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Today's Topics:

   1. missing files in he v6 fsaverage on the Martinos  Center
      network (Douglas N. Greve)
   2. Re: Group Analysis Covariates (Douglas N. Greve)
   3. Re: Freesurfer 7.1 hires error (Douglas N. Greve)
   4. Re: LGI problem (Angela Favaro)
   5. Are my slice-time corrected files being used in
      selxavg3-sess? (Mcnorgan, Christopher)
   6. freeview is RAM greedy in version 7.1.0 (Anton?n ?koch)
   7. Re: freeview is RAM greedy in version 7.1.0 (Ruopeng Wang)
   8. Re: freeview is RAM greedy in version 7.1.0 (fsbuild)
   9. Re: freeview is RAM greedy in version 7.1.0 (Anton?n ?koch)
  10. Command cannot recognise session from sessid file
      (Marco Ninghetto)
  11. Longitudinal processing with freesurfer 7.1.0 (Angela Favaro)
  12. Re: freeview is RAM greedy in version 7.1.0 (Ruopeng Wang)


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

Message: 1
Date: Fri, 22 May 2020 12:02:56 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: [Freesurfer] missing files in he v6 fsaverage on the Martinos
        Center network
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <fb258210-bab9-dfe2-2039-4ead9e6a64dc@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"; format=flowed

Sorry, I accidentally deleted some files from the v6 fsaverage located
on the Martinos Center network. They have been restored, but it might
have caused your recon-all process to fail if you had one running last
night.

Have a good weekend
doug




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

Message: 2
Date: Fri, 22 May 2020 12:14:06 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Group Analysis Covariates
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <23e96fb1-f2b5-8e23-112a-2d0cb9ec3d88@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Sorry, I left out a key ingredient. Use pmf below

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],:);
e = y - yhat;
pmf = yhat+e;



On 5/22/2020 11:55 AM, Hua, Jessica wrote:
>
> ????????External Email - Use Caution
>
> I just tried the revised code, and it gave me the adjusted values for
> each cluster by group. Is there a way to get covariate adjusted?
> values for each participant?
>
> ---
>
> Jessica Hua, M.A.
> Cognitive and Emotional Control Lab
> Doctoral Candidate?Clinical Psychology
> University of Missouri
>
> ------------------------------------------------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of
> freesurfer-request@nmr.mgh.harvard.edu
> <freesurfer-request@nmr.mgh.harvard.edu>
> *Sent:* Friday, May 22, 2020 10:09 AM
> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Freesurfer Digest, Vol 195, Issue 54
> 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: 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
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -------------- next part --------------
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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,
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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/ <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
> <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
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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>
> Content-Type: text/plain; charset="utf-8"
>
> ??????? External Email - Use Caution
>
> 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
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing
> listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwMDaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=ZG0QTsrPnW9eG-z3AwEI4cv-XX35unrH3etOYRJoyZQ&s=hVKW4UfzYP0jPJM1fTz38lH5pcJt1mCFU-DsHtx5O98&e=>
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=ZG0QTsrPnW9eG-z3AwEI4cv-XX35unrH3etOYRJoyZQ&s=hVKW4UfzYP0jPJM1fTz38lH5pcJt1mCFU-DsHtx5O98&e=
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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!
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> <DB7PR06MB41710FBC04D27C2F0F3DEF93F0B40@DB7PR06MB4171.eurprd06.prod.outlook.com>
>
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>
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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>
> Message-ID: <A9DADE70-B85C-470B-A5EB-03F53DBA7133@psych.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> ??????? External Email - Use Caution
>
>
> 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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>
> End of Freesurfer Digest, Vol 195, Issue 54
> *******************************************
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------------------------------

Message: 3
Date: Fri, 22 May 2020 12:23:07 -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: <22d1b406-0fe4-e319-2ed1-e6efa974fd1b@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Hi Richard, the conclusion among us is that you have run out of memory.
I'm not sure how much you will need, but with both hires and FLAIR, it
will be a lot

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

Message: 4
Date: Fri, 22 May 2020 18:59:13 +0200
From: Angela Favaro <angela.favaro@unipd.it>
Subject: Re: [Freesurfer] LGI problem
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <707B847E-E62D-443C-B3ED-D4DE076A5A8A@unipd.it>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi Doug,
I had the identical problem (failure at segmentation stage, as described below) in 4 subjects of my dataset. I have no possibility to run analyses on a linux machine?
Since all 4 subjects had no problem using Freesurfer 6, is it so wrong to use freesurfer 6 only for these 4 subjects?
Or have you any other suggestions?

