date:20160205

Re: [Freesurfer] DTI - Tracula question

2016-02-05 Thread Alan Francis

Hi Anastasia:

Thank you so much. Yes that is very helpful.

best,

Alan

On Fri, Feb 5, 2016 at 3:03 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Alan - Yes, you can give a single file for all data sets if they're all
> acquired with the same gradient table and slice prescription. As a test,
> you can extract the gradient tables from a couple of your data set's dicom
> headers and see how different they are. If there are only very small
> differences, using a single table for all will not make a difference.
>
> Hope this helps,
>
> a.y
>
>
> On Fri, 5 Feb 2016, Alan Francis wrote:
>
> Thanks Anastasia - that was very helpful. I have another question :  I am
>> working on a DTI dataset of around 70 subjects. This
>> dataset has ostensibly only 1 set of BVECS/BVALS. Can this set be
>> 'generically' used for all the images, given that they have been
>> acquired on the same scanner?
>>
>>
>>
>> thanks,
>>
>>
>>
>> Alan
>>
>>
>> On Wed, Feb 3, 2016 at 4:17 PM, Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>   Hi Alan - A nifti file with the gradient tables and b-values
>> embedded? All freesurfer programs can handle nifti
>>   volumes, compressed (.nii.gz) or not (.nii). You can pass those
>> volumes to TRACULA, and pass the gradient table and
>>   b-value table as separate files.
>>
>>   Run "mri_convert --help" to see all image file formats that we can
>> handle.
>>
>>   Hope this helps,
>>   a.y
>>
>>   On Wed, 3 Feb 2016, Alan Francis wrote:
>>
>> Hi Anastasia:
>>
>> I am working on a set of DTI data that were obtained at the
>> Martinos center. The data is in a single
>> nii.gz file. The BVECS and
>> BVALS files are also embedded in this. Could you please
>> advice me how do I code this in the DMRIRC file?
>>
>> Should I convert the nii.gz file into Analyze to get at the
>> BVECS/ BVALS?
>>
>> thank you so much,
>>
>> best regards,
>>
>> Alan
>>
>> --
>>
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>> Alan N. Francis PhD
>> NIDA T32  Fellow in Computational Neuroscience
>> Brain Imaging Center
>> McLean Hospital
>> Harvard Medical School
>> 115 Mill Street, Belmont, MA 02478
>> al...@bwh.harvard.edu
>> afran...@mclean.harvard.edu
>>
>>
>>
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>>
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>> Freesurfer mailing list
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>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> 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.
>>
>>
>>
>>
>> --
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>> Alan N. Francis PhD
>> NIDA T32  Fellow in Computational Neuroscience
>> Brain Imaging Center
>> McLean Hospital
>> Harvard Medical School
>> 115 Mill Street, Belmont, MA 02478
>> al...@bwh.harvard.edu
>> afran...@mclean.harvard.edu
>>
>>
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>>


-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*Alan N. Francis PhD*
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu


|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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Re: [Freesurfer] DTI - Tracula question

2016-02-05 Thread Anastasia Yendiki



As an add-on to the add-on, starting in 6.0 we'll be able to figure it out 
from the dicom header, so hopefully people won't have to worry about any 
of this in the future.


On Fri, 5 Feb 2016, Harms, Michael wrote:



As an add-on to this, note that using a single table for all subjects is 
probably only appropriate if the DWI was acquired with a
fixed orientation relative to the scanner gradient axes (e.g., strictly axial) 
for all subjects.  If the orientation was
customized individually for each subject (e.g., to align the imaging plane with 
the AC/PC), then it is unlikely that using a
single table for all subjects is appropriate.

cheers,
-MH

-- 
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From:  on behalf of Alan Francis 

Reply-To: Freesurfer support list 
Date: Friday, February 5, 2016 at 3:57 PM
To: Anastasia Yendiki 
Cc: Freesurfer support list 
Subject: Re: [Freesurfer] DTI - Tracula question

Hi Anastasia:

Thank you so much. Yes that is very helpful.

best,

Alan

On Fri, Feb 5, 2016 at 3:03 PM, Anastasia Yendiki 
 wrote:

  Hi Alan - Yes, you can give a single file for all data sets if they're 
all acquired with the same gradient table and
  slice prescription. As a test, you can extract the gradient tables from a 
couple of your data set's dicom headers and
  see how different they are. If there are only very small differences, 
using a single table for all will not make a
  difference.

  Hope this helps,

  a.y

  On Fri, 5 Feb 2016, Alan Francis wrote:

Thanks Anastasia - that was very helpful. I have another question : 
 I am working on a DTI dataset of
around 70 subjects. This
dataset has ostensibly only 1 set of BVECS/BVALS. Can this set be 
'generically' used for all the images,
given that they have been
acquired on the same scanner?

 

thanks,

 

Alan


On Wed, Feb 3, 2016 at 4:17 PM, Anastasia Yendiki 
 wrote:

      Hi Alan - A nifti file with the gradient tables and b-values 
embedded? All freesurfer programs can
handle nifti
      volumes, compressed (.nii.gz) or not (.nii). You can pass 
those volumes to TRACULA, and pass the
gradient table and
      b-value table as separate files.

      Run "mri_convert --help" to see all image file formats that 
we can handle.

      Hope this helps,
      a.y

      On Wed, 3 Feb 2016, Alan Francis wrote:

            Hi Anastasia:

            I am working on a set of DTI data that were obtained at 
the Martinos center. The data is in a
single
            nii.gz file. The BVECS and
            BVALS files are also embedded in this. Could you please 
advice me how do I code this in the
DMRIRC file?

            Should I convert the nii.gz file into Analyze to get at 
the BVECS/ BVALS?

            thank you so much,

            best regards,

            Alan

            --
            
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

            Alan N. Francis PhD
            NIDA T32  Fellow in Computational Neuroscience
            Brain Imaging Center
            McLean Hospital
            Harvard Medical School
            115 Mill Street, Belmont, MA 02478
            al...@bwh.harvard.edu
            afran...@mclean.harvard.edu
                                                                    
                                      
           
            
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|


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the e-mail
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but does not

Re: [Freesurfer] DTI - Tracula question

2016-02-05 Thread Alan Francis

That was helpful. Thanks Michael.

