Re: [Freesurfer] FreeSurfer 6 Error On Macbook M2

[fsbuild]

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The graphics packages used in Freeview have changed since the Freesurfer
 6 release, and also how they and the other Intel binaries are compiled for 
current 
versions of MacOS.  So a run time error, e.g., segfault, could occur when 
running under Rosetta on a silicon Mac. 

Please try one of the current MacOS Freesurfer 7 releases from the download 
page, 
  surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads
  
- R.




On 7/12/23 08:35, Prathifkumar, Thuvaragan 
(thuvaragan.prathifku...@sri.utoronto.ca) wrote:







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Caution

  
Hello,



I recently installed Free Surfer 6, and was following this 
guide:MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
https://secure-web.cisco.com/1NRP4tsM45lW3UFB3Jf_X6qXB5GUcDVNjcJDXPLcS2Shw2L-nOknee2bklELFhm3yl9E7Rg_e1a6Z_SQ2ZfTnwuQEKG5-KnkPaZcBauyjIwEOwRPMYqb8HYwMLBSgrsvfhb0GZp7WdPb75RgJdnnym7zlQQfS4S3YzdfJ0fgVTeHKHrhxNgPSaGawnn6Sh52Pg1ABE8N_OPg4P_vFqD7hjK-RxKVLT8Jib-xqRRcD3Jidq9IG95oj8STTmA080TSMeRYUyj01iX_iV4yIxwEinr-eAfaM7UrQ73Zw4byptTk6RqKYMulRZOkN3PhQvrcEfKaxS0YgIqgq9Tojw-7x5A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel6downloads



I got till Example 3, and Example 3 works perfectly. As attached as an image in 
this email.



For some reason, in Example 4, to open the GUI (freeview) based on 
thefully
 recon-ed subject bert in Example 3, I get an error and I'm not sure 
why. Why does that happen? Is it due to compatibility issues with the 
apple silicon chip? The error message
 is attached as an image in this email as well.



Any help is appreciated. Thank you.
  

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Re: [Freesurfer] Freesurfer 6 current state of submillimeter processing

[Greve, Douglas N.,Ph.D.]

Use the patch

On 10/10/2019 11:07 AM, Daniel Westfall wrote:

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Hi Everyone,

I just wanted to double check the current state of processing T3 submillimeter 
data with Freesurfer 6. We have two studies: one with 0.9 mm isotropic and the 
other with 0.8 mm isotropic. After doing some investigating, I found that there 
is either the option to run recon-all with the -hires flag 
(https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon) or I found that 
on the release notes for Freesurfer 6 there is a patch 
(https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/). I 
would guess that the patch method is the most recent version that I should use?

Thank you for the assistance.

Best,
Daniel



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[Freesurfer] Freesurfer 6 current state of submillimeter processing

[Daniel Westfall]

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Hi Everyone,

I just wanted to double check the current state of processing T3
submillimeter data with Freesurfer 6. We have two studies: one with 0.9 mm
isotropic and the other with 0.8 mm isotropic. After doing some
investigating, I found that there is either the option to run recon-all
with the -hires flag (
https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon) or I found
that on the release notes for Freesurfer 6 there is a patch (
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/). I
would guess that the patch method is the most recent version that I should
use?

Thank you for the assistance.

Best,
Daniel
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Re: [Freesurfer] FreeSurfer 6 vertex-wise cortical volume computation details?

[Tim Schäfer]

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Hi Doug,

thanks a lot for the clarification!

Tim

> On August 16, 2019 at 6:19 PM "Greve, Douglas N.,Ph.D." 
>  wrote:
> 
> 
> The algorithm in v6 is not as you describe. The function below is based 
> on Anderson Winkler's (cc'ed) work.
> 
> /*!
>    \fn MRISvolumeTH3(MRIS *w, MRIS *p, MRI *vol)
>    \brief Compute vertex-wise volume based on dividing each obliquely 
> truncated
>    trilateral pyramid into three tetrahedra. Based on Anderson M. Winkler's
>    srf2vol matlab script.
>    \params w is white surface, p is pial. Output is an MRI struct of 
> size nvertices
>   */
> MRI *MRISvolumeTH3(MRIS *w, MRIS *p, MRI *vol, MRI *mask, double *totvol)
> {
>    MRI *facevol;
>    int nthface, v1, v2, v3;
>    int vno, nfacenbrs, nthfacenbr, nbrfaceno;
>    MATRIX *Ap, *Bp, *Cp, *Aw, *Bw, *Cw;
>    MATRIX *C1 = NULL, *C2 = NULL, *C3 = NULL;
>    double T1, T2, T3, volsum, dval, vtxvolsum;
>    VERTEX *vtx;
> 
>    if (!vol) vol = MRIalloc(w->nvertices, 1, 1, MRI_FLOAT);
> 
>    Ap = MatrixAlloc(3, 1, MATRIX_REAL);
>    Bp = MatrixAlloc(3, 1, MATRIX_REAL);
>    Cp = MatrixAlloc(3, 1, MATRIX_REAL);
>    Aw = MatrixAlloc(3, 1, MATRIX_REAL);
>    Bw = MatrixAlloc(3, 1, MATRIX_REAL);
>    Cw = MatrixAlloc(3, 1, MATRIX_REAL);
> 
>    facevol = MRIalloc(w->nfaces, 1, 1, MRI_FLOAT);
>    volsum = 0.0;
>    for (nthface = 0; nthface < w->nfaces; nthface++) {
>      MRIsetVoxVal(facevol, nthface, 0, 0, 0, 0.0);
>      if (w->faces[nthface].ripflag) continue;
> 
>      v1 = w->faces[nthface].v[0];
>      v2 = w->faces[nthface].v[1];
>      v3 = w->faces[nthface].v[2];
> 
>      Ap->rptr[1][1] = p->vertices[v1].x;
>      Ap->rptr[2][1] = p->vertices[v1].y;
>      Ap->rptr[3][1] = p->vertices[v1].z;
>      Bp->rptr[1][1] = p->vertices[v2].x;
>      Bp->rptr[2][1] = p->vertices[v2].y;
>      Bp->rptr[3][1] = p->vertices[v2].z;
>      Cp->rptr[1][1] = p->vertices[v3].x;
>      Cp->rptr[2][1] = p->vertices[v3].y;
>      Cp->rptr[3][1] = p->vertices[v3].z;
> 
>      Aw->rptr[1][1] = w->vertices[v1].x;
>      Aw->rptr[2][1] = w->vertices[v1].y;
>      Aw->rptr[3][1] = w->vertices[v1].z;
>      Bw->rptr[1][1] = w->vertices[v2].x;
>      Bw->rptr[2][1] = w->vertices[v2].y;
>      Bw->rptr[3][1] = w->vertices[v2].z;
>      Cw->rptr[1][1] = w->vertices[v3].x;
>      Cw->rptr[2][1] = w->vertices[v3].y;
>      Cw->rptr[3][1] = w->vertices[v3].z;
> 
>      // As the Ap is the common vertex for all three, it can be used as 
> the origin.
>      Bp = MatrixSubtract(Bp, Ap, Bp);
>      Cp = MatrixSubtract(Cp, Ap, Cp);
>      Aw = MatrixSubtract(Aw, Ap, Aw);
>      Bw = MatrixSubtract(Bw, Ap, Bw);
>      Cw = MatrixSubtract(Cw, Ap, Cw);
> 
>      // The next lines compute the volume for each, using a scalar 
> triple product:
>      C1 = VectorCrossProduct(Bw, Cw, C1);
>      T1 = fabs(V3_DOT(Aw, C1));
> 
>      C2 = VectorCrossProduct(Cp, Bw, C2);
>      T2 = fabs(V3_DOT(Bp, C2));
> 
>      C3 = VectorCrossProduct(Cw, Bw, C3);
>      T3 = fabs(V3_DOT(Cp, C3));
> 
>      dval = (T1 + T2 + T3) / 6.0;
>      MRIsetVoxVal(facevol, nthface, 0, 0, 0, dval);
>      volsum += dval;
>    }
>    printf("Total face volume %g\n", volsum);
> 
>    vtxvolsum = 0;
>    for (vno = 0; vno < w->nvertices; vno++) {
>      vtx = >vertices[vno];
>      if (vtx->ripflag) continue;
>      if (mask && MRIgetVoxVal(mask, vno, 0, 0, 0) < 0.5) continue;
>      nfacenbrs = w->vertices_topology[vno].num;
>      volsum = 0.0;
>      for (nthfacenbr = 0; nthfacenbr < nfacenbrs; nthfacenbr++) {
>    nbrfaceno = w->vertices_topology[vno].f[nthfacenbr];
>    volsum += (MRIgetVoxVal(facevol, nbrfaceno, 0, 0, 0) / 3.0);
>    // divide by 3 because each face participates in 3 vertices
>      }
>      MRIsetVoxVal(vol, vno, 0, 0, 0, volsum);
>      vtxvolsum += volsum;
>    }
>    printf("Total vertex volume %g (mask=%d)\n", vtxvolsum, mask == NULL);
>    *totvol = vtxvolsum;
> 
>    MRIfree();
>    MatrixFree();
>    MatrixFree();
>    MatrixFree();
>    MatrixFree();
>    MatrixFree();
>    MatrixFree();
>    MatrixFree();
>    MatrixFree();
>    MatrixFree();
> 
>    return (vol);
> }
> 
> 
> On 8/15/2019 4:15 AM, Tim Schäfer wrote:
> >  External Email - Use Caution
> >
> > Dear FreeSurfer experts,
> >
> > can anybody refer me to a publication that explains in detail how 
> > vertex-wise cortical volume (the data in /surf/?h.volume) is 
> > computed in FreeSurfer 6?
> >
> > My understanding is the following:
> > * area is computed as 1/3 the area of all triangles meeting at that vertex.
> > * thickness is the shortest distance from the vertex (at white surface) to 
> > any vertex on pial, then the other way around from that pial vertex, 
> > divided by two.
> > * volume is area * thickness
> >
> > Is that true, and where can I read up on it?
> >
> > Thanks,
> >
> > Tim
> >
> > --
> > Dr. Tim Schäfer
> > Postdoc Computational Neuroimaging
> > Department of Child and Adolescent Psychiatry, 

Re: [Freesurfer] FreeSurfer 6 vertex-wise cortical volume computation details?

[Greve, Douglas N.,Ph.D.]

The algorithm in v6 is not as you describe. The function below is based 
on Anderson Winkler's (cc'ed) work.

