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Today's Topics:

   1. Re: Freesurfer 7.1 hires error (Douglas N. Greve)
   2. Re: question on partial volume correction (Barletta, Valeria)
   3. Re: question on partial volume correction (Douglas N. Greve)
   4. Re: Group Analysis Covariates (Hua, Jessica)
   5. Re: Group Analysis Covariates (Douglas N. Greve)
   6. Re: mris_register intermediate results display (Chris Adamson)
   7. Open Postdoctoral Scholar Position (Neva M Corrigan)
   8. Re: Infant Freesurfer: infant_recon_all error (Hoopes, Andrew)
   9. Re: circular/cyclic color map for polar data in   freeview
      {Disarmed} (Caspar M. Schwiedrzik)
  10. OHBM Brainhack registration is open! (Remi Gau)
  11. FW: Motion correction files contain 0 0 0 1
      (Camerino, I.L. (Ileana))


----------------------------------------------------------------------

Message: 1
Date: Thu, 21 May 2020 12:11:55 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer 7.1 hires error
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <9eaf8c24-3b80-eb34-7cd0-09080c152b03@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I don't know what is wrong. Can you upload the hires run? Instructions below

 From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log? into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.



On 5/21/2020 9:35 AM, Jones, Richard wrote:
>
> ????????External Email - Use Caution
>
> I ran freesurfer 7.1 with the following options:-
>
> -i ./study/T1_SAG/IM-0001-0001.dcm -FLAIR
> ./study/SAG_3D_FLAIR/IM-0001-0001.dcm -s TEST_050620 -3T ?mprage
> ?FLAIRpial ??hires ?parallel ?all
>
> The job failed, the logfile recon-all_hires.log is attached. I then
> reran the job with the same datasets but exchanged ?hires with
> ?conf2hires and used the subject ID TEST_050620c and the job completed
> successfully (the logfile for this job, recon-all_conf2hires.log, is
> also attached). Any idea what the problem is when using the ?hires option?
>
> Thanks
>
> *Richard*
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 2
Date: Thu, 21 May 2020 17:07:32 +0000
From: "Barletta, Valeria" <VBARLETTA@mgh.harvard.edu>
Subject: Re: [Freesurfer] question on partial volume correction
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>,
        "freesurfer-bounces@nmr.mgh.harvard.edu"
        <freesurfer-bounces@nmr.mgh.harvard.edu>, "Herranz Muelas, Elena"
        <EHERRANZMUELAS@mgh.harvard.edu>
Message-ID:
        <BL0PR04MB4722DCF726054FDD0F9496A4F9B70@BL0PR04MB4722.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="us-ascii"

Yes I need the lh and rh cerebral WM for sure, but not just the values, also an image.
And I need also a corrected image for the extra cerebral CSF. How can I get that?

Thank you very much,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Thursday, May 21, 2020 10:32 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] question on partial volume correction

It will certainly do cortex. We do not have a segmentation for subarachnoid spaces. Or are you just talking about extra cerebral CSF? We do have a segmentation for xCSF, but it is not the most beautiful thing in the world. For WM, the GTM will give you a PVC corrected value for the entire lh and rh cerebral WM (and cerebellar) segments. Is that all you need?

On 5/19/2020 11:36 AM, Barletta, Valeria wrote:
Dear Freesurfers,
We need to analyze PET data after correcting for partial volume effect in the cortex, white matter and subarachnoid space. Is Freesurfer's partial volume correction working on all these areas or only the grey matter volume and surface? Is there a way to use gtmseg on the white matter and outside the pial surface?

Thanks a lot,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823



_______________________________________________
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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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Message: 3
Date: Thu, 21 May 2020 14:05:49 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] question on partial volume correction
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <3904bd37-e3e4-4196-468c-586c4fcdbe18@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

You can try using --rbv. In theory, you can use mueller-gaertner
(--mgx), but I don't have it set up to look at WM or CSF. And be careful
because the extracerebral CSF segmentation is often not very good.