On Fri, Feb 5, 2016 at 5:19 PM, Harms, Michael  wrote:

>
> As an add-on to this, note that using a single table for all subjects is
> probably only appropriate if the DWI was acquired with a fixed orientation
> relative to the scanner gradient axes (e.g., strictly axial) for all
> subjects.  If the orientation was customized individually for each subject
> (e.g., to align the imaging plane with the AC/PC), then it is unlikely that
> using a single table for all subjects is appropriate.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From:  on behalf of Alan Francis <
> alandarkene...@gmail.com>
> Reply-To: Freesurfer support list 
> Date: Friday, February 5, 2016 at 3:57 PM
> To: Anastasia Yendiki 
> Cc: Freesurfer support list 
> Subject: Re: [Freesurfer] DTI - Tracula question
>
> Hi Anastasia:
>
> Thank you so much. Yes that is very helpful.
>
> best,
>
> Alan
>
> On Fri, Feb 5, 2016 at 3:03 PM, Anastasia Yendiki <
> ayend...@nmr.mgh.harvard.edu> wrote:
>
>>
>> Hi Alan - Yes, you can give a single file for all data sets if they're
>> all acquired with the same gradient table and slice prescription. As a
>> test, you can extract the gradient tables from a couple of your data set's
>> dicom headers and see how different they are. If there are only very small
>> differences, using a single table for all will not make a difference.
>>
>> Hope this helps,
>>
>> a.y
>>
>>
>> On Fri, 5 Feb 2016, Alan Francis wrote:
>>
>> Thanks Anastasia - that was very helpful. I have another question :  I am
>>> working on a DTI dataset of around 70 subjects. This
>>> dataset has ostensibly only 1 set of BVECS/BVALS. Can this set be
>>> 'generically' used for all the images, given that they have been
>>> acquired on the same scanner?
>>>
>>>
>>>
>>> thanks,
>>>
>>>
>>>
>>> Alan
>>>
>>>
>>> On Wed, Feb 3, 2016 at 4:17 PM, Anastasia Yendiki <
>>> ayend...@nmr.mgh.harvard.edu> wrote:
>>>
>>>   Hi Alan - A nifti file with the gradient tables and b-values
>>> embedded? All freesurfer programs can handle nifti
>>>   volumes, compressed (.nii.gz) or not (.nii). You can pass those
>>> volumes to TRACULA, and pass the gradient table and
>>>   b-value table as separate files.
>>>
>>>   Run "mri_convert --help" to see all image file formats that we can
>>> handle.
>>>
>>>   Hope this helps,
>>>   a.y
>>>
>>>   On Wed, 3 Feb 2016, Alan Francis wrote:
>>>
>>> Hi Anastasia:
>>>
>>> I am working on a set of DTI data that were obtained at the
>>> Martinos center. The data is in a single
>>> nii.gz file. The BVECS and
>>> BVALS files are also embedded in this. Could you please
>>> advice me how do I code this in the DMRIRC file?
>>>
>>> Should I convert the nii.gz file into Analyze to get at the
>>> BVECS/ BVALS?
>>>
>>> thank you so much,
>>>
>>> best regards,
>>>
>>> Alan
>>>
>>
>
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>
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Re: [Freesurfer] Volume analysis in native space vs. mni305 space

2016-02-05 Thread Rodriguez-Thompson, Anais

Hi FreeSurfer experts,

I'm writing to follow up on an email I sent on Monday.

I'm working in 5.3 and switching over to running my 1st level analysis in 
fsaverage. I noticed that when visualizing the volume output from the mni305 
analysis in tkmedit, there is only activation in subcortical regions and none 
in cortical regions.

I read in the FreeSurfer release notes for 5.1 that fsfast "now masks the 
volume-based analysis to include only subcortical areas."

I just wanted to confirm that we are not seeing cortical activation in the 
volume due to it being masked out.

Again, my commands are:
Pre-processing: preproc-sess -s GDDA001 -surface fsaverage lhrh -mni305 -fwhm 5 
-per-run -d $SUBJECTS_DIR -fsd bold -so siemens
Mkanalysis: mkanalysis-sess -analysis 
SIRP_LoadRegression_Stable5.3_012616_sm5_mni305 -mni305 2 -fwhm 5 -paradigm 
slopepar -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt 
-timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 
-per-run -TR 2 -stc siemens -force

Thanks,
Anais

On Feb 1, 2016, at 12:40 PM, Rodriguez-Thompson, Anais 
>
 wrote:

Hi FreeSurfer experts,

I'm in the process of switching over our first-level analyses from being run in 
native space to being run in fsaverage/mni305 space. Looking at the 
first-levels on an individual subject level, the volume analyses look fairly 
different (cortical signal especially is lost in the mni305 analysis). I've 
attached a couple of slides with images comparing the two volume analyses.

My commands for the mni305 analysis are...

Pre-processing: preproc-sess -s GDDA001 -surface fsaverage lhrh -mni305 -fwhm 5 
-per-run -d $SUBJECTS_DIR -fsd bold -so siemens
Mkanalysis: mkanalysis-sess -analysis 
SIRP_LoadRegression_Stable5.3_012616_sm5_mni305 -mni305 2 -fwhm 5 -paradigm 
slopepar -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt 
-timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 
-per-run -TR 2 -stc siemens -force
Mkcontrast: mkcontrast-sess -analysis 
SIRP_LoadRegression_Stable5.3_012616_sm5_mni305 -contrast 2vFix -a 2 -c 0

My commands for the native space analysis are...