/*!
   \fn MRISvolumeTH3(MRIS *w, MRIS *p, MRI *vol)
   \brief Compute vertex-wise volume based on dividing each obliquely 
truncated
   trilateral pyramid into three tetrahedra. Based on Anderson M. Winkler's
   srf2vol matlab script.
   \params w is white surface, p is pial. Output is an MRI struct of 
size nvertices
  */
MRI *MRISvolumeTH3(MRIS *w, MRIS *p, MRI *vol, MRI *mask, double *totvol)
{
   MRI *facevol;
   int nthface, v1, v2, v3;
   int vno, nfacenbrs, nthfacenbr, nbrfaceno;
   MATRIX *Ap, *Bp, *Cp, *Aw, *Bw, *Cw;
   MATRIX *C1 = NULL, *C2 = NULL, *C3 = NULL;
   double T1, T2, T3, volsum, dval, vtxvolsum;
   VERTEX *vtx;

   if (!vol) vol = MRIalloc(w->nvertices, 1, 1, MRI_FLOAT);

   Ap = MatrixAlloc(3, 1, MATRIX_REAL);
   Bp = MatrixAlloc(3, 1, MATRIX_REAL);
   Cp = MatrixAlloc(3, 1, MATRIX_REAL);
   Aw = MatrixAlloc(3, 1, MATRIX_REAL);
   Bw = MatrixAlloc(3, 1, MATRIX_REAL);
   Cw = MatrixAlloc(3, 1, MATRIX_REAL);

   facevol = MRIalloc(w->nfaces, 1, 1, MRI_FLOAT);
   volsum = 0.0;
   for (nthface = 0; nthface < w->nfaces; nthface++) {
     MRIsetVoxVal(facevol, nthface, 0, 0, 0, 0.0);
     if (w->faces[nthface].ripflag) continue;

     v1 = w->faces[nthface].v[0];
     v2 = w->faces[nthface].v[1];
     v3 = w->faces[nthface].v[2];

     Ap->rptr[1][1] = p->vertices[v1].x;
     Ap->rptr[2][1] = p->vertices[v1].y;
     Ap->rptr[3][1] = p->vertices[v1].z;
     Bp->rptr[1][1] = p->vertices[v2].x;
     Bp->rptr[2][1] = p->vertices[v2].y;
     Bp->rptr[3][1] = p->vertices[v2].z;
     Cp->rptr[1][1] = p->vertices[v3].x;
     Cp->rptr[2][1] = p->vertices[v3].y;
     Cp->rptr[3][1] = p->vertices[v3].z;

     Aw->rptr[1][1] = w->vertices[v1].x;
     Aw->rptr[2][1] = w->vertices[v1].y;
     Aw->rptr[3][1] = w->vertices[v1].z;
     Bw->rptr[1][1] = w->vertices[v2].x;
     Bw->rptr[2][1] = w->vertices[v2].y;
     Bw->rptr[3][1] = w->vertices[v2].z;
     Cw->rptr[1][1] = w->vertices[v3].x;
     Cw->rptr[2][1] = w->vertices[v3].y;
     Cw->rptr[3][1] = w->vertices[v3].z;

     // As the Ap is the common vertex for all three, it can be used as 
the origin.
     Bp = MatrixSubtract(Bp, Ap, Bp);
     Cp = MatrixSubtract(Cp, Ap, Cp);
     Aw = MatrixSubtract(Aw, Ap, Aw);
     Bw = MatrixSubtract(Bw, Ap, Bw);
     Cw = MatrixSubtract(Cw, Ap, Cw);

     // The next lines compute the volume for each, using a scalar 
triple product:
     C1 = VectorCrossProduct(Bw, Cw, C1);
     T1 = fabs(V3_DOT(Aw, C1));

     C2 = VectorCrossProduct(Cp, Bw, C2);
     T2 = fabs(V3_DOT(Bp, C2));

     C3 = VectorCrossProduct(Cw, Bw, C3);
     T3 = fabs(V3_DOT(Cp, C3));

     dval = (T1 + T2 + T3) / 6.0;
     MRIsetVoxVal(facevol, nthface, 0, 0, 0, dval);
     volsum += dval;
   }
   printf("Total face volume %g\n", volsum);

   vtxvolsum = 0;
   for (vno = 0; vno < w->nvertices; vno++) {
     vtx = >vertices[vno];
     if (vtx->ripflag) continue;
     if (mask && MRIgetVoxVal(mask, vno, 0, 0, 0) < 0.5) continue;
     nfacenbrs = w->vertices_topology[vno].num;
     volsum = 0.0;
     for (nthfacenbr = 0; nthfacenbr < nfacenbrs; nthfacenbr++) {
   nbrfaceno = w->vertices_topology[vno].f[nthfacenbr];
   volsum += (MRIgetVoxVal(facevol, nbrfaceno, 0, 0, 0) / 3.0);
   // divide by 3 because each face participates in 3 vertices
     }
     MRIsetVoxVal(vol, vno, 0, 0, 0, volsum);
     vtxvolsum += volsum;
   }
   printf("Total vertex volume %g (mask=%d)\n", vtxvolsum, mask == NULL);
   *totvol = vtxvolsum;

   MRIfree();
   MatrixFree();
   MatrixFree();
   MatrixFree();
   MatrixFree();
   MatrixFree();
   MatrixFree();
   MatrixFree();
   MatrixFree();
   MatrixFree();

   return (vol);
}


On 8/15/2019 4:15 AM, Tim Schäfer wrote:
>  External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> can anybody refer me to a publication that explains in detail how vertex-wise 
> cortical volume (the data in /surf/?h.volume) is computed in 
> FreeSurfer 6?
>
> My understanding is the following:
> * area is computed as 1/3 the area of all triangles meeting at that vertex.
> * thickness is the shortest distance from the vertex (at white surface) to 
> any vertex on pial, then the other way around from that pial vertex, divided 
> by two.
> * volume is area * thickness
>
> Is that true, and where can I read up on it?
>
> Thanks,
>
> Tim
>
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and 
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] FreeSurfer 6 vertex-wise cortical volume computation details?

[Tim Schäfer]

External Email - Use Caution

Dear FreeSurfer experts,

can anybody refer me to a publication that explains in detail how vertex-wise 
cortical volume (the data in /surf/?h.volume) is computed in 
FreeSurfer 6?

My understanding is the following: 
* area is computed as 1/3 the area of all triangles meeting at that vertex.
* thickness is the shortest distance from the vertex (at white surface) to any 
vertex on pial, then the other way around from that pial vertex, divided by two.
* volume is area * thickness

Is that true, and where can I read up on it?

Thanks,

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Nikita Nogovitsyn]

External Email - Use Caution

Thank you Eugenio, there were no error messages or any observations that may 
indicate the computing process experienced perturbations...

Nikita

On Jun 12, 2018, at 12:19, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:


External Email - Use Caution
Uuuummm it seems it died unexpectedly, but there’s no error at the end of the 
log… are you sure that’s the complete file?
If not: did you get any other message on the screen when you tried to run this?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 17:52
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files


External Email - Use Caution
My apologies. Here is the long-hippocampal-subfields-T1.log 
https://drive.google.com/open?id=1VIeYRRBT1fNOeucsYSW2R1792g7u5JBD



On Jun 12, 2018, at 10:45, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution

Thanks, Nikita.
Can you please send us the file long-hippocampal-subfields-T1.log, which you 
can find under the base subject, for one of the failing cases?
Cheers,
/E


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 17:36
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files

External Email - Use Caution
Hi Eugenio,

Thank you very much for your prompt reply.

I was trying to support the tread titled Re: [Freesurfer] freesurfer 6 
hippocampal longitudinal processing workflow question, more LH than RH files

We received results from the cross-sectional segmentations - this version 
worked just great! All the recon-all procedures were managed via Linux based 
computing cluster. (We never had any perturbations in the performance there; 
1000+ subjects were processed on the cross-sectional pipeline without problems).

Once we triggered the longitude version - we faced multiple challenges. We 
observer a strange thing: once the longitudal version reached some undefined 
number of subjects (30-50 jobs) it only produces the left hemisphere text file. 
The recon all log says there are no errors.

We were also not sure what would be the most appropriate way to employ the 
longitudal version given 3 time points of the observation.

Here are all log files from the long version: 
https://drive.google.com/open?id=1qT_auSyboq5tXTgepIAeqgkttiVXMPNq

Thank you very much for your input and help, Eugenio.

Sincerely,
Nikita



On Jun 12, 2018, at 10:05, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution

Hi Nikita,
Could you please be a bit more specific about your problem? What issue are you 
exactly referring to?
Also, can you please send us the log file of the hippocampal subfields (rather 
than of recon-all)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 16:49
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files

External Email - Use Caution
HI

I would like to report to have the same issue. There were no errors in the log 
yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: 
https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks
Nikita
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Uuuummm it seems it died unexpectedly, but there’s no error at the end of the 
log… are you sure that’s the complete file?
If not: did you get any other message on the screen when you tried to run this?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Nikita Nogovitsyn 

Reply-To: Freesurfer support list 
Date: Tuesday, 12 June 2018 at 17:52
To: Freesurfer support list 
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files


External Email - Use Caution
My apologies. Here is the long-hippocampal-subfields-T1.log 
https://drive.google.com/open?id=1VIeYRRBT1fNOeucsYSW2R1792g7u5JBD



On Jun 12, 2018, at 10:45, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution

Thanks, Nikita.
Can you please send us the file long-hippocampal-subfields-T1.log, which you 
can find under the base subject, for one of the failing cases?
Cheers,
/E


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 17:36
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files

External Email - Use Caution
Hi Eugenio,

Thank you very much for your prompt reply.

I was trying to support the tread titled Re: [Freesurfer] freesurfer 6 
hippocampal longitudinal processing workflow question, more LH than RH files

We received results from the cross-sectional segmentations - this version 
worked just great! All the recon-all procedures were managed via Linux based 
computing cluster. (We never had any perturbations in the performance there; 
1000+ subjects were processed on the cross-sectional pipeline without problems).

Once we triggered the longitude version - we faced multiple challenges. We 
observer a strange thing: once the longitudal version reached some undefined 
number of subjects (30-50 jobs) it only produces the left hemisphere text file. 
The recon all log says there are no errors.

We were also not sure what would be the most appropriate way to employ the 
longitudal version given 3 time points of the observation.

Here are all log files from the long version: 
https://drive.google.com/open?id=1qT_auSyboq5tXTgepIAeqgkttiVXMPNq

Thank you very much for your input and help, Eugenio.

Sincerely,
Nikita



On Jun 12, 2018, at 10:05, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution

Hi Nikita,
Could you please be a bit more specific about your problem? What issue are you 
exactly referring to?
Also, can you please send us the log file of the hippocampal subfields (rather 
than of recon-all)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 16:49
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files

External Email - Use Caution
HI

I would like to report to have the same issue. There were no errors in the log 
yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: 
https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks
Nikita
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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 . If the e-mail was sent to you in error
but does

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Nikita Nogovitsyn]

External Email - Use Caution

My apologies. Here is the long-hippocampal-subfields-T1.log 
https://drive.google.com/open?id=1VIeYRRBT1fNOeucsYSW2R1792g7u5JBD


On Jun 12, 2018, at 10:45, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:


External Email - Use Caution

Thanks, Nikita.
Can you please send us the file long-hippocampal-subfields-T1.log, which you 
can find under the base subject, for one of the failing cases?
Cheers,
/E


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 17:36
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files


External Email - Use Caution

Hi Eugenio,

Thank you very much for your prompt reply.

