Dear Douglas,

Thank you very much for your help, It seems to work now.
I got a table with all the FA values, for each segment, but I suspect a problem: I think that the values are too high (I set the threshold to 0.2-1), am I right ?
I'm attaching the table I got, and to be specific, I'm very much interested in the Corpus-Colosseum values, which are high (not surprising) but when I wanted to validate with some other structures, like the "left putamen" I saw 0.53 which is to my opinion too high ?
I would really appreciate if you can have a look at the table I attached here.

Thanks !

Rotem

2013/2/12 <freesurfer-request@nmr.mgh.harvard.edu>
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Today's Topics:

   1. Re: LME matlab toolbox - smooth error (jorge luis)
   2. Re: mean cortical thickness of significant clusters in qdec
      (Douglas N Greve)
   3. Re: A question regarding a "nii-read" error I get when
      running a script for FA values output (Douglas N Greve)
   4. Re: Temporal lobes not included (Kristina Nalbandian)
   5. Re: Temporal lobes not included (Bruce Fischl)
   6. Re: Temporal lobes not included (Douglas N Greve)
   7. Re: Freesurfer 5.2 CentOS 4 aparcstats2table error
      (Nick Schmansky)
   8. mc-sess Error (Daniel Cole)
   9. Re: mc-sess Error (Douglas N Greve)
  10. glmfit-sim trouble (Gabriel Gonzalez Escamilla)
  11. Re: Freesurfer 5.2 CentOS 4 aparcstats2table error
      (Garikoitz Lerma-Usabiaga)
  12. average subject (Linn Mittlestein)
  13. preparing NHP data for whole brain analysis
      (Caspar M. Schwiedrzik)
  14. Post-Doctoral position in brain imaging and computational
      morphometry ? University of Geneva (Narly Golestani)
  15. error when using stats import in qdec (Catherine Bois)
  16. Fwd: error when using stats import in qdec (Catherine Bois)
  17. Re: Fwd: error when using stats import in qdec (Catherine Bois)
  18. Re: Fwd: error when using stats import in qdec (Nick Schmansky)
  19. Re: Fwd: error when using stats import in qdec (Nick Schmansky)
  20. trac-all problem (Jon Wieser)
  21. two sample t-test of paired differences (J?rg Pfannm?ller)
  22. Re: average subject (Bruce Fischl)
  23. Re: average subject (Linn Mittlestein)
  24. Re: average subject (Douglas N Greve)
  25. Basic skullstrip Inquiry (Gabriel Obregon)
  26. Re: two sample t-test of paired differences (Douglas N Greve)
  27. Parallelizing on a different kind of cluster (Susan Kuo)
  28. Re: mean cortical thickness of significant clusters in qdec
      (Douglas N Greve)
  29. Re: trac-all -path error (Anastasia Yendiki)
  30. Re: R:  trac-all -path error (Anastasia Yendiki)
  31. Re: preparing NHP data for whole brain analysis (Douglas N Greve)
  32. Re: trac-all problem (Anastasia Yendiki)
  33. Re: Parallelizing on a different kind of cluster
      (Anastasia Yendiki)
  34. Re: Troubleshooting the preproc (Anastasia Yendiki)


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

Message: 1
Date: Mon, 11 Feb 2013 16:57:09 +0000 (GMT)
From: jorge luis <jbernal0019@yahoo.es>
Subject: Re: [Freesurfer] LME matlab toolbox - smooth error
To: Yolanda Vives <yvives@pic.es>,      "freesurfer@nmr.mgh.harvard.edu"
        <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <1360601829.82122.YahooMailNeo@web172101.mail.ir2.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"



Hi Yolanda

This is one of a few scripts in LME that requires an extra Matlab toolbox (maybe the only, besides the statistic toolbox). As it is documented in its header you are require to have the curve fitting toolbox installed to run it successfully.

Best
-Jorge






>________________________________
> De: Yolanda Vives <yvives@pic.es>
>Para: freesurfer@nmr.mgh.harvard.edu
>Enviado: Lunes 11 de febrero de 2013 6:14
>Asunto: [Freesurfer] LME matlab toolbox - smooth error
>
>Dear all
>
>I am a new user of the LME matlab toolbox and I have an error when
>running lme_lowessPlot due to the smooth function. Do I need a
>particular matlab toolbox to run this function? I have not seen any
>smooth function in the LME toolbox.
>
>Error in ==> lme_lowessPlot at 49
>? ? ybw = smooth(st,dat(ix),bw,'rlowess');
>
>Error in ==> LME at 14
>lme_lowessPlot(M(:,1),Y(:,1)+Y(:,2),0.70,M(:,2));
>
>Thank you in advance,
>Yolanda
>_______________________________________________
>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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>
>
>
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Message: 2
Date: Mon, 11 Feb 2013 13:03:43 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mean cortical thickness of significant
        clusters in qdec
To: "Richter, Julia" <Julia.Richter@med.uni-heidelberg.de>,
        "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>
Message-ID: <5119327F.5070402@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed


It may be a German operating system replacing 1.3 with 1,3. Maybe put it
in quotes, ie, "1.3"

On 02/11/2013 04:17 AM, Richter, Julia wrote:
> Dear Doug,
>
> this is what appears when I type my command in the command window:
>
> mri_glmfit-sim --cache 1.3 abs --cwpvalthresh .99
> ERROR: thresh 1,3, must be 1.3, 2.0, 3.0, 3.3, 4.0
>
> That's it...Any ideas why this is happening?
>
> Many thanks in advance!
>
> Best, Julia
>
> -----Urspr?ngliche Nachricht-----
> Von: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu]
> Gesendet: Donnerstag, 7. Februar 2013 17:32
> An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: AW: AW: [Freesurfer] mean cortical thickness of significant clusters in qdec
>
> it does not look like you changed the command line. Also, please cut and paste the info into the email instead of taking a snapshot.
> thanks
> doug
>
> On 02/04/2013 07:26 AM, Richter, Julia wrote:
>> This doesn't work either (see attachment)  :(
>>
>> -----Urspr?ngliche Nachricht-----
>> Von: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu]
>> Gesendet: Donnerstag, 31. Januar 2013 20:29
>> An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu
>> Betreff: Re: AW: [Freesurfer] mean cortical thickness of significant
>> clusters in qdec
>>
>> The threshold must be in the form of -log10(pthreshold). So, if you
>> want pthreshold=.05, then use 1.3 doug
>>
>>
>>
>> On 01/31/2013 07:37 AM, Richter, Julia wrote:
>>> Dear Doug,
>>>
>>> thanks for your reply. I tried the command you suggested, but I always get an error message that there is something wrong with my threshold. I took a screenshot of the command window and attached it to this mail. I will be very happy if you have a look at it.
>>>
>>> Looking forward to your answer,
>>>
>>> Best, Julia
>>>
>>> -----Urspr?ngliche Nachricht-----
>>> Von: freesurfer-bounces@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von
>>> Douglas Greve
>>> Gesendet: Mittwoch, 30. Januar 2013 17:16
>>> An: Richter, Julia; free surfer
>>> Betreff: Re: [Freesurfer] mean cortical thickness of significant
>>> clusters in qdec
>>>
>>> Oh, sorry, I thought you said you were using mri_glmfit-sim (which
>>> does not have an FDR option). Are you using the FDR in QDEC? If so,
>>> it will display the voxel-wise threshold that realizes the FDR
>>> threshold. You can then run mri_glmfit-sim --cache threshold sign
>>> --cwpvalthresh .99 where threshold is the voxelwise threshold from
>>> FDR and sign is either abs (absolute), pos, or neg. Setting
>>> cwpvalthresh=.99 tell it to report all clusters
>>>
>>> doug
>>>
>>> On 1/30/13 8:09 AM, Richter, Julia wrote:
>>>> No it is not...or I just do not find it.
>>>>
>>>> Might it be that I only get the xxx.y.ocn.dat if I correct for multiple comparisons with Monte Carlo? If yes, is there any possibility that I get this xxx.y.ocn.dat when correcting with FDR?
>>>>
>>>> Many thanks, Julia
>>>>
>>>> -----Urspr?ngliche Nachricht-----
>>>> Von: freesurfer-bounces@nmr.mgh.harvard.edu
>>>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von
>>>> Douglas N Greve
>>>> Gesendet: Dienstag, 29. Januar 2013 18:46
>>>> An: freesurfer@nmr.mgh.harvard.edu
>>>> Betreff: Re: [Freesurfer] mean cortical thickness of significant
>>>> clusters in qdec
>>>>
>>>> Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not?
>>>> doug
>>>>
>>>>
>>>> On 01/29/2013 11:03 AM, Richter, Julia wrote:
>>>>> Dear FreeSurfer experts,
>>>>>
>>>>> I did a group analysis in qdec, found several significant clusters
>>>>> and would now like to extract the mean cortical thickness of each
>>>>> significant cluster. I know that I have to run mri_glmfit-sim to do
>>>>> this, but I do not understand which commands I need to get the
>>>>> xxx.y.ocn.dat as output by running mri_glmfit-sim.
>>>>>
>>>>> Any ideas? Any help is appreciated. J
>>>>>
>>>>> Best wishes, Julia
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>> greve@nmr.mgh.harvard.edu
>>>> Phone Number: 617-724-2358
>>>> Fax: 617-726-7422
>>>>
>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>> FileDrop: 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.
>>>>
>>>>
>>>>
>>> _______________________________________________
>>> 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
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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