Preprocessing: preproc-sess -s GDDA001 -fwhm 5 -per-run -d $SUBJECTS_DIR -fsd 
bold
Mkanalysis: mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_050514 -TR 2 
-paradigm slopepar -event-related -runlistfile runlistfile -tpef tpef_1.5mm.txt 
-native -fwhm 5 -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 
-refeventdur 2
Mkcontrast: mkcontrast-sess -analysis SIRP_LoadRegression_Stable5_050514 
-contrast 2vFix -a 2 -c 0

I have a couple of questions regarding the differences between the two 
analyses. First, why is so much of the signal robustness from the native space 
volume analysis lost in the mni305 analysis? Second, why are the voxel sizes so 
different between the two analyses (with the native space analysis having a 
much larger voxel size)?

Thanks,
Anais

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Re: [Freesurfer] DTI - Tracula question

2016-02-05 Thread Alan Francis

Thanks Anastasia - that was very helpful. I have another question :  I am
working on a DTI dataset of around 70 subjects. This dataset has ostensibly
only 1 set of BVECS/BVALS. Can this set be 'generically' used for all the
images, given that they have been acquired on the same scanner?



thanks,



Alan

On Wed, Feb 3, 2016 at 4:17 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Alan - A nifti file with the gradient tables and b-values embedded? All
> freesurfer programs can handle nifti volumes, compressed (.nii.gz) or not
> (.nii). You can pass those volumes to TRACULA, and pass the gradient table
> and b-value table as separate files.
>
> Run "mri_convert --help" to see all image file formats that we can handle.
>
> Hope this helps,
> a.y
>
>
> On Wed, 3 Feb 2016, Alan Francis wrote:
>
> Hi Anastasia:
>>
>> I am working on a set of DTI data that were obtained at the Martinos
>> center. The data is in a single nii.gz file. The BVECS and
>> BVALS files are also embedded in this. Could you please advice me how do
>> I code this in the DMRIRC file?
>>
>> Should I convert the nii.gz file into Analyze to get at the BVECS/ BVALS?
>>
>> thank you so much,
>>
>> best regards,
>>
>> Alan
>>
>> --
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>> Alan N. Francis PhD
>> NIDA T32  Fellow in Computational Neuroscience
>> Brain Imaging Center
>> McLean Hospital
>> Harvard Medical School
>> 115 Mill Street, Belmont, MA 02478
>> al...@bwh.harvard.edu
>> afran...@mclean.harvard.edu
>>
>>
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> dispose of the e-mail.
>
>


-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*Alan N. Francis PhD*
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu


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Re: [Freesurfer] hello freesurfer developer~

2016-02-05 Thread Bruce Fischl


Hi A-reum

we use average Euclidean distance from gray to white and visa-versa. 
There are other (variational) techniques that we have messed around with, 
but none of our experiments have shown that they are any better, so we have 
stuck with the simplest thing.


cheers
Bruce


On Fri, 5 Feb 2016, A-reum Min wrote:


hello experts

i have some question to you

What method do you use when measuring the cortical thickness? 

(ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal
equation?)

plz answer me.

2016-01-17 0:53 GMT+09:00 A-reum Min :
  Thank you for u r answer.
I have some question to you.

i compared two groups(patients VS control) 

How can i extract the total vertices(ex.#1 vertex : cortical thickness
value) to 1 subject(patient) and average of patients ?
I want to compared asymmetry of brain (lateralization). So, i really
necessary above value(cortical thickness value of vertex). 

plz answer me.

Thank you.


2016-01-17 0:22 GMT+09:00 Bruce Fischl :
  Hi Areum

  every brain will have a somewhat different number of
  vertices depending on size and geometry. If you want them
  to be comparable you need to map them into the fsaverage
  space using e.g. the -qcache switch to recon-all (or
  mri_surf2surf directly if you prefer).

  cheers
  Bruce


  On Sat, 16 Jan 2016, A-reum Min wrote:

Hello expert.
I'm Areum.

I have some question to you.

A weeks ago, i compared two groups (OSA
patients VS control) and then the
number of vertices were confirmed. 

Each group has the same number of
vertices.(176416) -experiment 1.

And yesterday, i compared two groups(partial
sleep deprivation:PSD VS
control) and then the number of vertices were
confirmed.

Each group has the same number of
vertices(169548) -experiment 2.


1) Why isn't the same number of total
vertices? is it related rain size?


2) How can i extract the number of total
vertices(ex.#1 vertex : cortical
thickness value) to 1 subject(PSD) and average
of PSD ?
I want to compared asymmetry of brain
(lateralization). So, i really
necessary above value(cortical thickness value
of vertex). 

plz answer me.

Thank you.


2016-01-07 3:52 GMT+09:00 Bruce Fischl
:
      Hi A-reum

      did you talk to the Wash U group? If you
have nifti files they
      can be processed using recon-all (i.e.
recon-all -i  -s  -sd
 -all)

      cheers
      Bruce


      On Tue, 29 Dec 2015, A-reum Min wrote:

            hello experts!my name is areum.
            i have some question to you.i have
never seen before
            these NIFTI
            format(fig.1.png)
            I want to see these data
subjects's cortical
            thickness using qdec.
            how can i to do? plz answer me  

            2015-12-25 2:16 GMT+09:00 Bruce
Fischl
            :
                  Hi A-reum

                  you should probably ask the
Wash U HCP group.
            I'll cc Matt
                  Glasser who might be able to
answer your
            question
                  cheers
                  Bruce

                  On Thu, 24 Dec 2015, A-reum
Min wrote:

                        hello experts!my name
is areum.
                        i have some question
to you.
                        a few days ago i was
down load HCP(human
            connectom
                        project) data.
                        but.. how can i use
these HCP format.
                        i have never seen
before these
            format(fig.1.png)
                        I want to see HCP data
subjects's
            cortical thickness
                        using qdec.
                        how can i to do? 
                        plz answer me  

                        2015-11-10 7:49
GMT+09:00 A-reum Min
                        :
                              Hello experts!
                        I

Re: [Freesurfer] (no subject)

2016-02-05 Thread Alan Francis

Hello Achcha:

Detailed instructions on how to install FS on Windows via Virtual Box can
be found here:

https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtualImage

best,

Alan

On Fri, Jan 22, 2016 at 3:28 PM, Ачча Чимагомедова  wrote:

>
> Hello!
>
> My name is Achcha. I am a PhD student of Russian Medical Academy for
> Postgraduate Education. In my research "Dementia with Lewy bodies" (DLB) I
> am going to determine the association between the focal atrophy measures on
> MRI and to compare it with clinical features of DLB. I try to install
> FreeSurfer on my computer. But I have only Windows Operating System, that's
> why I have got and installed VirtualBox. Could you please send me detailed
> instructions and help to install FreeSurfer.
>
> Thank you,
>
> Kindest regards
>
> Achcha Chimagomedova
>
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*Alan N. Francis PhD*
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu

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Re: [Freesurfer] freeview command line generic overlay colormap question

2016-02-05 Thread Gardumi Anna (PSYCHOLOGY)

Dear all,



I am currently trying to automatically generate Freesurfer screenshots and, to 
this purpose, I need to change the color scale of the surface overlay to "Color 
Wheel - Inverse" and with specific min and max threshold.

Looking for a way to achieve this, I found this thread with similar request, 
but unfortunately no solution was posted. Thus Heath (who kindly replied to my 
email) suggested to re-post the question to the entire FreeSurfer community.



So far I am able only to set the min max threshold with the following command:

freeview -f 
$SUBJECTS_DIR/subj01/surf/lh.inflated:overlay=/pathToOverlay/MyOverlay.mgh:overlay_threshold=-10,10



Does anybody know the command line to set the overlay color scale to "Color 
Wheel (Inverse)"?



Thank you!

Any help is very much appreciated!



Best regards,

Anna


-
Anna Gardumi
Department of Cognitive Neuroscience | Faculty of Psychology & Neuroscience | 
Maastricht University
Postal address: PO Box 616, 6200MD, Maastricht, The Nederlands
Visiting address: Oxfordlaan 55, room 2.012, 6229EV
anna.gard...@maastrichtuniversity.nl



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[Freesurfer] tkregister2 - horizontal and coronal inverted in the functional only

2016-02-05 Thread Ilaria Sani

Dear All,

I have a functional and a T1 registered, but they are not in anatomical 
coordinates.
I put the anatomical in the desired position by using tkregister2.
I was hoping to use the output reg file to re-position the functional as well.

I got an unexpected output!
The functional looks reoriented BUT, coronal is horizontal, horizontal is 
coronal and sagittal is 90deg rotated.

How did it happen and how can I fix the problem?

Thanks,
Ilaria

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Re: [Freesurfer] tracula preproc complains about missing bvec-file

2016-02-05 Thread Anastasia Yendiki


Hi Peter - From your dicom header, it looks like the fields that it's 
looking for to guess which standard Siemens gradient table to use are not 
there. So you'll have to pass the gradient table and the b-value table as 
separate text files using bvecfile and bvalfile.

Starting in 6.0 this'll all be more seemless, I promise!

a.y

On Fri, 5 Feb 2016, Parzer, Peter wrote:

> Hi Anastasia,
>
> no, I did not define "bvecfile" and "bvalfile" in the configuration file, 
> because the tutorial says, that these variables are not needed if the data is 
> in Siemens DICOM format, and my data is in Siemens DICOM format. Do I need 
> this additional step to extract bvec and bval from die DICOM images? And what 
> is the best way to do it?
>
> Peter
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>  im Auftrag von Anastasia Yendiki 
> 
> Gesendet: Donnerstag, 4. Februar 2016 16:29
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] tracula preproc complains about missing bvec-file
>
> Hi Peter - Have you defined "bvecfile" in your configuration file? I
> suspect it doesn't know where to find the gradient table.
>
> a.y
>
> On Thu, 4 Feb 2016, Parzer, Peter wrote:
>
>> Hi,
>>
>> trying to do my first steps with tracula I got stuck early in the 
>> preprocessing step. The DICOM import and preparation for FSL seem to work 
>> (mri_convert, mri_probedicom, flip4fsl, fslswapdim, fslorient). But then 
>> trac-preproc wants to move a file named dwi_orig_flip.mghdti.bvecs that does 
>> not exist. What did I wrong?
>>
>> The command I used was
>>
>>  trac-all -prep -c dmrirc
>>
>> The content of the configuration file "dmrirc" was the minimum as described 
>> in the tutorial:
>>
>> setenv SUBJECTS_DIR /dat/Hirnreifung/Auswertung/freesurfer
>> set dtroot = /dat/Hirnreifung/Auswertung/freesurfer
>> set subjlist = (3001LT)
>> set dcmroot = /dat/Hirnreifung/Daten/DICOM
>> set dcmlist = (3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0001.dcm)
>>
>> dcminfo.dat and trac-all.log are in the attachments.
>>
>> Peter
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> at
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> 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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Re: [Freesurfer] Zero angle for retinotopy

2016-02-05 Thread dgw

Hi,

I know Doug is away, so he may correct me later, but I believe it
doesn't matter, as long as it is consistent across runs, and you know
what it is. It will just determine where the angle 0 activity goes (in
a color map etc.). The way FS-FAST does the mapping it just may mean
your colors don't line up with others.

hth
d

On Thu, Feb 4, 2016 at 11:52 PM,   wrote:
> Dear all,
>
>
>
> I am wondering about what the zero angle for retinotopy corresponds to in
> retinotopy analysis. I mean corresponding to the wedge being at zero angle
> in circular coordinate map (horizontal) or vertical up?
>
>
>
> Thank you,
>
> Best,
>
>
>
>
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>
>
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> addressed. If you believe this e-mail was sent to you in error and the
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> contains patient information, please contact the Partners Compliance
> HelpLine at
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> properly
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Re: [Freesurfer] DTI - Tracula question

2016-02-05 Thread Anastasia Yendiki



Hi Alan - Yes, you can give a single file for all data sets if they're all 
acquired with the same gradient table and slice prescription. As a test, 
you can extract the gradient tables from a couple of your data set's dicom 
headers and see how different they are. If there are only very small 
differences, using a single table for all will not make a difference.