Thank you for any help

Angela




> Il giorno 15 mag 2020, alle ore 23:26, Angela Favaro <angela.favaro@unipd.it> ha scritto:
>
>         External Email - Use Caution       
>
>
> Hi doug,
> I tried to re-run 3 or 4 times and always failed at the segmentation stage?
> I have no linux machine, but I can try in a mac computer with a different OS...
> thank you!
>
> Angela
>
>
>> Il giorno 15 mag 2020, alle ore 23:08, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> ha scritto:
>>
>> Hi Angela, I cannot replicate this error. If you re-run, does it always exit with error? You can try this quickly be running
>>
>> setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/Aachen
>> cd /Users/angelafavaro/Desktop/Aachen/subj220/mri
>> mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Users/angelafavaro/Desktop/Aachen/subj220/mri/transforms/cc_up.lta subj220
>>
>> One factor may be that I'm using CentOS and not Mac. Do you have a linux machine you can try it on?
>>
>>
>>
>> On 5/15/2020 10:59 AM, Angela Favaro wrote:
>>>         External Email - Use Caution       
>>>
>>> I have uploaded to you the data using the Martinos Center FileDrop
>>> Hope is a good option for you
>>>
>>> Thank you
>>> Angela
>>>
>>>> Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro <angela.favaro@unipd.it <mailto:angela.favaro@unipd.it>> ha scritto:
>>>>
>>>>         External Email - Use Caution       
>>>>
>>>>
>>>> Hi Doug,
>>>> I have some problem in uploading my subj.tar.gz using ftp. I am using a MacOs Catalina and, although I am able to connect to the FTP site and open the incoming window (also in binary mode), commands are not working...
>>>>
>>>> I am trying to overcome the problem.
>>>> Is there any other method to transfer the data set?
>>>> Thank you
>>>>
>>>> Angela
>>>>
>>>>> Il giorno 15 mag 2020, alle ore 00:15, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> ha scritto:
>>>>>
>>>>> Hmmm, I don't know. Can you upload the data set? Follow these instructions
>>>>>
>>>>> 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 <http://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 5/14/2020 5:03 PM, Angela Favaro wrote:
>>>>>>         External Email - Use Caution       
>>>>>>
>>>>>> Thank you Doug!
>>>>>> It works! Great!
>>>>>>
>>>>>>
>>>>>> I have another problem: I am reprocessing all my database with freesurfer 7.1.0, but in one subject segmentation failed.
>>>>>> I had no problem with this subjects using freesurfer 6
>>>>>> What can be the problem?
>>>>>>
>>>>>> I attach the log
>>>>>>
>>>>>> Thank you for any help!
>>>>>>
>>>>>> Angela
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> ha scritto:
>>>>>>>
>>>>>>>
>>>>>>> Someone just pointed out that I posted the wrong file. Here is the correct one. Copy it to the same folder
>>>>>>>
>>>>>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m <https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m>
>>>>>>>
>>>>>>>
>>>>>>> On 5/13/2020 11:01 PM, Douglas N. Greve wrote:
>>>>>>>>
>>>>>>>> Download this file
>>>>>>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m <https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m>
>>>>>>>> and copy it into $FREESURFER_HOME/matlab
>>>>>>>> and rerun. Let me know if that fixes it.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 5/13/2020 5:57 PM, Angela Favaro wrote:
>>>>>>>>>         External Email - Use Caution       
>>>>>>>>>
>>>>>>>>> Please find attached the log
>>>>>>>>> Thank you
>>>>>>>>> Angela
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> ha scritto:
>>>>>>>>>>