Message: 3
Date: Mon, 11 Feb 2013 13:31:14 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] A question regarding a "nii-read" error I
        get when running a script for FA values output
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <511938F2.3090101@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed


Try putting a slash "/" before "usr" on the input (--i) fille
doug

On 02/11/2013 04:50 AM, Rotem Saar wrote:
> Hi,
>
> My name is Rotem, I'm a PhD. student and recently started to work with
> freesurfer software (freesurfer-Linux-centos4-stable-pub-v5.1.0). QUESTION
> For several weeks, I have been trying to operate a script for FA
> values, with no success, and would really appreciate your help with
> shading some light regarding the problem and it's solution.
> I have a data set, after an anatomical segmentation (file is attached,
> named "Anatomical segmentation for fs", this is the script I'm using
> for brain anatomical segmentation). What I'm trying to run now is the
> DTI script, in which I run commands that at least for my understanding
> spouse to give me at the end a table with all the FA values for each
> brain region (ROI). The script I'm using to do this is attached and
> called "DTI_RUN_NEW_FOR_FS".
> _After running phase 5_, in which a mask file should be created
> (indeed I have checked and the file is created in the same folder it
> should be):
>
> fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_mask
> /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii
> /usr/local/freesurfer/subjects/FOLDER_NAME/mri/brainmask.mgz
> /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii
> DoAbs = 0
> Found 16777216 voxels in mask
> Writing masked volume to
> /usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii...done.
>
> _I run phase 6, and then get the following error message:_
>
> fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_segstats --seg
> /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab
> $FREESURFER_HOME/FreeSurferColorLUT.txt --i
> usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii
> --sum
> /usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME
>
> $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
> cwd
> cmdline mri_segstats --seg
> /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab
> /usr/local/freesurfer/FreeSurferColorLUT.txt --i
> usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii --sum
> /usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME
> sysname  Linux
> hostname fmri4-P67A-D3-B3
> machine  i686
> user     fmri4
> Loading /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz
> Loading
> usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii
> niiRead(): error opening file
> usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii
> ERROR: loading
> usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii
>
> I think the problem is between phase 5 and 6, and is related to file
> format (.nii) but don't have a hint regarding what can I do to solve
> this:( Can someone please write me the correct code line ?
>
> I would really appreciate your kind help since I run out of ideas for
> solutions.
>
> Thanks in advance,
>
> Rotem
>
>
>
> _______________________________________________
> 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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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

Message: 4
Date: Mon, 11 Feb 2013 12:09:00 -0800
From: Kristina Nalbandian <knalbandian@ucla.edu>
Subject: Re: [Freesurfer] Temporal lobes not included
To: Douglas Greve <greve@nmr.mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CAN5fwS0utT-E0nSSx1ny9ie9z+5BiKCXMhS7V7tEVns=S=bm3g@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Thank you for the reply!
  What is the command for running defect-seg? Will this only help me
visualize the defects or will it correct them as well?

Many thanks

On Fri, Feb 8, 2013 at 3:25 PM, Douglas Greve <greve@nmr.mgh.harvard.edu>wrote:

>  Kristina, you can also run defect-seg to create aseg segmentation of the
> defects. Follow the instructions in the --help to visualize. Look in that
> region for defects.
> doug
>
>
>
> On 2/8/13 5:56 PM, Bruce Fischl wrote:
>
> Hi Kristina
>
> I would guess you have a topological defect that is being fixed
> incorrectly. If you upload the subject I'm happy to take a look (in between
> rounds of shoveling)
>
> Bruce
>  On Fri, 8 Feb 2013, Kristina Nalbandian wrote:
>
> Hello,
>     I am trying to run cortical thickness on a few scans. After the
> initial
> recon-all -all command not all regions of grey and white matter were
> included. I have attached a picture of the problem (the right side
> temporal
> lobe is not included, but the the left side is). I tried adding control
> points and re-running the process with the command "-autorecon-all
> -autorecon2-cp -autorecon3 -subjid subject name" but I do not get a very
> improved result. If there anything else I can try?
>
> Thank you for all your help,
> Kristina Nalbandyan
> Neuroscience Undergraduate Interdepartmental Program, UCLA
>
>
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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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------------------------------

Message: 5
Date: Mon, 11 Feb 2013 15:11:02 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Temporal lobes not included
To: Kristina Nalbandian <knalbandian@ucla.edu>
Cc: freesurfer@nmr.mgh.harvard.edu, Douglas Greve
        <greve@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.00.1302111510250.30902@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"

it definitely won't correct them (otherwise we would have included it in
recon-all already). We are correcting them, just not the right way (e.g.
cutting instead of filling or visa-versa)

cheers
Bruce


On Mon, 11 Feb 2013, Kristina Nalbandian wrote:

> Thank you for the reply!
> ? What is the command for running defect-seg? Will this only help me visualize the defects or will it
> correct them as well?
>
> Many thanks
>
> On Fri, Feb 8, 2013 at 3:25 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
>       Kristina, you can also run defect-seg to create aseg segmentation of the defects. Follow
>       the instructions in the --help to visualize. Look in that region for defects.
>       doug
>
>
>       On 2/8/13 5:56 PM, Bruce Fischl wrote:
>       Hi Kristina
>
>       I would guess you have a topological defect that is being fixed incorrectly. If you
>       upload the subject I'm happy to take a look (in between rounds of shoveling)
>
>       Bruce
>       ?On Fri, 8 Feb 2013, Kristina Nalbandian wrote:
>
>             Hello,
>             ? ? I am trying to run cortical thickness on a few scans. After the
>             initial
>             recon-all -all command not all regions of grey and white matter were
>             included. I have attached a picture of the problem (the right side
>             temporal
>             lobe is not included, but the the left side is). I tried adding control
>             points and re-running the process with the command "-autorecon-all
>             -autorecon2-cp -autorecon3 -subjid subject name" but I do not get a
>             very
>             improved result. If there anything else I can try?
>
>             Thank you for all your help,
>             Kristina Nalbandyan
>             Neuroscience Undergraduate Interdepartmental Program, UCLA
>
>
>
> _______________________________________________
> 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.
>
>
>
>

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

Message: 6
Date: Mon, 11 Feb 2013 15:16:15 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Temporal lobes not included
To: Kristina Nalbandian <knalbandian@ucla.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5119518F.9090006@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

