Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

[Milde, Christopher]

Dear Doug,

Unfortunately, it doesn't make a difference if I'm using a dot or comma or 
simply type in 2 or 3 as a threshold. The terminal output always shows me the 
converted version with a comma 2.3 --> 2,3 or 2 --> 2,0 which is not recognized 
by the command. 

Maybe I have to change the default settings of floats in the bash using printf?

Sincerely yours,

Christopher

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve
Gesendet: Mittwoch, 10. Dezember 2014 17:31
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] multiple comparisons correction for individual 
hemispheres (native space)


Are you using 1.3 or 1,3 ?

On 12/09/2014 03:10 AM, Milde, Christopher wrote:
> Dear Doug,
>
> I tried to run MCC with cluster-sess but unfortunately I got the same error 
> message like when I'm using mri_glmfit-sim.
> It does not recognize the thresh (cluster-forming thresh)
>
> Here is the terminal output:
>
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /home/christopher/Desktop/freesurfer
> FSFAST_HOME   /home/christopher/Desktop/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /home/christopher/Desktop/freesurfer/subjects
> MNI_DIR   /home/christopher/Desktop/freesurfer/mni
> FSL_DIR   /usr/local/fsl
> [christopher@fu20a S1]$ proj_dir=/home/christopher/Desktop/freesurfer/S1
> [christopher@fu20a S1]$ cd $proj_dir
> [christopher@fu20a S1]$
> [christopher@fu20a S1]$ cluster-sess -s PM_02540 -c stim_DL -analysis 
> DL.sm5.rh -thresh 1.3 -cwp .05 -sign pos
> ERROR: thresh = 1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
>
> Sincerely yours,
>
> Christopher
>
>
>
> -Ursprüngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve
> Gesendet: Montag, 24. November 2014 20:34
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] multiple comparisons correction for individual 
> hemispheres (native space)
>
>
> Hi Christopher, sorry for the delay. I had a write a new program. You can 
> download it from here 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cluster-sess
> Let me know how it goes
>
> doug
>
> On 11/14/2014 06:05 AM, Milde, Christopher wrote:
>> Dear Freesurfer experts,
>>
>> I performed fMRI analysis using FSFast resulting in uncorrected significance 
>> maps (fsig.nii.gz). For selxavg3-sess I did not use the -fwhm flag (I rerun 
>> selxavg3-sess with -fwhm at moment).
>>
>> How can I use simulations for native space hemispheres?. I tried to adapt 
>> mri_glmfit-sim but unfortunately it failed...
>>
>> Sincerely yours,
>>
>> Christopher
>>
>> ___
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>> 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 
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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] subcortical segmentation only

[Lukas . Scheef]

Dear Bruce!

Thanks a lot for the response.  I try to get an idea about the minimal time
needed to get the subcortical volumes.

Best wishes,

Luke

> Re: [Freesurfer] subcortical segmentation only
> Bruce Fischl Wed, 10 Dec 2014 05:22:18 -0800
>
> Hi Luke
>
> you can run -autorecon1 and -autorecon2 if all you care about is the aseg
> (although we have tools for editing the cortical aseg labels with the
> surfaces that you will not be able to use in this case)
>
> cheers
> Bruce
> On Wed, 10 Dec 2014,
> lukas.sch...@ukb.uni-bonn.de wrote:
>
> >
> > Hi FS-folks!
> >
> > I would like to perform a subcortical segmentation only and I am not
sure
> > which preprocessing steps I would have to perform to achieve this goal.
> > So far I did always the full monty using reconall -all. Which reconall
> > stages are needed if only the subcortical segmentation is of interest?
> >
> > Best wishes and many thanks for you help!
> >
> > Luke
> >
> >
> >
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Re: [Freesurfer] use of high res T1 for subcortical segmentation

[Lukas . Scheef]

Dear Remi!

Would you mind to send me the new mri_tessellate?

Best wishes,

Luke

> Re: [Freesurfer] use of high res T1 for subcortical segmentation
> Remi Gau Wed, 10 Dec 2014 06:29:04 -0800
>
>  Hey,
>
> Someone corrects me if I am wrong, but it seems that the number of
> vertices currently allowed with freesurfer cannot accomodate more
> than a certain number of vertices.
> I suspect that the new version of Freesurfer should allow for more
vertices.
>
> On high res you might get such error message:
> mri_tessellate: max vertices 100 exceeded
> recon-all -s Subject_12 exited with ERRORS at Thu Apr 10 11:16:42 BST
2014
>
> Seems the issue has been raised before in this thread:
>
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html
>
> Zeke sent me a file of the new mri_tessellate: I can forward it to
> you if you want.
>
> Best
> Remi Gau
>
> On 10/12/14 10:24, lukas.sch...@ukb.uni-bonn.de wrote:
> Dear Remi!
>
> Thanks a lot for the fast response. Could comment further on your
> point that I might need a different version of mri_tesselate ...
> The spatial resolution I am talking about is 0.5x0.5x0.8 mm3.
>
> Best wihes,
>
> Luke
>
> > Yup.
> >
> > http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon
> >
> > Depending how far you intend to push it, you might need a different
> > version of the mri_tesselate function.
> >
> > Best
> >
> > Remi Gau
> >
> > On 10/12/14 08:44, lukas.sch...@ukb.uni-bonn.de wrote:
> > Hi folks!
> >
> > Is there any way to convince FS to make use of a high spatial
> > resolution (better than 1 x 1 x 1 mm3) for subcortical segmentation?
> >
> > Best wishes,
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[Freesurfer] Qdec coordinates

[Las Blawimo]

Dear experts,

I had a question regarding the output of my Qdec analyses. When I run a
Monte Carlo Z simulation on my results, I get the following output:

# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZCWP
CWPLowCWPHi   NVtxs   Annot
   12.930   94685921.76-48.9   -7.0   41.2  0.02170
0.01980  0.02360  2096  precentral
   22.525   33091935.62-21.2   22.2   35.2  0.01950
0.01770  0.02130  1634  superiorfrontal

When I then press the 'find cluster and goto max' button, I get a different
output:

Generating cluster stats using min threshold of 1.3...
Found 2 clusters
Contrast: 'lh-Avg-thickness-SensTOTAV-Cor', 10fwhm, DOF: 185
ClusterNo  Max   VtxMax  Size(mm2)   TalX   TalY   TalZ NVtxs Annotation
-  ---   --  -          - --
11.7100 109935.62   -22.7   24.0   51.0 1634
superiorfrontal
21.6635  12921.76   -52.5   -6.6   38.5 2096  precentral


I am assuming that that the second output gives the coordinates of the max
significant vertex. What does the first set of coordinates refer too? I
think it may the cluster's centre of mass, but I am not sure. Thank you!

Kind regards,

Las
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Re: [Freesurfer] retinotopy analysis viewing problem in Freesurfer 5

[zhang mingxia]

Thank you very much!

The map opened by rtview seems correct. As a new learner of retinotopic
analysis, I have one more basic quesion: What do the three files
(imag.nii.gz, real.nii.gz and fsig.nii.gz) represent? Hope some experienced
one can reply me!

Mingxia

On Thu, Dec 11, 2014 at 12:14 AM, Douglas N Greve  wrote:

>
> On 12/08/2014 09:19 PM, zhang mingxia wrote:
> > Hi Doug,
> >
> > I followed this guide:
> >
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis
> .
> > I used "tksurfer-sess" to view. Does "significant activation in the
> > visual cortex" mean the map from"tksurfer-sess -a rtopy.self.?h -s
> > sessid"? If so, yes.
> >
> > My question is (1) What do the maps from
>
> > "tksurfer-sess -a rtopy.self.?h -s sessid" -- this shows you the
> > significance map (-log10(p)) with eccen and polar in different frames
> > in the tksurfer overaly.
>
> > , "tksurfer-sess -a rtopy.self.?h -s sessid -map angle" This shows you
> > the angle with eccen and polar in different frames in the tksurfer
> overlay
>
> > , "tksurfer-sess -a rtopy.self.?h -s sessid -map angle.masked" This
> > shows you the angle with eccen and polar in different frames in the
> > tksurfer overlay with the angle masked to only those voxels that are
> > significant (p<.01).
>
> > and "tksurfer-sess -a rtopy.self.?h -s sessid -fieldsign" represent?
> > This shows you the field sign map.
>
> >
> > (2)I expected to get a red, green and blue map, but none of them is.
> > The first three are heat (yellow and red) and the fourth is red-blue.
> > This is the first time for me to do retinotopic analysis. The data is
> > from an experienced group for doing retinotopic research. I analyzed
> > four runs with two for eccen and two for polar. Do other people also
> > get this kind of color by using the script in the website above?
> tksurfer-sess will not generate a RGB colorwheel map. This functionality
> has been hard to continue to support. You can try rtview. You would use
> the RGB map to show the angle maps.
> >
> > (3)Which map is for delineating the boarder of visual area?
> field sign
> >
> > (4)Again, I expect to get a red, green and blue map as this people
> > asked
> > :
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21512.html.
> > How can I get a standard color?
> >
> > Thanks again!
> >
> > Mingxia
> >
> > On Tue, Dec 9, 2014 at 12:07 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > I'm not sure what you are asking for. Do you see significant
> > activation
> > in the visual cortex? What command are you running to view?
> >
> >
> > On 12/08/2014 09:48 AM, zhang mingxia wrote:
> > > Dear freesurfer experts,
> > >
> > > I used Freesurfer 5 to do the retinotopic analysis followed by
> > >
> >
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis
> .
> > > However, finally I didn't get a red, green and blue map as I
> > expected.
> > >
> > > This is the first time for me to analyze retinotopic data. I
> > have not
> > > quite understood what the raw angle map, the angle map masked by
> sig
> > > and field sign map meant. My purpose was to delineate the boarder
> of
> > > visual area. To my knowledge from previous study, I should get a
> > > colorful map. It seems I didn't get a right one (However, I exactly
> > > follow the guide and didn't get any error). Some other people seems
> > > having the same viewing problem: (He/She didn't have eccen data. I
> > > have both eccen and polar data. I also only got a heat map
> > instead of
> > > a red, green and blue one)
> > >
> >
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21512.html
> > >
> > > (1)Is it due to the threshold? How can I get a red, green and
> > blue map?
> > > (2) What does the three maps represent?
> > >
> > > Thanks a lot!
> > >
> > > Mingxia
> > >
> > >
> > > ___
> > > 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.

[Freesurfer] QDEC, Correction for multiple comparisons

[Xinfa Shi]

Hello,everyone

Your reply said I can't use alphasim with qdec.By the way ,Could I use
alphasim in other ways in FreeSurfer,for example command line ?

Best regards.

Xin-Fa Shi.
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Re: [Freesurfer] Getting voxel values from aseg.mgz

[Bruce Fischl]

  mri_extract_label
Usage: mri_extract_label [options]... 

Options:
-s   apply a Gaussian smoothing kernel
-t  apply the transform in  to extracted 
volume
-exit_none_foundexit 1 if label(s) not found
-dilate  dilate output volume  times
-erode   erode output volume  times

This program will extract a set of labeled voxels from an image.


so from the subject's mri dir you could do:

mri_extract_label aseg.mgz 17 53 hippo_labels.mgz

cheers
Bruce

On Thu, 11 
Dec 
2014, pradeep mahato wrote:

> There is no documentation or example for mri_extract_label.
> What should be the syntax for it. What kernel and xform file should be used.
> 
> On Wed, Dec 10, 2014 at 6:50 PM, Bruce Fischl 
> wrote:
>   Hi Pradeep
>
>   you can use mri_extract_label to copy just the hippocampal
>   labels out of
>   the segmentation if that is what you mean. The values for left
>   and right
>   hippocampus (17 and 53) can be found in
>   $FREESURFER_HOME/FreeSurferColorLUT.txt
>
>   cheers
>   Bruce
>   On
>   Wed, 10 Dec 2014, pradeep mahato wrote:
>
>   > After the recon-all process I want to access all the voxels in
>   the left
>   > hippocampus ( any subcortical region ) .
>   > Please tell me is there any method to extract this voxel
>   values from an
>   > segmented image.
>   >
>   > Thanking you
>   >
>   > Pradeep Kumar Mahato
>   >
>   >
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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.
> 
> 
> 
> 
> --
> Pradeep Kumar Mahato
> 
>
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Re: [Freesurfer] use of high res T1 for subcortical segmentation

[Bruce Fischl]

if you tell us what hardware/software platform you want it for we can 
post the current version, which I think has a limit of 10,000,000 
vertices and twice that many faces. Presumably that is enough?



cheers
Bruce

On Thu, 11 
Dec 2014, lukas.sch...@ukb.uni-bonn.de wrote:




Dear Remi!

Would you mind to send me the new mri_tessellate?

Best wishes,

Luke

> Re: [Freesurfer] use of high res T1 for subcortical segmentation
> Remi Gau Wed, 10 Dec 2014 06:29:04 -0800
>
>  Hey,
>
> Someone corrects me if I am wrong, but it seems that the number of
> vertices currently allowed with freesurfer cannot accomodate more
> than a certain number of vertices.
> I suspect that the new version of Freesurfer should allow for more
vertices.
>
> On high res you might get such error message:
> mri_tessellate: max vertices 1,000,000 exceeded
> recon-all -s Subject_12 exited with ERRORS at Thu Apr 10 11:16:42 BST 2014
>
> Seems the issue has been raised before in this thread:
> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html
>
> Zeke sent me a file of the new mri_tessellate: I can forward it to
> you if you want.
>
> Best
> Remi Gau
>
> On 10/12/14 10:24, lukas.sch...@ukb.uni-bonn.de wrote:
> Dear Remi!
>
> Thanks a lot for the fast response. Could comment further on your
> point that I might need a different version of mri_tesselate ...
> The spatial resolution I am talking about is 0.5x0.5x0.8 mm3.
>
> Best wihes,
>
> Luke
>
> > Yup.
> >
> > http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon
> >
> > Depending how far you intend to push it, you might need a different
> > version of the mri_tesselate function.
> >
> > Best
> >
> > Remi Gau
> >
> > On 10/12/14 08:44, lukas.sch...@ukb.uni-bonn.de wrote:
> > Hi folks!
> >
> > Is there any way to convince FS to make use of a high spatial
> > resolution (better than 1 x 1 x 1 mm3) for subcortical segmentation?
> >
> > Best wishes,
>


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Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

[lindsay hanford]

Hello,

Has anyone had a chance to look at this? I still haven't been able to solve
the problem.
Thanks!

Lindsay

On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford 
wrote:

> Hello Freesurfer Experts!
>
> I am encountering the dreaded mri_glmfit error:  matrix is ill-conditioned
> or badly scaled, condno = 1e+08. I have tried to troubleshoot how to solve
> this problem from other inquiries, however, I still have had no luck. I am
> trying to run a 4 group 1 variable analysis: with diagnosis being my
> variable of interest and trying to regress out the effects of sex and age.
>
>   1. Command line:
> mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C
> SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh
>   2. The FSGD file (if using one) (see attached)
>   3. And the design matrix:
>0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached)
>
> To the best of my knowledge, all my files are the right format and I
> believe I have adequate number of participants per group?
> I also tried mean centering my age variable. I had success when I ran just
> a two group analysis (diagnosis) not controlling for sex or age, however,
> as soon as I try to run four groups, I encounter this error. I have no idea
> how to proceed.
>
> I am looking forward to your response!
> Thanks,
>
>
> Lindsay
>
> --
> Lindsay Hanford, BSc, PhD Candidate
> McMaster Integrative Neuroscience Discovery & Study | *Department of
> Psychology, Neuroscience & Behaviour *
> McMaster University *|* 1280 Main Street West, PC329 Psychology Building
> *|* Hamilton, ON, L8S 4L8
> 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com
>
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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
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Re: [Freesurfer] use of high res T1 for subcortical segmentation

[Lukas . Scheef]

Hi Bruce!

I am working on a Mac, OS 10.10.1, FS version:
freesurfer-Darwin-lion-stable-pub-v5.3.0

All the best,

Luke

> Re: [Freesurfer] use of high res T1 for subcortical segmentation
> Bruce Fischl Thu, 11 Dec 2014 05:36:52 -0800
>
> if you tell us what hardware/software platform you want it for we
> can post the current version, which I think has a limit of 10,000,
> 000 vertices and twice that many faces. Presumably that is enough?
>
> cheers
> Bruce___
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Problem with mris_register: face not in vertex face list

[Wegbreit, Ezra]

Hi Bruce,

Thank you very much for this information.  Deleting the rh.sphere file and
re-running -make all did fix this issue and the brain now looks great.   I
wanted to confirm this so that if anyone else has the same issue they will
know what might work to fix it.

I had a question about the potential space issue.   Did you mean hard drive
space or RAM?  We have 7 TB of disk space on a Linux cluster - only 20% of
which is full.   When I ran recon-all, I submitted the script to a SLURM
batch system on the cluster, requesting 8 cpus and 24 GB of RAM.   Would
any of this explain why the rh.sphere file could have gotten corrupted?
Should I request even more RAM / more or fewer CPUs?  In general, recon-all
runs rather quickly on this setup.