I was trying to support the tread titled Re: [Freesurfer] freesurfer 6 
hippocampal longitudinal processing workflow question, more LH than RH files

We received results from the cross-sectional segmentations - this version 
worked just great! All the recon-all procedures were managed via Linux based 
computing cluster. (We never had any perturbations in the performance there; 
1000+ subjects were processed on the cross-sectional pipeline without problems).

Once we triggered the longitude version - we faced multiple challenges. We 
observer a strange thing: once the longitudal version reached some undefined 
number of subjects (30-50 jobs) it only produces the left hemisphere text file. 
The recon all log says there are no errors.

We were also not sure what would be the most appropriate way to employ the 
longitudal version given 3 time points of the observation.

Here are all log files from the long version: 
https://drive.google.com/open?id=1qT_auSyboq5tXTgepIAeqgkttiVXMPNq

Thank you very much for your input and help, Eugenio.

Sincerely,
Nikita


On Jun 12, 2018, at 10:05, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution

Hi Nikita,
Could you please be a bit more specific about your problem? What issue are you 
exactly referring to?
Also, can you please send us the log file of the hippocampal subfields (rather 
than of recon-all)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 16:49
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files

External Email - Use Caution
HI

I would like to report to have the same issue. There were no errors in the log 
yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: 
https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks
Nikita
___
Freesurfer mailing list
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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 . 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


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 . 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.

__

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Thanks, Nikita.
Can you please send us the file long-hippocampal-subfields-T1.log, which you 
can find under the base subject, for one of the failing cases?
Cheers,
/E


--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Nikita Nogovitsyn 

Reply-To: Freesurfer support list 
Date: Tuesday, 12 June 2018 at 17:36
To: Freesurfer support list 
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files


External Email - Use Caution
Hi Eugenio,

Thank you very much for your prompt reply.

I was trying to support the tread titled Re: [Freesurfer] freesurfer 6 
hippocampal longitudinal processing workflow question, more LH than RH files

We received results from the cross-sectional segmentations - this version 
worked just great! All the recon-all procedures were managed via Linux based 
computing cluster. (We never had any perturbations in the performance there; 
1000+ subjects were processed on the cross-sectional pipeline without problems).

Once we triggered the longitude version - we faced multiple challenges. We 
observer a strange thing: once the longitudal version reached some undefined 
number of subjects (30-50 jobs) it only produces the left hemisphere text file. 
The recon all log says there are no errors.

We were also not sure what would be the most appropriate way to employ the 
longitudal version given 3 time points of the observation.

Here are all log files from the long version: 
https://drive.google.com/open?id=1qT_auSyboq5tXTgepIAeqgkttiVXMPNq

Thank you very much for your input and help, Eugenio.

Sincerely,
Nikita


On Jun 12, 2018, at 10:05, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

External Email - Use Caution

Hi Nikita,
Could you please be a bit more specific about your problem? What issue are you 
exactly referring to?
Also, can you please send us the log file of the hippocampal subfields (rather 
than of recon-all)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 16:49
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files

External Email - Use Caution
HI

I would like to report to have the same issue. There were no errors in the log 
yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: 
https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks
Nikita
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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 . 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
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 . 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.

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Nikita Nogovitsyn]

External Email - Use Caution

Hi Eugenio,

Thank you very much for your prompt reply.

I was trying to support the tread titled Re: [Freesurfer] freesurfer 6 
hippocampal longitudinal processing workflow question, more LH than RH files

We received results from the cross-sectional segmentations - this version 
worked just great! All the recon-all procedures were managed via Linux based 
computing cluster. (We never had any perturbations in the performance there; 
1000+ subjects were processed on the cross-sectional pipeline without problems).

Once we triggered the longitude version - we faced multiple challenges. We 
observer a strange thing: once the longitudal version reached some undefined 
number of subjects (30-50 jobs) it only produces the left hemisphere text file. 
The recon all log says there are no errors.

We were also not sure what would be the most appropriate way to employ the 
longitudal version given 3 time points of the observation.

Here are all log files from the long version: 
https://drive.google.com/open?id=1qT_auSyboq5tXTgepIAeqgkttiVXMPNq

Thank you very much for your input and help, Eugenio.

Sincerely,
Nikita

On Jun 12, 2018, at 10:05, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:


External Email - Use Caution

Hi Nikita,
Could you please be a bit more specific about your problem? What issue are you 
exactly referring to?
Also, can you please send us the log file of the hippocampal subfields (rather 
than of recon-all)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com<http://www.jeiglesias.com/>
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nikita Nogovitsyn 
mailto:n.nogovit...@ucalgary.ca>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, 12 June 2018 at 16:49
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files


External Email - Use Caution

HI

I would like to report to have the same issue. There were no errors in the log 
yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: 
https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks
Nikita
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
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 . 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
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 . 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.

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Nikita,
Could you please be a bit more specific about your problem? What issue are you 
exactly referring to?
Also, can you please send us the log file of the hippocampal subfields (rather 
than of recon-all)?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Nikita Nogovitsyn 

Reply-To: Freesurfer support list 
Date: Tuesday, 12 June 2018 at 16:49
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing 
workflow question, more LH than RH files


External Email - Use Caution
HI

I would like to report to have the same issue. There were no errors in the log 
yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: 
https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks
Nikita
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 . 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.

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Nikita Nogovitsyn]

External Email - Use Caution

HI

I would like to report to have the same issue. There were no errors in the log 
yet the majority of results missing right hemisphere.

Attaching here the log file, or you can also access it via googledrive here: 
https://drive.google.com/open?id=13PVEWL4d6VuOJcIztWPTe83yz4Oi61Rv

Thanks
Nikita
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 . 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.

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Iglesias Gonzalez, Eugenio]

Hi Alan,
Can you please send me the log file for the longitudinal subfields?
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 3 May 2017, at 14:11, Martin Reuter 
> wrote:


Not sure what is going on, maybe Eugenio knows.

On 04/27/2017 10:29 PM, Salil Soman wrote:
Thank you for your email. Just to follow up, the rh and lh hippocampal 
hippoSfVolumes-T1.v10.txt files are present, but for a large number of cases, 
only the lh hippoSfVolumes-T1.long.v10.txt files are present. I reran the exact 
same recon-all -long command for all the cases, and I reran them after your 
suggestion, but there is no change in the number of missing 
rh.hippoSfVolumes-T1.long.v10.txt files. The log file for the longitudinal 
processing for recon-all says the process completed with no errors.

Is there anything else I should check?

Thanks!

On Fri, Apr 14, 2017 at 3:54 AM Alan Francis 
> wrote:
Hi Salil:

It could be that the HSF script may have `errored out' mid way through the 
analysis. If you go through the recon processing steps which are one of the 
output files, you will see exactly where the error occurred. Just reprocess 
that brain and see if that happens again.

Hope this helps,

best,

Alan



On Thu, Apr 13, 2017 at 4:49 PM, Salil Soman 
> wrote:
Hi,

I have run a number of cases through the FS6 hippocampal longitudinal 
processing steps listed at 
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields and 
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing

It seems that all steps completed, but when it came time to collect the 
results, I find I have many more lh.hippoSfVolumes-T1.long.v10.txt (67) than 
rh.hippoSfVolumes-T1.long.v10.txt files (25). Any suggestions on what I may be 
doing incorrectly?

Thanks!

Salil Soman

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Alan N. Francis PhD
Regional Sales Manager/ Application specialist
Nordic Neurolab
Boston.
a...@nordicneurolab.com


Previously:
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu
afran...@mclean.harvard.edu

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Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Martin Reuter]

Not sure what is going on, maybe Eugenio knows.


On 04/27/2017 10:29 PM, Salil Soman wrote:
Thank you for your email. Just to follow up, the rh and lh hippocampal 
hippoSfVolumes-T1.v10.txt files are present, but for a large number of 
cases, only the lh hippoSfVolumes-T1.long.v10.txt files are present. I 
reran the exact same recon-all -long command for all the cases, and I 
reran them after your suggestion, but there is no change in the number 
of missing rh.hippoSfVolumes-T1.long.v10.txt files. The log file for 
the longitudinal processing for recon-all says the process completed 
with no errors.


Is there anything else I should check?

Thanks!

On Fri, Apr 14, 2017 at 3:54 AM Alan Francis > wrote:


Hi Salil:

It could be that the HSF script may have `errored out' mid way
through the analysis. If you go through the recon processing steps
which are one of the output files, you will see exactly where the
error occurred. Just reprocess that brain and see if that happens
again.

Hope this helps,

best,

Alan



On Thu, Apr 13, 2017 at 4:49 PM, Salil Soman > wrote:

Hi,

I have run a number of cases through the FS6 hippocampal
longitudinal processing steps listed at

https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields
and
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing

It seems that all steps completed, but when it came time to
collect the results, I find I have many more
lh.hippoSfVolumes-T1.long.v10.txt (67) than
rh.hippoSfVolumes-T1.long.v10.txt files (25). Any suggestions
on what I may be doing incorrectly?

Thanks!

Salil Soman

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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
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*
Alan N. Francis PhD*
Regional Sales Manager/ Application specialist
Nordic Neurolab
Boston.
a...@nordicneurolab.com 


*Previously:*
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu 

|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|



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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Salil Soman]

Thank you for your email. Just to follow up, the rh and lh hippocampal
hippoSfVolumes-T1.v10.txt files are present, but for a large number of
cases, only the lh hippoSfVolumes-T1.long.v10.txt files are present. I
reran the exact same recon-all -long command for all the cases, and I reran
them after your suggestion, but there is no change in the number of missing
rh.hippoSfVolumes-T1.long.v10.txt files. The log file for the longitudinal
processing for recon-all says the process completed with no errors.

Is there anything else I should check?

Thanks!

On Fri, Apr 14, 2017 at 3:54 AM Alan Francis 
wrote:

> Hi Salil:
>
> It could be that the HSF script may have `errored out' mid way through the
> analysis. If you go through the recon processing steps which are one of the
> output files, you will see exactly where the error occurred. Just reprocess
> that brain and see if that happens again.
>
> Hope this helps,
>
> best,
>
> Alan
>
>
>
> On Thu, Apr 13, 2017 at 4:49 PM, Salil Soman  wrote:
>
>> Hi,
>>
>> I have run a number of cases through the FS6 hippocampal longitudinal
>> processing steps listed at 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields
>> and https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing
>>
>> It seems that all steps completed, but when it came time to collect the
>> results, I find I have many more lh.hippoSfVolumes-T1.long.v10.txt (67)
>> than rh.hippoSfVolumes-T1.long.v10.txt files (25). Any suggestions on what
>> I may be doing incorrectly?
>>
>> Thanks!
>>
>> Salil Soman
>>
>> ___
>> Freesurfer mailing list
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>>
>>
>> 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
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>> properly
>> dispose of the e-mail.
>>
>>
>
>
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> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>
> *Alan N. Francis PhD*
> Regional Sales Manager/ Application specialist
> Nordic Neurolab
> Boston.
> a...@nordicneurolab.com
>
>
> *Previously:*
> Instructor - Imaging Neuroscience
> Brain Imaging Center
> McLean Hospital
> Harvard Medical School
> 115 Mill Street, Belmont, MA 02478
> al...@bwh.harvard.edu 
> afran...@mclean.harvard.edu
>
>
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>
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[Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

[Salil Soman]

Hi,

I have run a number of cases through the FS6 hippocampal longitudinal
processing steps listed at
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields
and https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing

It seems that all steps completed, but when it came time to collect the
results, I find I have many more lh.hippoSfVolumes-T1.long.v10.txt (67)
than rh.hippoSfVolumes-T1.long.v10.txt files (25). Any suggestions on what
I may be doing incorrectly?

