Whole preprocessing with FAST without to perform a seed based analysis (stdp82@virgilio.it)
- Re: Brain to skull distance (Bruce Fischl)
- Re: Ventricles not filled (Bruce Fischl)
- Re: Faulty alignment to standard surface (Bruce Fischl)
- Re: tkmedit error (Bruce Fischl)
- Re: fsgd 4 groups, continuous dependent variable, 2 covariates (Douglas Greve)
- Re: Whole preprocessing with FAST without to perform a seed based analysis (Douglas Greve)
- Re: mri_vol2surf (Redwan Maatoug)
Message: 1 Date: Tue, 14 Mar 2017 15:45:17 +0100 (CET) From: stdp82@virgilio.it Subject: [Freesurfer] Whole preprocessing with FAST without to perform a seed based analysis To: freesurfer@nmr.mgh.harvard.edu Message-ID: 1222513272.4869241489502717860.JavaMail.httpd@fep-webmail-05 Content-Type: text/plain; charset="utf-8"
Hi list,in FS-FAST, on rs-fMRI data, is possible to run selxavg3-sess without -a option?I would use whole the FS-FAST to preprocess my data. I would include the mkanalysis-sess step but I would not perform a seed-based analysis. ThanksStefano
glad to hear it Bruce On Wed, 15 Mar 2017, Daan Wesselink wrote:
Dear Bruce,
Thank you for your help! This did the trick.
Kind regards,
Daan
Message: 4 Date: Tue, 14 Mar 2017 10:58:13 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Faulty alignment to standard surface To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1703141054510.10321@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
HI Daan
wow, that is a pretty unusual folding pattern, which I'm sure is the source of the issue. Are you sure which one is the central sulcus? If so, draw it (I guess using tksurfer as the current version of freeview doesn't have extensive surface drawing tools yet), probably by just "custom filling" the sulc, then rerun mris_register using the flag:
mris_register --help | grep "-L" Usage: grep [OPTION]... PATTERN [FILE]... Try 'grep --help' for more information. tiamat [C2.3T.recon] mris_register --help | grep "-L" -L <labelfile atlas_gcsa_file label_name>
where label_name is the exact name of the central sulcus label in the gcsa file you use, and can be obtained by looking in our color lookup table file such as FreeSurferColorLUT.txt, or just running mris_info on the gcsa file you are using (they are all in $FREESURFER_HOME/average).
cheers Bruce
On Tue, 14 Mar 2017, Daan Wesselink wrote:
Dear Douglas,
Thank you for your response. The surface placement on the individual seems correct (see?https://ibb.co/f4aeAa%C2%A0). However, if I load the annotation files, the labels are wrong. In this screenshot (https://ibb.co/cycFiv%C2%A0), I've loaded the BA annotation outlines and BA3a in yellow on the left hemisphere. It seems to think the wrong fold is the central sulcus.
Thanks,
Daan?
Message: 7 Date: Sun, 12 Mar 2017 19:00:21 -0400 From: Douglas Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Faulty alignment to standard surface To: freesurfer@nmr.mgh.harvard.edu Message-ID: 7ab364ef-539f-fd65-4346-db68d915ca05@nmr.mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
not sure what you mean. Can you send a pic? Is the surface placement on the individual correct (ie, are the white and pial surfaces properly placed on the T1)?
On 3/10/17 11:19 AM, Daan Wesselink wrote: > Dear experts, > > I've run the standard recon-all pipeline on a subject, for whom the > log does not report any errors and the white and pial surface follow > the structural nicely. However, the coregistration to the standard > surface has gone wrong: it seems like the central sulcus (e.g. labels > BA1, BA3a) is placed on top of the postcentral sulcus. > > Does someone know how to fix this problem and/or better identify the > step where it went wrong? > > Many thanks, > > Daan Wesselink > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 14 March 2017 at 15:50, freesurfer-request@nmr.mgh.harvard.edu 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. Whole preprocessing with FAST without to perform a seed based analysis (stdp82@virgilio.it) 2. Re: Brain to skull distance (Bruce Fischl) 3. Re: Ventricles not filled (Bruce Fischl) 4. Re: Faulty alignment to standard surface (Bruce Fischl) 5. Re: tkmedit error (Bruce Fischl) 6. Re: fsgd 4 groups, continuous dependent variable, 2 covariates (Douglas Greve) 7. Re: Whole preprocessing with FAST without to perform a seed based analysis (Douglas Greve) 8. Re: mri_vol2surf (Redwan Maatoug) ---------------------------------------------------------------------- Message: 1 Date: Tue, 14 Mar 2017 15:45:17 +0100 (CET) From: <stdp82@virgilio.it> Subject: [Freesurfer] Whole preprocessing with FAST without to perform a seed based analysis To: freesurfer@nmr.mgh.harvard.edu Message-ID: <1222513272.4869241489502717860.JavaMail.httpd@fep-webmail-05> Content-Type: text/plain; charset="utf-8" Hi list,in FS-FAST, on rs-fMRI data, is possible to run selxavg3-sess without -a option?I would use whole the FS-FAST to preprocess my data. I would include the mkanalysis-sess step but I would not perform a seed-based analysis. ThanksStefano
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Daan Wesselink