The command is defect-seg
doug
On 02/11/2013 03:09 PM, Kristina Nalbandian wrote:
> Thank you for the reply!
>   What is the command for running defect-seg? Will this only help me
> visualize the defects or will it correct them as well?
>
> Many thanks
>
> On Fri, Feb 8, 2013 at 3:25 PM, Douglas Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>     Kristina, you can also run defect-seg to create aseg segmentation
>     of the defects. Follow the instructions in the --help to
>     visualize. Look in that region for defects.
>     doug
>
>
>
>     On 2/8/13 5:56 PM, Bruce Fischl wrote:
>>     Hi Kristina
>>
>>     I would guess you have a topological defect that is being fixed
>>     incorrectly. If you upload the subject I'm happy to take a look
>>     (in between rounds of shoveling)
>>
>>     Bruce
>>      On Fri, 8 Feb 2013, Kristina Nalbandian wrote:
>>
>>>     Hello,
>>>         I am trying to run cortical thickness on a few scans. After
>>>     the initial
>>>     recon-all -all command not all regions of grey and white matter
>>>     were
>>>     included. I have attached a picture of the problem (the right
>>>     side temporal
>>>     lobe is not included, but the the left side is). I tried adding
>>>     control
>>>     points and re-running the process with the command "-autorecon-all
>>>     -autorecon2-cp -autorecon3 -subjid subject name" but I do not
>>>     get a very
>>>     improved result. If there anything else I can try?
>>>
>>>     Thank you for all your help,
>>>     Kristina Nalbandyan
>>>     Neuroscience Undergraduate Interdepartmental Program, UCLA
>>>
>>
>>
>>     _______________________________________________
>>     Freesurfer mailing list
>>     Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>     _______________________________________________
>     Freesurfer mailing list
>     Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>     The information in this e-mail is intended only for the person to
>     whom it is
>     addressed. If you believe this e-mail was sent to you in error and
>     the e-mail
>     contains patient information, please contact the Partners
>     Compliance HelpLine at
>     http://www.partners.org/complianceline . If the e-mail was sent to
>     you in error
>     but does not contain patient information, please contact the
>     sender and properly
>     dispose of the e-mail.
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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

Message: 7
Date: Mon, 11 Feb 2013 15:16:32 -0500
From: Nick Schmansky <nicks@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer 5.2 CentOS 4 aparcstats2table
        error
To: Garikoitz Lerma-Usabiaga <garikoitz@gmail.com>
Cc: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <1360613792.17432.609.camel@terrier.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Gari,

Can you try the attached fixed files?  Both aparcstats2table and
asegstats2table were fixed.

To install:

cp stats2tab.tar $FREESURFER_HOME/bin
cd $FREESURFER_HOME/bin
tar xf stats2tab.tar

Thanks again,

Nick


On Mon, 2013-02-11 at 17:06 +0100, Garikoitz Lerma-Usabiaga wrote:
> Thanks Nick!!
> is it a solution to run 5.2 aparcstats2table (Snow Leopard) in another
> machine, accessing the data from a network drive?
>
>
> or is it a solution to run the aparcstats2table provided in 5.1 in the
> same machine, but accessing the data created by the 5.2 version?
>
>
> many thanks again for your help,
> Gari
>
>
> On Mon, Feb 11, 2013 at 5:02 PM, Nick Schmansky
> <nicks@nmr.mgh.harvard.edu> wrote:
>         Gari,
>
>         A little googling tells me that the 'with' statement in python
>         was
>         introduced in python v2.5 in 2008, so unfortunately i think
>         you'll have to
>         update your python version, unless aparcstats2table can be
>         rewritten to
>         not use that statement.
>
>         Nick
>
>
>         > Hi Nick!
>         > this is the version:
>         > Centos 4 32b or 64b (x86_64)
>         > (Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06
>         EDT 2010
>         > x86_64
>         > x86_64 x86_64 GNU/Linux)
>         >
>         >
>         > and the python version is:
>         > Python 2.4.3 (#1, Feb 22 2012, 16:05:45)
>         > [GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2
>         > (python --version is not working)
>         >
>         > thanks!
>         > Gari
>         >
>         >
>         >
>         >
>         > On Mon, Feb 11, 2013 at 4:50 PM, Nick Schmansky
>         > <nicks@nmr.mgh.harvard.edu>wrote:
>         >
>         >> Gari,
>         >>
>         >> What OS are you running?  is this the Centos 4 32b or 64b
>         (x86_64)?
>         >>
>         >> can you tell me your python version?  this way:
>         >>
>         >> python --version
>         >>
>         >> Nick
>         >>
>         >>
>         >> > Hi fs experts,
>         >> > I have this error every time I try tu run
>         aparcstats2table :
>         >> >
>         >> >   File
>         "/home/glerma/fs/52/freesurfer/bin/aparcstats2table", line 221
>         >> >     with open(o.qdec, 'rb') as f:
>         >> >             ^
>         >> > SyntaxError: invalid syntax
>         >> >
>         >> >
>         >> >
>         >> > it appears each time I run aparcstats2table, even when I
>         write:
>         >> > aparcstats2table --help
>         >> >
>         >> >
>         >> > I have changed the environment variables in order to run
>         the 5.1
>         >> version,
>         >> > and it works as always.
>         >> >
>         >> >
>         >> > What else should I check?
>         >> > thanks!
>         >> > Gari
>         >> > _______________________________________________
>         >> > 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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------------------------------

Message: 8
Date: Mon, 11 Feb 2013 16:08:37 -0500
From: Daniel Cole <dcole10@u.rochester.edu>
Subject: [Freesurfer] mc-sess Error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CAM08fgnZzd3ZquJjJuvUXMvBKBV9PTwwmsDxp2-ndzPeHCfcKA@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hello Freesurfers,
I'm encountering an error when trying to run the following commands.

The command:
"csh

set SESSIONDIRECTORY     = $FUNCTIONALS_DIR

set SUBJECTDIRECTORY     = $SUBJECTS_DIR

set SESSIONNAME          = VGP03_151211

set ANATRUNFORREG        = 002

mc-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -fsd bold"


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


This is my error log:

">> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100

>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ??? Undefined
function or method 'fast_svbslice' for input arguments of type

'struct'.


Error in ==> MRIwrite at 83

  err = fast_svbslice(mri.vol,fstem,[],outbext,bmri);"



Any ideas or suggestions would be greatly appreciated!



--
Daniel Cole
University of Rochester
Brain and Cognitive Sciences
dcole10@u.rochester.edu
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Message: 9
Date: Mon, 11 Feb 2013 16:34:38 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mc-sess Error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <511963EE.8020809@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Make sure that $FREESURFER_HOME/fsfast/toolbox is in your matlab path
doug
On 02/11/2013 04:08 PM, Daniel Cole wrote:
> Hello Freesurfers,
> I'm encountering an error when trying to run the following commands.
>
> The command:
> "csh
>
> set SESSIONDIRECTORY     = $FUNCTIONALS_DIR
>
> set SUBJECTDIRECTORY     = $SUBJECTS_DIR
>
> set SESSIONNAME          = VGP03_151211
>
> set ANATRUNFORREG        = 002
>
>
> mc-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -fsd bold"
>
>
> ----------------------------------------------------------------
>
>
> This is my error log:
>
> ">> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100
>
> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ??? Undefined
> function or method 'fast_svbslice' for input arguments of type
>
> 'struct'.
>
>
> Error in ==> MRIwrite at 83
>
> err = fast_svbslice(mri.vol,fstem,[],outbext,bmri);"
>
>
>
> Any ideas or suggestions would be greatly appreciated!
>
>
>
> --
> Daniel Cole
> University of Rochester
> Brain and Cognitive Sciences
> dcole10@u.rochester.edu <mailto:dcole10@u.rochester.edu>
>
>
> _______________________________________________
> 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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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

Message: 10
Date: Mon, 11 Feb 2013 23:03:56 +0100
From: Gabriel Gonzalez Escamilla <ggonesc@upo.es>
Subject: [Freesurfer] glmfit-sim trouble
To: "Forum, Freesurfer" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <db670ef4369024e.511978dc@upo.es>
Content-Type: text/plain; charset="us-ascii"