Thanks!
Ezra

*___*
*Ezra Wegbreit, PhD*
NIMH T32 Post-doctoral Research Fellow in Child Mental Health
Pedi-MIND Program at Bradley Hospital
Department of Psychiatry and Human Behavior
Brown University Warren Alpert Medical School
(401) 432-1615
ezra_wegbr...@brown.edu

*___*


On Tue, Dec 9, 2014 at 4:13 PM, Bruce Fischl 
wrote:

> seems like the rh.sphere file is corrupted. Maybe you ran out of disk
> space? I would try deleting it and reruning with -make all
>
> cheers
> Bruce
>
> On Tue, 9 Dec 2014, Wegbreit, Ezra wrote:
>
>  Dear Freesurfer support community,
>>
>> I am having a recurring issue with re-running a participant after making
>> manual white matter edits (i.e., filling in holes in the wm.mgz file).   I
>> saved the new wm.mgz file and then reran using -make all (twice).  For
>> some
>> reason, Freesurfer stops at the Surf Reg step, but only for the right
>> hemisphere.  When I check the surfaces, I have lh white and pial, but only
>> rh white (no pial).
>>
>> Here is the error message I received both times (bold added for emphasis).
>>
>> "
>> Tue Dec  9 12:21:39 EST 2014
>> /gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/
>> Freesurfer_Analyses/da
>> ta/s4504
>> /gpfs/runtime/opt/freesurfer/5.3.0/bin/recon-all
>> -s/gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/
>> Freesurfer_Analyses/da
>> ta/s4504 -hemi rh -surfreg
>> #
>> #@# Surf Reg rh Tue Dec  9 12:21:40 EST 2014
>> /gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/
>> Freesurfer_Analyses/da
>> ta/s4504/scripts
>>
>>  mris_register -curv ../surf/rh.sphere/gpfs/runtime/opt/freesurfer/5.3.0/
>> average/rh.average.curvature.filled.buck
>> ner40.tif ../surf/rh.sphere.reg
>>
>> using smoothwm curvature for final alignment
>> $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
>>   $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
>> reading surface from ../surf/rh.sphere...
>> mrisFindNeighbors: ../surf/rh.sphere: face[205364].v[0] = 103504, but face
>> 205364 not in vertex 103504 face list
>>
>> No such file or directory
>> Linux node426 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC
>> 2013
>> x86_64 x86_64 x86_64 GNU/Linux
>> "
>>
>> I think my error is related to the following error that someone else
>> reported recently(http://www.mail-archive.com/freesurfer%40nmr.
>> mgh.harvard.edu/msg36707.html
>> ) though the function with the error (mris_euler_number) was different
>> than
>> the one I have.  Dr. Fischl's response was to suggest a re-run (which I
>> did)
>> and to suggest that the surfaces ended up too big and that this bug could
>> be
>> fixed in the future.   Could I have added too many WM voxels, making the
>> resulting surface too big?  I tried to be as conservative as possible,
>> while
>> still filling white matter holes in the anterior temporal lobes.
>>
>> I'm running Freesurfer v. 5.3.0 on a Linux system.
>>
>> Thanks in advance for answers!
>> Ezra
>> ___
>> Ezra Wegbreit, PhD
>> NIMH T32 Post-doctoral Research Fellow in Child Mental Health
>> Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human
>> Behavior
>> Brown University Warren Alpert Medical School
>> (401) 432-1615
>> ezra_wegbr...@brown.edu
>>
>>
>> ___
>>
>>
>>
> ___
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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.
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Re: [Freesurfer] Problem with mris_register: face not in vertex face list

[Bruce Fischl]

Hi Ezra

I have no idea why this would have happened. That's plenty of disk space 
and RAM.


sorry
Bruce

On Thu, 11 Dec 2014, Wegbreit, Ezra wrote:


Hi Bruce,

Thank you very much for this information.  Deleting the rh.sphere file and
re-running -make all did fix this issue and the brain now looks great.   I
wanted to confirm this so that if anyone else has the same issue they will
know what might work to fix it.

I had a question about the potential space issue.   Did you mean hard drive
space or RAM?  We have 7 TB of disk space on a Linux cluster - only 20% of
which is full.   When I ran recon-all, I submitted the script to a SLURM
batch system on the cluster, requesting 8 cpus and 24 GB of RAM.   Would any
of this explain why the rh.sphere file could have gotten corrupted?  Should
I request even more RAM / more or fewer CPUs?  In general, recon-all runs
rather quickly on this setup.

Thanks!
Ezra

___
Ezra Wegbreit, PhD
NIMH T32 Post-doctoral Research Fellow in Child Mental Health
Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human
Behavior
Brown University Warren Alpert Medical School
(401) 432-1615
ezra_wegbr...@brown.edu                                                     
                                                          
___


On Tue, Dec 9, 2014 at 4:13 PM, Bruce Fischl 
wrote:
  seems like the rh.sphere file is corrupted. Maybe you ran out of
  disk space? I would try deleting it and reruning with -make all

  cheers
  Bruce
  On Tue, 9 Dec 2014, Wegbreit, Ezra wrote:

Dear Freesurfer support community,

I am having a recurring issue with re-running a
participant after making
manual white matter edits (i.e., filling in holes in
the wm.mgz file).   I
saved the new wm.mgz file and then reran using -make
all (twice).  For some
reason, Freesurfer stops at the Surf Reg step, but
only for the right
hemisphere.  When I check the surfaces, I have lh
white and pial, but only
rh white (no pial).

Here is the error message I received both times
(bold added for emphasis).

"
Tue Dec  9 12:21:39 EST 2014
/gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/Freesurfer_Analyses/da

ta/s4504
/gpfs/runtime/opt/freesurfer/5.3.0/bin/recon-all 
-s/gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/Freesurfer_Analyses/
da
ta/s4504 -hemi rh -surfreg
#
#@# Surf Reg rh Tue Dec  9 12:21:40 EST 2014
/gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/Freesurfer_Analyses/da

ta/s4504/scripts

 mris_register 
-curv../surf/rh.sphere/gpfs/runtime/opt/freesurfer/5.3.0/average/rh.average.curv
ature.filled.buck
ner40.tif ../surf/rh.sphere.reg 

using smoothwm curvature for final alignment
$Id: mris_register.c,v 1.59 2011/03/02 00:04:33
nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01
nicks Exp $
reading surface from ../surf/rh.sphere...
mrisFindNeighbors: ../surf/rh.sphere:
face[205364].v[0] = 103504, but face
205364 not in vertex 103504 face list

No such file or directory
Linux node426 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed
Oct 16 18:37:12 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
"

I think my error is related to the following error
that someone else

reportedrecently(http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36
707.html
) though the function with the error
(mris_euler_number) was different than
the one I have.  Dr. Fischl's response was to
suggest a re-run (which I did)
and to suggest that the surfaces ended up too big
and that this bug could be
fixed in the future.   Could I have added too many
WM voxels, making the
resulting surface too big?  I tried to be as
conservative as possible, while
still filling white matter holes in the anterior
temporal lobes.  

I'm running Freesurfer v. 5.3.0 on a Linux system.  
 

Thanks in advance for answers!
Ezra
___
Ezra Wegbreit, PhD
NIMH T32 Post-doctoral Research Fellow in Child
Mental Health
Pedi-MIND Program at Bradley Hospital Department of
Psychiatry and Human
Behavior
Brown University Wa

Re: [Freesurfer] Problem with mris_register: face not in vertex face list

[Wegbreit, Ezra]

No worries.  Just checking to make sure there wasn't something I missed.

I appreciate your help, as I now have a workaround in case this issue
recurs.