>>>>>>>>>> Are you running this from recon-all? If so send the recon-all.log. If from the command line, send the command-line and all terminal output
>>>>>>>>>>
>>>>>>>>>> On 5/13/2020 5:28 PM, Angela Favaro wrote:
>>>>>>>>>>>         External Email - Use Caution       
>>>>>>>>>>>
>>>>>>>>>>> Hi Doug!
>>>>>>>>>>> yes, it run under version 6!
>>>>>>>>>>> Please let me know if it is something that can be solved
>>>>>>>>>>> Thank you
>>>>>>>>>>> Angela
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> ha scritto:
>>>>>>>>>>>>
>>>>>>>>>>>> Does it run under version 6? We are not really supporting lGI anymore, but maybe we can get it to work
>>>>>>>>>>>>
>>>>>>>>>>>> On 5/13/2020 4:24 PM, Angela Favaro wrote:
>>>>>>>>>>>>>         External Email - Use Caution       
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Hi all,
>>>>>>>>>>>>> I am using the new version of Freesurfer 7.1.0
>>>>>>>>>>>>> And I am finding problems in running gyrification analysis.
>>>>>>>>>>>>> I have Matlab 2016a (and 2019b) with the toolbox image processing
>>>>>>>>>>>>>
>>>>>>>>>>>>> The error is after the command find_corresponding_center_FSformat
>>>>>>>>>>>>>
>>>>>>>>>>>>> Matlab seems to start, but then the following message appears:
>>>>>>>>>>>>>
>>>>>>>>>>>>> >> Warning: Input argument must be a string.
>>>>>>>>>>>>> > In ver (line 41)
>>>>>>>>>>>>>   In freesurfer_read_surf (line 70)
>>>>>>>>>>>>>   In find_corresponding_center_FSformat (line 26)
>>>>>>>>>>>>> Error using fprintf
>>>>>>>>>>>>> Function is not defined for 'struct' inputs.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Error in freesurfer_read_surf (line 70)
>>>>>>>>>>>>> fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
>>>>>>>>>>>>>
>>>>>>>>>>>>> Error in find_corresponding_center_FSformat (line 26)
>>>>>>>>>>>>> [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
>>>>>>>>>>>>> 
>>>>>>>>>>>>> >>
>>>>>>>>>>>>> ERROR: find_corresponding_center_FSformat did not complete successfully!
>>>>>>>>>>>>>
>>>>>>>>>>>>> I tried with both the Matlab version, but the error is the same
>>>>>>>>>>>>> Any help is appreciated. Thank you so much
>>>>>>>>>>>>>
>>>>>>>>>>>>> Angela
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> 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>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> 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>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> 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>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> 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>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> 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>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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>
>>>>>
>>>>> _______________________________________________
>>>>> 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>
>>>> _______________________________________________
>>>> 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>
>>>
>>>
>>> _______________________________________________
>>> 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>
>> _______________________________________________
>> Freesurfer mailing list
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>
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Message: 5
Date: Fri, 22 May 2020 17:35:40 +0000
From: "Mcnorgan, Christopher" <cpmcnorg@buffalo.edu>
Subject: [Freesurfer] Are my slice-time corrected files being used in
        selxavg3-sess?
To: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <97D1FD5C-18DE-4A8C-A7F9-3292FBFCED5C@buffalo.edu>
Content-Type: text/plain; charset="us-ascii"