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

Message: 11
Date: Tue, 12 Feb 2013 01:02:12 +0100
From: Garikoitz Lerma-Usabiaga <garikoitz@gmail.com>
Subject: Re: [Freesurfer] Freesurfer 5.2 CentOS 4 aparcstats2table
        error
To: Nick Schmansky <nicks@nmr.mgh.harvard.edu>
Cc: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAMrepeYVjBCx=sLa7R9oVCZBwyh15XV75-iLNBzBmBhf3KQYMw@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Thanks Doug and Nick,
it works now,
Gari


On Mon, Feb 11, 2013 at 9:16 PM, Nick Schmansky
<nicks@nmr.mgh.harvard.edu>wrote:

> Gari,
>
> Can you try the attached fixed files?  Both aparcstats2table and
> asegstats2table were fixed.
>
> To install:
>
> cp stats2tab.tar $FREESURFER_HOME/bin
> cd $FREESURFER_HOME/bin
> tar xf stats2tab.tar
>
> Thanks again,
>
> Nick
>
>
> On Mon, 2013-02-11 at 17:06 +0100, Garikoitz Lerma-Usabiaga wrote:
> > Thanks Nick!!
> > is it a solution to run 5.2 aparcstats2table (Snow Leopard) in another
> > machine, accessing the data from a network drive?
> >
> >
> > or is it a solution to run the aparcstats2table provided in 5.1 in the
> > same machine, but accessing the data created by the 5.2 version?
> >
> >
> > many thanks again for your help,
> > Gari
> >
> >
> > On Mon, Feb 11, 2013 at 5:02 PM, Nick Schmansky
> > <nicks@nmr.mgh.harvard.edu> wrote:
> >         Gari,
> >
> >         A little googling tells me that the 'with' statement in python
> >         was
> >         introduced in python v2.5 in 2008, so unfortunately i think
> >         you'll have to
> >         update your python version, unless aparcstats2table can be
> >         rewritten to
> >         not use that statement.
> >
> >         Nick
> >
> >
> >         > Hi Nick!
> >         > this is the version:
> >         > Centos 4 32b or 64b (x86_64)
> >         > (Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06
> >         EDT 2010
> >         > x86_64
> >         > x86_64 x86_64 GNU/Linux)
> >         >
> >         >
> >         > and the python version is:
> >         > Python 2.4.3 (#1, Feb 22 2012, 16:05:45)
> >         > [GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2
> >         > (python --version is not working)
> >         >
> >         > thanks!
> >         > Gari
> >         >
> >         >
> >         >
> >         >
> >         > On Mon, Feb 11, 2013 at 4:50 PM, Nick Schmansky
> >         > <nicks@nmr.mgh.harvard.edu>wrote:
> >         >
> >         >> Gari,
> >         >>
> >         >> What OS are you running?  is this the Centos 4 32b or 64b
> >         (x86_64)?
> >         >>
> >         >> can you tell me your python version?  this way:
> >         >>
> >         >> python --version
> >         >>
> >         >> Nick
> >         >>
> >         >>
> >         >> > Hi fs experts,
> >         >> > I have this error every time I try tu run
> >         aparcstats2table :
> >         >> >
> >         >> >   File
> >         "/home/glerma/fs/52/freesurfer/bin/aparcstats2table", line 221
> >         >> >     with open(o.qdec, 'rb') as f:
> >         >> >             ^
> >         >> > SyntaxError: invalid syntax
> >         >> >
> >         >> >
> >         >> >
> >         >> > it appears each time I run aparcstats2table, even when I
> >         write:
> >         >> > aparcstats2table --help
> >         >> >
> >         >> >
> >         >> > I have changed the environment variables in order to run
> >         the 5.1
> >         >> version,
> >         >> > and it works as always.
> >         >> >
> >         >> >
> >         >> > What else should I check?
> >         >> > thanks!
> >         >> > Gari
> >         >> > _______________________________________________
> >         >> > 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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Message: 12
Date: Tue, 12 Feb 2013 12:00:17 +0000
From: Linn Mittlestein <linnmittle@gmail.com>
Subject: [Freesurfer] average subject
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CAPxBFyx7Wh=vvwYjt2xdgA3tSjkUL5kBxPAa4w0pkDEwmu0LPA@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear freesurfer experts,

i have a question regarding making my own average. I received this message

Tue Feb 12 10:54:34 GMT 2013
make_average_volume done

However, the stats file in the average subject is empty, and the tmp
folder, but the other folders are not empty. Is this "normal"? Does the
above message indicate that the make_subject is done, or should it say
"finished without error etc".

Thank you for your help,

Kind Regards Linn
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------------------------------

Message: 13
Date: Tue, 12 Feb 2013 07:55:12 -0500
From: "Caspar M. Schwiedrzik" <cschwiedrz@mail.rockefeller.edu>
Subject: [Freesurfer] preparing NHP data for whole brain analysis
To: "Freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CA+bX-3-MUFUJDTfTEN-eWrQPKm=4n5r58bSZ402M4tnghS0kmw@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear Freesurfer experts,
I am trying to prepare some NHP functional data for a whole brain group
analysis, and I was wondering which sequence of steps you would recommend,
given that the data cannot be processed with recon-all.
I have surfaces from 4 subjects, but one subject for which I do not have an
anatomy of sufficient quality and won't be able to obtain one. I would also
like to align the data to the 112RM atlas by Mclaren et al.
I was thinking that I could probably align the functional data per subject
to the atlas, and then use this registration with func2sph-sess to align
all subjects for the group analysis (again to the atlas). Does that make
sense, given that I have only four out of five individual surfaces?

A second question is when to smooth the data. I assume that it makes most
sense to smooth it after it has been transformed into surface space. Would
that be sphsmooth-sess?

Finally, when doing the analysis, I would use isxavg-re-sess or isxavg-fe-
sess, correct?

I am using Freesurfer v5.1.
Thank you very much for your advice,
Caspar
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------------------------------

Message: 14
Date: Tue, 12 Feb 2013 14:43:34 +0000
From: Narly Golestani <Narly.Golestani@unige.ch>
Subject: [Freesurfer] Post-Doctoral position in brain imaging and
        computational morphometry ? University of Geneva
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <F28880B1C6E2D84A80B0FF0AD77D54389D4FA3@hotel.isis.unige.ch>
Content-Type: text/plain; charset="Windows-1252"


Post-Doctoral applications are invited in the newly established Brain and Language Lab at the Department of Clinical Neuroscience at the University of Geneva, in collaboration with the Swiss Institute of Technology (EPFL) in Lausanne, Switzerland.  Projects will include the development of new data-driven computational morphometry methods for analysis of structural magnetic resonance imaging (MRI) data, and application of these to large datasets in the context of normal variability, disease, and expertise.

Candidates should have a degree in Biomedical Engineering, Computational Neuroscience, or a related field with a strong mathematical and computational background. Ideally they should have experience in brain image analysis, pattern recognition, machine learning, statistics as well as excellent programming skills.

We offer a competitive starting salary of 68, 964 CHF/year, or more depending on experience.

The position is available immediately, and applications will be considered until the position is filled.  Informal inquiries can be addressed to Narly Golestani (Narly.Golestani@unige.ch).   Applications including a CV, a statement of research interests, and the names and full contact details of three referees should be sent to: Narly.Golestani@unige.ch.



