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Today's Topics:

  1. preprocessing error (Maryam Vaziri Pashkam)
  2. Re: preprocessing error (Douglas Greve)
  3. convert surface label on to functional image (Zhangyuanchao)
  4. References/materials for interaction analysis in  freesurfer
     (Bhavani Shankara Bagepally)
  5. Re: dt_recon error (Yuko Yotsumoto)
  6. Re: dt_recon error (Yuko Yotsumoto)
  7. Re: run preproc-sess with -nomc (Thunell Evelina)
  8. Re: mri_ca_register from virtual box (Lorenzo Busti)
  9. Re: mri_ca_register from virtual box (Lorenzo Busti)
 10. Converting thickness maps to vtk (Navid Shiee)
 11. Re: tracula and snow leopard: can't allocate region /     memory
     error (Anastasia Yendiki)
 12. tracula failed to find header file for -t (Scott Hayes)


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

Message: 1
Date: Sun, 11 Dec 2011 14:34:05 -0500
From: Maryam Vaziri Pashkam <mvaziri.p@gmail.com>
Subject: [Freesurfer] preprocessing error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
       <CAEEXA4cePaYDO8EPMpma7ThADfnd1qcYfg2HnnHz+7sVrVBTjw@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi,

I am running preprocessing on my data using freesurfer 5.1, fsl 4.1.7, and
matlab R2009a (I also tried it with matlab 2007a) on Harvard cluster and I
am receiving an error. I connect to the cluster using terminal and SSH
connection in mac.

the preprocessing is stalled in the middle with this error:

++ Max displacement in automask = 0.79 (mm) at sub-brick 3
Can't connect? tcp_connect[connect]: Connection timed out
++ Wrote dataset to disk in 004/tmp.mc-afni2.20850/outvol.nii.gz
** Warning: overwriting file 004/fmcpr.mcdat
Can't connect? tcp_connect[connect]: Connection timed out
Can't connect? tcp_connect[connect]: Connection timed out
Can't connect? tcp_connect[connect]: Connection timed out


It does not stop running and output an error. But rather keeps printing the
last line and does not move forward. Any idea where the problem might be?


Thanks,
Maryam
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Message: 2
Date: Sun, 11 Dec 2011 15:39:34 -0500
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] preprocessing error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <4EE51506.6090001@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"

what command are you running (I mean the full command line -- hard to
debug without it). The preprocessing should not require matlab. Just
guessing, this does not look like a FS problem.
doug

On 12/11/11 2:34 PM, Maryam Vaziri Pashkam wrote:
> Hi,
>
> I am running preprocessing on my data using freesurfer 5.1, fsl 4.1.7,
> and matlab R2009a (I also tried it with matlab 2007a) on Harvard
> cluster and I am receiving an error. I connect to the cluster using
> terminal and SSH connection in mac.
>
> the preprocessing is stalled in the middle with this error:
>
> ++ Max displacement in automask = 0.79 (mm) at sub-brick 3
> Can't connect? tcp_connect[connect]: Connection timed out
> ++ Wrote dataset to disk in 004/tmp.mc-afni2.20850/outvol.nii.gz
> ** Warning: overwriting file 004/fmcpr.mcdat
> Can't connect? tcp_connect[connect]: Connection timed out
> Can't connect? tcp_connect[connect]: Connection timed out
> Can't connect? tcp_connect[connect]: Connection timed out
>
>
> It does not stop running and output an error. But rather keeps
> printing the last line and does not move forward. Any idea where the
> problem might be?
>
>
> Thanks,
> Maryam
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 3
Date: Mon, 12 Dec 2011 13:24:21 +0800 (CST)
From: Zhangyuanchao <woshizhangyc@yahoo.cn>
Subject: [Freesurfer] convert surface label on to functional image
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
       <1323667461.98732.YahooMailClassic@web92411.mail.cnh.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