Best wishes,
Ezra

*___*
*Ezra Wegbreit, PhD*
NIMH T32 Post-doctoral Research Fellow in Child Mental Health
Pedi-MIND Program at Bradley Hospital
Department of Psychiatry and Human Behavior
Brown University Warren Alpert Medical School
(401) 432-1615
ezra_wegbr...@brown.edu

*___*


On Thu, Dec 11, 2014 at 12:17 PM, Bruce Fischl 
wrote:

> Hi Ezra
>
> I have no idea why this would have happened. That's plenty of disk space
> and RAM.
>
> sorry
> Bruce
>
>
> On Thu, 11 Dec 2014, Wegbreit, Ezra wrote:
>
>  Hi Bruce,
>>
>> Thank you very much for this information.  Deleting the rh.sphere file and
>> re-running -make all did fix this issue and the brain now looks great.   I
>> wanted to confirm this so that if anyone else has the same issue they will
>> know what might work to fix it.
>>
>> I had a question about the potential space issue.   Did you mean hard
>> drive
>> space or RAM?  We have 7 TB of disk space on a Linux cluster - only 20% of
>> which is full.   When I ran recon-all, I submitted the script to a SLURM
>> batch system on the cluster, requesting 8 cpus and 24 GB of RAM.   Would
>> any
>> of this explain why the rh.sphere file could have gotten corrupted?
>> Should
>> I request even more RAM / more or fewer CPUs?  In general, recon-all runs
>> rather quickly on this setup.
>>
>> Thanks!
>> Ezra
>>
>> ___
>> Ezra Wegbreit, PhD
>> NIMH T32 Post-doctoral Research Fellow in Child Mental Health
>> Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human
>> Behavior
>> Brown University Warren Alpert Medical School
>> (401) 432-1615
>> ezra_wegbr...@brown.edu
>>
>>
>> ___
>>
>>
>> On Tue, Dec 9, 2014 at 4:13 PM, Bruce Fischl 
>> wrote:
>>   seems like the rh.sphere file is corrupted. Maybe you ran out of
>>   disk space? I would try deleting it and reruning with -make all
>>
>>   cheers
>>   Bruce
>>   On Tue, 9 Dec 2014, Wegbreit, Ezra wrote:
>>
>> Dear Freesurfer support community,
>>
>> I am having a recurring issue with re-running a
>> participant after making
>> manual white matter edits (i.e., filling in holes in
>> the wm.mgz file).   I
>> saved the new wm.mgz file and then reran using -make
>> all (twice).  For some
>> reason, Freesurfer stops at the Surf Reg step, but
>> only for the right
>> hemisphere.  When I check the surfaces, I have lh
>> white and pial, but only
>> rh white (no pial).
>>
>> Here is the error message I received both times
>> (bold added for emphasis).
>>
>> "
>> Tue Dec  9 12:21:39 EST 2014
>> /gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/
>> Freesurfer_Analyses/da
>>
>> ta/s4504
>> /gpfs/runtime/opt/freesurfer/5.3.0/bin/recon-all
>> -s/gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/
>> Freesurfer_Analyses/
>> da
>> ta/s4504 -hemi rh -surfreg
>> #
>> #@# Surf Reg rh Tue Dec  9 12:21:40 EST 2014
>> /gpfs/data/ddickstein/MRI_REVISED_STRUCTURE/Projects/
>> Freesurfer_Analyses/da
>>
>> ta/s4504/scripts
>>
>>  mris_register -curv../surf/rh.sphere/gpfs/
>> runtime/opt/freesurfer/5.3.0/average/rh.average.curv
>> ature.filled.buck
>> ner40.tif ../surf/rh.sphere.reg
>>
>> using smoothwm curvature for final alignment
>> $Id: mris_register.c,v 1.59 2011/03/02 00:04:33
>> nicks Exp $
>>   $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01
>> nicks Exp $
>> reading surface from ../surf/rh.sphere...
>> mrisFindNeighbors: ../surf/rh.sphere:
>> face[205364].v[0] = 103504, but face
>> 205364 not in vertex 103504 face list
>>
>> No such file or directory
>> Linux node426 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed
>> Oct 16 18:37:12 UTC 2013
>> x86_64 x86_64 x86_64 GNU/Linux
>> "
>>
>> I think my error is related to the following error
>> that someone else
>> reportedrecently(http://www.mail-archive.com/freesurfer%
>> 40nmr.mgh.harvard.edu/msg36
>> 707.html
>> ) though the function with the error
>> (mris_euler_number) was different than
>> the one I have.  Dr. Fischl's response was to
>> suggest a re-run (which I did)
>> and to suggest that the surfaces ended u

Re: [Freesurfer] retinotopy analysis viewing problem in Freesurfer 5

[Douglas N Greve]

imag is the imaginary (sine) part of the signal
real is the real part (cosine)
fsig is the significance (-log10(p)) where p is computed from an F test 
of the real and imag components


On 12/11/2014 05:09 AM, zhang mingxia wrote:
> Thank you very much!
>
> The map opened by rtview seems correct. As a new learner of 
> retinotopic analysis, I have one more basic quesion: What do the three 
> files (imag.nii.gz, real.nii.gz and fsig.nii.gz) represent? Hope some 
> experienced one can reply me!
>
> Mingxia
>
> On Thu, Dec 11, 2014 at 12:14 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> On 12/08/2014 09:19 PM, zhang mingxia wrote:
> > Hi Doug,
> >
> > I followed this guide:
> >
> 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis.
> > I used "tksurfer-sess" to view. Does "significant activation in the
> > visual cortex" mean the map from"tksurfer-sess -a rtopy.self.?h -s
> > sessid"? If so, yes.
> >
> > My question is (1) What do the maps from
>
> > "tksurfer-sess -a rtopy.self.?h -s sessid" -- this shows you the
> > significance map (-log10(p)) with eccen and polar in different
> frames
> > in the tksurfer overaly.
>
> > , "tksurfer-sess -a rtopy.self.?h -s sessid -map angle" This
> shows you
> > the angle with eccen and polar in different frames in the
> tksurfer overlay
>
> > , "tksurfer-sess -a rtopy.self.?h -s sessid -map angle.masked" This
> > shows you the angle with eccen and polar in different frames in the
> > tksurfer overlay with the angle masked to only those voxels that are
> > significant (p<.01).
>
> > and "tksurfer-sess -a rtopy.self.?h -s sessid -fieldsign" represent?
> > This shows you the field sign map.
>
> >
> > (2)I expected to get a red, green and blue map, but none of them is.
> > The first three are heat (yellow and red) and the fourth is
> red-blue.
> > This is the first time for me to do retinotopic analysis. The
> data is
> > from an experienced group for doing retinotopic research. I analyzed
> > four runs with two for eccen and two for polar. Do other people also
> > get this kind of color by using the script in the website above?
> tksurfer-sess will not generate a RGB colorwheel map. This
> functionality
> has been hard to continue to support. You can try rtview. You
> would use
> the RGB map to show the angle maps.
> >
> > (3)Which map is for delineating the boarder of visual area?
> field sign
> >
> > (4)Again, I expect to get a red, green and blue map as this people
> > asked
> >
> 
> :https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21512.html.
> > How can I get a standard color?
> >
> > Thanks again!
> >
> > Mingxia
> >
> > On Tue, Dec 9, 2014 at 12:07 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> >
> > I'm not sure what you are asking for. Do you see significant
> > activation
> > in the visual cortex? What command are you running to view?
> >
> >
> > On 12/08/2014 09:48 AM, zhang mingxia wrote:
> > > Dear freesurfer experts,
> > >
> > > I used Freesurfer 5 to do the retinotopic analysis followed by
> > >
> >
> 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis.
> > > However, finally I didn't get a red, green and blue map as I
> > expected.
> > >
> > > This is the first time for me to analyze retinotopic data. I
> > have not
> > > quite understood what the raw angle map, the angle map
> masked by sig
> > > and field sign map meant. My purpose was to delineate the
> boarder of
> > > visual area. To my knowledge from previous study, I should
> get a
> > > colorful map. It seems I didn't get a right one (However,
> I exactly
> > > follow the guide and didn't get any error). Some other
> people seems
> > > having the same viewing problem: (He/She didn't have eccen
> data. I
> > > have both eccen and polar data. I also only got a heat map
> > instead of
> > > a red, green and blue one)
> > >
> >
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21512.html
> > >
> > > (1)Is it due to the threshold? How can I get a red, green and
> > blue map?
> > > (2) What does the three maps represent?
> > >
> > > Thanks a lot!
> > >
> > > Mingxia
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> 

Re: [Freesurfer] Tracula_critical issue

[Anastasia Yendiki]

Hi Mohamad - What you did with your binarization was that you lowered the 
threshold all the way to zero, i.e., included all the voxels that had any
probability > 0 to be in the tract. This means that you included more 
voxels than the default, which is to threshold at 20% of the max 
probability. Changing the threshold to get a broader ROI would be an 
alternative to running more iterations to get a more realiable 
distribution. How either of those approaches would behave depends on the 
noise level in the data. Also, you averaged the FA/MD/etc over those 
voxels without multiplying with their probability, which corresponds to 
the unweigthed average that trac-all gives you. Note that trac-all calls 
the dmri_pathstats command to compute the stats, and you can run that 
command with a different threshold to get the same behavior as what you 
did. You can find an example of the dmri_pathstats command line in the 
trac-all.log file of any of your subjects.

