[Freesurfer] mri_cnr

[Jürgen Hänggi]

Dear FS experts

There is a reviewer question with respect to the voxels/vertices used to
compute the SNR and CNR with FreeSurfer's mri_cnr function.
Do we right that SNR/CNR computation is based only on the voxels that are
located at the interface between the white and pial surface?

Thanks in advance
Regards
Jürgen Hänggi


Jürgen Hänggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

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Re: [Freesurfer] mri_cnr

[Bruce Fischl]

yes, that is correct.
Bruce
On Mon, 10 Nov 2014, Jürgen Hänggi wrote:


Dear FS experts

There is a reviewer question with respect to the voxels/vertices used to
compute the SNR and CNR with FreeSurfer's mri_cnr function.
Do we right that SNR/CNR computation is based only on the voxels that are
located at the interface between the white and pial surface?

Thanks in advance
Regards
Jürgen Hänggi

---
-
Jürgen Hänggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)  
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)  

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Re: [Freesurfer] edit failure

[Octavian Lie]

Thank you, Bruce

I tried to upload the subject (tar.gz, 183 Mb) to the ftp, followed
instructions

ftp surfer.nmr.mgh.harvard.edu
anonymous
my email
cd transfer/incoming
put /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz

and I get this:

local: /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz
remote: /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz
200 PORT command successful. Consider using PASV.
553 Could not create file.

Please advise,

Octavian

On Sun, Nov 9, 2014 at 9:44 PM, Bruce Fischl 
wrote:

> Hi Octavian
> If you upload the subject we will take a look
> Cheers
> Bruce
>
>
>
> > On Nov 9, 2014, at 10:40 PM, Octavian Lie 
> wrote:
> >
> > Dear all,
> >
> > 1. in the attached there is a gyrus that does not incorporated into
> surfaces, whatever I do (wm edits/topological defects-cloning voxels from
> brainmask.mgz or T1.mgz into wm.mgz, save volume then run recon-all
> autorecon2-wm autorecon 3), or control points addition to wm in
> brainmask.mgz, then run the -cp flag. Is there any other solution left to
> clone the white matter (and pial voxels) left out? is
> brain.finalsurfs.manedit.mgz a solution?
> >
> > 2. Unrelated, after manual pial edits and reruning the recon-all
> autorecon-pial command, the pial surface generated is mostly OK, however
> where there have been heavy dura editing the surface looks granular. Is
> there a workaround (along with better hands), such as smoothing the final
> pia a bit more (preferably in the recon-all pipeline as to be convergent
> with other segmentation results).
> >
> > I appreciate your help,
> >
> > Octavian
> > 
> > 
> > ___
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] mri_surfcluster and "sub-clustering"

[Douglas N Greve]

There is not an explicit program to do this. You can re-run 
mri_surfcluster with a lower threshold and mask to the big cluster to 
force all the results to be within that cluster.
doug

On 11/06/2014 04:29 AM, Sophie Maingault wrote:
> Dear FS experst,
>
> I used the command mri_surfcluster. For one analysis, I obtained 6 
> clusters with one huge of 473 cm2 which corresponds to several 
> "sub-clusters" because it was expanded through a large part of the 
> cortex (covering several anatomical regions). Is there a way to 
> separate one apparent cluster in several sub clusters by extracting 
> several maximum vertices and not only one per cluster ?
>
> Best,
>
> *Sophie Maingault –Doctorante/PhD student*
>
> GIN (Groupe d'Imagerie Neurofonctionnelle)
> UMR 5296 –Université de Bordeaux –CNRS/CEA
> 146, rue Léo Saignat – Case 71
> 33076 Bordeaux cedex
>
>
>
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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
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Re: [Freesurfer] edit failure

[Bruce Fischl]

try changing the local dir to /usr/local/fs5.3/freesurfer/subjects and just 
putting the file without a path

cheers
Bruce


On Mon, 10 Nov 2014, Octavian Lie wrote:

> Thank you, Bruce
> 
> I tried to upload the subject (tar.gz, 183 Mb) to the ftp, followed
> instructions
> 
> ftp surfer.nmr.mgh.harvard.edu
> anonymous
> my email
> cd transfer/incoming
> put /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz
> 
> and I get this:
> 
> local: /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz remote:
> /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz
> 200 PORT command successful. Consider using PASV.
> 553 Could not create file.
> 
> Please advise,
> 
> Octavian
> 
> On Sun, Nov 9, 2014 at 9:44 PM, Bruce Fischl 
> wrote:
>   Hi Octavian
>   If you upload the subject we will take a look
>   Cheers
>   Bruce
> 
> 
>
>   > On Nov 9, 2014, at 10:40 PM, Octavian Lie
>wrote:
>   >
>   > Dear all,
>   >
>   > 1. in the attached there is a gyrus that does not incorporated
>   into surfaces, whatever I do (wm edits/topological
>   defects-cloning voxels from brainmask.mgz or T1.mgz into wm.mgz,
>   save volume then run recon-all autorecon2-wm autorecon 3), or
>   control points addition to wm in brainmask.mgz, then run the -cp
>   flag. Is there any other solution left to clone the white matter
>   (and pial voxels) left out? is brain.finalsurfs.manedit.mgz a
>   solution?
>   >
>   > 2. Unrelated, after manual pial edits and reruning the
>   recon-all autorecon-pial command, the pial surface generated is
>   mostly OK, however where there have been heavy dura editing the
>   surface looks granular. Is there a workaround (along with better
>   hands), such as smoothing the final pia a bit more (preferably
>   in the recon-all pipeline as to be convergent with other
>   segmentation results).
>   >
>   > I appreciate your help,
>   >
>   > Octavian
> > 
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> ___
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> 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
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> and properly
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> 
> 
> 
>
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Re: [Freesurfer] error with fast_selxavg3

[Douglas N Greve]

There are a bunch of columns in the design matrix that are 0, meaning 
that it expects some kind of stimulus to be there but it was not in the 
parfile. Do you only have eccen for this or do you also have polar?
doug


On 11/08/2014 11:25 AM, Francesca Strappini wrote:
> Hi, I attached the file, thank you!
>
> Best
> Francesca
>
> 2014-11-06 18:58 GMT+02:00 Douglas N Greve  >:
>
>
> Can you send me
> 
> /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat
>
> On 11/06/2014 09:53 AM, Francesca Strappini wrote:
> > Dear all,
> >
> > I'm trying to run a retinotopy analysis in several subjects but it
> > crashed with an error in one subject. I ran this command line:
> >
> > selxavg3-sess -a rtopy.HS.rh -s SUBJ09
> >
> >
> > and this is the last part of the output with the error message.
> > Any help would be much appreciated.
> >
> > Best
> > Francesca
> >
> >
> > < M A T L A B (R) >
> >   Copyright 1984-2013 The MathWorks, Inc.
> > R2013b (8.2.0.701) 64-bit (glnxa64)
> >   August 13, 2013
> >
> >  
> > Your MATLAB license will expire in 56 days.
> > Please contact your system administrator or
> > MathWorks to renew this license.
> >  
> >
> > To get started, type one of these: helpwin, helpdesk, or demo.
> > For product information, visit www.mathworks.com
> 
> > .
> >
> > >> >> >> >> >> >> >>
> > sxa3pwd =
> >
> > /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed
> >
> > >>
> > sxa3cmd =
> >
> > /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.HS.rh -s
> SUBJ09
> >
> > >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
> >
> > #@# SUBJ09 ###
> > /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09
> > -
> > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
> > /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> > /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> > /usr/local/freesurfer/matlab/MRIread.m
> > -
> > outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed
> > Extension format = nii.gz
> > nruns = 4
> > autostimdur =
> >
> >
> > outanadir =
> >
> 
> /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh
> > Found 110059/126364 (87.1) voxels in mask
> > Creating Design Matrix
> >  ... creation time =  0.005 sec
> > DoMCFit = 1
> > ntptot = 960, nX = 36, DOF = 924
> > Saving X matrix to
> >
> 
> /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat
> > Error using svd
> > Input to SVD must not contain NaN or Inf.
> >
> > Error in cond (line 36)
> > s = svd(A);
> >
> > Error in fast_selxavg3 (line 279)
> >   XCond = cond(XtX);
> >
> >
> > --
> > Francesca Strappini, Ph.D.
> > Neurobiology Department
> > Weizmann Institute of Science
> > 234 Herzl Street, Rehovot 7610001 Israel
> > Tel.: +972 58 444 2584
> > E-mail: francesca.strapp...@weizmann.ac.il
> 
> >  >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> 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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>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe t