hi, expert,
By mapping a surface label to a functional template, I want to extract the corresponding cortical gray matter region in the functional space. I know I should use the mri_label2vol command.?
In the help page of mri_label2vol, I see some examples of this command.
2. Convert a surface label into a binary mask in the functional space.Fill in all the cortical gray matter. Require that a functional voxelbe filled at least 30% by the label:
mri_label2vol???--label lh-avg_central_sulcus.label???--temp f.nii???--reg register.dat???--fillthresh .3???--proj frac 0 1 .1???--subject bert --hemi lh??--o cent-lh.nii
3. Convert a surface label into a binary mask in the functional space.Sample a 1mm ribbon 2mm below the gray/white surface. Do not require a?fill threshold:
mri_label2vol???--label lh-avg_central_sulcus.label???--temp f.nii???--reg register.dat???--proj abs -3 -2 .1???--subject bert --hemi lh??--o cent-lh.nii
I want to extract the cortical gray matter on the functional images corresponding to the surface label.?I do not know which of the above commands could obtain the result I want and which parameters I should use to obtain what I want.
For example 3, I do not quite catch what "Sample a 1mm ribbon 2mm below the gray/white surface. " this sentence means.?
Thanks for your help!

Best
Yuanchao
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Message: 4
Date: Mon, 12 Dec 2011 12:34:05 +0530
From: Bhavani Shankara Bagepally <bshankara@gmail.com>
Subject: [Freesurfer] References/materials for interaction analysis in
       freesurfer
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
       <CAMx_rAr2CQARrGFD5ENr4kFiye-+XwNiVh-vpkTex55zeCaTYg@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear Sir/Freesurfer experts,

We are working of genes and gene- gene interaction on cortical thickness
using freesurfer. Please let me know if there any material/publications for
validation of free surfer based analysis mainly on gene-gene interaction or
any of the Interaction statistics using freesurfer.

Many thanks in advance


--
Dr. BHAVANI SHANKARA BAGEPALLY
MBBS, (PhD in Clinical Neuroscience) NIMHANS,
Bangalore,
INDIA-560029
email:  bshankara@gmail.com
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Message: 5
Date: Mon, 12 Dec 2011 18:18:47 +0900
From: Yuko Yotsumoto <yukoyy@a7.keio.jp>
Subject: Re: [Freesurfer] dt_recon error
To: Douglas Greve <greve@nmr.mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID: <92101EFC-A3B5-4EBC-8B51-3DC3921059A1@a7.keio.jp>
Content-Type: text/plain; charset="us-ascii"

Thanks Doug,

In the dt_recon help,

> The bvalues are in a simple text file, one for each direction
> (including b=0). The bvectors (gradient directions) are also in a
> simple text file with three components on each row. These also include
> the b=0 values. There must be as many rows in the bvals/bvecs
> as there are frames in the input.


I got the bvectors from Siemens tech. The file looks similar to one in $FREESURFER_HOME/diffusion/mgh-dti-seqpack

However, I am still not sure about bvalues.

> The bvalues are in a simple text file, one for each direction
> (including b=0).


I think I'm using b-value=700, and I have 64 directions.
Should I have b-values for each of the 64 directions? Then the text file should have 64 rows and each row has the same value?

Thank you for your help!
Yuko


On Dec 10, 2011, at 1:42 PM, Douglas Greve wrote:

> Hi Yuko, it will get the bvals and bvecs from a set of tables
> distributed with FS. But the dicom has to have some information in it
> that tells it which table to use. It looks like your dicom did not have
> this information (it is not in the info dump created from the dicom). So
> you'll have to create text files of the bval/bvecs. The expected format
> is given in the help. You'll have to ask someone who knows about your
> sequences as to what the actual values you should use.
> doug
>
> On 12/9/11 10:09 PM, Yuko Yotsumoto wrote:
>> Hi Doug,
>>
>> Thank you for your reply.
>>> If so, then it cannot extract the bvecs and bvals. If you supply them in a file on the command line
>> I don't quite understand how --b works with dt_recon.
>>
>> I did:
>> dt_recon --i /Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm --s AGY11 --o /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
>>
>> and it stopped after creating dwi.nii and dwi-ec.nii.
>> I thought dt_recon is the command to compute bvals and bvecs. How do I supply bvecs and bvals on the command line?
>>
>> Yuko
>>
>>
>> On Dec 10, 2011, at 2:24 AM, Douglas N Greve wrote:
>>
>>> Hi Yuko, your dicom file might be from a different versioned scanner than dt_recon is used to seeing. If so, then it cannot extract the bvecs and bvals. If you supply them in a file on the command line, it should run properly.
>>> doug
>>>
>>> Yuko Yotsumoto wrote:
>>>> Hello,
>>>>
>>>> I'm having a problem with dt_recon on data scanned by Siemens TrioTim.
>>>> I'm using v4.5.0, with Mac OS 10.6.8.
>>>>
>>>> dt_recon ran for a while, and stopped with an error "ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat"
>>>>
>>>> I found the same errors reported to this mailing list, but found no solution.
>>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019755.html
>>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07935.html
>>>>
>>>> In YDTI/YD11A/ folder, I have the following files
>>>> dt_recon.log
>>>> dwi-ec.ecclog
>>>> dwi-ec.nii
>>>> dwi-infodump.dat
>>>> dwi.nii
>>>> mri_glmfit.log
>>>>
>>>> In dwi-infodump.dat, I see bunch of lines, but I don't see "sWiPMemBlock.alFree".
>>>>
>>>> Please help!
>>>> Thanks,
>>>> Yuko Yotsumoto
>>>>
>>>>
>>>>
>>>>
>>>> #@#-------------------------------
>>>> Fitting Tensors
>>>> Wed Dec  7 10:15:52 JST 2011
>>>> cd /Users/yuko/Documents/FreeSurfer/subjects
>>>> mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat
>>>>
>>>> $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $
>>>> cwd /Users/yuko/Documents/FreeSurfer/subjects
>>>> cmdline mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat sysname  Darwin
>>>> hostname Yukos-iMac.local
>>>> machine  i386
>>>> user     yuko
>>>> FixVertexAreaFlag = 1
>>>> UseMaskWithSmoothing     1
>>>> OneSampleGroupMean 0
>>>> y    /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii
>>>> logyflag 1
>>>> X    /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat
>>>> usedti  1
>>>> glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
>>>> IllCondOK 0
>>>> DoFFx 0
>>>> Creating output directory /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
>>>> Loading y from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii
>>>> Using DTI
>>>> bValue = 700
>>>> ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>>
>>>
>>> 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

-----------------------------------
Yuko Yotsumoto, Ph. D.
Associate Professor (research)
The Global Centers of Excellence Program, Keio University

TEL:011-81-3-5427-1156 x 23851
e-mail: yukoyy@a7.keio.jp
HP  : http://web.keio.jp/~yukoyy/
------------------------------------

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Message: 6
Date: Mon, 12 Dec 2011 19:15:30 +0900
From: Yuko Yotsumoto <yukoyy@a7.keio.jp>
Subject: Re: [Freesurfer] dt_recon error
To: Douglas Greve <greve@nmr.mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID: <942CDBDD-4F07-4485-AB91-2A9FBBEBD952@a7.keio.jp>
Content-Type: text/plain; charset="us-ascii"

Doug,

Never mind. I think I just figured it out!0

Yuko

On Dec 12, 2011, at 6:18 PM, Yuko Yotsumoto wrote:

> Thanks Doug,
>
> In the dt_recon help,
>
>> The bvalues are in a simple text file, one for each direction
>> (including b=0). The bvectors (gradient directions) are also in a
>> simple text file with three components on each row. These also include
>> the b=0 values. There must be as many rows in the bvals/bvecs
>> as there are frames in the input.
>
>
> I got the bvectors from Siemens tech. The file looks similar to one in $FREESURFER_HOME/diffusion/mgh-dti-seqpack
>
> However, I am still not sure about bvalues.
>
>> The bvalues are in a simple text file, one for each direction
>> (including b=0).
>
>
> I think I'm using b-value=700, and I have 64 directions.
> Should I have b-values for each of the 64 directions? Then the text file should have 64 rows and each row has the same value?
>
> Thank you for your help!
> Yuko
>
>
> On Dec 10, 2011, at 1:42 PM, Douglas Greve wrote:
>
>> Hi Yuko, it will get the bvals and bvecs from a set of tables
>> distributed with FS. But the dicom has to have some information in it
>> that tells it which table to use. It looks like your dicom did not have
>> this information (it is not in the info dump created from the dicom). So
>> you'll have to create text files of the bval/bvecs. The expected format
>> is given in the help. You'll have to ask someone who knows about your
>> sequences as to what the actual values you should use.
>> doug
>>
>> On 12/9/11 10:09 PM, Yuko Yotsumoto wrote:
>>> Hi Doug,
>>>
>>> Thank you for your reply.
>>>> If so, then it cannot extract the bvecs and bvals. If you supply them in a file on the command line
>>> I don't quite understand how --b works with dt_recon.
>>>
>>> I did:
>>> dt_recon --i /Users/yuko/Documents/FreeSurfer/raw/AGY11ADTI/DTIs/IM-0011-0001.dcm --s AGY11 --o /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
>>>
>>> and it stopped after creating dwi.nii and dwi-ec.nii.
>>> I thought dt_recon is the command to compute bvals and bvecs. How do I supply bvecs and bvals on the command line?
>>>
>>> Yuko
>>>
>>>
>>> On Dec 10, 2011, at 2:24 AM, Douglas N Greve wrote:
>>>
>>>> Hi Yuko, your dicom file might be from a different versioned scanner than dt_recon is used to seeing. If so, then it cannot extract the bvecs and bvals. If you supply them in a file on the command line, it should run properly.
>>>> doug
>>>>
>>>> Yuko Yotsumoto wrote:
>>>>> Hello,
>>>>>
>>>>> I'm having a problem with dt_recon on data scanned by Siemens TrioTim.
>>>>> I'm using v4.5.0, with Mac OS 10.6.8.
>>>>>
>>>>> dt_recon ran for a while, and stopped with an error "ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat"
>>>>>
>>>>> I found the same errors reported to this mailing list, but found no solution.
>>>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019755.html
>>>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07935.html
>>>>>
>>>>> In YDTI/YD11A/ folder, I have the following files
>>>>> dt_recon.log
>>>>> dwi-ec.ecclog
>>>>> dwi-ec.nii
>>>>> dwi-infodump.dat
>>>>> dwi.nii
>>>>> mri_glmfit.log
>>>>>
>>>>> In dwi-infodump.dat, I see bunch of lines, but I don't see "sWiPMemBlock.alFree".
>>>>>
>>>>> Please help!
>>>>> Thanks,
>>>>> Yuko Yotsumoto
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> #@#-------------------------------
>>>>> Fitting Tensors
>>>>> Wed Dec  7 10:15:52 JST 2011
>>>>> cd /Users/yuko/Documents/FreeSurfer/subjects
>>>>> mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat
>>>>>
>>>>> $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $
>>>>> cwd /Users/yuko/Documents/FreeSurfer/subjects
>>>>> cmdline mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat sysname  Darwin
>>>>> hostname Yukos-iMac.local
>>>>> machine  i386
>>>>> user     yuko
>>>>> FixVertexAreaFlag = 1
>>>>> UseMaskWithSmoothing     1
>>>>> OneSampleGroupMean 0
>>>>> y    /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii
>>>>> logyflag 1
>>>>> X    /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat
>>>>> usedti  1
>>>>> glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
>>>>> IllCondOK 0
>>>>> DoFFx 0
>>>>> Creating output directory /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A
>>>>> Loading y from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii
>>>>> Using DTI
>>>>> bValue = 700
>>>>> ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>>
>>>>
>>>> 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
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Message: 7
Date: Mon, 12 Dec 2011 10:55:05 +0000
From: Thunell Evelina <evelina.thunell@epfl.ch>
Subject: Re: [Freesurfer] run preproc-sess with -nomc
To: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <33467ED5-576F-4313-8738-332E1FD89764@epfl.ch>
Content-Type: text/plain; charset="us-ascii"