        External Email - Use Caution       

Hi all,
There was some ambiguity in communication from a previous MR technician regarding the slice ordering in our BOLD data.
preproc-sess was applied to our data:
preproc-sess -sf SUBJECTS -surface fsaverage lhrh -per-run -fsd bold -sliceorder up -fwhm 4
I then ran selxavg3-sess on the data, followed by mri_glmfit to produce contrast maps

As an experiment, I deleted the fmcpr.up.* data, and re-ran preproc-sess, this time specifying sliceorder down:
preproc-sess -sf SUBJECTS -surface fsaverage lhrh -per-run -fsd bold -sliceorder down -fwhm 4
After re-running selxavg3-sess and mri_glmfit on the reverse-stc-corrected data, the contrast maps were identical, which seemed peculiar, given that the slice time corrections for a 2-second TR were in the opposite direction.

I note that when I run selxavg3-sess, it generates a set of fmcpr.sm4 files, and I suspect that the GLM is run on those novel non-stc files. Is there a switch I am missing in the call to selxavg3-sess or mkanalysis-sess that will ensure that will allow me to ensure that the GLM is run on fmcpr.[STC].sm4.fsaverage.[rl]h.nii.gz?

Thanks
/**********************************************
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo,
* The State University of New York
* http://ccnlab.buffalo.edu/
* Office: 716.645.0236
* Lab: 716.645.0222
**********************************************/

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Message: 6
Date: Fri, 22 May 2020 20:42:30 +0200
From: Anton?n ?koch <ansk@ikem.cz>
Subject: [Freesurfer] freeview is RAM greedy in version 7.1.0
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <1034089660-17457@posta.ikem.cz>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Dear experts,


I want to use freeview for viewing Gordon surface labels on inflated surface with custom coloring. I am using commandline like


freeview -viewport 3d -f $SUBJECTS_DIR/fsaverage/lh.inflated:label=L_Auditory_10.label:label_color=255,191,0:label=L_Auditory_11.label:label_color=255,140,0....etc (the commandline contains 161 labels)



I observe that freeview in version 7.1.0 consumes much more RAM than in version 6.0, using identical command line.

The difference is enormous: While in version 6.0 freeview consumes 1.5 GB RAM to successfully display all labels, freeview in version 7.1.0 consumes all memory available on the server (32 GB RAM) while only about 30 labels are actually loaded (then server start to swap and I am forced to kill freeview process).


Are you aware of such behaviour?



Regards,



Antonin Skoch


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Message: 7
Date: Fri, 22 May 2020 14:49:40 -0400
From: Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freeview is RAM greedy in version 7.1.0
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <FFFC8368-69BB-439B-9CE0-7BDA2B0C1DB5@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Antonin,

Thanks for the report. We?ll look into this.

Best,
Ruopeng

> On May 22, 2020, at 2:42 PM, Anton?n ?koch <ansk@ikem.cz> wrote:
>
>         External Email - Use Caution       
>
>
> Dear experts,
>
> I want to use freeview for viewing Gordon surface labels on inflated surface with custom coloring. I am using commandline like
>
> freeview -viewport 3d -f $SUBJECTS_DIR/fsaverage/lh.inflated:label=L_Auditory_10.label:label_color=255,191,0:label=L_Auditory_11.label:label_color=255,140,0....etc (the commandline contains 161 labels)
>
> I observe that freeview in version 7.1.0 consumes much more RAM than in version 6.0, using identical command line.
> The difference is enormous: While in version 6.0 freeview consumes 1.5 GB RAM to successfully display all labels, freeview in version 7.1.0 consumes all memory available on the server (32 GB RAM) while only about 30 labels are actually loaded (then server start to swap and I am forced to kill freeview process).
>
> Are you aware of such behaviour?
>
> Regards,
>
> Antonin Skoch
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 8
Date: Sat, 23 May 2020 03:03:52 +0200
From: fsbuild <fsbuild@contbay.com>
Subject: Re: [Freesurfer] freeview is RAM greedy in version 7.1.0
To: freesurfer@nmr.mgh.harvard.edu
Cc: ansk@ikem.cz
Message-ID: <1590195832.5ec876786a050@trashmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Please also let us know the version of the OS you are comparing running both the 6.0.0 and 7.1.0 release on.
- R.

On May 22, 2020, at 14:49, Ruopeng Wang &lt;rpwang@nmr.mgh.harvard.edu&gt; wrote:Hi Antonin,Thanks for the report. We?ll look into this.Best,RuopengOn May 22, 2020, at 2:42 PM, Anton?n ?koch &lt;ansk@ikem.cz&gt; wrote:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;External Email - Use Caution&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Dear experts,I want to use freeview for viewing Gordon surface labels on inflated surface with custom coloring. I am using commandline likefreeview -viewport 3d -f $SUBJECTS_DIR/fsaverage/lh.inflated:label=L_Auditory_10.label:label_color=255,191,0:label=L_Auditory_11.label:label_color=255,140,0....etc (the commandline contains 161 labels)I observe that freeview in version 7.1.0 consumes much more RAM than in version 6.0, using identical command line.&nbsp;The difference is enormous: While in version 6.0 freeview consumes 1.5 GB RAM to successfully display all labels, freeview in version 7.1.0 consumes all memory available on the server (32 GB RAM) while only about 30 labels are actually loaded (then server start to swap and I am forced to kill freeview process).Are you aware of such behaviour?Regards,Antonin Skoch_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 9
Date: Sat, 23 May 2020 08:08:48 +0200
From: Anton?n ?koch <ansk@ikem.cz>
Subject: Re: [Freesurfer] freeview is RAM greedy in version 7.1.0
To: fsbuild <fsbuild@contbay.com>, freesurfer@nmr.mgh.harvard.edu
Message-ID: <1075843798-25980@posta.ikem.cz>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi,