Best,
a.y

On Mon, 24 Nov 2014, Alshikho, Mohamad J. wrote:

> Dear Anastasia,
> Thank you very much for your answer.
> In my analysis I have two groups 23 patients and 27 controls. My problem 
> right now is that this change in the results (from the output of trac-all 
> -path -c)  gave me different P values between the groups, sometimes the 
> results are significant and sometimes it is not! Till today I repeated this 
> analysis many times and I collected the results after 5 consecutive runs (all 
> the tracts for all the subjects)
>
> Recently and In order to find a solution for this problem I used the 
> following command line to generate the mean metrics and the tracts volume:
>
> fslstats - dti_FA.nii.gz -k path.pd_bin.nii.gz -M -V   [ I binarized 
> "path.pd.nii.gz" (the output of trac-all -path -c for every tract) using 
> fslmaths path.pd.nii.gz -thr 0.999 path.pd_bin.nii.gz and I used this 
> treashold to make my mask conservative as possible]
>
> In this case I got stable numbers. i.e when I run this command line again the 
> results are the same.
> Kindly is this valid? can I use "fslstats" instead of the third step in 
> Tracula "trac-all -path -c" to calculate the mean metrics and the tract's 
> volume?
>
> Also what is the difference between fslstats and trac-all -path -c 
> (technically)
>
> I highly appreciate your support
>
> Mohamad
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
> [ayend...@nmr.mgh.harvard.edu]
> Sent: Friday, November 21, 2014 5:10 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tracula_critical issue
>
> Hi Mohamad - As it's a probabilistic method that's sampling from a
> distribution, there is a bit of randomness built in (which should decrease
> as you increase the number of samples that you collect). You'll find that
> the the weighted average measures are the most reliable, as they are less
> affected by the tails of the distribution.
>
> a.y
>
> On Wed, 5 Nov 2014, Alshikho, Mohamad J. wrote:
>
>> Hi Anastasia,
>> I started recently using Tracula to do tractography for my DTI data. I did 
>> the analysis exactly as mentioned
>> in wiki. The problem is that when I am repeating the third step (trac-all 
>> -path -c ) for the same subjects to
>> generate the statistics; Tracula is updating all the information mentioned 
>> in the file "pathstats.overal.txt"
>> regarding the tract's volume and the tract's metrics values.
>> Every time the output is different. I think we have a problem in the scripts 
>> or something like this?
>>
>> Attached are three "pathstats.overal.txt" files for the same subject after 
>> three consecutive runs for the
>> "trac-all -path -c" (the same subject)
>>
>>
>> Looking forward for your support
>> Thanks
>>
>>
>
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Re: [Freesurfer] TRACULA- DKI?

[Anastasia Yendiki]

Hi Cat - Currently the only stats that are produced automatically are 
FA/MD/RD/AD. But if you have volumes of other parameters, you could always 
use the tracts from trac-all and extract mean values of those parameters 
within each tract with something like mri_segstats, fslastats, etc.

Best,
a.y

On Tue, 25 Nov 2014, Cat Chong wrote:

> Dear Tracula Team,
> 
> Quick question: Is Tracula able to to process diffusion kurtosis data, and
> yield, let's say, 'mean kurtosis' parameters for specific fiber tracts?
> cheers,
> Cat
> 
>
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Re: [Freesurfer] TRACULA mask error

[Anastasia Yendiki]

Hi Amanda - The final masks used by tracula are derived from the 
structural and not the diffusion data, i.e., they are the whole-brain 
FreeSurfer segmentations (from mri/aparc+aseg.mgz) mapped onto diffusion 
space and dilated slightly. It may be that there was something wrong with 
the FreeSurfer reconstructions of those subjects (if, for example, the T1 
contrast was poorer in part of the brain and the part was not included in 
the brain mask), or that there was misregistration between the T1 and 
diffusion. You can troubleshoot this by looking at the aparc+aseg in 
diffusion space (from the dlabel/diff directory, over the FA map (from the 
dmri directory).

If you still have trouble deciding what went wrong, you can upload a zip 
file for me with all the directories created by trac-all (dmri, dlabel, 
etc) for one of these subjects, here:
https://gate.nmr.mgh.harvard.edu/filedrop2/

Best,
a.y

On Thu, 27 Nov 2014, Worker, Amanda wrote:

> 
> Dear All,
> 
> 
> I have run all of the pre-processing steps on my DTI data and as I am
> checking my nodif_brain_mask I have realised that some of the masks have
> become distorted and twisted in some way. I have attached screenshots of
> both the raw data (which looks fine) and the white mask (which is
> distorted). In addition, as I have read that it is important to check the
> dtifit_V1 and dtifit_FA I have also included these in the word document,
> incase this helps.
> 
> 
> This distortion has occured for approximately a quarter of the subjects that
> I have processed and the rest look good. Please can you let me know if you
> have any ideas about what has gone wrong and how to fix this?
> 
> 
> Thanks in advance for your help,
> 
> 
> Amanda
> 
> 
>
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Re: [Freesurfer] TRACULA with Philips par-rec format

[Anastasia Yendiki]

Hi - Any format that can be handled by mri_convert (run "mri_convert 
--help" to see the list) can be run through freesurfer and tracula. If 
mri_convert doesn't work on your format, you'll have to find a converter 
that can convert it into one of the formats on that list (like nifti).


Hope this helps,
a.y

On Tue, 2 Dec 2014, Woo-Suk Tae wrote:


Dear TRACULA exports
I've successfully processed with Philips DICOM DTI data.
But, I have Philips 32 directional DTI data with par-rec format.
How can I process par-rec data in TRACUAL?

Best regards! 

 

Woo-Suk, Tae  Ph.D.
Research Professor, Neuroimaging Lab.
Neuroscience Research Institute,
Clinical Research Institute,
Kangwon National University Hospital
Chuncheon, Korea
office: 82-33-258-9164
mobile: 82-10-9120-4629
email: ws...@kangwon.ac.kr
  woos...@gmail.com
-

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Re: [Freesurfer] Command '-qa' in TRACULA

[Anastasia Yendiki]

Hi Anri - This is not a command itself, it's an option of the trac-all 
command. So you need to run:

trac-all -qa -c the_name_of_your_configuration_file

Or, if you just run the entire preprocessing:
trac-all -prep -c the_name_of_your_configuration_file
then the motion QA measures will be computed by default as one of the 
many steps of the preprocessing.


You can run "trac-all" without any arguments to see usage information on 
all the the different options.


Hope this helps,
a.y

On Tue, 9 Dec 2014, Anri WATANABE wrote:


Thank you, Anastasia.
I had downloaded the updated software and unzipped it, but I couldn't find
the command "-qa."
I found "-qa" in the trac-all text file in the updated software.
However there are no "-qa" in terminal when I run "trac-all."
Do I have to move the file somewhere?

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2014-11-22 7:22 GMT+09:00 Anastasia Yendiki :

  Hi Anri - See here, and follow the link "software update":
         
  http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Arguments

  The -qa option was added after 5.3 was released.

  a.y

  On Mon, 10 Nov 2014, Anri WATANABE wrote:

Dear FreeSurfer experts,

I'm running pre-processing steps in TRACULA
separatelly and could neither find the context about
quality
assessment step nor run the command 'trac-all -qa -c
.
I downloaded TRACULA in FreeSurfer 5.3, MacOSX lion
(64-bit).
Could anyone solve this problem?
Thank you.

Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
WATANABE ANRI
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of
Medicine

**


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Re: [Freesurfer] TRACULA fmajor recon failure: needing help

[Anastasia Yendiki]

Hi Emad - Those missing voxels in the mask in the middle of the corpus 
callosum could very well be what's not allowing that tract to be 
preconstructed.


The file used to create the brain mask from the freesurfer recon is not 
mri/brainmask.mgz, but mri/aparc+aseg.mgz, which is mapped to diffusion 
space and dilated a bit. This gives you the final mask, which is in 
dlabel/diff/aparc+aseg_mask... You can edit this final mask directly in 
diffusion space, and then rerun the trac-all steps that come after -masks. 
(The editing tutorial on the wiki is about rerunning recon-all, which you 
do not have to do if there is nothing wrong with the freesurfer recon.)


Hope this helps,
a.y

On Tue, 9 Dec 2014, Emad Ahmadi wrote:


Hello FreeSurfers!

I am using TRACULA to reconstruct white matter pathways in a patient 
with traumatic brain injury. TRACULA has failed to reconstruct forceps 
major, and I’m trying to track down why.


I overlaid the FA map (dmri/dtifit_FA.nii.gz) on top of the masked aparc+aseg 
(dlabel/diff/aparc+aseg.flt.nii.gz), and I feel fmajor is partially cut by the 
mask. Attached please find a slide deck containing the images.

Now I’m trying to edit the brain mask to include the midline of the brain near 
the splenium of corpus callosum in the mask. I have two questions:

1. Is my feeling right? Is this small cut of the midline brain the reason of 
fmajor recon failure?
2. In the online editorial for brain mask editing, it’s mentioned how to 
“shrink” the brain mask, but I cannot find how to “expand” it. I’d appreciate 
any help.