Hi Douglas,

I do most of my analysis in matlab and SPM. For this one part of my experiment - it's a retinotopic mapping that I will use to ensure that my ROIs are in V1 - I'm using Freesurfer. I have done slice time correction, motion correction and coregistration between functional runs and of the structural image already in SPM. I thought that since these flags exist they would just skip a step in the processing and send the data directly to the next step. But since it's not the case I'll have to do it some other way instead, maybe just redo the whole preprocessing in Freesurfer on the already preprocessed data. (Running the analysis with selxavg3-sess -analysis retlh -s SessXX -no-preproc doesn't work.)
Anyway, the important thing is that the retinotopic mapping data stay coregistered with the rest of the functional data. If I can do this step in Freesurfer instead (and the rest of the preprocessing) that would be an option.

Thanks a lot,
Evelina

On Dec 9, 2011, at 7:06 PM, Douglas N Greve wrote:

Hi Evelina, why do you want to run it without MC? I'm not sure it will run that way. When you run it with -noreg, it causes it not to run the registration. For the preprocessing you have set up, it requires that the registration be run at some point because it needs it to map the fmri to the surface.
doug

Thunell Evelina wrote:

Hi,

Does anyone know how to correctly use the -nomc and -noreg flags?

When I run:
preproc-sess -fwhm 0 -surface self lhrh -s SessLP -fsd bold -nomc
I get the error message:
ERROR: could not determine file for /Applications/freesurfer/sessions/retinotopy/SessLP/bold/001/fmcpr

I also tried
preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold -noreg
which gives the error:
ERROR: cannot find /Applications/freesurfer/sessions/retinotopy/SessLPpolar/bold/001/register.dof6.dat
Try running register-sess with -per-run

When I do
preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold
it works fine and finishes without errors (preproc-sess done)

(I'm using  freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on Mac OS X 10.6.8)

Thanks a lot for any help,
Evelina
------------------------------------------------------------------------

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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



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
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Message: 8
Date: Mon, 12 Dec 2011 15:41:01 +0100
From: Lorenzo Busti <lorebusti@gmail.com>
Subject: Re: [Freesurfer] mri_ca_register from virtual box
To: Nick Schmansky <nicks@nmr.mgh.harvard.edu>
Cc: Freesurfer@nmr.mgh.harvard.edu
Message-ID:
       <CAKKhoR=p1ZsCK8VBijzENctOTmNX5n5x9fvjEtkUre6xRWykLQ@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

*No.. it doesn't work. The RAM is not enough.

We abandoned that machine..

Now we are working with a 64 Bit Computer Dual-core CPU @ 2.10 GHz with 8
GB of RAM.

And.. IT WORKS!!!!!

We completed the autorecon1, autorecon2 and autorecon3 stages with succes!!

We use a virtual box under Windows 7 bat we are not able to allocate more
than 3.5 GB to run freesurfer.

At that hight the selecting bar of the virual box is still green (it
becomes red near 4 GB) but passing 3.5 GB the virtual box does not start

and  it  returns the following error
*

Opening a session for virtual machine frees2 failed.

VT-x is not available. (VERR_VMX_NO_VMX).

Unknown error creating VM (VM_VMX_NO_VMX).