I am testing version


freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

against version
freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b

My system is:
Debian GNU/Linux 8.9 (jessie)


I tried to merge labels corresponding the same network into one, i.e. I have now only 11 labels, comprising almost all cortical surface. This seems to spare a bit RAM, but still it required approx. 38 GB RAM to load all labels.


Antonin



 Od:   fsbuild <fsbuild@contbay.com>
 Komu:   <freesurfer@nmr.mgh.harvard.edu>
 Kopie:   <ansk@ikem.cz>
 Odesl?no:   23.5.2020 3:03
 P?edm?t:   Re: [Freesurfer] freeview is RAM greedy in version 7.1.0

Please also let us know the version of the OS you are comparing running both the 6.0.0 and 7.1.0 release on.


- R.



On May 22, 2020, at 14:49, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu> wrote:


Hi Antonin,


Thanks for the report. We?ll look into this.


Best,
Ruopeng



On May 22, 2020, at 2:42 PM, Anton?n ?koch <ansk@ikem.cz> wrote:



????????External Email - Use Caution????????


Dear experts,


I want to use freeview for viewing Gordon surface labels on inflated surface with custom coloring. I am using commandline like


freeview -viewport 3d -f $SUBJECTS_DIR/fsaverage/lh.inflated:label=L_Auditory_10.label:label_color=255,191,0:label=L_Auditory_11.label:label_color=255,140,0....etc (the commandline contains 161 labels)



I observe that freeview in version 7.1.0 consumes much more RAM than in version 6.0, using identical command line.?

The difference is enormous: While in version 6.0 freeview consumes 1.5 GB RAM to successfully display all labels, freeview in version 7.1.0 consumes all memory available on the server (32 GB RAM) while only about 30 labels are actually loaded (then server start to swap and I am forced to kill freeview process).


Are you aware of such behaviour?



Regards,



Antonin Skoch


_______________________________________________
Freesurfer mailing list
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: 10
Date: Sat, 23 May 2020 10:28:23 +0200
From: Marco Ninghetto <m.ninghetto@nencki.edu.pl>
Subject: [Freesurfer] Command cannot recognise session from sessid
        file
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAAwR5PxbJHRpEj7Aoy_pXB8j=VB=p9XB9bcyrh4nQmmohQcg9Q@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

  Dear experts,
I looked through your mailing list, but I cannot find any question like
mine.
When I run whatever command in my analysis for retinotopy, I have to
specify subject after subject using:

-s subj001 -s subj002 -s subj00x

and so on. To avoid that, inside my project directory, I have the "sessid"
(actually two sessid files) file in which are listed all the names of the
subjects.
I don't know why, when I try to run:

-sf sessid1

I get the error, like (random command from my pipeline):

brain@neurodebian:/media/main/fs_pRFs_functionals$ isxconcat-sess -sf
sessid1 -a rtopy.fsaverage.lh/ -call -o retgroup_ng
ERROR: finding sessions
       ERROR: cound not find session SUBJ02NG

I tried to write differently inside the sessid file, I tried to use the
name of the structural folders instead of the functional ones, but nothing
seems to work.
My sessid file is something like this:

SUBJ02NG
SUBJ06NG
SUBJ07NG
SUBJ08NG

and so on.Each subject's session folder name:

SUBJ02NG
SUBJ06NG
SUBJ07NG
SUBJ08NG

The names listed are the same for the name of the session folder for each
subject, but still, FS tells me that it cannot find the session.

[image: tree.png]
Inside each subject folder, there is the  "bold" folder and inside that,
together with the runs folders, there is the analysis folder.