Thank you so much,
Emad


Emad Ahmadi, MD
---
Research Fellow
Department of Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu

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Re: [Freesurfer] trac-all -path error "Segmentation Fault (Core Dumped)"

[Anastasia Yendiki]

Hi Thomas - No bother at all! If you search for the word "error" in your 
trac-all.log, you'll see that it couldn't find the MNI template, which 
means that some of the pre-processing steps did not complete. You can 
either remove the "mnitemp" line from your configuration file (so that it 
uses the default $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz) or edit 
that line to include the correct path to the MNI template. You'll then 
need to rerun the pre-processing, or at least the steps including the 
inter-subject registration and beyond (run trac-all without arguments to 
see the sequence of steps included in the pre-processing).

Hope this helps,
a.y

On Wed, 10 Dec 2014, Thomas DeRamus wrote:

> Freesurfer Experts,
> 
> Sorry to bother you again, but I'm having an issue with the 3rd step of
> Tracula. I was able to run -prep just fine, and I ran bedpostx locally
> (there was an error in the step 2 command apparently, used command "bedpostx
> ///dmri/"), but every time I run the third step with the -path
> command I get the error "Segmentation fault (core dumped) foreach: No
> match."
> 
> The foreach error has me thinking there is something wrong with my dmrirc
> file or my folder structure.
> 
> I'd appreciate any feedback you are willing to give on this error.
> 
> I've attached the trac-all.log for one subject, but it gives the same error
> even when different subjects are used or this one is removed.
> 
> --
> Thomas DeRamusUAB Department of Psychology, Behavioral Neuroscience
> Graduate Research Trainee
> Civitan International Research Center
> 1719 6th Ave S, Suite 235J, Birmingham, AL 35233
> Phone: 205-934-0971 Email: tpdera...@gmail.com, faus...@uab.edu
> 
>
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Re: [Freesurfer] Question re. Tracula motion measures

[Anastasia Yendiki]

Hi - The fact that the first 2 parameters are all zero (translation and 
rotation) means that it didn't find the file that it expects to derive 
those parameters from. Currently, this is the eddy_correct log file that 
contains the affine registration matrices from each DWI volume to the 
first volume. This file is called dmri/dwi.ecclog and it is produced by 
the first of the pre-processing steps of trac-all (the -prep step).

The other 2 motion parameters are "0 1" when there are no slices with 
excessive signal drop-out found in the DWIs, which is an entirely 
plausible scenario and hopefully the case for most of your data sets.

The motion parameters that trac-all extracts are described here:
http://www.sciencedirect.com/science/article/pii/S1053811913011312

Hope this helps,
a.y

On Wed, 10 Dec 2014, Yuwen Hung wrote:

> Hi,
> I ran our pipeline script that contains DTI_prep and Tracula, and when I 
> extracted the individual motion data, they are mostly zeros (see below)
> Is this normal? If this is a problem, can anyone please let me know if there 
> any way to fix this (e.g. re-run the motion script..)?
> Your help would be greatly appreciated!
>
> ps: I just need to examine the motions between 2 groups (below are all data 
> from the 2 groups).
>
> AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0.0419463 1.02647
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0.370763 1.23369
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0.414365 1.13071
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
> 0 0 0 1
>
> Thanks so much for helping!
>
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Re: [Freesurfer] From bedpostX and recon-all to tracula

[Anastasia Yendiki]

Hi Kate - The screenshot looks more like a low-b image from a diffusion 
scan than a field map. In case this helps, the phase map data will have 
either 2 volumes (2 phase maps acquired at different echo times) or 1 
volume (the difference of 2 such phase maps).


Best,
a.y

On Thu, 11 Dec 2014, Katherine Damme wrote:


Hello


Has anyone else had the problem of tracula not recognizing the format of the
phase map?

 I opened the B0 in fslview and it appeared normal (see screenshot). Any
help that you can offer would be greatly appreciated! Thank you!

Thank you!

Kate Damme


On Fri, Nov 21, 2014 at 4:02 PM, Anastasia Yendiki
 wrote:

  Hi Kate - The -prep, -bedp, and -path steps need to be run
  separately, in that order. You can't run them all at once
  unfortunately. See:
         
  http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula

  a.y

  On Wed, 29 Oct 2014, Katherine Damme wrote:

Sorry for the delay. I signed up for the course and
hoped that it would answer my question, but I am
still
unsure what went wrong.

Thank you.

On Tue, Sep 9, 2014 at 12:14 PM, Anastasia Yendiki
 wrote:

      Can you please attach the trac-all.log file,
which has the entire output from beginning to end?
      Ofter something goes wrong earlier that causes
the program to fail later in the process.

      Also, we'll need your original configuration
file. Thanks!

      On Mon, 8 Sep 2014, Katherine Damme wrote:

            Hello Freesurfer Community!
             
            Thank you Anastasia and Christopher, I
am still getting ending with errors and the log
            file gives no clue that I have been able
to detect, see attached.

            Any help would be appreciated!


            On Thu, Sep 4, 2014 at 4:29 PM,
Anastasia Yendiki 
            wrote:

                  Hi Kate - There is an example
configuration file for tracula in your
                  freesurfer distribution
($FREESURFER_HOME/bin/dmrirc.example). The same
                  file is also here:
                 
http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

                  If you attach your configuration
file and the log file
                  (scripts/trac-all.log), we can try
to troubleshoot.

                  a.y

                  On Wed, 3 Sep 2014, Katherine
Damme wrote:

                  > Hello Freesurfer Community!
                  > I have sucessfully completed
diffusion preprocessing in FSL and the
                  > recon-all of the structural
image and would like to use tracula for the
                  > tract reconstruction. I keep
having trouble with my configuration file.
                  >
                  > Does anyone have a bedpostX
tracula config file they could share as an
                  > example?H
                  >
                  > Thank you!
                  >
                  > Kate
                  >
                  >
           
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but do

Re: [Freesurfer] From bedpostX and recon-all to tracula

[Katherine Damme]

I am sorry, I am a bit confused. What am I supposed to be specifying under
the b0mlist and b0plist?

I thought that it was the B0 low-b image from diffusion.

Thank you!

On Thu, Dec 11, 2014 at 2:25 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Kate - The screenshot looks more like a low-b image from a diffusion
> scan than a field map. In case this helps, the phase map data will have
> either 2 volumes (2 phase maps acquired at different echo times) or 1
> volume (the difference of 2 such phase maps).
>
> Best,
> a.y
>
>
> On Thu, 11 Dec 2014, Katherine Damme wrote:
>
>  Hello
>>
>>
>> Has anyone else had the problem of tracula not recognizing the format of
>> the
>> phase map?
>>
>>  I opened the B0 in fslview and it appeared normal (see screenshot). Any
>> help that you can offer would be greatly appreciated! Thank you!
>>
>> Thank you!
>>
>> Kate Damme
>>
>>
>> On Fri, Nov 21, 2014 at 4:02 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Kate - The -prep, -bedp, and -path steps need to be run
>>   separately, in that order. You can't run them all at once
>>   unfortunately. See:
>>
>>   http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula
>>
>>   a.y
>>
>>   On Wed, 29 Oct 2014, Katherine Damme wrote:
>>
>> Sorry for the delay. I signed up for the course and
>> hoped that it would answer my question, but I am
>> still
>> unsure what went wrong.
>>
>> Thank you.
>>
>> On Tue, Sep 9, 2014 at 12:14 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Can you please attach the trac-all.log file,
>> which has the entire output from beginning to end?
>>   Ofter something goes wrong earlier that causes
>> the program to fail later in the process.
>>
>>   Also, we'll need your original configuration
>> file. Thanks!
>>
>>   On Mon, 8 Sep 2014, Katherine Damme wrote:
>>
>> Hello Freesurfer Community!
>>
>> Thank you Anastasia and Christopher, I
>> am still getting ending with errors and the log
>> file gives no clue that I have been able
>> to detect, see attached.
>>
>> Any help would be appreciated!
>>
>>
>> On Thu, Sep 4, 2014 at 4:29 PM,
>> Anastasia Yendiki 
>> wrote:
>>
>>   Hi Kate - There is an example
>> configuration file for tracula in your
>>   freesurfer distribution
>> ($FREESURFER_HOME/bin/dmrirc.example). The same
>>   file is also here:
>>
>> http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
>>
>>   If you attach your configuration
>> file and the log file
>>   (scripts/trac-all.log), we can try
>> to troubleshoot.
>>
>>   a.y
>>
>>   On Wed, 3 Sep 2014, Katherine
>> Damme wrote:
>>
>>   > Hello Freesurfer Community!
>>   > I have sucessfully completed
>> diffusion preprocessing in FSL and the
>>   > recon-all of the structural
>> image and would like to use tracula for the
>>   > tract reconstruction. I keep
>> having trouble with my configuration file.
>>   >
>>   > Does anyone have a bedpostX
>> tracula config file they could share as an
>>   > example?H
>>   >
>>   > Thank you!
>>   >
>>   > Kate
>>   >
>>   >
>>
>> ___
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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.
>>
>>
>>
>>
>>

Re: [Freesurfer] From bedpostX and recon-all to tracula

[Anastasia Yendiki]

No, those are field maps used to correct for inhomogeneities in the main 
magnetic field (which in MRI lingo is referred to as the B0 field, not to 
be confused with the b=0 images). You can skip that correction (you have 
to skip it if you don't have field maps).