[Freesurfer] Infinite loop in mri_convert

[Nooshin Zadeh]

Dear FreeSurfer experts,


I get a new message when I use "mri_convert" command to convert dicom to
mgz. I used to apply this command before and there was no problem. I wonder
what is the reason that I receive the following message. In addition, it
does not create mgz file, and goes to infinite loop.

*mri_convert  "/M1/t1_se_ax_5/IM-0004-0001.dcm"  "/FS/M1/mri/orig/001.mgz"*
mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /M1/t1_se_ax_5/IM-0004-0001.dcm...
Getting Series No
Scanning Directory
INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5
INFO: Scanning for Series Number 5INFO: found 37 files in series
INFO: loading series header info.

I appreciate if you can advise me.



Regards,
Nooshin
PhD Candidate
Departments of Electrical & Computer Engineering
University of Miami
Email: n.za...@miami.edu
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Re: [Freesurfer] Infinite loop in mri_convert

[Bruce Fischl]

Hi Nooshin

if you upload the dicoms we will take a look

Bruce
On Mon, 10 Nov 2014, Nooshin 
Zadeh wrote:



Dear FreeSurfer experts,

I get a new message when I use "mri_convert" command to convert dicom to
mgz. I used to apply this command before and there was no problem. I wonder
what is the reason that I receive the following message. In addition, it
does not create mgz file, and goes to infinite loop.

mri_convert  "/M1/t1_se_ax_5/IM-0004-0001.dcm"  "/FS/M1/mri/orig/001.mgz"
mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
reading from /M1/t1_se_ax_5/IM-0004-0001.dcm...
Getting Series No 
Scanning Directory 
INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5
INFO: Scanning for Series Number 5INFO: found 37 files in series
INFO: loading series header info.

I appreciate if you can advise me.



Regards,
Nooshin
PhD Candidate
Departments of Electrical & Computer Engineering
University of Miami
Email: n.za...@miami.edu

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Re: [Freesurfer] Infinite loop in mri_convert

[Douglas N Greve]

The messages don't look problematic. What do you mean it goes into an 
infinite loop?
doug

On 11/10/2014 12:14 PM, Nooshin Zadeh wrote:
> Dear FreeSurfer experts,
>
>
> I get a new message when I use "mri_convert" command to convert dicom 
> to mgz. I used to apply this command before and there was no problem. 
> I wonder what is the reason that I receive the following message. In 
> addition, it does not create mgz file, and goes to infinite loop.
>
> *mri_convert  "/M1/t1_se_ax_5/IM-0004-0001.dcm" 
>  "/FS/M1/mri/orig/001.mgz"*
> mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz
> $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $
> reading from /M1/t1_se_ax_5/IM-0004-0001.dcm...
> Getting Series No
> Scanning Directory
> INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5
> INFO: Scanning for Series Number 5INFO: found 37 files in series
> INFO: loading series header info.
>
> I appreciate if you can advise me.
>
>
>
> Regards,
> Nooshin
> PhD Candidate
> Departments of Electrical & Computer Engineering
> University of Miami
> Email: n.za...@miami.edu 
>
>
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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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Re: [Freesurfer] Different significant regions with different cluster wise thresholds

[Douglas N Greve]

Can you upload the gtlmdir and I'll take a look?