On 5/21/2020 1:07 PM, Barletta, Valeria wrote:
> Yes I need the lh and rh cerebral WM for sure, but not just the
> values, also an image.
> And I need also a corrected image for the extra cerebral CSF. How can
> I get that?
>
> Thank you very much,
>
> Valeria Barletta, MD
> Massachusetts General Hospital
> 149 13th Street, Charlestown MA 02129
> (617)-724-8823
> ------------------------------------------------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
> <dgreve@mgh.harvard.edu>
> *Sent:* Thursday, May 21, 2020 10:32 AM
> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] question on partial volume correction
> It will certainly do cortex. We do not have a segmentation for
> subarachnoid spaces. Or are you just talking about extra cerebral CSF?
> We do have a segmentation for xCSF, but it is not the most beautiful
> thing in the world. For WM, the GTM will give you a PVC corrected
> value for the entire lh and rh cerebral WM (and cerebellar) segments.
> Is that all you need?
>
> On 5/19/2020 11:36 AM, Barletta, Valeria wrote:
>> Dear Freesurfers,
>> We need to analyze PET data after correcting for partial volume
>> effect in the cortex, white matter and subarachnoid space. Is
>> Freesurfer's partial volume correction working on all these areas or
>> only the grey matter volume and surface? Is there a way to use gtmseg
>> on the white matter and outside the pial surface?
>>
>> Thanks a lot,
>>
>> Valeria Barletta, MD
>> Massachusetts General Hospital
>> 149 13th Street, Charlestown MA 02129
>> (617)-724-8823
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> 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

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Message: 4
Date: Thu, 21 May 2020 18:12:20 +0000
From: "Hua, Jessica" <jphc55@mail.missouri.edu>
Subject: Re: [Freesurfer] Group Analysis Covariates
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <MN2PR01MB566370502B085E7067AAFBF793B70@MN2PR01MB5663.prod.exchangelabs.com>
       
Content-Type: text/plain; charset="iso-2022-jp"

        External Email - Use Caution       

I apologize for resending all of this info, but my email is acting up and every time I try to respond to the other email, my Outlook freezes.

Here is info from our thread. I modified it to include the analysis in which I found significant clusters (i.e., looking at thickness with only age and sex as covariates and not ICV):

After running the permutation and finding significant clusters, I am trying to calculate the value for each participant for these significant clusters.

The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the adjusted values accounting for age and sex (this is a three group design).


The X matrix was 240x12 (see attached file)

  *   Column 1: 1s for Group 1 and 0s for Group 2 and 0s for Group 3
  *   Column 2: 0s for Group 1 and 1s for Group 2 and 0s for Group 3
  *   Column 3: 0s for Group 1 and 0s for Group 2 and 1s for Group 3
  *   Column 4: Age for Group 1 and 0s for Group 2 and 0s for Group 3
  *   Column 5: 0s for Group 1 and Age for Group 2 and 0s for Group 3
  *   Column 6: 0s for Group 1 and 0s for Group 2 and Age for Group 3
  *   Column 7: Sex for Group 1 and 0s for Group 2 and 0s for Group 3
  *   Column 8: 0s for Group 1 and Sex for Group 2 and 0s for Group 3
  *   Column 9: 0s for Group 1 and 0s for Group 2 and Sex for Group 3

Your code:
There is not an easy way to do it, but you can do it in matlab
cd glmdir
X = load('Xg.dat');
y = load('perm.th30.abs.y.ocn.dat');
beta = inv(X'*X)*X'*y;
yhat = X(:,[1 2 3]*beta([1 2 3])

When running your code, below are the errors I got in Matlab. Do you know how I can fix the code?

>> X = load('Xg.dat');
>> y = load('perm.th30.abs.y.ocn.dat');
>> y = load('perm.th30.abs.y.ocn.dat');
>> beta = inv(X'*X)*X'*y;
>> yhat = X(:,[1 2 3]*beta([1 2 3])
 yhat = X(:,[1 2 3]*beta([1 2 3])
                                 ?
Error: Invalid expression. When calling a function
or indexing a variable, use parentheses. Otherwise,
check for mismatched delimiters.