Output Code:

E_FAIL (0x80004005)

Component:

Console

Interface:

IConsole {515e8e8d-f932-4d8e-9f32-79a52aead882}




What does it means?


Thanks!!

L. Busti



2011/12/6 Lorenzo Busti <lorebusti@gmail.com>

> I'm going to check with more ram dedicated.
>
> Many Thanks
>
> Lorenzo Busti
>
>
> 2011/12/5 Nick Schmansky <nicks@nmr.mgh.harvard.edu>
>
>> 1.5GB is probably not enough.  typically we recommend that recon-all
>> have at least 3GB available to it, which can be very hard to do on a
>> virtual machine (since windows takes 1GB, the vm linux takes another
>> 1GB, which leaves 2GB for processes).  i would setup your vm to use the
>> maximum memory allowed (just dont run stuff in windows at the same
>> time).
>>
>> n.
>>
>>
>> On Mon, 2011-12-05 at 15:01 +0100, Lorenzo Busti wrote:
>> > Hi everyone
>> > I got this error while running one of my subjects
>> >
>> >
>> > mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed
>> >
>> > ERROR: mri_ca_register with non-zero status 252
>> >
>> > but continuing despite the error
>> >
>> > #--------------------------------------
>> >
>> > #@# CA Reg Inv Thu Nov 24 05:15:42 EST 2011
>> >
>> > /home/virtualuser/freesurfer/subjects/Petrollini2/mri
>> >
>> >
>> >
>> >  mri_ca_register -invert-and-save transforms/talairach.m3z
>> >
>> >
>> >
>> > Loading, Inverting, Saving, Exiting ...
>> >
>> > Reading transforms/talairach.m3z
>> >
>> > ERROR: cannot find or read transforms/talairach.m3z
>> >
>> > ERROR: mri_ca_register with non-zero status 0
>> >
>> > Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59
>> > UTC 2009 i686 GNU/Linux
>> >
>> >
>> >
>> > recon-all -s Petrollini2 exited with ERRORS at Thu Nov 24 05:15:43 EST
>> > 2011
>> >
>> >
>> >
>> > To report a problem,
>> > see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> >
>> >
>> > I'm working with a virtual machine on a 32 bit computer with 4GB of
>> > RAM(2-core Intel processor 2.00 GHz). I raised the ram dedicated to
>> > the virtual machine to 1,5 GB: this is the max value permitted before
>> > the selecting bar of the virtual box changes from green to red (is it
>> > sufficent?)
>> >
>> > I have free space for data.
>> >
>> > Can you help me in solving this problem?
>> >
>> > Thanks
>> >
>> > Lorenzo Busti
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > 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: 9
Date: Mon, 12 Dec 2011 15:50:37 +0100
From: Lorenzo Busti <lorebusti@gmail.com>
Subject: Re: [Freesurfer] mri_ca_register from virtual box
To: Nick Schmansky <nicks@nmr.mgh.harvard.edu>
Cc: Freesurfer@nmr.mgh.harvard.edu
Message-ID:
       <CAKKhoRkXidz4L08z+YvfFo58ha0_UbU2_iHYsMwGSOv4CM-RUg@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Ops.. I'm sorry..
the selecting bar of our virtual box changes from green to red at 5.4 GB
(not 4 GB.. i was wrong!)

but if i allocate more than 3.5 GB it does not start!

Thanks!