On 11/06/2014 08:19 PM, Bronwyn Overs wrote:
> I believe it is the cluster-forming threshold. I was running the 
> following:
> mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 
> 1.3 abs --cwpvalthresh  0.05 --2spaces
> mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 
> 2 abs --cwpvalthresh  0.05 --2spaces
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
>
> Neuroscience Research Australia
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>
> neura.edu.au 
>
> Follow @neuraustralia on twitter 
> Follow NeuRA on facebook 
> Subscribe to 
> the NeuRA Magazine 
>
> On 7/11/2014 4:03 am, Douglas N Greve wrote:
>> Do you mean cluster-wise threshold or cluster-forming threshold?
>>
>> On 11/06/2014 01:12 AM, Bronwyn Overs wrote:
>>> Dear Freesurfer Mailing list,
>>>
>>> While running a glm anlaysis with monte carlo correction (using
>>> cluster wise thresholds of .05 & .01), I encountered the following issue:
>>> When examining the clusters formed for each of the different cluster
>>> wise thresholds, the .05 threshold resulted in a superior temporal
>>> cluster, while the .01 threshold resulted in a two lateral occipital
>>> clusters that did not overlap with the cluster from the .05 threshold.
>>>
>>> Do you know why there would be no overlap between significant regions
>>> at different cluster wise thresholds? I was aware that a cluster which
>>> is significant at .05 may split or be smaller at .01, but I do not
>>> know why entirely different regions would be significant.
>>> -- 
>>>
>>> Kind regards,
>>>
>>> Bronwyn Overs
>>> Research Assistant
>>>
>>> Neuroscience Research Australia
>>>
>>> Neuroscience Research Australia
>>> Margarete Ainsworth Building
>>> Barker Street Randwick Sydney NSW 2031 Australia
>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>>>
>>> neura.edu.au
>>>
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>>> the NeuRA Magazine
>>>
>>>
>>>
>>> ___
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
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
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Re: [Freesurfer] edit failure

[Octavian Lie]

Dear Bruce,

It worked, I transferred it and is ready for view.
The original recon was with the command
recon-all -3T -openmp 8 -notal-check (the raw volume was analyze).
I noted a small gyrus excluded from the surfaces, located in the right
hemisphere posteriorly; the recon also did not include two other regions in
the left hemisphere (one mesial gyrus, and a wedge-shaped region, also
posteriorly located), but I am insterested mainly in the right hemisphere,
and I suspect the solution would be the same.
After the original recon, I did some pial editing (although not perfect),
and tried control points and wm/topological defect corrections. As suchs,
the wm.mgz included was edited to extend into the excluded areas for
correction.
Thank you for helping, as always. Please let me know if there is a fix,
such as cloning voxels from T1.mgz into brain.finalsufs,manedit.mgz.

Octavian

On Mon, Nov 10, 2014 at 11:09 AM, Bruce Fischl 
wrote:

> try changing the local dir to /usr/local/fs5.3/freesurfer/subjects and just
> putting the file without a path
>
> cheers
> Bruce
>
>
> On Mon, 10 Nov 2014, Octavian Lie wrote:
>
> > Thank you, Bruce
> >
> > I tried to upload the subject (tar.gz, 183 Mb) to the ftp, followed
> > instructions
> >
> > ftp surfer.nmr.mgh.harvard.edu
> > anonymous
> > my email
> > cd transfer/incoming
> > put /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz
> >
> > and I get this:
> >
> > local: /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz
> remote:
> > /usr/local/fs5.3/freesurfer/subjects/rightgyrusfailure.tar.gz
> > 200 PORT command successful. Consider using PASV.
> > 553 Could not create file.
> >
> > Please advise,
> >
> > Octavian
> >
> > On Sun, Nov 9, 2014 at 9:44 PM, Bruce Fischl  >
> > wrote:
> >   Hi Octavian
> >   If you upload the subject we will take a look
> >   Cheers
> >   Bruce
> >
> >
> >
> >   > On Nov 9, 2014, at 10:40 PM, Octavian Lie
> >wrote:
> >   >
> >   > Dear all,
> >   >
> >   > 1. in the attached there is a gyrus that does not incorporated
> >   into surfaces, whatever I do (wm edits/topological
> >   defects-cloning voxels from brainmask.mgz or T1.mgz into wm.mgz,
> >   save volume then run recon-all autorecon2-wm autorecon 3), or
> >   control points addition to wm in brainmask.mgz, then run the -cp
> >   flag. Is there any other solution left to clone the white matter
> >   (and pial voxels) left out? is brain.finalsurfs.manedit.mgz a
> >   solution?
> >   >
> >   > 2. Unrelated, after manual pial edits and reruning the
> >   recon-all autorecon-pial command, the pial surface generated is
> >   mostly OK, however where there have been heavy dura editing the
> >   surface looks granular. Is there a workaround (along with better
> >   hands), such as smoothing the final pia a bit more (preferably
> >   in the recon-all pipeline as to be convergent with other
> >   segmentation results).
> >   >
> >   > I appreciate your help,
> >   >
> >   > Octavian
> > > 
> > > 
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > 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.
> >
> >
> >
> >
> ___
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Re: [Freesurfer] error with fast_selxavg3