Thanks!

Salil Soman
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Re: [Freesurfer] Freesurfer 6 - Segfault - mri_ca_register

[Bruce Fischl]

Hi FLorian

the problem is that you have cortical labels from the aparc+aseg in your 
.gca file, and these exceed the max label we are expecting in a .gca atlas. 
Is there a reason you need them and not just left and right cortical gray 
matter labels? I don't think labeling folds will be terribly accurate with 
a volume morph, and there are downstream steps in recon-all that will do 
strange things if they can't find any cortical gray matter labels.


BTW: you may not know that you can directly visualize a .gca file with 
freeview. Just load it in freeview and it will come up as a multi-frame 
volume (frame 0 is the mean of the most likely class, frame 1 is the most 
likely class, and frame 2 is the prior of the most likely class). This is 
only a subset of what we store in the atlas, but it's a nice way to take a 
quick look and make sure everything looks ok

cheers
Bruce


On Tue, 24 Jan 2017, Florian Krismer wrote:


Hi Bruce,

It’s a custom atlas with minor changes that was build with the 
rebuild_gca_atlas.csh script.
What is puzzling to me is the fact that if I omit the align-after flag the 
mri_ca_register command works perfectly fine.

Many thanks & best wishes,
Florian


Am 24.01.17, 21:48 schrieb "Bruce Fischl" :

   I think that should be enough, but your data doesn't segfault for me. I
   also noticed the following in your recon-all.log file:

   usr/local/freesurfer/bin/recon-all
   -all -gca RB_all_2017-01-23.gca -gca-skull RB_all_withskull_2017-01-23.gca
   -subjid vco1573test_mpr


   are you using your own version of our atlases? Or did you rename them? I
   don't think we rebuilt any in 2017.

   cheers
   Bruce


   On
   Tue, 24 Jan 2017, Florian Krismer wrote:

   > Hi Bruce,
   >
   > it is a virtual machine with 8GB RAM dedicated to it. Any idea how much 
RAM would be enough?
   >
   > Thanks,
   > Florian
   >
   >
   >
   > Am 24.01.17, 21:39 schrieb "Bruce Fischl" 
:
   >
   >Hi Florian
   >
   >how much RAM do you have in that machine? I think it is not enough
   >cheers
   >Bruce
   >On
   >Tue, 24 Jan 2017, Florian Krismer wrote:
   >
   >> Dear FreeSurfer Developers,
   >>
   >> I'm attempting to run recon-all on a test subject (through recon-all 
–all –subjid test001 in Freesurfer 6). Recon-all hangs at the mri_ca_register command 
throwing a Segfault error.
   >>
   >> This is the corresponding part of the recon-all.log:
   >> 
---
   >> mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
   >>
   >> not handling expanded ventricles...
   >> using previously computed transform transforms/talairach.lta
   >> renormalizing sequences with structure alignment, equivalent to:
   >> -renormalize
   >> -regularize_mean 0.500
   >> -regularize 0.500
   >> using MR volume brainmask.mgz to mask input volume...
   >>
   >> == Number of threads available to mri_ca_register for OpenMP = 1 ==
   >> reading 1 input volumes...
   >> logging results to talairach.log
   >> reading input volume 'norm.mgz'...
   >> reading GCA 
'/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
   >> label assignment complete, 0 changed (0.00%)
   >> det(m_affine) = 1.26 (predicted orig area = 6.3)
   >> Segmentation fault
   >> 
---
   >>
   >>
   >> When debugging the error through gdb I get the following, additional 
information:
   >>
   >> 
---
   >>
   >> [florian@freesurfer]$ gdb --args mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
   >> GNU gdb (GDB) Red Hat Enterprise Linux (7.2-90.el6)
   >> Copyright (C) 2010 Free Software Foundation, Inc.
   >> License GPLv3+: GNU GPL version 3 or later 

   >> This is free software: you are free to change and redistribute it.
   >> There is NO WARRANTY, to the extent permitted by law.  Type "show 
copying"
   >> and "show warranty" for details.
   >> This GDB was configured as "x86_64-redhat-linux-gnu".
   >> For bug reporting instructions, please see:
   >> 

Re: [Freesurfer] Freesurfer 6 - Segfault - mri_ca_register

[Bruce Fischl]

Hi FLorian

I think you are not running the release, but a slightly earlier version 
(from the info at the top of your recon-all.log).


Can you try running with the standard atlases and see if that works? And if 
it does, upload your rebuilt atlases so I can try to replicate the crash?


cheers
Bruce


On Tue, 24 Jan 2017, Florian Krismer wrote:


Hi Bruce,

It’s a custom atlas with minor changes that was build with the 
rebuild_gca_atlas.csh script.
What is puzzling to me is the fact that if I omit the align-after flag the 
mri_ca_register command works perfectly fine.

Many thanks & best wishes,
Florian


Am 24.01.17, 21:48 schrieb "Bruce Fischl" :

   I think that should be enough, but your data doesn't segfault for me. I
   also noticed the following in your recon-all.log file:

   usr/local/freesurfer/bin/recon-all
   -all -gca RB_all_2017-01-23.gca -gca-skull RB_all_withskull_2017-01-23.gca
   -subjid vco1573test_mpr


   are you using your own version of our atlases? Or did you rename them? I
   don't think we rebuilt any in 2017.

   cheers
   Bruce


   On
   Tue, 24 Jan 2017, Florian Krismer wrote:

   > Hi Bruce,
   >
   > it is a virtual machine with 8GB RAM dedicated to it. Any idea how much 
RAM would be enough?
   >
   > Thanks,
   > Florian
   >
   >
   >
   > Am 24.01.17, 21:39 schrieb "Bruce Fischl" 
:
   >
   >Hi Florian
   >
   >how much RAM do you have in that machine? I think it is not enough
   >cheers
   >Bruce
   >On
   >Tue, 24 Jan 2017, Florian Krismer wrote:
   >
   >> Dear FreeSurfer Developers,
   >>
   >> I'm attempting to run recon-all on a test subject (through recon-all 
–all –subjid test001 in Freesurfer 6). Recon-all hangs at the mri_ca_register command 
throwing a Segfault error.
   >>
   >> This is the corresponding part of the recon-all.log:
   >> 
---
   >> mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
   >>
   >> not handling expanded ventricles...
   >> using previously computed transform transforms/talairach.lta
   >> renormalizing sequences with structure alignment, equivalent to:
   >> -renormalize
   >> -regularize_mean 0.500
   >> -regularize 0.500
   >> using MR volume brainmask.mgz to mask input volume...
   >>
   >> == Number of threads available to mri_ca_register for OpenMP = 1 ==
   >> reading 1 input volumes...
   >> logging results to talairach.log
   >> reading input volume 'norm.mgz'...
   >> reading GCA 
'/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
   >> label assignment complete, 0 changed (0.00%)
   >> det(m_affine) = 1.26 (predicted orig area = 6.3)
   >> Segmentation fault
   >> 
---
   >>
   >>
   >> When debugging the error through gdb I get the following, additional 
information:
   >>
   >> 
---
   >>
   >> [florian@freesurfer]$ gdb --args mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
   >> GNU gdb (GDB) Red Hat Enterprise Linux (7.2-90.el6)
   >> Copyright (C) 2010 Free Software Foundation, Inc.
   >> License GPLv3+: GNU GPL version 3 or later 

   >> This is free software: you are free to change and redistribute it.
   >> There is NO WARRANTY, to the extent permitted by law.  Type "show 
copying"
   >> and "show warranty" for details.
   >> This GDB was configured as "x86_64-redhat-linux-gnu".
   >> For bug reporting instructions, please see:
   >> ...
   >> Reading symbols from /usr/local/freesurfer/bin/mri_ca_register...(no 
debugging symbols found)...done.
   >> (gdb) run
   >> Starting program: /usr/local/freesurfer/bin/mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
   >> warning: no loadable sections found in added symbol-file 
system-supplied DSO at 0x77ffa000
   >   

Re: [Freesurfer] Freesurfer 6 - Segfault - mri_ca_register

[Florian Krismer]

Hi Bruce,

It’s a custom atlas with minor changes that was build with the 
rebuild_gca_atlas.csh script. 
What is puzzling to me is the fact that if I omit the align-after flag the 
mri_ca_register command works perfectly fine.

Many thanks & best wishes,
Florian


Am 24.01.17, 21:48 schrieb "Bruce Fischl" 
:

I think that should be enough, but your data doesn't segfault for me. I 
also noticed the following in your recon-all.log file:

usr/local/freesurfer/bin/recon-all
-all -gca RB_all_2017-01-23.gca -gca-skull RB_all_withskull_2017-01-23.gca 
-subjid vco1573test_mpr


are you using your own version of our atlases? Or did you rename them? I 
don't think we rebuilt any in 2017.

cheers
Bruce


On 
Tue, 24 Jan 2017, Florian Krismer wrote:

> Hi Bruce,
>
> it is a virtual machine with 8GB RAM dedicated to it. Any idea how much 
RAM would be enough?
>
> Thanks,
> Florian
>
>
>
> Am 24.01.17, 21:39 schrieb "Bruce Fischl" 
:
>
>Hi Florian
>
>how much RAM do you have in that machine? I think it is not enough
>cheers
>Bruce
>On
>Tue, 24 Jan 2017, Florian Krismer wrote:
>
>> Dear FreeSurfer Developers,
>>
>> I'm attempting to run recon-all on a test subject (through recon-all 
–all –subjid test001 in Freesurfer 6). Recon-all hangs at the mri_ca_register 
command throwing a Segfault error.
>>
>> This is the corresponding part of the recon-all.log:
>> 
---
>> mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
>>
>> not handling expanded ventricles...
>> using previously computed transform transforms/talairach.lta
>> renormalizing sequences with structure alignment, equivalent to:
>>  -renormalize
>>  -regularize_mean 0.500
>>  -regularize 0.500
>> using MR volume brainmask.mgz to mask input volume...
>>
>> == Number of threads available to mri_ca_register for OpenMP = 1 ==
>> reading 1 input volumes...
>> logging results to talairach.log
>> reading input volume 'norm.mgz'...
>> reading GCA 
'/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
>> label assignment complete, 0 changed (0.00%)
>> det(m_affine) = 1.26 (predicted orig area = 6.3)
>> Segmentation fault
>> 
---
>>
>>
>> When debugging the error through gdb I get the following, additional 
information:
>>
>> 
---
>>
>> [florian@freesurfer]$ gdb --args mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
>> GNU gdb (GDB) Red Hat Enterprise Linux (7.2-90.el6)
>> Copyright (C) 2010 Free Software Foundation, Inc.
>> License GPLv3+: GNU GPL version 3 or later 