Hope this helps,

a.y

On Fri, 5 Feb 2016, Alan Francis wrote:


Thanks Anastasia - that was very helpful. I have another question :  I am 
working on a DTI dataset of around 70 subjects. This
dataset has ostensibly only 1 set of BVECS/BVALS. Can this set be 'generically' 
used for all the images, given that they have been
acquired on the same scanner?

 

thanks,

 

Alan


On Wed, Feb 3, 2016 at 4:17 PM, Anastasia Yendiki 
 wrote:

  Hi Alan - A nifti file with the gradient tables and b-values embedded? 
All freesurfer programs can handle nifti
  volumes, compressed (.nii.gz) or not (.nii). You can pass those volumes 
to TRACULA, and pass the gradient table and
  b-value table as separate files.

  Run "mri_convert --help" to see all image file formats that we can handle.

  Hope this helps,
  a.y

  On Wed, 3 Feb 2016, Alan Francis wrote:

Hi Anastasia:

I am working on a set of DTI data that were obtained at the 
Martinos center. The data is in a single
nii.gz file. The BVECS and
BVALS files are also embedded in this. Could you please advice me 
how do I code this in the DMRIRC file?

Should I convert the nii.gz file into Analyze to get at the BVECS/ 
BVALS?

thank you so much,

best regards,

Alan

--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu
afran...@mclean.harvard.edu
                                                                    
                                      
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|


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Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu
afran...@mclean.harvard.edu
                                                                                
                          
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Re: [Freesurfer] DTI - Tracula question

2016-02-05 Thread Harms, Michael







As an add-on to this, note that using a single table for all subjects is probably only appropriate if the DWI was acquired with a fixed orientation relative to the scanner gradient axes (e.g., strictly axial) for all subjects.  If the orientation was customized
 individually for each subject (e.g., to align the imaging plane with the AC/PC), then it is unlikely that using a single table for all subjects is appropriate.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From:  on behalf of Alan Francis 
Reply-To: Freesurfer support list 
Date: Friday, February 5, 2016 at 3:57 PM
To: Anastasia Yendiki 
Cc: Freesurfer support list 
Subject: Re: [Freesurfer] DTI - Tracula question








Hi Anastasia:


Thank you so much. Yes that is very helpful.


best,


Alan


On Fri, Feb 5, 2016 at 3:03 PM, Anastasia Yendiki 
 wrote:


Hi Alan - Yes, you can give a single file for all data sets if they're all acquired with the same gradient table and slice prescription. As a test, you can extract the gradient tables from a couple of your data set's dicom headers and see how different they
 are. If there are only very small differences, using a single table for all will not make a difference.

Hope this helps,

a.y



On Fri, 5 Feb 2016, Alan Francis wrote:


Thanks Anastasia - that was very helpful. I have another question :  I am working on a DTI dataset of around 70 subjects. This
dataset has ostensibly only 1 set of BVECS/BVALS. Can this set be 'generically' used for all the images, given that they have been
acquired on the same scanner?

 

thanks,

 

Alan


On Wed, Feb 3, 2016 at 4:17 PM, Anastasia Yendiki  wrote:

      Hi Alan - A nifti file with the gradient tables and b-values embedded? All freesurfer programs can handle nifti
      volumes, compressed (.nii.gz) or not (.nii). You can pass those volumes to TRACULA, and pass the gradient table and
      b-value table as separate files.

      Run "mri_convert --help" to see all image file formats that we can handle.

      Hope this helps,
      a.y

      On Wed, 3 Feb 2016, Alan Francis wrote:

            Hi Anastasia:

            I am working on a set of DTI data that were obtained at the Martinos center. The data is in a single
            nii.gz file. The BVECS and
            BVALS files are also embedded in this. Could you please advice me how do I code this in the DMRIRC file?

            Should I convert the nii.gz file into Analyze to get at the BVECS/ BVALS?

            thank you so much,

            best regards,

            Alan

            --
            |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

            Alan N. Francis PhD
            NIDA T32  Fellow in Computational Neuroscience
            Brain Imaging Center
            McLean Hospital
            Harvard Medical School
            115 Mill Street, Belmont, MA 02478
            al...@bwh.harvard.edu
            afran...@mclean.harvard.edu
                                                                                                                      
            |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|


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--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu
afran...@mclean.harvard.edu
                                                                                                          
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|









-- 




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

Alan N. Francis PhD
NIDA T32  Fellow in Computational

Re: [Freesurfer] TRACULA Longitudinal can't find subject folder

2016-02-05 Thread Anastasia Yendiki



Hi again Deniz - This may be confusing but with longitudinal TRACULA there 
are separate trac-all.log files in each time point's directory and in the 
within-subject template's directory. The former are for things that are 
run independently for each time point (mainly pre-processing) and the 
latter for things that are run jointly for all time points (like 
tractography).


I suspect that the first error probably occured earlier, and it can be 
found in the log file of one of the time points.


In your configuration file, use bvecfile if you're using a single gradient 
table for all data sets and bveclist if you have a different one for each 
time point.


Hope this helps,

a.y

On Fri, 5 Feb 2016, Deniz Gursel wrote:


Dear Anastasia,

Thank you very much for your fast solution. Indeed, I was missing the related 
folders, I haven’t run the recon-all myself and I copied only the final folder 
and not the whole as a mistake. Now, I passed that error and got stuck with a 
new one.