[Francesca Strappini]

Hi Doug, thanks for the answer. I have both, 2 runs of polar angle and 2 of
eccentricity.

Francesca

On Monday, November 10, 2014, Douglas N Greve 
wrote:

>
> There are a bunch of columns in the design matrix that are 0, meaning
> that it expects some kind of stimulus to be there but it was not in the
> parfile. Do you only have eccen for this or do you also have polar?
> doug
>
>
> On 11/08/2014 11:25 AM, Francesca Strappini wrote:
> > Hi, I attached the file, thank you!
> >
> > Best
> > Francesca
> >
> > 2014-11-06 18:58 GMT+02:00 Douglas N Greve  
> > >:
> >
> >
> > Can you send me
> >
>  
> /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat
> >
> > On 11/06/2014 09:53 AM, Francesca Strappini wrote:
> > > Dear all,
> > >
> > > I'm trying to run a retinotopy analysis in several subjects but it
> > > crashed with an error in one subject. I ran this command line:
> > >
> > > selxavg3-sess -a rtopy.HS.rh -s SUBJ09
> > >
> > >
> > > and this is the last part of the output with the error message.
> > > Any help would be much appreciated.
> > >
> > > Best
> > > Francesca
> > >
> > >
> > > < M A T L A B (R) >
> > >   Copyright 1984-2013 The MathWorks, Inc.
> > > R2013b (8.2.0.701) 64-bit (glnxa64)
> > >   August 13, 2013
> > >
> > >  
> > > Your MATLAB license will expire in 56 days.
> > > Please contact your system administrator or
> > > MathWorks to renew this license.
> > >  
> > >
> > > To get started, type one of these: helpwin, helpdesk, or demo.
> > > For product information, visit www.mathworks.com
> > 
> > > .
> > >
> > > >> >> >> >> >> >> >>
> > > sxa3pwd =
> > >
> > > /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed
> > >
> > > >>
> > > sxa3cmd =
> > >
> > > /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.HS.rh -s
> > SUBJ09
> > >
> > > >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> > > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
> > >
> > > #@# SUBJ09 ###
> > > /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09
> > > -
> > > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
> > > /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> > > /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> > > /usr/local/freesurfer/matlab/MRIread.m
> > > -
> > > outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed
> > > Extension format = nii.gz
> > > nruns = 4
> > > autostimdur =
> > >
> > >
> > > outanadir =
> > >
> >
>  /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh
> > > Found 110059/126364 (87.1) voxels in mask
> > > Creating Design Matrix
> > >  ... creation time =  0.005 sec
> > > DoMCFit = 1
> > > ntptot = 960, nX = 36, DOF = 924
> > > Saving X matrix to
> > >
> >
>  
> /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat
> > > Error using svd
> > > Input to SVD must not contain NaN or Inf.
> > >
> > > Error in cond (line 36)
> > > s = svd(A);
> > >
> > > Error in fast_selxavg3 (line 279)
> > >   XCond = cond(XtX);
> > >
> > >
> > > --
> > > Francesca Strappini, Ph.D.
> > > Neurobiology Department
> > > Weizmann Institute of Science
> > > 234 Herzl Street, Rehovot 7610001 Israel
> > > Tel.: +972 58 444 2584
> > > E-mail: francesca.strapp...@weizmann.ac.il 
> > 
> > >  > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu 
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu   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:
> > ft