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

Message: 15
Date: Tue, 12 Feb 2013 14:57:08 +0000
From: Catherine Bois <C.Bois@sms.ed.ac.uk>
Subject: [Freesurfer] error when using stats import in qdec
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <20130212145708.12284tex8czyt44k@www.staffmail.ed.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
        format="flowed"

Dear all,

I have a question;

I am trying to load data into qdec; the data table is loaded fine
(although it lists age as continuous for some region, rather than
discreet). However, When i try to generate the stats table, this error
comes up. Does this mean I somehow have to manually set the subjects
directory to where my subjects are (rather than the default that seems
to be used), using the "generate stats table" option? If so, how is
this done? Or is it a preprocessing step I have missed out?

mkdir: cannot create directory
`/usr/local2/freesurfer510/subjects/qdec': Permission denied
ERROR: In
/usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line
230
vtkKWQdecApp (0x30732c58):
     Script:
vtkTemp2 GenerateStatsDataTables
     Returned Error on line 1:
Uncaught exception: command failed: mkdir -p
/usr/local2/freesurfer510/subjects/qdec/stats_tables/

Stack trace:
Uncaught exception: command failed: mkdir -p
/usr/local2/freesurfer510/subjects/qdec/stats_tables/

     while executing
"vtkTemp2 GenerateStatsDataTables"

Grateful for your help

Regards Catherine



--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.




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

Message: 16
Date: Tue, 12 Feb 2013 14:58:45 +0000
From: Catherine Bois <C.Bois@sms.ed.ac.uk>
Subject: [Freesurfer] Fwd: error when using stats import in qdec
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <20130212145845.59463tf238ggo6uc@www.staffmail.ed.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
        format="flowed"


Dear all,

I have a question;

I am trying to load data into qdec; the data table is loaded fine
(although it lists age as continuous for some region, rather than
discreet). However, When i try to generate the stats table, this error
comes up. Does this mean I somehow have to manually set the subjects
directory to where my subjects are (rather than the default that seems
to be used), using the "generate stats table" option? If so, how is
this done? Or is it a preprocessing step I have missed out?

mkdir: cannot create directory
`/usr/local2/freesurfer510/subjects/qdec': Permission denied
ERROR: In
/usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line
230
vtkKWQdecApp (0x30732c58):
     Script:
vtkTemp2 GenerateStatsDataTables
     Returned Error on line 1:
Uncaught exception: command failed: mkdir -p
/usr/local2/freesurfer510/subjects/qdec/stats_tables/

Stack trace:
Uncaught exception: command failed: mkdir -p
/usr/local2/freesurfer510/subjects/qdec/stats_tables/

     while executing
"vtkTemp2 GenerateStatsDataTables"

Grateful for your help

Regards Catherine



--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



----- End forwarded message -----


--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.




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

Message: 17
Date: Tue, 12 Feb 2013 15:09:09 +0000
From: Catherine Bois <C.Bois@sms.ed.ac.uk>
Subject: Re: [Freesurfer] Fwd: error when using stats import in qdec
To: freesurfer@nmr.mgh.harvard.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID: <20130212150909.43115jzcpryvfh0c@www.staffmail.ed.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
        format="flowed"

Sorry, just to clarify; it lists age as a discreet variable rather
than continuous for some reason, not the other way round as I
accidentally wrote=)

Regards


Quoting Catherine Bois <C.Bois@sms.ed.ac.uk> on Tue, 12 Feb 2013
14:58:45 +0000:

>
> Dear all,
>
> I have a question;
>
> I am trying to load data into qdec; the data table is loaded fine
> (although it lists age as continuous for some region, rather than
> discreet). However, When i try to generate the stats table, this
> error comes up. Does this mean I somehow have to manually set the
> subjects directory to where my subjects are (rather than the default
> that seems to be used), using the "generate stats table" option? If
> so, how is this done? Or is it a preprocessing step I have missed out?
>
> mkdir: cannot create directory
> `/usr/local2/freesurfer510/subjects/qdec': Permission denied
> ERROR: In
> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
> line 230
> vtkKWQdecApp (0x30732c58):
>     Script:
> vtkTemp2 GenerateStatsDataTables
>     Returned Error on line 1:
> Uncaught exception: command failed: mkdir -p
> /usr/local2/freesurfer510/subjects/qdec/stats_tables/
>
> Stack trace:
> Uncaught exception: command failed: mkdir -p
> /usr/local2/freesurfer510/subjects/qdec/stats_tables/
>
>     while executing
> "vtkTemp2 GenerateStatsDataTables"
>
> Grateful for your help
>
> Regards Catherine
>
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
> ----- End forwarded message -----
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>



--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.




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

Message: 18
Date: Tue, 12 Feb 2013 10:13:50 -0500 (EST)
From: "Nick Schmansky" <nicks@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Fwd: error when using stats import in qdec
To: "Catherine Bois" <C.Bois@sms.ed.ac.uk>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <50668.66.30.255.161.1360682030.squirrel@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1

Catherine,

Is your SUBJECTS_DIR enviro var setup properly prior to starting qdec?
That is, set to your own writable subjects directory?  I noticed in the
error message that it looks like the subjects dir is the default one under
the /freesurfer dir, which is read-only.

One option is to put this line at the top of your qdec.table.dat file:

SUBJECTS_DIR  /path/to/my/subjects

so that you dont have to remember to set it prior to starting qdec.

Also, age would be a continuous var even if its an integer, discrete is
what we assign to classes like male/female or patient/control.

Nick


>
> Dear all,
>
> I have a question;
>
> I am trying to load data into qdec; the data table is loaded fine
> (although it lists age as continuous for some region, rather than
> discreet). However, When i try to generate the stats table, this error
> comes up. Does this mean I somehow have to manually set the subjects
> directory to where my subjects are (rather than the default that seems
> to be used), using the "generate stats table" option? If so, how is
> this done? Or is it a preprocessing step I have missed out?
>
> mkdir: cannot create directory
> `/usr/local2/freesurfer510/subjects/qdec': Permission denied
> ERROR: In
> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
> line
> 230
> vtkKWQdecApp (0x30732c58):
>      Script:
> vtkTemp2 GenerateStatsDataTables
>      Returned Error on line 1:
> Uncaught exception: command failed: mkdir -p
> /usr/local2/freesurfer510/subjects/qdec/stats_tables/
>
> Stack trace:
> Uncaught exception: command failed: mkdir -p
> /usr/local2/freesurfer510/subjects/qdec/stats_tables/
>
>      while executing
> "vtkTemp2 GenerateStatsDataTables"
>
> Grateful for your help
>
> Regards Catherine
>
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
> ----- End forwarded message -----
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>



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

Message: 19
Date: Tue, 12 Feb 2013 10:15:23 -0500 (EST)
From: "Nick Schmansky" <nicks@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Fwd: error when using stats import in qdec
To: "Catherine Bois" <C.Bois@sms.ed.ac.uk>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <50675.66.30.255.161.1360682123.squirrel@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1

Catherine,

Thats odd, can you email me your qdec.table.dat file?  qdec parses
'discretes' if they're non-numerical, so maybe there is a stray character
thats messing it up.

Nick


> Sorry, just to clarify; it lists age as a discreet variable rather
> than continuous for some reason, not the other way round as I
> accidentally wrote=)
>
> Regards
>
>
> Quoting Catherine Bois <C.Bois@sms.ed.ac.uk> on Tue, 12 Feb 2013
> 14:58:45 +0000:
>
>>
>> Dear all,
>>
>> I have a question;
>>
>> I am trying to load data into qdec; the data table is loaded fine
>> (although it lists age as continuous for some region, rather than
>> discreet). However, When i try to generate the stats table, this
>> error comes up. Does this mean I somehow have to manually set the
>> subjects directory to where my subjects are (rather than the default
>> that seems to be used), using the "generate stats table" option? If
>> so, how is this done? Or is it a preprocessing step I have missed out?
>>
>> mkdir: cannot create directory
>> `/usr/local2/freesurfer510/subjects/qdec': Permission denied
>> ERROR: In
>> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
>> line 230
>> vtkKWQdecApp (0x30732c58):
>>     Script:
>> vtkTemp2 GenerateStatsDataTables
>>     Returned Error on line 1:
>> Uncaught exception: command failed: mkdir -p
>> /usr/local2/freesurfer510/subjects/qdec/stats_tables/
>>
>> Stack trace:
>> Uncaught exception: command failed: mkdir -p
>> /usr/local2/freesurfer510/subjects/qdec/stats_tables/
>>
>>     while executing
>> "vtkTemp2 GenerateStatsDataTables"
>>
>> Grateful for your help
>>
>> Regards Catherine
>>
>>
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>>
>> ----- End forwarded message -----
>>
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>