Any idea on what I'm doing wrong?
Thank you so much,
Marco
--
---------------------------------------------------
Marco Ninghetto, PhD candidate
Laboratory of Neuroplasticity
Nencki Institute of Experimental Biology
Polish Academy of Sciences
3 Pasteur Street, 02-093 Warsaw, Poland
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main
    |reconstructed
                |sub_02
                |sub-03
                |sub-06
                ...
    |
    |functionals
                |sessid1
                |SUBJ02NG
                |SUBJ06NG
                |SUBJ010NG
                |sessid2
                |SUBJ03YG
                |SUBJ04YG
                ...
                |rtopy.anal.folder


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

Message: 11
Date: Sat, 23 May 2020 10:41:02 +0200
From: Angela Favaro <angela.favaro@unipd.it>
Subject: [Freesurfer] Longitudinal processing with freesurfer 7.1.0
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <4132529B-6331-4E82-B9F0-1F7BAB060658@unipd.it>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Dear Freesurfer experts,
I am trying to process a dataset with a longitudinal design.
However, after building the template, at the ?recon-all -long? command I got this error:

longmc Done
/Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri
\n cp -f --preserve=timestamps /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz ./brainmask_template4.mgz \n
cp: illegal option -- -
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
       cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory
ERROR:
Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 CEST 2020

For more details, see the log file /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log


Thank you for any help!

Angela
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Message: 12
Date: Sat, 23 May 2020 09:03:08 -0400
From: Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freeview is RAM greedy in version 7.1.0
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: fsbuild <fsbuild@contbay.com>
Message-ID: <70BA8E7A-F758-4577-9813-E75D3CD35C57@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Antonin,

I?ve fixed the bug. You can download the latest freeview build here:
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview <https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview>

Best,
Ruopeng

> On May 23, 2020, at 2:08 AM, Anton?n ?koch <ansk@ikem.cz> wrote:
>
>         External Email - Use Caution       
>
>
> Hi,
>
> I am testing version
>
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> against version
> freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
> My system is:
> Debian GNU/Linux 8.9 (jessie)
>
> I tried to merge labels corresponding the same network into one, i.e. I have now only 11 labels, comprising almost all cortical surface. This seems to spare a bit RAM, but still it required approx. 38 GB RAM to load all labels.
>
> Antonin
>
>
> Od: fsbuild <fsbuild@contbay.com>
> Komu: <freesurfer@nmr.mgh.harvard.edu>
> Kopie: <ansk@ikem.cz>
> Odesl?no: 23.5.2020 3:03
> P?edm?t: Re: [Freesurfer] freeview is RAM greedy in version 7.1.0
>
> Please also let us know the version of the OS you are comparing running both the 6.0.0 and 7.1.0 release on.
>
> - R.
>
>> On May 22, 2020, at 14:49, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu> wrote:
>>
>> Hi Antonin,
>>
>> Thanks for the report. We?ll look into this.
>>
>> Best,
>> Ruopeng
>>
>>> On May 22, 2020, at 2:42 PM, Anton?n ?koch <ansk@ikem.cz <mailto:ansk@ikem.cz>> wrote:
>>>
>>>         External Email - Use Caution       
>>>
>>>
>>> Dear experts,
>>>
>>> I want to use freeview for viewing Gordon surface labels on inflated surface with custom coloring. I am using commandline like
>>>
>>> freeview -viewport 3d -f $SUBJECTS_DIR/fsaverage/lh.inflated:label=L_Auditory_10.label:label_color=255,191,0:label=L_Auditory_11.label:label_color=255,140,0....etc (the commandline contains 161 labels)
>>>
>>> I observe that freeview in version 7.1.0 consumes much more RAM than in version 6.0, using identical command line.
>>> The difference is enormous: While in version 6.0 freeview consumes 1.5 GB RAM to successfully display all labels, freeview in version 7.1.0 consumes all memory available on the server (32 GB RAM) while only about 30 labels are actually loaded (then server start to swap and I am forced to kill freeview process).
>>>
>>> Are you aware of such behaviour?
>>>
>>> Regards,
>>>
>>> Antonin Skoch
>>>
>>> _______________________________________________
>>> 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
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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*******************************************