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

[Caspar M. Schwiedrzik]

Hi!
A quick follow-up:
I have a taskreg file with 6 continuous predictors. I would like to run
specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6).
>From what I gather, selxavg3-sess will run automatic contrasts on taskregs,
but the automatic contrasts are against baseline. This is not what I need
at this point.
mk-contrast-sess does not like what I am putting in because I do not have a
paradigm file in which condition numbers are specified.
Is there a way to compute specific contrasts between multiple taskregs, and
if not, is there a workaround?
Thank you very much, Caspar


2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik :

> Hi!
> I have several external regressors in my analysis that I configure with
> -taskreg in mkanalysis-sess (something like -notask -taskreg nameoffile 6).
> I was wondering how to set up mkcontrast-sess to contrast these regerssors
> given that I do not have a paradigm file for them.
> Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5?
>
> Thanks, Caspar
>
>
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] error with fast_selxavg3

[Douglas N Greve]

Check in the rtopy.par file for the polar and make sure it actually says 
polar (and not eccen) inside

On 11/10/2014 01:23 PM, Francesca Strappini wrote:
> Hi Doug, thanks for the answer. I have both, 2 runs of polar angle and 
> 2 of eccentricity.
>
> Francesca
>
> On Monday, November 10, 2014, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> There are a bunch of columns in the design matrix that are 0, meaning
> that it expects some kind of stimulus to be there but it was not
> in the
> parfile. Do you only have eccen for this or do you also have polar?
> doug
>
>
> On 11/08/2014 11:25 AM, Francesca Strappini wrote:
> > Hi, I attached the file, thank you!
> >
> > Best
> > Francesca
> >
> > 2014-11-06 18:58 GMT+02:00 Douglas N Greve
> 
> > >:
> >
> >
> > Can you send me
> >
>  
> /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat
> >
> > On 11/06/2014 09:53 AM, Francesca Strappini wrote:
> > > Dear all,
> > >
> > > I'm trying to run a retinotopy analysis in several
> subjects but it
> > > crashed with an error in one subject. I ran this command line:
> > >
> > > selxavg3-sess -a rtopy.HS.rh -s SUBJ09
> > >
> > >
> > > and this is the last part of the output with the error
> message.
> > > Any help would be much appreciated.
> > >
> > > Best
> > > Francesca
> > >
> > >
> > > < M A T L A B (R) >
> > >   Copyright 1984-2013 The MathWorks, Inc.
> > > R2013b (8.2.0.701) 64-bit (glnxa64)
> > >   August 13, 2013
> > >
> > > 
> > > Your MATLAB license will expire in 56 days.
> > > Please contact your system administrator or
> > > MathWorks to renew this license.
> > > 
> > >
> > > To get started, type one of these: helpwin, helpdesk, or demo.
> > > For product information, visit www.mathworks.com
> 
> > 
> > > .
> > >
> > > >> >> >> >> >> >> >>
> > > sxa3pwd =
> > >
> > > /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed
> > >
> > > >>
> > > sxa3cmd =
> > >
> > > /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a
> rtopy.HS.rh -s
> > SUBJ09
> > >
> > > >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> > > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
> > >
> > > #@# SUBJ09 ###
> > > /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09
> > > -
> > > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve
> Exp $
> > > /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> > > /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> > > /usr/local/freesurfer/matlab/MRIread.m
> > > -
> > > outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed
> > > Extension format = nii.gz
> > > nruns = 4
> > > autostimdur =
> > >
> > >
> > > outanadir =
> > >
> >
>  
> /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh
> > > Found 110059/126364 (87.1) voxels in mask
> > > Creating Design Matrix
> > >  ... creation time =  0.005 sec
> > > DoMCFit = 1
> > > ntptot = 960, nX = 36, DOF = 924
> > > Saving X matrix to
> > >
> >
>  
> /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat
> > > Error using svd
> > > Input to SVD must not contain NaN or Inf.
> > >
> > > Error in cond (line 36)
> > > s = svd(A);
> > >
> > > Error in fast_selxavg3 (line 279)
> > >   XCond = cond(XtX);
> > >
> > >
> > > --
> > > Francesca Strappini, Ph.D.
> > > Neurobiology Department
> > > Weizmann Institute of Science
> > > 234 Herzl Street, Rehovot 7610001 Israel
> > > Tel.: +972 58 444 2584
> > > E-mail: francesca.strapp...@weizmann.ac.il 
> > 
> > >  > >
> > >
> > >
> > > ___
> > 

