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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
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Message: 2
Date: Tue, 14 Mar 2017 10:51:30 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Brain to skull distance
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<alpine.LRH.2.20.1703141050410.10321@door.nmr. >mgh.harvard.edu
Content-Type: text/plain; charset="utf-8"
Hi Youssif
you can save BEM surfaces with the -surf option to mri_watershed, but you
would probably get more accurate measures if you have a T2 (or PD) scan.
cheers
Bruce
On Tue, 14
Mar 2017, yusif Al-kheder wrote:
> Hello,
> Is it possible to use freesurfer to determine the distance between the skull
> and brain?
>
> Youssif?
>
>
------------------------------
Message: 3
Date: Tue, 14 Mar 2017 10:53:36 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Ventricles not filled
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<alpine.LRH.2.20.1703141053190.10321@door.nmr. >mgh.harvard.edu
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Manuel
yes, you can either fill them in the wm or edit the aseg
cheers
Bruce
On Tue, 14 Mar 2017, Manuel Delgado wrote:
> Dear Freesurfer list,
> Does anybody know how to deal with the parts of the ventricles that have not
> been filled in yellow when editing the white matter mask? (see enclosed
> image) Is it necessary to fill them as other parts of the wm that have not
> been included, such as vascular lesions? If I fill them using this, will
> that parts be considered white matter instead of ventricles? Or this is not
> relevant?
>
> Kind regards,
> Manuel
>
>
------------------------------
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
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
>
>
>
>
------------------------------
Message: 5
Date: Tue, 14 Mar 2017 11:04:20 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] tkmedit error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<alpine.LRH.2.20.1703141103500.10321@door.nmr. >mgh.harvard.edu
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Veronica
if freeview works for you then you should just use it. We have deprecated
tkmedit and are trying not to invest any time or energy in it any longer.
cheers
Bruce
On Tue, 14 Mar 2017, Veronica Munoz wrote:
> Dear all,
>
> I'm trying to use tkmedit to verify my recon-all results but I get these
> messages rather than the visualization of my volumes.
> Am I missing a library ?
> I've been using freeview and it works just fine but I would like to solve my
> problem.
>
> Thank you in advance.
> Best regards,
>
> Veronica M.R.
>
>
------------------------------
Message: 6
Date: Tue, 14 Mar 2017 11:10:40 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] fsgd 4 groups, continuous dependent
variable, 2 covariates
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <7201036e-cc8c-c7aa-70c1-1405f922eeda@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset="utf-8"
See if one of these examples works for you
http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
having two covariates is a straight forward extension of one
On 3/14/17 7:47 AM, Donna Cosgrove wrote:
> ?Hi Freesurfer experts,
>
> I am looking at the effect of a genetic risk score (GRS) on cortical
> surface/thickness. I have two groups: patients, controls (male and
> female).
>
> GroupDescriptorFile1
> TitleGRS_all_lh_surf_fwhm10
> MeasurementNamethickness
> ClassSexFemaleControl
> ClassSexMaleControl
> ClassSexFemalePatient
> ClassSexMalePatient
>
>
> I want to include total brain volume and age as covariates. Is this
> possible using an fsgd file? Is there an example you could give? ?
>
> Any advice would be great.
> Thanking you in advance
> Donna
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
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Message: 7
Date: Tue, 14 Mar 2017 11:14:06 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Whole preprocessing with FAST without to
perform a seed based analysis
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <4252f471-c127-da69-c6f7-0ce0083f2092@nmr.mgh.harvard. >edu
Content-Type: text/plain; charset="windows-1252"
just use preproc-sess
On 3/14/17 10:45 AM, stdp82@virgilio.it wrote:
> 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.
> Thanks
> Stefano
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
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Message: 8
Date: Mon, 13 Mar 2017 17:48:16 -0700
From: Redwan Maatoug <redwanmaatoug@gmail.com>
Subject: Re: [Freesurfer] mri_vol2surf
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >
Message-ID:
<CAKdBfSm650c-QK1DEakUxGOoqrGamtRqoN- zBuWQdj31-7nE+Q@mail.gmail.com >
Content-Type: text/plain; charset="utf-8"
Thank you very much Douglas,
I think that I probably miss something.
There is no error in the terminal but when i launch tksurfer, I have the
following screenshot (screen1). The overlay is loaded but the coordinates
are 0.00000 and the overlay is not in a different color that the brain.
I have attached, in case, the brain file and the volumetric file.
As you can see, I have followed all the instructions :
1) bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg MNI152.dat
--t1 --init-coreg
2) mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat
--hemi lh --o ./multidem.mgh
3) tksurfer fsaverage lh inflated -overlay multidem.mgh -fminmax .5 1
Thank you,
Best,
Redwan Maatoug
Resident in psychiatry
Stanford University
Amit Etkin lab
On 13 March 2017 at 14:51, Douglas N Greve <greve@nmr.mgh.harvard.edu>
wrote:
> The file you created is not a label so don't try to load it with -label.
> Instead use -overlay file.mgh -fminmax .5 1
>
>
>
> On 03/13/2017 05:40 PM, Redwan Maatoug wrote:
> > Hi Douglas,
> >
> > Sorry to bother you, again.
> > Actually, my command was t1 and not t2 but even with t1 nothing works.
> > So if my command line is exact, do you think it is a problem with my
> > files ?