On Thu, 11 Dec 2014, Katherine Damme wrote:


I am sorry, I am a bit confused. What am I supposed to be specifying under
the b0mlist and b0plist?

I thought that it was the B0 low-b image from diffusion. 

Thank you!

On Thu, Dec 11, 2014 at 2:25 PM, Anastasia Yendiki
 wrote:

  Hi Kate - The screenshot looks more like a low-b image from a
  diffusion scan than a field map. In case this helps, the phase
  map data will have either 2 volumes (2 phase maps acquired at
  different echo times) or 1 volume (the difference of 2 such
  phase maps).

  Best,
  a.y

  On Thu, 11 Dec 2014, Katherine Damme wrote:

Hello


Has anyone else had the problem of tracula not
recognizing the format of the
phase map?

 I opened the B0 in fslview and it appeared normal
(see screenshot). Any
help that you can offer would be greatly
appreciated! Thank you!

Thank you!

Kate Damme


On Fri, Nov 21, 2014 at 4:02 PM, Anastasia Yendiki
 wrote:

      Hi Kate - The -prep, -bedp, and -path steps
need to be run
      separately, in that order. You can't run them
all at once
      unfortunately. See:
             
     
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula

      a.y

      On Wed, 29 Oct 2014, Katherine Damme wrote:

            Sorry for the delay. I signed up for the
course and
            hoped that it would answer my question,
but I am
            still
            unsure what went wrong.

            Thank you.

            On Tue, Sep 9, 2014 at 12:14 PM,
Anastasia Yendiki
             wrote:

                  Can you please attach the
trac-all.log file,
            which has the entire output from
beginning to end?
                  Ofter something goes wrong earlier
that causes
            the program to fail later in the
process.

                  Also, we'll need your original
configuration
            file. Thanks!

                  On Mon, 8 Sep 2014, Katherine
Damme wrote:

                        Hello Freesurfer Community!
                         
                        Thank you Anastasia and
Christopher, I
            am still getting ending with errors and
the log
                        file gives no clue that I
have been able
            to detect, see attached.

                        Any help would be
appreciated!


                        On Thu, Sep 4, 2014 at 4:29
PM,
            Anastasia Yendiki

                        wrote:

                              Hi Kate - There is an
example
            configuration file for tracula in your
                              freesurfer
distribution
            ($FREESURFER_HOME/bin/dmrirc.example).
The same
                              file is also here:
                             
           
http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

                              If you attach your
configuration
            file and the log file
                             
(scripts/trac-all.log), we can try
            to troubleshoot.

                              a.y

                              On Wed, 3 Sep 2014,
Katherine
            Damme wrote:

                              > Hello Freesurfer
Community!
                              > I have sucessfully
completed
            diffusion preprocessing in FSL and the
                              > recon-all of the
structural
            image and would like to use tracula for
the
                              > tract
reconstruction. I keep
            having trouble with my configuration
file.
                              >
                 

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

[Douglas N Greve]

Your FSGD file appears to have been made under windows or using an 
editor that is not simple text. The contrast matrix looks ok.

doug

On 12/01/2014 02:41 PM, lindsay hanford wrote:
> Hello Freesurfer Experts!
>
> I am encountering the dreaded mri_glmfit error:  matrix is 
> ill-conditioned or badly scaled, condno = 1e+08. I have tried to 
> troubleshoot how to solve this problem from other inquiries, however, 
> I still have had no luck. I am trying to run a 4 group 1 variable 
> analysis: with diagnosis being my variable of interest and trying to 
> regress out the effects of sex and age.
>
>   1. Command line:
> mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C 
> SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh
>   2. The FSGD file (if using one) (see attached)
>   3. And the design matrix:
>0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached)
>
> To the best of my knowledge, all my files are the right format and I 
> believe I have adequate number of participants per group?
> I also tried mean centering my age variable. I had success when I ran 
> just a two group analysis (diagnosis) not controlling for sex or age, 
> however, as soon as I try to run four groups, I encounter this error. 
> I have no idea how to proceed.
>
> I am looking forward to your response!
> Thanks,
>
>
> Lindsay
>
> -- 
> Lindsay Hanford, BSc, PhD Candidate
> McMaster Integrative Neuroscience Discovery & Study| *Department of 
> Psychology, Neuroscience & Behaviour *
> McMaster University *|* 1280 Main Street West, PC329 Psychology 
> Building *|* Hamilton, ON, L8S 4L8
> 905 525 9140 x24784***|*lindsay.hanf...@gmail.com 
> 
>
>
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-- 
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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] QDEC, Correction for multiple comparisons

[Douglas N Greve]

No

On 12/11/2014 06:48 AM, Xinfa Shi wrote:
> Hello,everyone
>
> Your reply said I can't use alphasim with qdec.By the way ,Could I use 
> alphasim in other ways in FreeSurfer,for example command line ?
>
> Best regards.
>
> Xin-Fa Shi.
>
>
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-- 
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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
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Re: [Freesurfer] QDEC cluster stats

[Douglas N Greve]

You should run mri_glmfit-sim from the command line passing it the QDEC 
glmdir as output and the same thresholds you used in QDEC. This will 
create several output files one of which will include the means inside 
each cluster. Run it with --help to get more info.

doug

On 12/10/2014 12:16 PM, Worker, Amanda wrote:
>
> Hi All,
>
>
> I am using QDEC to run a correlation analysis and I have a lot of 
> large significant clusters that encompass various different cortical 
> regions. I am hoping to extract mean thickness' from the significant 
> clusters in order to create a plot to display the correlations. Can 
> anyone tell me where to find or how to generate stats (e.g. mean 
> thickness/SD) for each significant cluster? At the moment I am only 
> able to visualise the regions or plot correlations for regional 
> thickness' but this doesn't reflect the significant clusters. Do I 
> need to draw an ROI around the cluster and generate the stats?
>
>
> Best wishes,
>
>
> Amanda
>
>
>
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-- 
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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
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Re: [Freesurfer] Can one adjust CWP Threshold in Qdec?

[Douglas N Greve]

Once you have the CWP image loaded, the Threshold value sets the CWP.
doug

On 12/03/2014 10:12 AM, Claire Morley wrote:
> Hi Freesurfer Experts,
> I was wondering if there is a way for me to adjust the default CWP of 
> p <.01 to p <.05 on Qdec? I saw that it is possible using cwpvalthresh 
> .05 with glmfit, but as I have set up everything with Qdec, it would 
> be much easier and save me time to do this via Qdec.
>
> Thanks so much for your help!
>
> Claire
>
>
>
> -- 
>
> /We shall not cease from exploration. And the end of all our exploring 
> will be to arrive where we started and know the place for the first 
> time- T.S. Eliot/
>
>
>
>
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-- 
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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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[Freesurfer] obtaining the level of smoothness in the data

[Marie Schaer]

Hi all,

I'd like to know whether there is a command line that I could use to extract 
the level of smoothness in my data, the same way qdec does it automatically, 
i.e. writing the fwhm.dat that is then used to define which precomputed CSD 
file should be used in the Monte Carlo Simulation. Is there any simple command 
which I could use, inputing the y.mgh and getting as an output the fwhm.dat. 

Sorry to disturb for such a small question, I've been looking everywhere but 
don't find any solution to this. 

Otherwise, is there any way that we can change the default smoothing level 
accepted by qdec, i.e. having other values in there that 5, 10, 15, 20 or 25? 