>> This is free software: you are free to change and redistribute it.
>> There is NO WARRANTY, to the extent permitted by law.  Type "show 
copying"
>> and "show warranty" for details.
>> This GDB was configured as "x86_64-redhat-linux-gnu".
>> For bug reporting instructions, please see:
>> ...
>> Reading symbols from /usr/local/freesurfer/bin/mri_ca_register...(no 
debugging symbols found)...done.
>> (gdb) run
>> Starting program: /usr/local/freesurfer/bin/mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
>> warning: no loadable sections found in added symbol-file 
system-supplied DSO at 0x77ffa000
>> [Thread debugging using libthread_db enabled]
>> not handling expanded ventricles...
>> using previously computed transform transforms/talairach.lta
>> renormalizing sequences with structure alignment, equivalent to:
> 

Re: [Freesurfer] Freesurfer 6 - Segfault - mri_ca_register

[Bruce Fischl]

I think that should be enough, but your data doesn't segfault for me. I 
also noticed the following in your recon-all.log file:


usr/local/freesurfer/bin/recon-all
-all -gca RB_all_2017-01-23.gca -gca-skull RB_all_withskull_2017-01-23.gca 
-subjid vco1573test_mpr



are you using your own version of our atlases? Or did you rename them? I 
don't think we rebuilt any in 2017.


cheers
Bruce


On 
Tue, 24 Jan 2017, Florian Krismer wrote:



Hi Bruce,

it is a virtual machine with 8GB RAM dedicated to it. Any idea how much RAM 
would be enough?

Thanks,
Florian



Am 24.01.17, 21:39 schrieb "Bruce Fischl" :

   Hi Florian

   how much RAM do you have in that machine? I think it is not enough
   cheers
   Bruce
   On
   Tue, 24 Jan 2017, Florian Krismer wrote:

   > Dear FreeSurfer Developers,
   >
   > I'm attempting to run recon-all on a test subject (through recon-all –all 
–subjid test001 in Freesurfer 6). Recon-all hangs at the mri_ca_register command 
throwing a Segfault error.
   >
   > This is the corresponding part of the recon-all.log:
   > 
---
   > mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
   >
   > not handling expanded ventricles...
   > using previously computed transform transforms/talairach.lta
   > renormalizing sequences with structure alignment, equivalent to:
   > -renormalize
   > -regularize_mean 0.500
   > -regularize 0.500
   > using MR volume brainmask.mgz to mask input volume...
   >
   > == Number of threads available to mri_ca_register for OpenMP = 1 ==
   > reading 1 input volumes...
   > logging results to talairach.log
   > reading input volume 'norm.mgz'...
   > reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
   > label assignment complete, 0 changed (0.00%)
   > det(m_affine) = 1.26 (predicted orig area = 6.3)
   > Segmentation fault
   > 
---
   >
   >
   > When debugging the error through gdb I get the following, additional 
information:
   >
   > 
---
   >
   > [florian@freesurfer]$ gdb --args mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
   > GNU gdb (GDB) Red Hat Enterprise Linux (7.2-90.el6)
   > Copyright (C) 2010 Free Software Foundation, Inc.
   > License GPLv3+: GNU GPL version 3 or later 

   > This is free software: you are free to change and redistribute it.
   > There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
   > and "show warranty" for details.
   > This GDB was configured as "x86_64-redhat-linux-gnu".
   > For bug reporting instructions, please see:
   > ...
   > Reading symbols from /usr/local/freesurfer/bin/mri_ca_register...(no 
debugging symbols found)...done.
   > (gdb) run
   > Starting program: /usr/local/freesurfer/bin/mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
   > warning: no loadable sections found in added symbol-file system-supplied 
DSO at 0x77ffa000
   > [Thread debugging using libthread_db enabled]
   > not handling expanded ventricles...
   > using previously computed transform transforms/talairach.lta
   > renormalizing sequences with structure alignment, equivalent to:
   > -renormalize
   > -regularize_mean 0.500
   > -regularize 0.500
   > using MR volume brainmask.mgz to mask input volume...
   >
   > == Number of threads available to 
/usr/local/freesurfer/bin/mri_ca_register for OpenMP = 1 ==
   > reading 1 input volumes...
   > logging results to talairach.log
   > reading input volume 'norm.mgz'...
   > reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
   > freeing gibbs priors...done.
   > average std[0] = 5.0
   > label assignment complete, 0 changed (0.00%)
   > det(m_affine) = 1.26 (predicted orig area = 6.3)
   >
   > Program received signal SIGSEGV, Segmentation fault.
   > _int_free (av=0x76bb4120, p=0x619a5f30, have_lock=0) at malloc.c:5000
   > 5000if (__builtin_expect (!prev_inuse(nextchunk), 0))
   > (gdb)
   > 

Re: [Freesurfer] Freesurfer 6 - Segfault - mri_ca_register

[Florian Krismer]

Hi Bruce,

it is a virtual machine with 8GB RAM dedicated to it. Any idea how much RAM 
would be enough?

Thanks,
Florian



Am 24.01.17, 21:39 schrieb "Bruce Fischl" 
:

Hi Florian

how much RAM do you have in that machine? I think it is not enough
cheers
Bruce
On 
Tue, 24 Jan 2017, Florian Krismer wrote:

> Dear FreeSurfer Developers,
>
> I'm attempting to run recon-all on a test subject (through recon-all –all 
–subjid test001 in Freesurfer 6). Recon-all hangs at the mri_ca_register 
command throwing a Segfault error.
>
> This is the corresponding part of the recon-all.log:
> 
---
> mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
>
> not handling expanded ventricles...
> using previously computed transform transforms/talairach.lta
> renormalizing sequences with structure alignment, equivalent to:
>   -renormalize
>   -regularize_mean 0.500
>   -regularize 0.500
> using MR volume brainmask.mgz to mask input volume...
>
> == Number of threads available to mri_ca_register for OpenMP = 1 ==
> reading 1 input volumes...
> logging results to talairach.log
> reading input volume 'norm.mgz'...
> reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
> label assignment complete, 0 changed (0.00%)
> det(m_affine) = 1.26 (predicted orig area = 6.3)
> Segmentation fault
> 
---
>
>
> When debugging the error through gdb I get the following, additional 
information:
>
> 
---
>
> [florian@freesurfer]$ gdb --args mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
> GNU gdb (GDB) Red Hat Enterprise Linux (7.2-90.el6)
> Copyright (C) 2010 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later 

> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
> and "show warranty" for details.
> This GDB was configured as "x86_64-redhat-linux-gnu".
> For bug reporting instructions, please see:
> ...
> Reading symbols from /usr/local/freesurfer/bin/mri_ca_register...(no 
debugging symbols found)...done.
> (gdb) run
> Starting program: /usr/local/freesurfer/bin/mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
> warning: no loadable sections found in added symbol-file system-supplied 
DSO at 0x77ffa000
> [Thread debugging using libthread_db enabled]
> not handling expanded ventricles...
> using previously computed transform transforms/talairach.lta
> renormalizing sequences with structure alignment, equivalent to:
>   -renormalize
>   -regularize_mean 0.500
>   -regularize 0.500
> using MR volume brainmask.mgz to mask input volume...
>
> == Number of threads available to 
/usr/local/freesurfer/bin/mri_ca_register for OpenMP = 1 == 
> reading 1 input volumes...
> logging results to talairach.log
> reading input volume 'norm.mgz'...
> reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
> freeing gibbs priors...done.
> average std[0] = 5.0
> label assignment complete, 0 changed (0.00%)
> det(m_affine) = 1.26 (predicted orig area = 6.3)
>
> Program received signal SIGSEGV, Segmentation fault.
> _int_free (av=0x76bb4120, p=0x619a5f30, have_lock=0) at malloc.c:5000
> 5000  if (__builtin_expect (!prev_inuse(nextchunk), 0))
> (gdb) 
> 
---
>
>
> I run the command on a virtual machine (using XEN as hypervisor software) 
with 2 cores and 8gb RAM assigned to the virtual machine.
> Some basic information about the platform:
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 
(download date 24-Jan-17)
> 2) Platform: CentOS 

Re: [Freesurfer] Freesurfer 6 - Segfault - mri_ca_register

[Bruce Fischl]

Hi Florian

how much RAM do you have in that machine? I think it is not enough
cheers
Bruce
On 
Tue, 24 Jan 2017, Florian Krismer wrote:



Dear FreeSurfer Developers,

I'm attempting to run recon-all on a test subject (through recon-all –all 
–subjid test001 in Freesurfer 6). Recon-all hangs at the mri_ca_register 
command throwing a Segfault error.

This is the corresponding part of the recon-all.log:
---
mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z

not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_ca_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.26 (predicted orig area = 6.3)
Segmentation fault
---


When debugging the error through gdb I get the following, additional 
information:

---

[florian@freesurfer]$ gdb --args mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-90.el6)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later 
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
...
Reading symbols from /usr/local/freesurfer/bin/mri_ca_register...(no debugging 
symbols found)...done.
(gdb) run
Starting program: /usr/local/freesurfer/bin/mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
warning: no loadable sections found in added symbol-file system-supplied DSO at 
0x77ffa000
[Thread debugging using libthread_db enabled]
not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to /usr/local/freesurfer/bin/mri_ca_register for 
OpenMP = 1 == 
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
freeing gibbs priors...done.
average std[0] = 5.0
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.26 (predicted orig area = 6.3)

Program received signal SIGSEGV, Segmentation fault.
_int_free (av=0x76bb4120, p=0x619a5f30, have_lock=0) at malloc.c:5000
5000    if (__builtin_expect (!prev_inuse(nextchunk), 0))
(gdb) 
---


I run the command on a virtual machine (using XEN as hypervisor software) with 
2 cores and 8gb RAM assigned to the virtual machine.
Some basic information about the platform:
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 
(download date 24-Jan-17)
2) Platform: CentOS release 6.8 (Final)
3) uname –a: Linux  4.4.27-x86_64-jb1 #1 SMP Thu Oct 27 13:51:17 CEST 2016 
x86_64 x86_64 x86_64 GNU/Linux
4) mri_ca_register –all-info: ProgramName: mri_ca_register  ProgramArguments: 
-all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/01/24-17:30:37-GMT  
BuildTimeStamp: Dec 29 2016 17:01:05  CVS: $Id: mri_ca_register.c,v 1.96.2.3 
2016/10/27 22:25:10 zkaufman
5) libgcc.i686 4.4.7-17.el6

Does anyone have any thoughts on how to trouble-shoot this one?
The funny thing is that if I remove the –align-after flag, the command works 
like a charm (I couldn’t find any documentation describing the purpose of 
–align-after?).