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

Message: 20
Date: Tue, 12 Feb 2013 09:49:07 -0600 (CST)
From: Jon Wieser <wieser@uwm.edu>
Subject: [Freesurfer] trac-all problem
To: freesurfer  <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <1024806192.314376.1360684147269.JavaMail.root@mail06.pantherlink.uwm.edu>

Content-Type: text/plain; charset="utf-8"

hello

i am trying to process the dti  data with trac-all.  I am new to tracula
my input images are 3300 dicoms,   60 slices and 55 dti diffusions
i have attached my dmrirc_single_subject file


i did the following command:

trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject

and got the result:



INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012
INFO: Diffusion root is /Studies/MJMRI/MJ0012
Actual FREESURFER_HOME /Applications/freesurfer
trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd
#-------------------------------------
/Applications/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Mon Feb 11 12:41:04 CST 2013
mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz
mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1...
Starting DICOMRead2()
dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1
dcmdir = /Studies/MJMRI/MJ0012//s780
Ref Series No = 13
Found 3304 files, checking for dicoms
Found 3300 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 0 2
Vs: 0 0 1
Second Sorting
Counting frames
nframes = 55
nslices = 60
ndcmfiles = 3300
PE Dir = COL (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
jpegUID:           --1.2.840.10008.1.2.4--
Loading pixel data
TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (-0, -0, 1)
writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz...
mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 > /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat
flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 2
fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz
INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals, converting to FSL format
INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs, converting to FSL format
mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs
mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals
eddy_correct /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0000
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0016
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0017
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0018
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0019
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0020
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0021
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0022
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0023
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0024
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0025
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0026
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0027
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0028
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0029
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0030
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0031
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0032
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0033
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0034
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0035
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0036
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0037
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0038
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0039
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0040
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0041
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0042
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0043
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0044
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0045
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0046
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0047
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0048
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0049
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0050
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0051
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0052
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0053
processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0054
mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot
xfmrot /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.ecclog /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs
fslroi /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/lowb.nii.gz 0

Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize>
       fslroi <input> <output> <tmin> <tsize>

       fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize>
Note: indexing (in both time and space) starts with 0 not 1!
Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun  7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Mon Feb 11 13:25:16 CST 2013


can you tell me how to fix this?
Thanks
Jon Wieser
UW-Milwaukee
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------------------------------

Message: 21
Date: Tue, 12 Feb 2013 16:51:20 +0100
From: J?rg Pfannm?ller <pfannmoelj@uni-greifswald.de>
Subject: [Freesurfer] two sample t-test of paired differences
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <20130212165120.64610635.pfannmoelj@uni-greifswald.de>
Content-Type: text/plain; charset=US-ASCII

Hello,

I have two different results from a paired difference analysis lets call it A and B. How can I do a two sample t-test with those results (A-B)? Somehow I am stuck in using isxconcat-sess on the group results A and B. Help is highly appreciated.

Cheers Joerg




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

Message: 22
Date: Tue, 12 Feb 2013 11:14:20 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] average subject
To: Linn Mittlestein <linnmittle@gmail.com>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <alpine.LRH.2.00.1302121114150.21699@gate.nmr.mgh.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

Hi Linn
that sounds normal to me

cheers
Bruce
On Tue, 12 Feb 2013, Linn Mittlestein wrote:

> Dear freesurfer experts,
>
> i have a question regarding making my own average. I received this message
>
> Tue Feb 12 10:54:34 GMT 2013
> make_average_volume done
>
> However, the stats file in the average subject is empty, and the tmp folder,
> but the other folders are not empty. Is this "normal"? Does the above
> message indicate that the make_subject is done, or should it say "finished
> without error etc".
>
> Thank you for your help,
>
> Kind Regards Linn
>
>
>


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

Message: 23
Date: Tue, 12 Feb 2013 16:15:28 +0000
From: Linn Mittlestein <linnmittle@gmail.com>
Subject: Re: [Freesurfer] average subject
To: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CAPxBFywt9didOeYfsg7pRVCt9Oo-NtWWU2Y86vB_eidLu7+nOA@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear Bruce,

Thank you for your reply

Regards, Linn


On Tue, Feb 12, 2013 at 4:14 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>wrote:

> Hi Linn
> that sounds normal to me
>
> cheers
> Bruce
>
> On Tue, 12 Feb 2013, Linn Mittlestein wrote:
>
>  Dear freesurfer experts,
>>
>> i have a question regarding making my own average. I received this message
>>
>> Tue Feb 12 10:54:34 GMT 2013
>> make_average_volume done
>>
>> However, the stats file in the average subject is empty, and the tmp
>> folder,
>> but the other folders are not empty. Is this "normal"? Does the above
>> message indicate that the make_subject is done, or should it say "finished
>> without error etc".
>>
>> Thank you for your help,
>>
>> Kind Regards Linn
>>
>>
>>
>>
>
> 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<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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Message: 24
Date: Tue, 12 Feb 2013 11:29:03 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] average subject
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <511A6DCF.9000800@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Linn, make_average_subject does not compile statistics so this is normal.
doug


On 02/12/2013 11:14 AM, Bruce Fischl wrote:
> Hi Linn
> that sounds normal to me
>
> cheers
> Bruce
> On Tue, 12 Feb 2013, Linn Mittlestein wrote:
>
>> Dear freesurfer experts,
>>
>> i have a question regarding making my own average. I received this message
>>
>> Tue Feb 12 10:54:34 GMT 2013
>> make_average_volume done
>>
>> However, the stats file in the average subject is empty, and the tmp folder,
>> but the other folders are not empty. Is this "normal"? Does the above
>> message indicate that the make_subject is done, or should it say "finished
>> without error etc".
>>
>> Thank you for your help,
>>
>> Kind Regards Linn
>>
>>
>>
> _______________________________________________
> 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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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

Message: 25
Date: Tue, 12 Feb 2013 11:29:48 -0500
From: Gabriel Obregon <obregon@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Basic skullstrip Inquiry
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <5C5C6F12-D35D-40E1-850B-AE1BCED6D8B0@nmr.mgh.harvard.edu>
Content-Type: text/plain;       charset=us-ascii

Hi,

I'm using the -gcut flag for the first time and I've noticed that the skull stripping process is still leaving small fragments of dura behind. Will this affect my surfaces? Should I manually edit the brainmask volume to remove as much of these fragments as I can?

Also, should I only be concerned about the GM and cerebellum edges when checking for over-aggressive cutting, or are other brain structures important as well, e.g. optic chiasm?

Thanks,

--G



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

Message: 26
Date: Tue, 12 Feb 2013 11:32:33 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] two sample t-test of paired differences
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <511A6EA1.30701@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Joerg, see http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples and
look at the 2 group with 0 covariates.
doug

On 02/12/2013 10:51 AM, J?rg Pfannm?ller wrote:
> Hello,
>
> I have two different results from a paired difference analysis lets call it A and B. How can I do a two sample t-test with those results (A-B)? Somehow I am stuck in using isxconcat-sess on the group results A and B. Help is highly appreciated.
>
> Cheers Joerg
>
>
> _______________________________________________
> 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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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

Message: 27
Date: Tue, 12 Feb 2013 11:35:08 -0500
From: Susan Kuo <susan.kuo.run@gmail.com>
Subject: [Freesurfer] Parallelizing on a different kind of cluster
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CAL9UXA7O66R38zvxub73GBARf+3isW63kj+pz71h_+fJ4spJ5Q@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi TRACULA Experts,

  Is there a way of parallelizing BEDPOSTX on a cluster, not using the
bedpostx_seychelles option since I'm on a non-MGH cluster?