Thanks a lot in advance for your reply,

Marie



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Re: [Freesurfer] obtaining the level of smoothness in the data

[Douglas Greve]

Hi Marie, you can use mris_fwhm, something like

mris_fwhm --i y.mgh --subject fsaverage --hemi lh --cortex --dat fwhm.dat

doug

On 12/11/14 8:40 PM, Marie Schaer wrote:
> Hi all,
>
> I'd like to know whether there is a command line that I could use to extract 
> the level of smoothness in my data, the same way qdec does it automatically, 
> i.e. writing the fwhm.dat that is then used to define which precomputed CSD 
> file should be used in the Monte Carlo Simulation. Is there any simple 
> command which I could use, inputing the y.mgh and getting as an output the 
> fwhm.dat.
>
> Sorry to disturb for such a small question, I've been looking everywhere but 
> don't find any solution to this.
>
> Otherwise, is there any way that we can change the default smoothing level 
> accepted by qdec, i.e. having other values in there that 5, 10, 15, 20 or 25?
>
> Thanks a lot in advance for your reply,
>
> Marie
>
>
>
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Re: [Freesurfer] Command '-qa' in TRACULA

[Anri WATANABE]

Thanks, Anastasia.
I'm worried about that a quality assessment step is not run because there
are no presentation about "-qa" when I type "trac-all" in terminal (other
steps are presented.)
Do you mean QA step will be run even if no mention about it?

Thanks in advance,
Anri



 **
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
 **
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
 **

2014-12-12 4:48 GMT+09:00 Anastasia Yendiki :
>
>
> Hi Anri - This is not a command itself, it's an option of the trac-all
> command. So you need to run:
> trac-all -qa -c the_name_of_your_configuration_file
>
> Or, if you just run the entire preprocessing:
> trac-all -prep -c the_name_of_your_configuration_file
> then the motion QA measures will be computed by default as one of the many
> steps of the preprocessing.
>
> You can run "trac-all" without any arguments to see usage information on
> all the the different options.
>
> Hope this helps,
> a.y
>
>
> On Tue, 9 Dec 2014, Anri WATANABE wrote:
>
>  Thank you, Anastasia.
>> I had downloaded the updated software and unzipped it, but I couldn't find
>> the command "-qa."
>> I found "-qa" in the trac-all text file in the updated software.
>> However there are no "-qa" in terminal when I run "trac-all."
>> Do I have to move the file somewhere?
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>> 2014-11-22 7:22 GMT+09:00 Anastasia Yendiki > >:
>>
>>   Hi Anri - See here, and follow the link "software update":
>>
>>   http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Arguments
>>
>>   The -qa option was added after 5.3 was released.
>>
>>   a.y
>>
>>   On Mon, 10 Nov 2014, Anri WATANABE wrote:
>>
>> Dear FreeSurfer experts,
>>
>> I'm running pre-processing steps in TRACULA
>> separatelly and could neither find the context about
>> quality
>> assessment step nor run the command 'trac-all -qa -c
>> .
>> I downloaded TRACULA in FreeSurfer 5.3, MacOSX lion
>> (64-bit).
>> Could anyone solve this problem?
>> Thank you.
>>
>> Anri
>>
>>
>> 
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> 
>> **
>> WATANABE ANRI
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of
>> Medicine
>> 
>> **
>>
>>
>> ___
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>>
>>
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>> 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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>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
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Re: [Freesurfer] obtaining the level of smoothness in the data

[Marie Schaer]

Awesome Doug, that's exactly what I wanted, thanks a lot for the prompt answer!

Have a nice evening,

Marie

On Dec 11, 2014, at 6:38 PM, Douglas Greve 
 wrote:

> 
> Hi Marie, you can use mris_fwhm, something like
> 
> mris_fwhm --i y.mgh --subject fsaverage --hemi lh --cortex --dat fwhm.dat
> 
> doug
> 
> On 12/11/14 8:40 PM, Marie Schaer wrote:
>> Hi all,
>> 
>> I'd like to know whether there is a command line that I could use to extract 
>> the level of smoothness in my data, the same way qdec does it automatically, 
>> i.e. writing the fwhm.dat that is then used to define which precomputed CSD 
>> file should be used in the Monte Carlo Simulation. Is there any simple 
>> command which I could use, inputing the y.mgh and getting as an output the 
>> fwhm.dat.
>> 
>> Sorry to disturb for such a small question, I've been looking everywhere but 
>> don't find any solution to this.
>> 
>> Otherwise, is there any way that we can change the default smoothing level 
>> accepted by qdec, i.e. having other values in there that 5, 10, 15, 20 or 25?
>> 
>> Thanks a lot in advance for your reply,
>> 
>> Marie
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
> 
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> 
> 
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> at
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Re: [Freesurfer] Command '-qa' in TRACULA

[Anri WATANABE]

I tried to run trac-all -qa -c the_name_of_my_configuration_file after trac-all
-corr -c the_name_of_my_configuration_file, but it failed.
I pasted the log below and do you have any advices?

Thank you,
Anri


[watanabeanris-Mac-Pro:~] watanabeanri% trac-all -corr -c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial

INFO: SUBJECTS_DIR is /volumes/mybook/Anri/diffusion_recons

INFO: Diffusion root is /volumes/mybook/Anri/diffusion_tutorial

Actual FREESURFER_HOME /Applications/freesurfer

trac-preproc -c
/volumes/mybook/Anri/diffusion_tutorial/HC_002/scripts/dmrirc.local -log
/volumes/mybook/Anri/diffusion_tutorial/HC_002/scripts/trac-all.log -cmd
/volumes/mybook/Anri/diffusion_tutorial/HC_002/scripts/trac-all.cmd

#-

/Applications/freesurfer/bin/trac-preproc

#-


*-I omitted a part of log in an image correction step-*


Computing mean across frames

Writing to /volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb.nii.gz

bet /volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb.nii.gz
/volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb_brain.nii.gz -m -f
0.3

mv -f
/volumes/mybook/Anri/diffusion_tutorial/HC_002/dmri/lowb_brain_mask.nii.gz
/volumes/mybook/Anri/diffusion_tutorial/HC_002/dlabel/diff

#-

trac-preproc finished without error at Fri Dec 12 14:04:04 JST 2014

[watanabeanris-Mac-Pro:~] watanabeanri% trac-all -qa -c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial

ERROR: flag -qa unrecognized

-qa -c /volumes/mybook/Anri/diffusion_tutorial/dmrirc.tutorial

[watanabeanris-Mac-Pro:~] watanabeanri%


 **
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
 **
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
 **

2014-12-12 11:38 GMT+09:00 Anri WATANABE :
>
> Thanks, Anastasia.
> I'm worried about that a quality assessment step is not run because there
> are no presentation about "-qa" when I type "trac-all" in terminal (other
> steps are presented.)
> Do you mean QA step will be run even if no mention about it?
>
> Thanks in advance,
> Anri
>
>
>
>  **
> 京都府立医科大学附属病院
> 精神科・心療内科
> 渡辺 杏里
>  **
> Anri WATANABE, M.D.
> Department of Psychiatry,
> University Hospital, Kyoto Prefectural University of Medicine
>  **
>
> 2014-12-12 4:48 GMT+09:00 Anastasia Yendiki 
> :
>>
>>
>> Hi Anri - This is not a command itself, it's an option of the trac-all
>> command. So you need to run:
>> trac-all -qa -c the_name_of_your_configuration_file
>>
>> Or, if you just run the entire preprocessing:
>> trac-all -prep -c the_name_of_your_configuration_file
>> then the motion QA measures will be computed by default as one of the
>> many steps of the preprocessing.
>>
>> You can run "trac-all" without any arguments to see usage information on
>> all the the different options.
>>
>> Hope this helps,
>> a.y
>>
>>
>> On Tue, 9 Dec 2014, Anri WATANABE wrote:
>>
>>  Thank you, Anastasia.
>>> I had downloaded the updated software and unzipped it, but I couldn't
>>> find
>>> the command "-qa."
>>> I found "-qa" in the trac-all text file in the updated software.
>>> However there are no "-qa" in terminal when I run "trac-all."
>>> Do I have to move the file somewhere?
>>>
>>> **
>>> 京都府立医科大学附属病院
>>> 精神科・心療内科
>>> 渡辺 杏里
>>> **
>>> Anri WATANABE, M.D.
>>> Department of Psychiatry,
>>> University Hospital, Kyoto Prefectural University of Medicine
>>> **
>>>
>>> 2014-11-22 7:22 GMT+09:00 Anastasia Yendiki <
>>> ayend...@nmr.mgh.harvard.edu>:
>>>
>>>   Hi Anri - See here, and follow the link "software update":
>>>
>>>   http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Arguments
>>>
>>>   The -qa option was added after 5.3 was released.
>>>
>>>   a.y
>>>
>>>   On Mon, 10 Nov 2014, Anri WATANABE wrote:
>>>
>>> Dear FreeSurfer experts,
>>>
>>> I'm running pre-processing steps in TRACULA
>>> separatelly and could neither find the context about
>>> quality
>>> assessment step nor run the command 'trac-all -qa -c
>>> .
>>> I downloaded TRACULA in FreeSurfer 5.3, MacOSX lion
>>> (64-bit).
>>> Could anyone solve this problem?
>>> Thank you.
>>>
>>> Anri
>>>
>>>
>>> ***