> >
> > Thank you,
> >
> > Redwan Maatoug
> > Resident in psychiatry
> > Stanford University
> > Amit Etkin lab
> >
> > On 13 March 2017 at 13:41, Douglas N Greve <greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu >> wrote:
> >
> > Use --t1 (I assume the --tw was supposed to be --t2, which is
> > wrong for
> > that mni152 volume)
> >
> >
> > On 03/09/2017 08:58 PM, Redwan Maatoug wrote:
> > > Hi Douglas,
> > >
> > > Indeed you have already helped me !
> > > Thank you for your help and for your time.
> > >
> > > I have tried to do, as you said.
> > > I have used the brain image for the registration and then I have
> > > tried to convert my ROI nifti volumetric file into a surface file
> > > using this registration file.
> > >
> > > I do not know what is wrong with my command line and I tried
> > many many
> > > things.
> > >
> > > I have attached two files
> > > (MNI152_T1_2mm_brain.nii is the brain file,
> > > multdemand_MCC_SMA_thr50.nii.gz is the ROI file).
> > >
> > > I have tried the following commands :
> > > 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg
> > > MNI152.dat --tw --init-coreg*
> > >
> > > 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg
> > > MNI152.dat --hemi lh --o ./multidem.mgh*
> > >
> > > I do not know if the output format .mgh is correct.
> > > Anyway when I launch it with :
> > > *tksurfer fsaverage lh inflated -label multidem.mgh*
> > >
> > > the multidem.mgh file does not appear.
> > >
> > > Thank you by advance for your advice,
> > > Best,
> > > Redwan
> > >
> > > On 9 March 2017 at 09:09, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu >
> > > <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu >>> wrote:
> > >
> > > didn't I respond to this earlier this week? the images
> > appear to be
> > > binarized regions of interest and not whole (or ever partial)
> > > brain. To
> > > run the registration, you will need an actual brain. If you
> > > created the
> > > ROI from a brain image, then use that image to create the reg,
> > > then run
> > > vol2surf using that reg with the ROI as input
> > >
> > >
> > > On 03/07/2017 03:02 PM, Redwan Maatoug wrote:
> > > > Hi experts,
> > > >
> > > > I try to convert my volumetric nifti file to surface files.
> > > >
> > > > My nifti volumetric file looks like : 1. screenshot
> > > > I have first registered the volumetric file using bbregister
> > > with this
> > > > command line :
> > > > *bbregister --s fsaverage --mov segment_7.nii --reg
> > > segment_7.dat --t1
> > > > --init-coreg*
> > > >
> > > > then I have used the following command line and the file
> > looks like
> > > > screenshot 1 attached :
> > > > *tkregister2 --mov segment_7.nii --reg register7.dat --surf*
> > > >
> > > > And after that, I have tried to convert my volumetric file to
> > > surface
> > > > file with this command line :
> > > >
> > > > *mri_vol2surf --src segment_7.nii --srcreg register7.dat
> > --hemi
> > > lh --o
> > > > ./segment_7-lh.nii --float2int round*
> > > >
> > > > But with this command when I load the file with freeview
> > it does not
> > > > work and with tkregister the file is empty.
> > > >
> > > > Or this one :
> > > >
> > > > *mri_vol2surf --src segment_7.nii --srcreg register7.dat
> > --hemi
> > > lh --o
> > > > ./segment_7-lh.w --out_type paint --float2int tkregister*
> > > >
> > > > But with this command I have this warning :
> > > > Warning: all vertex values are zero
> > > >
> > > > Could you please help me to convert my volumetric files
> > because I am
> > > > probably doing someting wrong. All my files come from an
> > Atlas and I
> > > > just need to convert them to surfaces files.
> > > >
> > > > Thank you for your help,
> > > > Redwan
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu >
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu >>
> > > >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ >freesurfer
> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ >>freesurfer
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu >
> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu
> >>
> > > Phone Number: 617-724-2358 <tel:617-724-2358>
> > <tel:617-724-2358 <tel:617-724-2358>>
> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
> > <tel:617-726-7422>>
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/ >BugReporting
> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/ BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/ >>BugReporting
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > <https://gate.nmr.mgh.harvard.edu/filedrop2 >
> > > <https://gate.nmr.mgh.harvard.edu/filedrop2
> > <https://gate.nmr.mgh.harvard.edu/filedrop2 >>
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index. >html
> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index. html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index. >>html
> > > Outgoing:
> > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ greve/
> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ >greve/
> > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/
> greve/
> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ >>greve/
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu >
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu >>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ >freesurfer
> > >
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ >>freesurfer
> > >
> > >
> > > The information in this e-mail is intended only for the
> > person to
> > > whom it is
> > > addressed. If you believe this e-mail was sent to you in
> > error and
> > > the e-mail
> > > contains patient information, please contact the Partners
> > > Compliance HelpLine at
> > > http://www.partners.org/complianceline
> > <http://www.partners.org/complianceline >
> > > <http://www.partners.org/complianceline
> > <http://www.partners.org/complianceline >> . If the e-mail was sent
> > > to you in error
> > > but does not contain patient information, please contact the
> > > sender and properly
> > > dispose of the e-mail.
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu >
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ >freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu >
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> > Fax: 617-726-7422 <tel:617-726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/ >BugReporting
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > <https://gate.nmr.mgh.harvard.edu/filedrop2 >
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index. >html
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ greve/
> > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ >greve/
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.har
> vard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ >freesurfer
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 <(617)%20724-2358>
> Fax: 617-726-7422 <(617)%20726-7422>
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/ freesurfer
>
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End of Freesurfer Digest, Vol 157, Issue 43
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