Many thanks for your support & best wishes,

Re: [Freesurfer] Freesurfer 6 - Segfault - mri_ca_register

[Bruce Fischl]

Hi Florian

can you tar and gzip that subject dir and we will take a look?

cheers
Bruce
On Tue, 24 
Jan 2017, Florian Krismer wrote:



Dear FreeSurfer Developers,

I'm attempting to run recon-all on a test subject (through recon-all –all 
–subjid test001 in Freesurfer 6). Recon-all hangs at the mri_ca_register 
command throwing a Segfault error.

This is the corresponding part of the recon-all.log:
---
mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z

not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_ca_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.26 (predicted orig area = 6.3)
Segmentation fault
---


When debugging the error through gdb I get the following, additional 
information:

---

[florian@freesurfer]$ gdb --args mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-90.el6)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later 
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
...
Reading symbols from /usr/local/freesurfer/bin/mri_ca_register...(no debugging 
symbols found)...done.
(gdb) run
Starting program: /usr/local/freesurfer/bin/mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
warning: no loadable sections found in added symbol-file system-supplied DSO at 
0x77ffa000
[Thread debugging using libthread_db enabled]
not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to /usr/local/freesurfer/bin/mri_ca_register for 
OpenMP = 1 == 
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
freeing gibbs priors...done.
average std[0] = 5.0
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.26 (predicted orig area = 6.3)

Program received signal SIGSEGV, Segmentation fault.
_int_free (av=0x76bb4120, p=0x619a5f30, have_lock=0) at malloc.c:5000
5000    if (__builtin_expect (!prev_inuse(nextchunk), 0))
(gdb) 
---


I run the command on a virtual machine (using XEN as hypervisor software) with 
2 cores and 8gb RAM assigned to the virtual machine.
Some basic information about the platform:
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 
(download date 24-Jan-17)
2) Platform: CentOS release 6.8 (Final)
3) uname –a: Linux  4.4.27-x86_64-jb1 #1 SMP Thu Oct 27 13:51:17 CEST 2016 
x86_64 x86_64 x86_64 GNU/Linux
4) mri_ca_register –all-info: ProgramName: mri_ca_register  ProgramArguments: 
-all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/01/24-17:30:37-GMT  
BuildTimeStamp: Dec 29 2016 17:01:05  CVS: $Id: mri_ca_register.c,v 1.96.2.3 
2016/10/27 22:25:10 zkaufman
5) libgcc.i686 4.4.7-17.el6

Does anyone have any thoughts on how to trouble-shoot this one?
The funny thing is that if I remove the –align-after flag, the command works 
like a charm (I couldn’t find any documentation describing the purpose of 
–align-after?).

Many thanks for your support & best wishes,

[Freesurfer] Freesurfer 6 - Segfault - mri_ca_register

[Florian Krismer]

Dear FreeSurfer Developers,

I'm attempting to run recon-all on a test subject (through recon-all –all 
–subjid test001 in Freesurfer 6). Recon-all hangs at the mri_ca_register 
command throwing a Segfault error. 

This is the corresponding part of the recon-all.log:
---
mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z 

not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_ca_register for OpenMP = 1 == 
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.26 (predicted orig area = 6.3)
Segmentation fault
---


When debugging the error through gdb I get the following, additional 
information:

---

[florian@freesurfer]$ gdb --args mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-90.el6)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later 
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
...
Reading symbols from /usr/local/freesurfer/bin/mri_ca_register...(no debugging 
symbols found)...done.
(gdb) run
Starting program: /usr/local/freesurfer/bin/mri_ca_register -rusage 
/usr/local/freesurfer/subjects/test001/touch/rusage.mri_ca_register.dat 
-nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz 
norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.m3z
warning: no loadable sections found in added symbol-file system-supplied DSO at 
0x77ffa000
[Thread debugging using libthread_db enabled]
not handling expanded ventricles...
using previously computed transform transforms/talairach.lta
renormalizing sequences with structure alignment, equivalent to:
-renormalize
-regularize_mean 0.500
-regularize 0.500
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to /usr/local/freesurfer/bin/mri_ca_register for 
OpenMP = 1 == 
reading 1 input volumes...
logging results to talairach.log
reading input volume 'norm.mgz'...
reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'...
freeing gibbs priors...done.
average std[0] = 5.0
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.26 (predicted orig area = 6.3)

Program received signal SIGSEGV, Segmentation fault.
_int_free (av=0x76bb4120, p=0x619a5f30, have_lock=0) at malloc.c:5000
5000    if (__builtin_expect (!prev_inuse(nextchunk), 0))
(gdb) 
---


I run the command on a virtual machine (using XEN as hypervisor software) with 
2 cores and 8gb RAM assigned to the virtual machine.
Some basic information about the platform:
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 
(download date 24-Jan-17)
2) Platform: CentOS release 6.8 (Final)
3) uname –a: Linux  4.4.27-x86_64-jb1 #1 SMP Thu Oct 27 13:51:17 CEST 2016 
x86_64 x86_64 x86_64 GNU/Linux
4) mri_ca_register –all-info: ProgramName: mri_ca_register  ProgramArguments: 
-all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/01/24-17:30:37-GMT  
BuildTimeStamp: Dec 29 2016 17:01:05  CVS: $Id: mri_ca_register.c,v 1.96.2.3 
2016/10/27 22:25:10 zkaufman
5) libgcc.i686 4.4.7-17.el6 

Does anyone have any thoughts on how to trouble-shoot this one?
The funny thing is that if I remove the –align-after flag, the command works 
like a charm (I couldn’t find any documentation describing the purpose of 
–align-after?).

Many thanks for your support & best wishes,
Florian








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Re: [Freesurfer] Freesurfer 6 beta testing: mri_glmfit-sim error

[Douglas Greve]

Looks like the most up-to-date version of mri_surfcluster did not get 
into the distribution. Try this one


https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster


On 11/18/16 9:06 PM, Elijah Mak wrote:

Hi Freesurfer Team,

I came across the following error while running mri_glmfit-sim. What 
is vwsigmax?

Thanks for your help again.

The full log is as follows:

$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Sat Nov 19 02:00:45 GMT 2016
Darwin dhcp-10-240-201-24.cp.wireless.private.cam.ac.uk 
 14.5.0 
Darwin Kernel Version 14.5.0: Thu Jun 16 19:58:21 PDT 2016; 
root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64


MacPro

setenv SUBJECTS_DIR /Volumes/TITAN/cth_wmh_study

FREESURFER_HOME //Users/MacPro/Documents/freesurfer_b6


Original mri_glmfit command line:
cmdline mri_glmfit.bin --y y.mgh --fsgd FSGDs/FSGD_Z_cthVsCTH_AD_age 
dods --C Contrasts/C --surf fsaverage lh --cortex --glmdir 
Glmdirs/ProjectAD


DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 20.927757
CSD 
//Users/MacPro/Documents/freesurfer_b6/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/abs/th30/mc-z.csd
mri_surfcluster --in Glmdirs/ProjectAD/C/sig.mgh --mask 
Glmdirs/ProjectAD/mask.mgh --cwsig 
Glmdirs/ProjectAD/C/cache.th30.abs.sig.cluster.mgh --sum 
Glmdirs/ProjectAD/C/cache.th30.abs.sig.cluster.summary --ocn 
Glmdirs/ProjectAD/C/cache.th30.abs.sig.ocn.mgh --annot aparc 
--cwpvalthresh 0.05 --o 
Glmdirs/ProjectAD/C/cache.th30.abs.sig.masked.mgh --no-fixmni --csd 
//Users/MacPro/Documents/freesurfer_b6/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/abs/th30/mc-z.csd 
--csdpdf Glmdirs/ProjectAD/C/cache.th30.abs.pdf.dat --vwsig 
Glmdirs/ProjectAD/C/cache.th30.abs.sig.voxel.mgh --vwsigmax 
Glmdirs/ProjectAD/C/cache.th30.abs.sig.voxel.max.dat --oannot 
Glmdirs/ProjectAD/C/cache.th30.abs.sig.ocn.annot --bonferroni 2 --surf 
white


ERROR: Option --vwsigmax unknown

Best Wishes,

Elijah



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[Freesurfer] Freesurfer 6 beta testing: mri_glmfit-sim error

[Elijah Mak]

Hi Freesurfer Team,

I came across the following error while running mri_glmfit-sim. What is
vwsigmax?
Thanks for your help again.

The full log is as follows:

$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Sat Nov 19 02:00:45 GMT 2016
Darwin dhcp-10-240-201-24.cp.wireless.private.cam.ac.uk 14.5.0 Darwin
Kernel Version 14.5.0: Thu Jun 16 19:58:21 PDT 2016;
root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64

MacPro

setenv SUBJECTS_DIR /Volumes/TITAN/cth_wmh_study

FREESURFER_HOME //Users/MacPro/Documents/freesurfer_b6


Original mri_glmfit command line:
cmdline mri_glmfit.bin --y y.mgh --fsgd FSGDs/FSGD_Z_cthVsCTH_AD_age dods
--C Contrasts/C --surf fsaverage lh --cortex --glmdir Glmdirs/ProjectAD

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 20.927757
CSD
//Users/MacPro/Documents/freesurfer_b6/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/abs/th30/mc-z.csd
mri_surfcluster --in Glmdirs/ProjectAD/C/sig.mgh --mask
Glmdirs/ProjectAD/mask.mgh --cwsig
Glmdirs/ProjectAD/C/cache.th30.abs.sig.cluster.mgh --sum
Glmdirs/ProjectAD/C/cache.th30.abs.sig.cluster.summary --ocn
Glmdirs/ProjectAD/C/cache.th30.abs.sig.ocn.mgh --annot aparc --cwpvalthresh
0.05 --o Glmdirs/ProjectAD/C/cache.th30.abs.sig.masked.mgh --no-fixmni
--csd
//Users/MacPro/Documents/freesurfer_b6/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/abs/th30/mc-z.csd
--csdpdf Glmdirs/ProjectAD/C/cache.th30.abs.pdf.dat --vwsig
Glmdirs/ProjectAD/C/cache.th30.abs.sig.voxel.mgh --vwsigmax
Glmdirs/ProjectAD/C/cache.th30.abs.sig.voxel.max.dat --oannot
Glmdirs/ProjectAD/C/cache.th30.abs.sig.ocn.annot --bonferroni 2 --surf white

ERROR: Option --vwsigmax unknown

Best Wishes,

Elijah
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Re: [Freesurfer] FreeSurfer 6 beta and mac osx el capitan

[Damien MARIE]

Hi,

I downloaded the archive with Firefox instead of Safari and problem is solved. 
Strangely, the archive downloaded with Safari was not full.