L. Busti

2011/12/12 Lorenzo Busti <lorebusti@gmail.com>

> *No.. it doesn't work. The RAM is not enough.
>
> We abandoned that machine..
>
> Now we are working with a 64 Bit Computer Dual-core CPU @ 2.10 GHz with 8
> GB of RAM.
>
> And.. IT WORKS!!!!!
>
> We completed the autorecon1, autorecon2 and autorecon3 stages with
> succes!!
>
> We use a virtual box under Windows 7 bat we are not able to allocate more
> than 3.5 GB to run freesurfer.
>
> At that hight the selecting bar of the virual box is still green (it
> becomes red near 4 GB) but passing 3.5 GB the virtual box does not start
>
> and  it  returns the following error
> *
>
> Opening a session for virtual machine frees2 failed.
>
> VT-x is not available. (VERR_VMX_NO_VMX).
>
> Unknown error creating VM (VM_VMX_NO_VMX).
>
>
>
> Output Code:
>
> E_FAIL (0x80004005)
>
> Component:
>
> Console
>
> Interface:
>
> IConsole {515e8e8d-f932-4d8e-9f32-79a52aead882}
>
>
>
>
> What does it means?
>
>
> Thanks!!
>
> L. Busti
>
>
>
>
> 2011/12/6 Lorenzo Busti <lorebusti@gmail.com>
>
>> I'm going to check with more ram dedicated.
>>
>> Many Thanks
>>
>> Lorenzo Busti
>>
>>
>> 2011/12/5 Nick Schmansky <nicks@nmr.mgh.harvard.edu>
>>
>>> 1.5GB is probably not enough.  typically we recommend that recon-all
>>> have at least 3GB available to it, which can be very hard to do on a
>>> virtual machine (since windows takes 1GB, the vm linux takes another
>>> 1GB, which leaves 2GB for processes).  i would setup your vm to use the
>>> maximum memory allowed (just dont run stuff in windows at the same
>>> time).
>>>
>>> n.
>>>
>>>
>>> On Mon, 2011-12-05 at 15:01 +0100, Lorenzo Busti wrote:
>>> > Hi everyone
>>> > I got this error while running one of my subjects
>>> >
>>> >
>>> > mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed
>>> >
>>> > ERROR: mri_ca_register with non-zero status 252
>>> >
>>> > but continuing despite the error
>>> >
>>> > #--------------------------------------
>>> >
>>> > #@# CA Reg Inv Thu Nov 24 05:15:42 EST 2011
>>> >
>>> > /home/virtualuser/freesurfer/subjects/Petrollini2/mri
>>> >
>>> >
>>> >
>>> >  mri_ca_register -invert-and-save transforms/talairach.m3z
>>> >
>>> >
>>> >
>>> > Loading, Inverting, Saving, Exiting ...
>>> >
>>> > Reading transforms/talairach.m3z
>>> >
>>> > ERROR: cannot find or read transforms/talairach.m3z
>>> >
>>> > ERROR: mri_ca_register with non-zero status 0
>>> >
>>> > Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59
>>> > UTC 2009 i686 GNU/Linux
>>> >
>>> >
>>> >
>>> > recon-all -s Petrollini2 exited with ERRORS at Thu Nov 24 05:15:43 EST
>>> > 2011
>>> >
>>> >
>>> >
>>> > To report a problem,
>>> > see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> >
>>> >
>>> > I'm working with a virtual machine on a 32 bit computer with 4GB of
>>> > RAM(2-core Intel processor 2.00 GHz). I raised the ram dedicated to
>>> > the virtual machine to 1,5 GB: this is the max value permitted before
>>> > the selecting bar of the virtual box changes from green to red (is it
>>> > sufficent?)
>>> >
>>> > I have free space for data.
>>> >
>>> > Can you help me in solving this problem?
>>> >
>>> > Thanks
>>> >
>>> > Lorenzo Busti
>>> >
>>> >
>>> >
>>> >
>>> > _______________________________________________
>>> > 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: 10
Date: Mon, 12 Dec 2011 10:13:01 -0500
From: Navid Shiee <navid@jhu.edu>
Subject: [Freesurfer] Converting thickness maps to vtk
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
       <CAMn7hwjTsYQ4EiUevNeSbKNKAUwg8gfYQ=TpbHWTX7p8V8CeDA@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hello,

I was wondering if there is a command like mris_convert to create a
thickness map in vtk format (either on the white or pial surface) ?