Thanks!
Susie Kuo
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Message: 28
Date: Tue, 12 Feb 2013 11:41:48 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mean cortical thickness of significant
        clusters in qdec
To: "Richter, Julia" <Julia.Richter@med.uni-heidelberg.de>,
        "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>
Message-ID: <511A70CC.8030701@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Anyone know how to reset the LOCAL? Even if temporarily to see if this
is the problem?
doug


On 02/12/2013 08:23 AM, Richter, Julia wrote:
> It says the same even if I put 1.3 in quotes. :( Any other possibility to get access to the data?
>
>
> -----Urspr?ngliche Nachricht-----
> Von: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu]
> Gesendet: Montag, 11. Februar 2013 19:04
> An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: AW: AW: AW: [Freesurfer] mean cortical thickness of significant clusters in qdec
>
>
> It may be a German operating system replacing 1.3 with 1,3. Maybe put it in quotes, ie, "1.3"
>
> On 02/11/2013 04:17 AM, Richter, Julia wrote:
>> Dear Doug,
>>
>> this is what appears when I type my command in the command window:
>>
>> mri_glmfit-sim --cache 1.3 abs --cwpvalthresh .99
>> ERROR: thresh 1,3, must be 1.3, 2.0, 3.0, 3.3, 4.0
>>
>> That's it...Any ideas why this is happening?
>>
>> Many thanks in advance!
>>
>> Best, Julia
>>
>> -----Urspr?ngliche Nachricht-----
>> Von: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu]
>> Gesendet: Donnerstag, 7. Februar 2013 17:32
>> An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu
>> Betreff: Re: AW: AW: [Freesurfer] mean cortical thickness of
>> significant clusters in qdec
>>
>> it does not look like you changed the command line. Also, please cut and paste the info into the email instead of taking a snapshot.
>> thanks
>> doug
>>
>> On 02/04/2013 07:26 AM, Richter, Julia wrote:
>>> This doesn't work either (see attachment)  :(
>>>
>>> -----Urspr?ngliche Nachricht-----
>>> Von: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu]
>>> Gesendet: Donnerstag, 31. Januar 2013 20:29
>>> An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu
>>> Betreff: Re: AW: [Freesurfer] mean cortical thickness of significant
>>> clusters in qdec
>>>
>>> The threshold must be in the form of -log10(pthreshold). So, if you
>>> want pthreshold=.05, then use 1.3 doug
>>>
>>>
>>>
>>> On 01/31/2013 07:37 AM, Richter, Julia wrote:
>>>> Dear Doug,
>>>>
>>>> thanks for your reply. I tried the command you suggested, but I always get an error message that there is something wrong with my threshold. I took a screenshot of the command window and attached it to this mail. I will be very happy if you have a look at it.
>>>>
>>>> Looking forward to your answer,
>>>>
>>>> Best, Julia
>>>>
>>>> -----Urspr?ngliche Nachricht-----
>>>> Von: freesurfer-bounces@nmr.mgh.harvard.edu
>>>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von
>>>> Douglas Greve
>>>> Gesendet: Mittwoch, 30. Januar 2013 17:16
>>>> An: Richter, Julia; free surfer
>>>> Betreff: Re: [Freesurfer] mean cortical thickness of significant
>>>> clusters in qdec
>>>>
>>>> Oh, sorry, I thought you said you were using mri_glmfit-sim (which
>>>> does not have an FDR option). Are you using the FDR in QDEC? If so,
>>>> it will display the voxel-wise threshold that realizes the FDR
>>>> threshold. You can then run mri_glmfit-sim --cache threshold sign
>>>> --cwpvalthresh .99 where threshold is the voxelwise threshold from
>>>> FDR and sign is either abs (absolute), pos, or neg. Setting
>>>> cwpvalthresh=.99 tell it to report all clusters
>>>>
>>>> doug
>>>>
>>>> On 1/30/13 8:09 AM, Richter, Julia wrote:
>>>>> No it is not...or I just do not find it.
>>>>>
>>>>> Might it be that I only get the xxx.y.ocn.dat if I correct for multiple comparisons with Monte Carlo? If yes, is there any possibility that I get this xxx.y.ocn.dat when correcting with FDR?
>>>>>
>>>>> Many thanks, Julia
>>>>>
>>>>> -----Urspr?ngliche Nachricht-----
>>>>> Von: freesurfer-bounces@nmr.mgh.harvard.edu
>>>>> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von
>>>>> Douglas N Greve
>>>>> Gesendet: Dienstag, 29. Januar 2013 18:46
>>>>> An: freesurfer@nmr.mgh.harvard.edu
>>>>> Betreff: Re: [Freesurfer] mean cortical thickness of significant
>>>>> clusters in qdec
>>>>>
>>>>> Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not?
>>>>> doug
>>>>>
>>>>>
>>>>> On 01/29/2013 11:03 AM, Richter, Julia wrote:
>>>>>> Dear FreeSurfer experts,
>>>>>>
>>>>>> I did a group analysis in qdec, found several significant clusters
>>>>>> and would now like to extract the mean cortical thickness of each
>>>>>> significant cluster. I know that I have to run mri_glmfit-sim to
>>>>>> do this, but I do not understand which commands I need to get the
>>>>>> xxx.y.ocn.dat as output by running mri_glmfit-sim.
>>>>>>
>>>>>> Any ideas? Any help is appreciated. J
>>>>>>
>>>>>> Best wishes, Julia
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>> greve@nmr.mgh.harvard.edu
>>>>> Phone Number: 617-724-2358
>>>>> Fax: 617-726-7422
>>>>>
>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>>> FileDrop: 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.
>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> 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
>> greve@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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

Message: 29
Date: Tue, 12 Feb 2013 11:43:58 -0500 (EST)
From: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] trac-all -path error
To: stdp82@virgilio.it
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <alpine.LRH.2.00.1302121141000.8686@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"


Hi Stefano - What are the contents of the bedpostX output directory? In
your case, that'd be this directory:
/Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX

a.y

On Mon, 11 Feb 2013, stdp82@virgilio.it wrote:

> Hi list,
> I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I have this error:
>
> Loading mask from
> /Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
> Loading BEDPOST parameter samples from /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX
> niiRead(): error opening file
> /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz
> ERROR: Could not read
> /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz
>
> From?http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22066.html?
> I'm deducing that the error may be related trace-all upload.
>
> I have doing this upload but I visualize always the same error.
>
> I attached tract-all uploades file that live in /Applications/freesurfer/bin.
>
> Please, could you check it?
>
> I have also other question. May I run the second step of trac-all (bedpostx) using FSL on other pc? In this
> way, could I directly run in FSL dmri folder? Do you think that I should rename some files?
>
> Thanks,
>
>
> Stefano
>
>

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

Message: 30
Date: Tue, 12 Feb 2013 11:45:55 -0500 (EST)
From: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] R:  trac-all -path error
To: stdp82@virgilio.it
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <alpine.LRH.2.00.1302121144290.8686@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"


Hi Stefano - There is no need to attach the trac-all script, I am quite
familiar with it. Perhaps you could attach the configuration file that you
set up?