Damien 

> On 10 Oct 2016, at 16:56, Damien MARIE  wrote:
> 
> Hi,
> 
> I would like to install the FreeSurfer 6 beta on my macbook pro (OS X El 
> capitan 10.11.6, XQuartz 2.7.9 installed).
> 
> I allowed applications downloaded from Anywhere in privacy and settings, and 
> disabled csrutil (the System Integrity Protection, a security feature that 
> hobbles some of the capabilities of root since this OS release). No matter 
> what I try,  I cannot decompress the archive.
> 
> Using the terminal and sudo : 
> tar: Error opening archive: Failed to open 
> '/Users/dmarie2/Applications/freesurfer-Darwin-OSX-dev.tar.gz’
> 
> Or by double clicking :
> Unable to expand “freesurfer-Darwin-OSX-dev.tar.gz (Error 1 - Operation not 
> permitted).
> 
> I was wondering if somebody experienced this issue and would eventually have 
> a solution.
> 
> Thank you and best,
> 
> Damien

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[Freesurfer] FreeSurfer 6 beta and mac osx el capitan

[Damien MARIE]

Hi,

I would like to install the FreeSurfer 6 beta on my macbook pro (OS X El 
capitan 10.11.6, XQuartz 2.7.9 installed).

I allowed applications downloaded from Anywhere in privacy and settings, and 
disabled csrutil (the System Integrity Protection, a security feature that 
hobbles some of the capabilities of root since this OS release). No matter what 
I try,  I cannot decompress the archive.

Using the terminal and sudo : 
tar: Error opening archive: Failed to open 
'/Users/dmarie2/Applications/freesurfer-Darwin-OSX-dev.tar.gz’

Or by double clicking :
Unable to expand “freesurfer-Darwin-OSX-dev.tar.gz (Error 1 - Operation not 
permitted).

I was wondering if somebody experienced this issue and would eventually have a 
solution.

Thank you and best,

Damien
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Re: [Freesurfer] Freesurfer 6 beta error on OSX 10.7

[Z K]

Hello James,

Is it only the mris_decimate binary that gives this error? What happens 
if you try to perform a recon-all on the subjects bert under 
$FREESURFER_HOME/subjects... Does it get far or does it spit out the 
same error?

   $> 
   $> export SUBJECTS_DIR=/Applications/subjects
   $> recon-all -s bert -all

-Zeke

On 03/10/2016 12:50 PM, James Bennett wrote:
> Dear Freesurfer developers
>
> I've just tried out the beta version of Freesurfer 6.0 on my Mac, which
> I downloaded from
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/, mainly
> because I need to use the mris_decimate function. However, issuing
>
> mris_decimate -d 0.25 inputfile outputfile
>
> returns this error:
>
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: ___emutls_get_address
>Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>Expected in: /usr/lib/libSystem.B.dylib
>
> Trace/BPT trap: 5
>
> I'm running OS X 10.7, and I've seen similar errors reported on the
> mailing list relating to OS X compatibility problems. Is this the case
> here, and is there a mris_decimate binary that works on 10.7 that could
> be made available?
>
> Many thanks in advance for your help
> James
>
>
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[Freesurfer] Freesurfer 6 beta error on OSX 10.7

[James Bennett]

Dear Freesurfer developers

I've just tried out the beta version of Freesurfer 6.0 on my Mac, which I
downloaded from
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/, mainly
because I need to use the mris_decimate function. However, issuing

mris_decimate -d 0.25 inputfile outputfile

returns this error:

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

Trace/BPT trap: 5

I'm running OS X 10.7, and I've seen similar errors reported on the mailing
list relating to OS X compatibility problems. Is this the case here, and is
there a mris_decimate binary that works on 10.7 that could be made
available?

Many thanks in advance for your help
James
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[Freesurfer] FreeSurfer 6 Release Date & El Capitan SIP issues

[Shady El Damaty]

Hi,

I was curious to know what the tentative release date for FreeSurfer 6 is.  I’m 
currently running FreeSurfer on multiple machines with El Capitan installed and 
I’m wondering whether it’s worth installing the beta distribution or rather 
uninstalling SIP on each of these many machines.

Also is there any documentation on any specific bugs to watch out for with El 
Capitan and FreeSurfer 5.3?  I’ve been running some functions and haven’t found 
any errors yet.  

Thank you,
Shady El Damaty

PS - how does FreeSurfer 6 plan to get around SIP?
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Re: [Freesurfer] FreeSurfer 6 Release Date & El Capitan SIP issues

[Z K]

On 01/28/2016 01:11 PM, Shady El Damaty wrote:
> Hi,
>
> I was curious to know what the tentative release date for FreeSurfer 6 is.  
> I’m currently running FreeSurfer on multiple machines with El Capitan 
> installed and I’m wondering whether it’s worth installing the beta 
> distribution or rather uninstalling SIP on each of these many machines.
>

The release date for FreeSurfer 6 has been hard to nail down but we are 
in the final stages. I hesitate to give a solid date but I would say a 
month is a fair estimate.


> Also is there any documentation on any specific bugs to watch out for with El 
> Capitan and FreeSurfer 5.3?  I’ve been running some functions and haven’t 
> found any errors yet.
>

I would only expect you to encounter errors if you were calling scripts 
which call freesurfer binaries (e.g. recon-all). If your just calling 
the binaries themselves then those should run successfully.

>
> PS - how does FreeSurfer 6 plan to get around SIP?

We plan on getting around it using two methods. 1) creating wrapper 
scripts for some binaries. 2) Adding a source file in existing scripts 
to recreate the library path that were stripped by SIP.

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>
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Re: [Freesurfer] freesurfer 6 error: dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib

[zkaufman]

Did you source the Freesurfer setup script?

  $> export FREESURFER_HOME=/Applications/freesurfer6
  $> source $FREESURFER_HOME/SetUpFreeSurfer.sh




> Hello All,
>
> I installed freesurfer 6 on a mac running OS-X Yosemite 10.10.4. I am
> getting the following error when I run recon-all from freesurfer 6.
>
> Can you please suggest how to fix it ?
>
> Thank you,
>
> Ri
>
> ri@Magi [0] ~/ri/SampleDatasets$ export
> FREESURFER_HOME= ;export
> SUBJECTS_DIR=/Applications/freesurfer6/subjects;export
> PATH=/Applications/freesurfer6/bin:$PATH;/Applications/freesurfer6/bin/recon-all
> -s Dataset1-only-T1 -i Dataset1/MPRAGE.nii.gz -all
> Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015
> Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015
> INFO: SUBJECTS_DIR is /Applications/freesurfer6/subjects
> Actual FREESURFER_HOME /Applications/freesurfer6
> Darwin Magi.uphs.upenn.edu 14.4.0 Darwin Kernel Version 14.4.0: Thu May 28
> 11:35:04 PDT 2015; root:xnu-2782.30.5~1/RELEASE_X86_64 x86_64
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_convert
>   Reason: image not found
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_convert
>   Reason: image not found
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_make_uchar
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_normalize
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_watershed
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_gcut
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_segment
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_label2label
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_em_register
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_ca_normalize
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_ca_register
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_ca_label
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_pretess
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_fill
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_tessellate
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_concatenate_lta
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mri_normalize_tp2
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mris_smooth
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mris_inflate
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mris_curvature
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mris_sphere
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mris_fix_topology
>   Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
>   Referenced from: /Applications/freesurfer6/bin/mris_topo_fixer
>   

[Freesurfer] Freesurfer 6 - matlab crash

[Scott Quadrelli]

Hi, 

I’m running freesurfer 6 on a cluster. I am having issues with the matlab 
crashing during the hippocampal segmentation. I am allocating 10gb for each 
job, however that hasn’t fixed the problem. Sometime the segmentation works 
fine, however many segmentations fail due to matlab crash. I have attached two 
example crash reports one with ‘segmentation violation’ the other common one is 
‘Abort signal detection’. 

What else should we be looking at to fix the problem ?

Cheers,

Scott





matlab_crash_dump.20760-1
Description: application/applefile


matlab_crash_dump.20760-1
Description: Binary data


matlab_crash_dump.19123-1
Description: application/applefile


matlab_crash_dump.19123-1
Description: Binary data
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[Freesurfer] freesurfer 6 error: dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib

[Ritobrato Datta]

Hello All,

I installed freesurfer 6 on a mac running OS-X Yosemite 10.10.4. I am getting 
the following error when I run recon-all from freesurfer 6. 

Can you please suggest how to fix it ?

Thank you,

Ri

ri@Magi [0] ~/ri/SampleDatasets$ export 
FREESURFER_HOME=/Applications/freesurfer6;export 
SUBJECTS_DIR=/Applications/freesurfer6/subjects;export 
PATH=/Applications/freesurfer6/bin:$PATH;/Applications/freesurfer6/bin/recon-all
 -s Dataset1-only-T1 -i Dataset1/MPRAGE.nii.gz -all
Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015
Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015
INFO: SUBJECTS_DIR is /Applications/freesurfer6/subjects
Actual FREESURFER_HOME /Applications/freesurfer6
Darwin Magi.uphs.upenn.edu 14.4.0 Darwin Kernel Version 14.4.0: Thu May 28 
11:35:04 PDT 2015; root:xnu-2782.30.5~1/RELEASE_X86_64 x86_64
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_convert
  Reason: image not found
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_convert
  Reason: image not found
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_make_uchar
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_normalize
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_watershed
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_gcut
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_segment
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_label2label
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_em_register
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_ca_normalize
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_ca_register
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_ca_label
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_pretess
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_fill
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_tessellate
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_concatenate_lta
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mri_normalize_tp2
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_smooth
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_inflate
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_curvature
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_sphere
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_fix_topology
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_topo_fixer
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_ca_label
  Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
  Referenced from: /Applications/freesurfer6/bin/mris_euler_number
  

[Freesurfer] Freesurfer 6 exits with errors after recon edits on skullstrip

[Tuominen, Lauri Johannes]

Dear Freesurfer experts,

I ran recon-all on launchpad using /usr/local/freesurfer/stable6/bin/recon-all. 
This command worked nicely, but part of the occipital cortex was missing and I 
therefore ran the following command ( both in freesurfer6 ):

  recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -s atib

This took care of the brain mask problem that I had with the previous recon. So 
I then ran on launchpad:

 recon-all -s atib -autorecon2 -autorecon3 -hippocampal-subfields-T1'

The last command exits with errors. Please find the log-files attached.

Thank you for your help!