Thanks,

--
Navid Shiee
Ph.D. Candidate
Laboratory of MEDical Image Computing (MEDIC)
Image Analysis and Communication Laboratory (IACL)
Johns Hopkins University
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------------------------------

Message: 11
Date: Mon, 12 Dec 2011 10:20:59 -0500 (EST)
From: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] tracula and snow leopard: can't allocate
       region /        memory error
To: Scott Hayes <smhayes@bu.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
       <alpine.LRH.2.00.1112121017410.7728@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"


Hi Scott - Sending to the list is always good so that others can find it
in the archives when they have similar problems.

Do you specify the .dcm or .mgz file in your dmrirc? Does dwi.nii.gz have
the right dimensions/frames?

a.y

On Mon, 12 Dec 2011, Scott Hayes wrote:

> Thanks for the prompt response Anastasia--I ran it over the weekend
> and it worked.
>
> I've subsequently encountered a new issue (copied below from the
> trac-all.log). The file (dwi.nii.gz) exists in the correct location
> (it was written there by tracula).  I use unpacksdcmdir for unpacking
> the dicoms, and then point the config file to the appropriate .mgz
> file, so I'm not doing anything particularly unusual in terms of
> unpacking or messing w/ the headers (We scan on a Siemens 3T tim
> trio.)  I can send this to the listserv if you prefer.
> Best,
> Scott
>
> fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k
> /Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz
> -m -s | awk '{print $1/$2}' >
> /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt
> ** ERROR (nifti_image_read): failed to find header file for '-t'
> ** ERROR: nifti_image_open(-t): bad header info
> Error: failed to open file -t
> ERROR: Could not open image -t
> Image Exception : #22 :: Failed to read volume -t
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>
>
>
> On Fri, Dec 9, 2011 at 12:44 PM, Anastasia Yendiki
> <ayendiki@nmr.mgh.harvard.edu> wrote:
>>
>> Hi Scott - Here are the tracula executables for snow leopard that we posted
>> in response to that thread:
>>
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz
>>
>> Let me know if this solves the memory errors.
>>
>> a.y
>>
>>
>> On Fri, 9 Dec 2011, Scott Hayes wrote:
>>
>>> Hi Anastasia,
>>> I've encountered an error using tracula w/ snow leopard OS that was
>>> previously reported on the FS listserv:
>>>
>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18829.html
>>>
>>> I'm wondering if there is a documented solution available?
>>> Recompiling from source code would be beyond my expertise.
>>>
>>> David: ?I'm cc'ing you just as a heads up--all of the workstations in
>>> the imaging center run snow leopard OS.
>>>
>>> Best,
>>> Scott
>>>
>>
>>
>> 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: 12
Date: Mon, 12 Dec 2011 11:31:57 -0500
From: Scott Hayes <smhayes@bu.edu>
Subject: [Freesurfer] tracula failed to find header file for -t
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
       <CAF9YUDZ+PSCiq-Axs5L2M6Tg3E5qsrN0JYc9qr9kmJxg+pyK1g@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi,
I have received the following error message (copied from trac-all.log file).

fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k
/Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz
-m -s | awk '{print $1/$2}' >
/Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt
** ERROR (nifti_image_read): failed to find header file for '-t'
** ERROR: nifti_image_open(-t): bad header info
Error: failed to open file -t
ERROR: Could not open image -t
Image Exception : #22 :: Failed to read volume -t
terminate called after throwing an instance of 'RBD_COMMON::BaseException'


The file (dwi.nii.gz) exists in the correct location, and appears to
have the correct number of frames (60 directions + 10 b0).
We scan on a Siemens 3T tim trio.  I unpack the data using
unpacksdcmdir and I specify the resulting .mgz file in the tracula
config file.  Running locally on mac os 10.6.8.

Any suggestions would be appreciated.
Thanks,
Scott


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

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