Re: [Freesurfer] Running a contrast on multiple taskregs in FSFAST

[Douglas N Greve]

To get sig maps for  an individual, this is problematic but I could 
probably come up with a work-around. For a group analysis, you can 
simply compute each taskreg separately, then subtract the two prior to 
running mri_glmfit.
doug

On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote:
> Hi!
> A quick follow-up:
> I have a taskreg file with 6 continuous predictors. I would like to 
> run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6).
> From what I gather, selxavg3-sess will run automatic contrasts on 
> taskregs, but the automatic contrasts are against baseline. This is 
> not what I need at this point.
> mk-contrast-sess does not like what I am putting in because I do not 
> have a paradigm file in which condition numbers are specified.
> Is there a way to compute specific contrasts between multiple 
> taskregs, and if not, is there a workaround?
> Thank you very much, Caspar
>
>
> 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik 
> mailto:cschwie...@rockefeller.edu>>:
>
> Hi!
> I have several external regressors in my analysis that I configure
> with -taskreg in mkanalysis-sess (something like -notask -taskreg
> nameoffile 6).
> I was wondering how to set up mkcontrast-sess to contrast these
> regerssors given that I do not have a paradigm file for them.
> Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5?
>
> Thanks, Caspar
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
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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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] Running a contrast on multiple taskregs in FSFAST

[Caspar M. Schwiedrzik]

Hi Doug,
thanks for your reply. I would like to feed the differences into a FFX
group analysis, so I think I will need to resort to your workaround. It
would be great if you could provide that. Thanks! Caspar

2014-11-10 13:45 GMT-05:00 Douglas N Greve :

>
> To get sig maps for  an individual, this is problematic but I could
> probably come up with a work-around. For a group analysis, you can
> simply compute each taskreg separately, then subtract the two prior to
> running mri_glmfit.
> doug
>
> On 11/10/2014 01:36 PM, Caspar M. Schwiedrzik wrote:
> > Hi!
> > A quick follow-up:
> > I have a taskreg file with 6 continuous predictors. I would like to
> > run specific contrasts, e.g., predictor 1 vs. mean(predictor 2:6).
> > From what I gather, selxavg3-sess will run automatic contrasts on
> > taskregs, but the automatic contrasts are against baseline. This is
> > not what I need at this point.
> > mk-contrast-sess does not like what I am putting in because I do not
> > have a paradigm file in which condition numbers are specified.
> > Is there a way to compute specific contrasts between multiple
> > taskregs, and if not, is there a workaround?
> > Thank you very much, Caspar
> >
> >
> > 2014-11-06 15:23 GMT-05:00 Caspar M. Schwiedrzik
> > mailto:cschwie...@rockefeller.edu>>:
> >
> > Hi!
> > I have several external regressors in my analysis that I configure
> > with -taskreg in mkanalysis-sess (something like -notask -taskreg
> > nameoffile 6).
> > I was wondering how to set up mkcontrast-sess to contrast these
> > regerssors given that I do not have a paradigm file for them.
> > Can I just do something like -a 1 -c 2 -c 3 -c 4 -c 5?
> >
> > Thanks, Caspar
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> 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/
>
> ___
> 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.
>
>
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Re: [Freesurfer] freeview fault: PETSC Error ... PERSISTENT

[Krieger, Donald N.]