In the inter-subject registration step, I get the error:

#@# Image corrections Fri Feb  5 14:34:25 CET 2016
mri_convert 
/data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii 
/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz
mri_convert 
/data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii 
/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from 
/data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii...
crypt_gkey = FS1gOHzYgoG2U
TR=10443.18, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998789, 0.0474208, 0.0131247)
j_ras = (0.0473438, 0.99886, -0.00611764)
k_ras = (0.0133998, 0.00548885, 0.999895)
writing to 
/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz...
crypt_gkey = FS1gOHzYgoG2U
if: Expression Syntax.
#-
/sw/freesurfer/5.3.0/bin/trac-preproc
#-
#@# Inter-subject registration (base template) Fri Feb  5 14:34:30 CET 2016
cp 
/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/mni2anatorig.mat
 
/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/anatorig2mni.mat
 /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94/dmri/xfms
cp: cannot stat 
‘/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/mni2anatorig.mat’:
 No such file or directory
cp: cannot stat 
‘/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/anatorig2mni.mat’:
 No such file or directory
Linux slow.mri.tu-muenchen.de 3.7.10-1.40-desktop #1 SMP PREEMPT Thu Jul 10 
11:22:12 UTC 2014 (9b06319) x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Feb  5 14:34:30 CET 2016

I am attaching the trac_all.log, trac_all.error and dmrirc for you.
Also, before the error, at the image correction step, there is “if: expression 
syntax” message which I couldn’t figure out why it happens. I looked it up and 
seems like some Unix error. I encountered it many times, when I was running 
another cross-sectional study and sometimes it went away magically.

Thank you very much for your time and help.




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[Freesurfer] use as seed a ROI.label as seed in FS-FAST

2016-02-05 Thread stdp82

Hi list,
I would like to use as seed in FS-FAST a ROI.label which I have drawn on a 
cluster in tksurfer.How can I do it?Should I use mri_label2vol?
Thanks.
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Re: [Freesurfer] seq.info

2016-02-05 Thread Ji Won Bang

Or my guess is that this seq.info is not necessary for the further
analysis.. so I can go ahead without it?

Best,
Ji Won

2016-02-05 15:06 GMT-05:00 Ji Won Bang :

> If I use:
> unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir /scan.info
>
> I can get sequencename, nrows, ncols, nslcs, ntrs, but how can I check the
> exact value of slcpixelsize?
>
> Thanks,
> Ji Won
>
> 2016-02-05 14:54 GMT-05:00 Ji Won Bang :
>
>> Dear. Freesurfer team
>>
>> I used dcmunpack to convert DCM to nii.
>>
>> This command didn't generate seq.info (I couldn't find it).
>>
>> I'd like to create one by myself
>>
>> Do you know how I can check the scan parameters:
>> sequencename
>> nrows
>> ncols
>> nslcs
>> rowpixelsize
>> colpixelsize
>> slcpixelsize
>> ntrs
>> TR
>>
>> I know that when I use: unpacksdcmdir -src dicomdir -targ targetdir
>> -scanonly targetdir /scan.info
>>
>> I can get sequencename, nrows, ncols... but then from where can I check
>> the others?
>>
>> Thank you very much.
>>
>> Best,
>> Ji Won
>>
>
>
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Re: [Freesurfer] seq.info

2016-02-05 Thread Ji Won Bang

If I use:
unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir /scan.info

I can get sequencename, nrows, ncols, nslcs, ntrs, but how can I check the
exact value of slcpixelsize?

Thanks,
Ji Won

2016-02-05 14:54 GMT-05:00 Ji Won Bang :

> Dear. Freesurfer team
>
> I used dcmunpack to convert DCM to nii.
>
> This command didn't generate seq.info (I couldn't find it).
>
> I'd like to create one by myself
>
> Do you know how I can check the scan parameters:
> sequencename
> nrows
> ncols
> nslcs
> rowpixelsize
> colpixelsize
> slcpixelsize
> ntrs
> TR
>
> I know that when I use: unpacksdcmdir -src dicomdir -targ targetdir
> -scanonly targetdir /scan.info
>
> I can get sequencename, nrows, ncols... but then from where can I check
> the others?
>
> Thank you very much.
>
> Best,
> Ji Won
>
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[Freesurfer] seq.info

2016-02-05 Thread Ji Won Bang

Dear. Freesurfer team

I used dcmunpack to convert DCM to nii.

This command didn't generate seq.info (I couldn't find it).

I'd like to create one by myself

Do you know how I can check the scan parameters:
sequencename
nrows
ncols
nslcs
rowpixelsize
colpixelsize
slcpixelsize
ntrs
TR

I know that when I use: unpacksdcmdir -src dicomdir -targ targetdir
-scanonly targetdir /scan.info

I can get sequencename, nrows, ncols... but then from where can I check the
others?

Thank you very much.

Best,
Ji Won
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Re: [Freesurfer] tracula preproc complains about missing bvec-file

2016-02-05 Thread Parzer, Peter

Hi Anastasia,

no, I did not define "bvecfile" and "bvalfile" in the configuration file, 
because the tutorial says, that these variables are not needed if the data is 
in Siemens DICOM format, and my data is in Siemens DICOM format. Do I need this 
additional step to extract bvec and bval from die DICOM images? And what is the 
best way to do it?

Peter

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Anastasia Yendiki 

Gesendet: Donnerstag, 4. Februar 2016 16:29
An: Freesurfer support list
Betreff: Re: [Freesurfer] tracula preproc complains about missing bvec-file

Hi Peter - Have you defined "bvecfile" in your configuration file? I
suspect it doesn't know where to find the gradient table.

a.y

On Thu, 4 Feb 2016, Parzer, Peter wrote:

> Hi,
>
> trying to do my first steps with tracula I got stuck early in the 
> preprocessing step. The DICOM import and preparation for FSL seem to work 
> (mri_convert, mri_probedicom, flip4fsl, fslswapdim, fslorient). But then 
> trac-preproc wants to move a file named dwi_orig_flip.mghdti.bvecs that does 
> not exist. What did I wrong?
>
> The command I used was
>
>  trac-all -prep -c dmrirc
>
> The content of the configuration file "dmrirc" was the minimum as described 
> in the tutorial:
>
> setenv SUBJECTS_DIR /dat/Hirnreifung/Auswertung/freesurfer
> set dtroot = /dat/Hirnreifung/Auswertung/freesurfer
> set subjlist = (3001LT)
> set dcmroot = /dat/Hirnreifung/Daten/DICOM
> set dcmlist = (3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0001.dcm)
>
> dcminfo.dat and trac-all.log are in the attachments.
>
> Peter
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[Freesurfer] problem mri_convert

2016-02-05 Thread Righart, Ruthger

Dear FreeSurfers,

On one of our Linux machines we encounter the following error message 
when calling mri_convert:

/lib64/libz.so.1: no version information available (required by 
mri_convert)
/usr/lib64/libstdc++.so6:  version GLIBCXX_3.4.11 not found (required
by mri_convert)

Mri_convert has worked before without any problem. Any advices how to 
resolve this would be very welcome!