Thanks,
a.y

On Mon, 11 Feb 2013, stdp82@virgilio.it wrote:

> I'm attaching my trac-all file for check.Thanks,
>
> Stefano
>
> ----Messaggio originale----
> Da: stdp82@virgilio.it
> Data: 11-feb-2013 14.42
> A: <freesurfer@nmr.mgh.harvard.edu>
> Cc: <ayendiki@nmr.mgh.harvard.edu>
> Ogg: [Freesurfer] trac-all -path error
>
> Hi list,
> I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I have this error:
>
> Loading mask from
> /Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
> Loading BEDPOST parameter samples from /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX
> niiRead(): error opening file
> /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz
> ERROR: Could not read
> /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz
>
> From?http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22066.html?
> I'm deducing that the error may be related trace-all upload.
>
> I have doing this upload but I visualize always the same error.
>
> I attached tract-all uploades file that live in /Applications/freesurfer/bin.
>
> Please, could you check it?
>
> I have also other question. May I run the second step of trac-all (bedpostx) using FSL on other pc? In this
> way, could I directly run in FSL dmri folder? Do you think that I should rename some files?
>
> Thanks,
>
>
> Stefano
>
>
>
>

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

Message: 31
Date: Tue, 12 Feb 2013 11:49:04 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] preparing NHP data for whole brain analysis
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <511A7280.8090100@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Caspar, with 5.1 you would not use any of those programs (ie,
func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use FSFAST,
then see the tutorial for getting started. You'll need to set up the
directory structure properly, then run preproc-sess, mkanalysis-sess,
and selxavg3-sess. For the group analysis you'll run isxconcat-sess
followed by mri_glmfit and mri_glmfit-sim. If you don't have anatomicals
for all subjects and you just want to use the average subject, then put
the average subject into the subjectname file when you set up the
directory structure.

doug


On 02/12/2013 07:55 AM, Caspar M. Schwiedrzik wrote:
> Dear Freesurfer experts,
> I am trying to prepare some NHP functional data for a whole brain
> group analysis, and I was wondering which sequence of steps you would
> recommend, given that the data cannot be processed with recon-all.
> I have surfaces from 4 subjects, but one subject for which I do not
> have an anatomy of sufficient quality and won't be able to obtain one.
> I would also like to align the data to the 112RM atlas by Mclaren et al.
> I was thinking that I could probably align the functional data per
> subject to the atlas, and then use this registration with
> func2sph-sess to align all subjects for the group analysis (again to
> the atlas). Does that make sense, given that I have only four out of
> five individual surfaces?
>
> A second question is when to smooth the data. I assume that it makes
> most sense to smooth it after it has been transformed into surface
> space. Would that be sphsmooth-sess?
>
> Finally, when doing the analysis, I would use isxavg-re-sess or
> isxavg-fe-sess, correct?
>
> I am using Freesurfer v5.1.
> Thank you very much for your advice,
> 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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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

Message: 32
Date: Tue, 12 Feb 2013 11:49:18 -0500 (EST)
From: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] trac-all problem
To: Jon Wieser <wieser@uwm.edu>
Cc: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.00.1302121146120.8686@door.nmr.mgh.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed


Hi Jon - My guess is you didn't define the nb0 variable in your
configuration file, see here:
        http://www.freesurfer.net/fswiki/dmrirc

The new version, which will come out in a few days, will be able to figure
it out without you having to specify it but with the current version you
have to.

Hope this helps,
a.y

On Tue, 12 Feb 2013, Jon Wieser wrote:

> hello
>
> i am trying to process the dti  data with trac-all.  I am new to tracula
> my input images are 3300 dicoms,   60 slices and 55 dti diffusions
> i have attached my dmrirc_single_subject file
>
>
> i did the following command:
>
> trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject
>
> and got the result:
>
>
>
> INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012
> INFO: Diffusion root is /Studies/MJMRI/MJ0012
> Actual FREESURFER_HOME /Applications/freesurfer
> trac-preproc -c /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd
> #-------------------------------------
> /Applications/freesurfer/bin/trac-preproc
> #-------------------------------------
> #@# Image corrections Mon Feb 11 12:41:04 CST 2013
> mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz
> mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz
> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
> reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1...
> Starting DICOMRead2()
> dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1
> dcmdir = /Studies/MJMRI/MJ0012//s780
> Ref Series No = 13
> Found 3304 files, checking for dicoms
> Found 3300 dicom files in series.
> First Sorting
> Computing Slice Direction
> Vs: 0 0 2
> Vs: 0 0 1
> Second Sorting
> Counting frames
> nframes = 55
> nslices = 60
> ndcmfiles = 3300
> PE Dir = COL (dicom read)
> TransferSyntaxUID: --1.2.840.10008.1.2.1--
> jpegUID:           --1.2.840.10008.1.2.4--
> Loading pixel data
> TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00
> i_ras = (-1, 0, 0)
> j_ras = (0, -1, 0)
> k_ras = (-0, -0, 1)
> writing to /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz...
> mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 > /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat
> flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz
> INFO: input image orientation is LPS
> INFO: input image determinant is 2
> fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz
> INFO: left-right orientation was flipped by fslswapdim
> fslorient -forceradiological /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz
> INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals, converting to FSL format
> INFO: found /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs, converting to FSL format
> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs
> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals
> eddy_correct /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0000
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0016
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0017
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0018
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0019
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0020
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0021
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0022
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0023
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0024
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0025
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0026
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0027
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0028
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0029
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0030
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0031
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0032
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0033
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0034
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0035
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0036
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0037
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0038
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0039
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0040
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0041
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0042
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0043
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0044
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0045
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0046
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0047
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0048
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0049
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0050
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0051
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0052
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0053
> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0054
> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot
> xfmrot /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.ecclog /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs
> fslroi /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz /Studies/MJMRI/MJ0012/freesurfer/dmri/lowb.nii.gz 0
>
> Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize>
>       fslroi <input> <output> <tmin> <tsize>
>
>       fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize>
> Note: indexing (in both time and space) starts with 0 not 1!
> Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun  7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
>
> trac-preproc exited with ERRORS at Mon Feb 11 13:25:16 CST 2013
>
>
> can you tell me how to fix this?
> Thanks
> Jon Wieser
> UW-Milwaukee
>


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

Message: 33
Date: Tue, 12 Feb 2013 11:56:23 -0500 (EST)
From: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Parallelizing on a different kind of cluster
To: Susan Kuo <susan.kuo.run@gmail.com>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <alpine.LRH.2.00.1302121150420.8686@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"


Hi Susie - FSL's bedpostx script works for parallelization on the type of
cluster they have at Oxford, and bedpostx_seychelles is a modified version
of it that also works on our cluster. Other than that, support for all
possible cluster setups at other centers is beyond the scope of our
research, but perhaps the existing script is useful as a starting point
for making it work on your cluster.

Hope this helps,
a.y

On Tue, 12 Feb 2013, Susan Kuo wrote:

> Hi TRACULA Experts,?
> ? Is there a way of parallelizing BEDPOSTX on a cluster, not using the bedpostx_seychelles option since I'm
> on a non-MGH cluster??
>
> Thanks!
> Susie Kuo
>
>

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

Message: 34
Date: Tue, 12 Feb 2013 11:58:01 -0500 (EST)
From: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Troubleshooting the preproc
To: Susan Kuo <susan.kuo.run@gmail.com>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <alpine.LRH.2.00.1302121157120.8686@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"


Hi Susie - avscale is part of the FSL package. You have to make sure FSL
is installed and in your path.

a.y

On Wed, 6 Feb 2013, Susan Kuo wrote:

> Hi FreeSurfer community,?? I am currently trying to troubleshoot my preprocessing part of TRACULA with the
> tutorial dataset (for Diff001?as the subject, specifically), running trac-all -corr -c <config dmrirc>. I am
> running the commands in subjectID/scripts/trac-all.cmd?one by one because I've had problems with some of the
> steps. Specifically, flip4fsl?didn't work. I instead used fslswapdim -x -y z?(flip4fsl?uses fslswapdim x -y
> z, which doesn't generate the correct orientation for FSL in fact), followed by fslorient
> -forceradiological. I successfully ran eddy_current thereafter. Now I am stuck again, at FreeSurfer's
> xfmrot, which should look like:?
>
> xfmrot <transform file> <input vector file> [<output vector file>]
>
> I specifically typed in:?
>
> xfmrot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi.ecclog
> /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs.norot
> /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs
>
>
> and received the following iterative errors:
>
> avscale: Command not found.
> R: Subscript out of range.
> R: Subscript out of range.
> R: Subscript out of range.
>
> Can any of you help me??
>
> Thank you,?
> Susie K
>
>

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

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End of Freesurfer Digest, Vol 108, Issue 14
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