Did you mean:
>> yhat = X(:,[1 2 3]*beta([1 2 3]))
Error using  *
Incorrect dimensions for matrix multiplication.
Check that the number of columns in the first matrix
matches the number of rows in the second matrix. To
perform elementwise multiplication, use '.*'.

>> yhat = X(:,[1 2 3].*beta([1 2 3]))
Index in position 2 is invalid. Array indices must
be positive integers or logical values.

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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------------------------------

Message: 5
Date: Thu, 21 May 2020 14:16:17 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Group Analysis Covariates
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <c41a095e-9d64-06a7-09f2-7e1ac13c1dee@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Typo
 

On 5/21/2020 2:12 PM, Hua, Jessica wrote:
>
> ????????External Email - Use Caution
>
> I apologize for resending all of this info, but my email is acting up
> and every time I try to respond to the other email, my Outlook freezes.
>
> Here is info from our thread. I modified it to include the analysis in
> which I found significant clusters (i.e., looking at thickness with
> only age and sex as covariates and not ICV):
>
> After running the permutation and finding significant clusters, I am
> trying to calculate the value for each participant for these
> significant clusters.
>
> The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to
> get the adjusted values accounting for age and sex (this is a three
> group design).
>
> The X matrix was 240x12 (see attached file)
>
>   * Column 1: 1s for Group 1 and 0s for Group 2 and 0s for Group 3
>   * Column 2: 0s for Group 1 and 1s for Group 2 and 0s for Group 3
>   * Column 3: 0s for Group 1 and 0s for Group 2 and 1s for Group 3
>   * Column 4: Age for Group 1 and 0s for Group 2 and 0s for Group 3
>   * Column 5: 0s for Group 1 and Age for Group 2 and 0s for Group 3
>   * Column 6: 0s for Group 1 and 0s for Group 2 and Age for Group 3
>   * Column 7: Sex for Group 1 and 0s for Group 2 and 0s for Group 3
>   * Column 8: 0s for Group 1 and Sex for Group 2 and 0s for Group 3
>   * Column 9: 0s for Group 1 and 0s for Group 2 and Sex for Group 3
> Your code:
> There is not an easy way to do it, but you can do it in matlab
> cd glmdir
> X = load('Xg.dat');
> y = load('perm.th30.abs.y.ocn.dat');
> beta = inv(X'*X)*X'*y;
> yhat = X(:,[1 2 3]*beta([1 2 3])
>
> When running your code, below are the errors I got in Matlab. Do you
> know how I can fix the code?
>
> >> X = load('Xg.dat');
> >> y = load('perm.th30.abs.y.ocn.dat');
> >> y = load('perm.th30.abs.y.ocn.dat');
> >> beta = inv(X'*X)*X'*y;
> >> yhat = X(:,[1 2 3]*beta([1 2 3])
> ?yhat = X(:,[1 2 3]*beta([1 2 3])
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ??
> Error: Invalid expression. When calling a function
> or indexing a variable, use parentheses. Otherwise,
> check for mismatched delimiters.
>
> Did you mean:
> >> yhat = X(:,[1 2 3]*beta([1 2 3]))
> Error using ?*
> Incorrect dimensions for matrix multiplication.
> Check that the number of columns in the first matrix
> matches the number of rows in the second matrix. To
> perform elementwise multiplication, use '.*'.
>
> >> yhat = X(:,[1 2 3].*beta([1 2 3]))
> Index in position 2 is invalid. Array indices must
> be positive integers or logical values.
>
> ---
>
> Jessica Hua, M.A.
> Cognitive and Emotional Control Lab
> Doctoral Candidate?Clinical Psychology
> University of Missouri
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 6
Date: Fri, 22 May 2020 00:25:27 +0000
From: Chris Adamson <chris.adamson@mcri.edu.au>
Subject: Re: [Freesurfer] mris_register intermediate results display
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <43A4603348D2AC409B1B958EFE5C8B9403198040B8@MITSMXMBX02V.mcri.edu.au>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Yeah that works, thanks a lot.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve
Sent: Friday, 22 May 2020 1:08 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_register intermediate results display