Best Regards,

Ruthger
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Re: [Freesurfer] Brain stem segmentation-- FS6

2016-02-05 Thread Eugenio Iglesias

Hi Mohamad,
you might have run out of memory. Could you please try allocating more RAM for 
the job?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

- Original Message -
From: "Mohamad J. Alshikho" 
To: "Freesurfer support list" 
Sent: Thursday, February 4, 2016 11:01:50 PM
Subject: [Freesurfer] Brain stem segmentation-- FS6

Dear Freesurfer experts,
I am working on brain stem segmentation analysis using the new module included 
in FS6.

The analysis ran properly for 38/40 subjects. I have an issue with two subjects.

I sent my jobs to the cluster as always using the following command line:  
pbsubmit -c " recon-all -subjid  -brainstem-structures  " -f  &

After a while I received an email that the job is done:
PBS Job Id: 11020983.launchpad.nmr.mgh.harvard.edu
Job Name:   pbsjob_2045
Exec host:  compute-0-111/3
Execution terminated
Exit_status=0
resources_used.cput=00:42:33
resources_used.mem=3220236kb
resources_used.vmem=7319444kb
resources_used.walltime=00:44:45

I checked the subject's folder /mri/ looking for the files : 
"brainstemSsLabels.v10.1mm.mgz" , "brainstemSsLabels.v10.mgz" but I was unable 
to find them.

I checked the job history in the cluster and it returns as ( quotation -- the 
last lines):

Resolution level 3 iteration 3 deformation iterations 19
Number of Meshes: 1
Using CG optimizer
Did one deformation step of max. 0.0097272 voxels in 4.1676 seconds

minLogLikelihoodTimesPrior =

   1.0786e+07

Resolution level 3 iteration 3 deformation iterations 20
Number of Meshes: 1
Using CG optimizer
Did one deformation step of max. 0.016365 voxels in 4.1717 seconds

minLogLikelihoodTimesPrior =

   1.0786e+07

Fitting mesh to image data mask took 2144.0218 seconds
Error using kvlAtlas3D_Matlab
std::bad_alloc

Error in kvlRasterizeAtlasMesh (line 11)



Error in segmentSubject (line 1078)





Started at Thu Feb 4 15:57:18 EST 2016 
Ended   at Thu Feb 4 16:41:59 EST 2016
#@#%# recon-all-run-time-hours 0.745
recon-all -s CTRL039 finished without error at Thu Feb  4 16:42:00 EST 2016



It stated that the job was ended properly without errors but  the previous 
lines ( before the final stamp) showed errors and the files 
"brainstemSsLabels.v10.1mm.mgz" , "brainstemSsLabels.v10.mgz" are missing ... 

Kindly what I am doing wrong?
Any suggestions are highly appreciated !!

Mohamad
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[Freesurfer] Combining lh. and rh. surfaces

2016-02-05 Thread Maheen Siddiqui

Dear FreeSurfer Users,


I have been using the recon-all FreeSurfer command to reconstruct surfaces
from T1 weighted MRI scan. I need to import the surfaces I have into Homer2
Atlas Viewer and for this I need whole surface/volume files rather than the
individual hemispheres. Does anybody have experience combining the
hemispheres?


Many thanks,


Maheen


Maheen Siddiqui



BBSRC LIDo PhD Student

Centre for Brain and Cognitive Development

Birkbeck, University of London

London
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[Freesurfer] FreeSurfer group analysis: mri_glmfit-sim

2016-02-05 Thread Silas

Dear FS team,


I'm currently making a group analysis using the "command-line" group analysis 
stream in freesurfer.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng

[https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]

FsTutorial/GroupAnalysisDng - Free Surfer 
Wiki
surfer.nmr.mgh.harvard.edu
Introduction. This tutorial is designed to introduce you to the "command-line" 
group analysis stream in FreeSurfer (as opposed to QDEC which is GUI-driven), 
including ...



1) I would like to do a surface based analysis where i'm only investigating a 
certain area or label - instead of doing a whole brain analysis. This can be 
done by introducing --label surface_area_of_interest.label when running 
mri_glmfit. Would this give me different results from doing a whole brain 
analysis - or would it just exclude the results from outside the label? And how 
about after clusterwise correction for multiple comparisons?

-> is there a better way to do this than following the command-line group 
analysis stream in freesurfer?


2) When running mri_glmfit-sim i'm investigating the output ending with 
-voxel.mgh - how do i interpret the results of this file? When investigating 
the file in freeview what is the meaning of the units when configuring the 
overlay?