Best,
Lauri Tuominen

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Re: [Freesurfer] Freesurfer 6 exits with errors after recon edits on skullstrip

[Bruce Fischl]

Hi Lauri

I think you forgot to attach the logs

Bruce


On Thu, 10 Dec 2015, Tuominen, Lauri Johannes wrote:


Dear Freesurfer experts,

I ran recon-all on launchpad using
/usr/local/freesurfer/stable6/bin/recon-all. This command worked nicely, but
part of the occipital cortex was missing and I therefore ran the following
command ( both in freesurfer6 ):

  recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -s atib

This took care of the brain mask problem that I had with the previous recon.
So I then ran on launchpad:

 recon-all -s atib -autorecon2 -autorecon3 -hippocampal-subfields-T1'

The last command exits with errors. Please find the log-files attached.

Thank you for your help!

Best,
Lauri Tuominen
 

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Re: [Freesurfer] FreeSurfer 6 recon-all exiting with errors at -cortparc step

[Zaretskaya, Natalia]

Hi Bruce,

I re-ran the -cortparc step with the current dev version
freesurfer-Linux-centos6_x86_64-dev-20151209

It took ~6 hours and the error is still the same. It seems to run through the 
left hemisphere, but crashes on the right one.

Cheers!
Natalia

On 09 Dec 2015, at 14:37, Bruce Fischl 
> wrote:

HI Natalia

can you try the dev version? I'm pretty sure I fixed this. You can just rerun 
mris_ca_label. We'll hopefully be cutting a new stable 6 sometime soon

cheers
Bruce


On Wed, 9 Dec 2015, Zaretskaya, Natalia wrote:

Dear all,
I am running recon-all with FreeSurfer 6 stable version on launchpad and
have it exiting with errors with all of my 43 brains, always at the same
stage (-cortparc). The same brains used to run through recon-all smoothly
with the dev version just a month or so ago, and I am not doing anything
essentially different than before, except using FreeSurfer 6, so I am
wondering what’s wrong. The output of recon-all before the error looks o.k.
I attached an example recon-all.log file.
Many thanks in advance for your help!
Natalia
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Re: [Freesurfer] FreeSurfer 6 recon-all exiting with errors at -cortparc step

[Bruce Fischl]

HI Natalia

can you try the dev version? I'm pretty sure I fixed this. You can just 
rerun mris_ca_label. We'll hopefully be cutting a new stable 6 sometime 
soon


cheers
Bruce


On Wed, 9 Dec 2015, Zaretskaya, Natalia wrote:


Dear all,

I am running recon-all with FreeSurfer 6 stable version on launchpad and
have it exiting with errors with all of my 43 brains, always at the same
stage (-cortparc). The same brains used to run through recon-all smoothly
with the dev version just a month or so ago, and I am not doing anything
essentially different than before, except using FreeSurfer 6, so I am
wondering what’s wrong. The output of recon-all before the error looks o.k.

I attached an example recon-all.log file.

Many thanks in advance for your help!
Natalia





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Re: [Freesurfer] Freesurfer 6 - exited with errors

[Douglas N Greve]

You may need to download the Matlab Compiler Runtime (MCR) for Matlab 2012b.
To do so, please run the following commands (you might need root 
permissions):

LINUX:

cd $FREESURFER_HOME
curl 
"http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile=get=runtime2012bLinux.tar.gz;
 
-o "runtime2012b.tar.gz"
tar xvf runtime2012b.tar.gz

MAC:

cd $FREESURFER_HOME
curl 
"http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile=get=runtime2012bMAC.tar.gz;
 
-o "runtime2012b.tar.gz"
tar xvf runtime2012b.tar.gz



On 12/08/2015 05:52 AM, Scott Quadrelli wrote:
> Thanks Doug and Bruce for your response.
>
> Here is the result of the command Doug requested:
>
> *$ mris_anatomical_stats -th3 -mgz -f 
> ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot 
> -c ./BA_exvivo.thresh.ctab C02DL_t1 rh white*
>
> INFO: using TH3 volume calc
>
> INFO: assuming MGZ format for volumes.
>
> computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
>
> reading volume 
> /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/mri/wm.mgz...
>
> reading input surface 
> /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.white...
>
> Using TH3 vertex volume calc
>
> Total face volume 229272
>
> Total vertex volume 224839 (mask=0)
>
> reading input pial surface 
> /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.pial...
>
> reading input white surface 
> /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/surf/rh.white...
>
> reading colortable from annotation file...
>
> colortable with 15 entries read (originally 
> /usr/local/freesurfer/6.0.beta/average/colortable_BA.txt)
>
> Saving annotation colortable ./BA_exvivo.thresh.ctab
>
>
> table columns are:
>
> number of vertices
>
> total surface area (mm^2)
>
> total gray matter volume (mm^3)
>
> average cortical thickness +- standard deviation (mm)
>
> integrated rectified mean curvature
>
> integrated rectified Gaussian curvature
>
> folding index
>
> intrinsic curvature index
>
> structure name
>
>
> atlas_icv (eTIV) = 1539395 mm^3 (det: 1.265500 )
>
> lhCtxGM: 216981.653 216526.000 diff=  455.7  pctdiff= 0.210
>
> rhCtxGM: 224488.981 223971.000 diff=  518.0  pctdiff= 0.231
>
> lhCtxWM: 221893.625 222489.000 diff= -595.4  pctdiff=-0.268
>
> rhCtxWM: 224605.205 224852.000 diff= -246.8  pctdiff=-0.110
>
> SubCortGMVol  51078.000
>
> SupraTentVol  967354.464 (965462.000) diff=1892.464 pctdiff=0.196
>
> SupraTentVolNotVent  940904.464 (939012.000) diff=1892.464 pctdiff=0.201
>
> BrainSegVol  453.000 (1108301.000) diff=3152.000 pctdiff=0.284
>
> BrainSegVolNotVent  1080460.000 (1080411.464) diff=48.536 pctdiff=0.004
>
> BrainSegVolNotVent  1080460.000
>
> CerebellumVol 141268.000
>
> VentChorVol   26450.000
>
> 3rd4th5thCSF   4543.000
>
> CSFVol  1413.000, OptChiasmVol 158.000
>
> MaskVol 1614399.000
>
>   663321   1164  2.414 0.317 0.126 0.029   10 0.7  
> BA1_exvivo
>
>  1878   1200   2522  2.055 0.423 0.096 0.018   13 1.5  
> BA2_exvivo
>
>   846653728  1.608 0.324 0.159 0.0359 1.3  
> BA3a_exvivo
>
>  1782   1155   1902  1.588 0.371 0.089 0.0189 1.5  
> BA3b_exvivo
>
>   930539   1396  2.423 0.439 0.108 0.0308 1.4  
> BA4a_exvivo
>
>  1048718   1669  2.480 0.403 0.093 0.0214 1.0  
> BA4p_exvivo
>
>  6264   3392   9732  2.494 0.482 0.103 0.030   66 7.5  
> BA6_exvivo
>
>   951631   1818  2.403 0.428 0.123 0.027   16 1.1  
> BA44_exvivo
>
>   915650   1780  2.212 0.349 0.139 0.031   16 1.0  
> BA45_exvivo
>
>  3074   2189   3724  1.675 0.473 0.134 0.035   33 4.8  
> V1_exvivo
>
>  4690   2886   4907  1.698 0.528 0.151 0.041   79 8.3  
> V2_exvivo
>
>   324198535  2.216 0.477 0.135 0.0365 0.5  
> MT_exvivo
>
>   285170847  3.400 0.783 0.132 0.0364 0.4  
> perirhinal_exvivo
>
>   245177522  2.386 0.732 0.126 0.0202 0.2  
> entorhinal_exvivo
>
>
> The annotation seems to be fine, I have attached a screenshot of the 
> second command.
>
> The initial command I ran was: "recon-all -all -s bert 
> -hippocampal-subfields-T1”
> However I noticed there was no /[lr]h.hippoSfLabels-T1.v10.mgz 
> /output. When I tried to run the just the hippocampal segmentation I 
> got an error that the matlab dependencies weren’t installed, so 
> presumably that is why I received the original message ?!
>
> Cheers,
>
> Scott
>
> From: "quadrel...@me.com " 
> >
> Date: Tuesday, 8 December 2015 8:57 am
> To:  >
> Subject: Freesurfer 6 - exited with errors
>
> Hi All,
>
> I am trying to track down the source of an error on one of my first 
> runs using freesurfer 6.
>
> I have attached the relevant logs. Any help would be 

Re: [Freesurfer] Freesurfer 6 - exited with errors

[Bruce Fischl]

Hi Scott,

hmmm, I know it says "exited with ERRORS", but I don't actually see any 
errors. Did it appear to finish properly? Are the results visually ok?


ZBruce

On 
Tue, 8 Dec 2015, Scott Quadrelli wrote:



Hi All, 

I am trying to track down the source of an error on one of my first runs using 
freesurfer 6.

I have attached the relevant logs. Any help would be much appreciated.

Cheers,

Scott


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Re: [Freesurfer] Freesurfer 6 - exited with errors

[Douglas N Greve]

Not sure. Can you run this command

cd /home/quadrellis/civ_ptsd/structural_fs/C02DL_t1/label
mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b 
-a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab C02DL_t1 rh white

and send  the terminal output. Does it not fail for the left hemi?

Also, run
tksurferfv C02DL rh inflated -annot BA_exvivo.thresh.annot

to see if there is a problem with the annotation

doug



On 12/07/2015 05:57 PM, Scott Quadrelli wrote:
> Hi All,
>
> I am trying to track down the source of an error on one of my first 
> runs using freesurfer 6.
>
> I have attached the relevant logs. Any help would be much appreciated.
>
> Cheers,
>
> Scott
>
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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/

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[Freesurfer] FreeSurfer 6

[Pedro Paulo de Magalhães Oliveira Junior]

Hey Guys,

Sorry if this is a frequently asked question.

Do we have an updated ETA for version 6 of Freesurfer? We are planning on
upgrading our 1024-node cluster and version 6 is a big deal for us.

Best

Pedro Paulo Jr.
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
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[Freesurfer] Freesurfer 6 estimated release date?

[Elijah Mak]

Hello,

I have just read Iglesias et al (2015) hippocampal subfields paper in
Neuroimage with great interest.

Do you have an estimate on the release date of Freesurfer 6 for Mac OSX?
Apologies in advance if this has already been answered elsewhere on this
site.

Many thanks.

Best Wishes,
Elijah

-- 

Elijah Mak, Gates Scholar

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] Freesurfer 6 estimated release date?

[Z K]

We are anticipating a beta release in about two weeks time followed by the 
version 6 release about one week later. 

-Zeke


 On May 2, 2015, at 9:35 AM, Elijah Mak fk...@medschl.cam.ac.uk wrote:
 
 Hello,
 
 I have just read Iglesias et al (2015) hippocampal subfields paper in 
 Neuroimage with great interest. 
 
 Do you have an estimate on the release date of Freesurfer 6 for Mac OSX? 
 Apologies in advance if this has already been answered elsewhere on this site.
 
 Many thanks.
 
 Best Wishes,
 Elijah
 
 -- 
 Elijah Mak, Gates Scholar
 PhD Candidate | Psychiatry
 University of Cambridge
 Trinity College, Cambridge, CB2 1TQ
 
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