I would just map the ?h.curv from one subject to another and then display them on a single surface and flip back and forth. Would that work for you?
On 5/21/2020 9:30 AM, Chris Adamson wrote:

        External Email - Use Caution
Freesurfer devs,

Apologies if this has already been asked. I?m looking for a way that I can look at the progress of mris_register to investigate the accuracy of registration. Given that the registration is done on the 2D parameterisations of the curvature maps, how can I take a spherical surface and write out a tif file with the curvature maps of the surface that I?m registering and the target surface. I presume I need to use mrisp_write but it is unclear how I choose the curvature map to write in the image.

Thanks in advance,

Chris.

Dr Chris Adamson
Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT)
Software Engineer, Cardiovascular Research (0.7 EFT)

Murdoch Childrens Research Institute
The Royal Children?s Hospital
Flemington Road, Parkville, VIC 3052 Australia
E chris.adamson@mcri.edu.au<mailto:chris.adamson@mcri.edu.au>
www.mcri.edu.au<http://www.mcri.edu.au/>



This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children?s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.



_______________________________________________

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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>

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Message: 7
Date: Fri, 22 May 2020 00:56:30 +0000
From: Neva M Corrigan <nevao@uw.edu>
Subject: [Freesurfer] Open Postdoctoral Scholar Position
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <A8503AF5-0C82-463C-BA34-17607B478C06@contoso.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Open Postdoctoral Scholar Position

The University of Washington Institute for Learning & Brain Sciences (I-LABS; http://ilabs.washington.edu/) located in Seattle, WA is seeking a Postdoctoral Scholar to conduct analyses of human MRI brain imaging data.  I-LABS is an interdisciplinary research unit dedicated to discovering the fundamental principles of human learning, with a special emphasis on early learning and brain development. The Postdoctoral Scholar will contribute to a team responsible for creating breakthrough findings in infant, child and adolescent brain development.


Applicants should have a Ph.D. in Psychology, Linguistics, Cognitive Science, Biomedical Engineering, Neuroscience, or relate field. Extensive prior experience in analysis of MRI data in a scientific setting is essential. Programming and scripting skills are required, with Matlab or Python as well as Unix scripting experience at a minimum.  Familiarity with common MRI image processing software packages (such as FSL, SPM, ANTS, FreeSurfer, or AFNI) is a must. Previous experience in working with pediatric MRI data is highly desired.
Full position details and application submission are available at:  https://apply.interfolio.com/75530. Review of applications will begin May 1st, 2020; applications will be accepted until the position is filled.

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Message: 8
Date: Fri, 22 May 2020 02:17:56 +0000
From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: [Freesurfer] Infant Freesurfer: infant_recon_all error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <6762C52C-20F5-49A0-A818-4FB1B63BA863@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Fleur,
It?s definitely running with tcsh. Can you provide a bit more context for the error? Like is there any terminal output preceding it?
Andrew

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fleur Warton <fleur.warton@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, May 20, 2020 at 6:13 AM
To: fsbuild <fsbuild@contbay.com>
Cc: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Infant Freesurfer: infant_recon_all error


        External Email - Use Caution
Hi,

Thanks for the reply! The output for 'file' was tcsh. I switched to tcsh (just in that session) but got the same error when running infant_recon_all

 if: Expression Syntax

Kind regards,
--

Fleur Warton

Postdoctoral Research Fellow
Division of Biomedical Engineering
Faculty of Health Sciences
University of Cape Town


On Wed, May 20, 2020 at 11:42 AM fsbuild <fsbuild@contbay.com<mailto:fsbuild@contbay.com>> wrote:
Hello Fleur,

You should be able to do,
$ file `which infant_recon_all`
... and the output should tell you if it it is a csh script, a Bourne shell script, a binary, etc.