Hi Nick,



I downloaded the most recent version of freeview.bin using wget as you 
suggested and ran it on two different machines.

It appeared to load a volume file fully whereas before it was crashing when 
showing it had loaded only 1%.

But it still crashes after that with the message below my signature.



I tried a few different .mgz files including the original one with the same 
result.  Both the machines on which I ran it have 8 GBytes of RAM.  Any other 
thoughts would be welcome.



Regards,



Don



[0]PETSC ERROR: 


[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range

[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find m

emory corruption errors

[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run

[0]PETSC ERROR: to get more information on the crash.

[0]PETSC ERROR: - Error Message 


[0]PETSC ERROR: Signal received!

[0]PETSC ERROR: 


[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124

[0]PETSC ERROR: See docs/changes/index.html for recent updates.

[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.

[0]PETSC ERROR: See docs/index.html for manual pages.

[0]PETSC ERROR: 


[0]PETSC ERROR: Unknown Name on a linux-gnu named donHome1TB by kriegerd Mon 
Nov 10 13:48:15 2014

[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt

[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010

[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-sha

red=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3

[0]PETSC ERROR: 


[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file

[unset]: aborting job:

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0







> -Original Message-

> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-

> boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky, MGH

> Sent: Tuesday, November 04, 2014 11:59 PM

> To: Freesurfer support list

> Subject: Re: [Freesurfer] freeview fault: PETSC Error ...

>

> you can try downloading our nightly 'dev' build of freeview, from here:

>

> https://surfer.nmr.mgh.harvard.edu/fswiki/Download

>

> or here's a quicker way (this is a one-line command... wget ):

>

> wget

> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x

> 86_64/freeview.bin

>

> and copy it to $FREESURFER_HOME/bin

> then

> chmod a+x $FREESURFER_HOME/bin/freeview.bin

>

> N.

>

>

> On Tue, 2014-11-04 at 12:35 +, Krieger, Donald N. wrote:

> > I recently downloaded and installed

> > freesurfer-Linux-centos6_x86_64-table-pub-v5.3.0.tar.gz .

> >

> > I had been running this version previously but had to reload

> > everything due to a disk crash.

> >

> >

> >

> > recon-all –all goes to completion with no errors.

> >

> > freeview starts up fine but fails on loading a volume file with the

> > PETC error listed below.

> >

> > I found several references to this error in the archive but no

> > resolution for my problem.

> >

> > Any thoughts would be welcome – thanks.

> >

> >

> >

> > [0]PETSC ERROR:

> > --

> > --

> >

> > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,

> > probably memory access out of range

> >

> > [0]PETSC ERROR: Try option -start_in_debugger or

> > -on_error_attach_debugger

> >

> > [0]PETSC ERROR: or see

> > http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.ht

> > ml#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man

> > libgmalloc on Apple to find memory corruption errors

> >

> > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,

> > and run

> >

> > [0]PETSC ERROR: to get more information on the crash.

> >

> > [0]PETSC ERROR: - Error Message

> > 

> >

> > [0]PETSC ERROR: S

[Freesurfer] inverted dicoms

[will brown]

Hi all,

I have files that are 2D axial slices that are left-right inverted, so the
left side of the brain is on the right side of each slice. Do I need to do
anything to the dicoms before importing them into freesurfer?

Thanks,
Will
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Re: [Freesurfer] inverted dicoms

[Bruce Fischl]

Hi Will

not if the dicoms have the correct ras2vox matrix (which they should). 
Try visualizing them in freeview and see if the anatomical labels it 
shows are correct

cheers
Bruce
On Tue, 11 Nov 2014, will brown wrote:

> Hi all,
> 
> I have files that are 2D axial slices that are left-right inverted, so the
> left side of the brain is on the right side of each slice. Do I need to do
> anything to the dicoms before importing them into freesurfer?
> 
> Thanks,
> Will
> 
>
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