Unless you explicitly made csh or bash your default shell, then at the dollar sign prompt the default shell in Ubuntu is "dash" and not bash or Bourne shell.   If the file command reports it's a Bourne shell then it might be a bash script.  Or a bash script with a hash bang line of /bin/sh will run using dash shell on Ubuntu and can exit with that error on bash syntax/grammar.  You can eliminate that possibility by first running bash, and then the script,

$ bash
$ infant_recon_all --s SUBJ --age AGE
(with I presume arguments substituted for SUBJ and AGE)

- R.
Fleur Warton<mailto:fleur.warton@gmail.com>
May 20, 2020 at 04:05

        External Email - Use Caution
Hi,

I recently installed the Infant FreeSurfer package. When I try to run
infant_recon_all (specific command: infant_recon_all --s SUBJ --age AGE)

 I get the error

if: Expression Syntax

I tried switching shells from bash to tcsh but got the same error.

The FreeSurfer version is freesurfer-infant-20200205
My platform is Ubuntu 18.04

Any suggestions how to fix this?

Kind regards,

Fleur




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Message: 9
Date: Fri, 22 May 2020 07:54:52 +0200
From: "Caspar M. Schwiedrzik" <cschwiedrz@mail.rockefeller.edu>
Subject: Re: [Freesurfer] circular/cyclic color map for polar data in
        freeview {Disarmed}
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CA+bX-39G02LgOc5-dJeq5ewKOMB2ahN3k+Fgp8cQvZLCK0GB=g@mail.gmail.com>
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Hi!
Jumping in on this, since it has come up many times but is without a
solution so far: the issue is that the color code is now mapped onto a
straight color bar, not a circle. At the same time, it is not documented
what color refers to which angle. That makes it very difficult to work with
this kind of color bar. It would be very helpful to reintroduce the circle,
and to explicitly document how angles are mapped to colors.
Thank you!
Caspar

On Thu, May 21, 2020 at 16:41 Douglas N. Greve <dgreve@mgh.harvard.edu>
wrote:

> When you say it is "linear" do you mean it does not wrap-around?
>
>
>
> On 5/19/2020 8:47 PM, Devavrat Vartak PhD wrote:
>
>         External Email - Use Caution
> Hello freesurfer community,
>
> I am trying to setup a retinotopy pipeline. I have analysed pRF data
> generating polar angle and eccentricity maps which I project onto an
> inflated surface / flattened surface in freeview.
>
> Is there a way to display a circular/cyclic colour map (for the polar
> angle data) in the overlay screen?, the existing 'colour wheel' option
> seems to be linear?
>
>
> Thank you!
>
> Best,
> DV
>
>
>
> _______________________________________________
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Message: 10
Date: Fri, 22 May 2020 14:33:44 +0200
From: Remi Gau <remi_gau@hotmail.com>
Subject: [Freesurfer] OHBM Brainhack registration is open!
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Message: 11
Date: Fri, 22 May 2020 13:47:39 +0000
From: "Camerino, I.L. (Ileana)" <I.Camerino@psych.ru.nl>
Subject: [Freesurfer] FW: Motion correction files contain 0 0 0 1
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
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From: "Camerino, I.L. (Ileana)" <I.Camerino@psych.ru.nl>
Date: Friday, 22 May 2020 at 14:27
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Motion correction files contain 0 0 0 1


Dear Freesurfer developpers,

I performed tractography analyses by using tracula implemented in freesurfer version 6.0.

I am performing the quality check as suggested in: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs. The problem is that all my motion files (for all subjects) contain the same values: 0 0 0 1.

I checked the archive but I could not find an answer to a similar question in there.

Please could you suggest me what went wrong? is it possible to recalculate only the motion estimation without having to run again recon all?
Thank you in advance



Ileana Camerino

PhD candidate
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognition

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