Best, Silas
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Re: [Freesurfer] TRACULA Longitudinal can't find subject folder

2016-02-05 Thread Deniz Gursel

Dear Anastasia,Thank you very much for your fast solution. Indeed, I was missing the related folders, I haven’t run the recon-all myself and I copied only the final folder and not the whole as a mistake. Now, I passed that error and got stuck with a new one.In the inter-subject registration step, I get the error:#@# Image corrections Fri Feb  5 14:34:25 CET 2016mri_convert /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gzmri_convert /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $reading from /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii...crypt_gkey = FS1gOHzYgoG2UTR=10443.18, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-0.998789, 0.0474208, 0.0131247)j_ras = (0.0473438, 0.99886, -0.00611764)k_ras = (0.0133998, 0.00548885, 0.999895)writing to /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz...crypt_gkey = FS1gOHzYgoG2Uif: _expression_ Syntax.#-/sw/freesurfer/5.3.0/bin/trac-preproc #-#@# Inter-subject registration (base template) Fri Feb  5 14:34:30 CET 2016cp /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/mni2anatorig.mat /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/anatorig2mni.mat /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94/dmri/xfmscp: cannot stat ‘/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/mni2anatorig.mat’: No such file or directorycp: cannot stat ‘/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/anatorig2mni.mat’: No such file or directoryLinux slow.mri.tu-muenchen.de 3.7.10-1.40-desktop #1 SMP PREEMPT Thu Jul 10 11:22:12 UTC 2014 (9b06319) x86_64 x86_64 x86_64 GNU/Linuxtrac-preproc exited with ERRORS at Fri Feb  5 14:34:30 CET 2016I am attaching the trac_all.log, trac_all.error and dmrirc for you.Also, before the error, at the image correction step, there is “if: _expression_ syntax” message which I couldn’t figure out why it happens. I looked it up and seems like some Unix error. I encountered it many times, when I was running another cross-sectional study and sometimes it went away magically.Thank you very much for your time and help.

trac-all.error
Description: Binary data


trac-all.log
Description: Binary data


dmrirc.long
Description: Binary data
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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

2016-02-05 Thread Nabin Koirala

I did that but it still does not work, it is almost the same error except
the condno is now 15521.8 before it was 27492.1, though I am not sure if
that tells something about the error. Could it be something else ?
Thank you.

Regards,
Nabin

On Thu, Feb 4, 2016 at 5:59 PM, Douglas Greve 
wrote:

> I'm not sure what the difference is. Compute the mean of the 2nd column,
> then subtract that number from the values in the 2nd column.
> doug
>
>
> On 2/2/16 7:30 AM, Nabin Koirala wrote:
>
> Thank you for your response . Sorry but for my understanding, should i
> substract the mean from the data (demean) or you mean to remove the value
> which is equal to the mean ?
>
> Thank you.
>
> Regards,
> Nabin
>
> On Mon, Feb 1, 2016 at 5:21 PM, Douglas N Greve  > wrote:
>
>> Try removing the mean from your covariate
>>
>> On 01/30/2016 01:31 PM, Nabin Koirala wrote:
>> > Dear Freesurfer forum,
>> >
>> > 'I am trying to run qdec analysis for a group of subjects to see if
>> > correlation exists but I am getting this error only for this
>> >  particular set of data but could not figure out what is exactly wrong
>> > with it. Your suggestion would be greatly appreciated.
>> >
>> > Following is the terminal output for the process:
>> > ..
>> > Saving design matrix to
>> /g/f/h/s/freesurfer/subjects/qdec/Untitled/Xg.dat
>> > Normalized matrix condition is 27492.1
>> > Design matrix --
>> >  1.000   0.408;
>> >  1.000   0.417;
>> >  1.000   0.417;
>> >  1.000   0.405;
>> >  1.000   0.412;
>> >  1.000   0.412;
>> >  1.000   0.411;
>> >  1.000   0.417;
>> >  1.000   0.405;
>> >  1.000   0.406;
>> >  1.000   0.402;
>> >  1.000   0.419;
>> >  1.000   0.413;
>> >  1.000   0.413;
>> > 
>> > ERROR: matrix is ill-conditioned or badly scaled, condno = 27492.1
>> > 
>> > Possible problem with experimental design:
>> > Check for duplicate entries and/or lack of range of
>> > continuous variables within a class.
>> > If you seek help with this problem, make sure to send:
>> >   1. Your command line:
>> > mri_glmfit --y /g/f/h/s/freesurfer/subjects/qdec/Untitled/y.mgh
>> > --fsgd /g/f/h/s/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods
>> > --glmdir /g/f/h/s/freesurfer/subjects/qdec/Untitled --surf fsaverage
>> > lh --label /g/f/h/s/freesurfer/subjects/fsaverage/label/lh.aparc.label
>> > --C
>> >
>> /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
>> > --C
>> >
>> /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-alpha1-Cor.mat
>> >
>> >   2. The FSGD file (if using one)
>> >   3. And the design matrix above
>> > Error in Analyze: command failed: mri_glmfit --y
>> > /g/f/h/s/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd
>> > /g/f/h/s/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir
>> > /g/f/h/s/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label
>> > /g/f/h/s/freesurfer/subjects/fsaverage/label/lh.aparc.label --C
>> >
>> /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
>> > --C
>> >
>> /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-alpha1-Cor.mat
>> >
>> > Many thanks in advance.
>> >
>> > Regards,
>> > Nabin
>> >
>> >
>> > ___
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>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
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Re: [Freesurfer] Combining lh. and rh. surfaces

2016-02-05 Thread Jesu Kiran Jk

Hi Maheen,

I have been using SIMNIBS (www.simnibs.de) script for the exact same thing.
This script gives a mesh output.

Perhaps that helps,..

Kind regards,
Jesu

Jesu Kiran Spurgen
Postgraduate Student in Advanced Medical Imaging
KU Leuven, Belgium

On Fri, Feb 5, 2016 at 1:29 PM, Maheen Siddiqui  wrote:

>
> Dear FreeSurfer Users,
>
>
> I have been using the recon-all FreeSurfer command to reconstruct surfaces
> from T1 weighted MRI scan. I need to import the surfaces I have into Homer2
> Atlas Viewer and for this I need whole surface/volume files rather than the
> individual hemispheres. Does anybody have experience combining the
> hemispheres?
>
>
> Many thanks,
>
>
> Maheen
>
>
> Maheen Siddiqui
>
>
>
> BBSRC LIDo PhD Student
>
> Centre for Brain and Cognitive Development
>
> Birkbeck, University of London
>
> London
>
>
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> HelpLine at
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Re: [Freesurfer] hello freesurfer developer~

2016-02-05 Thread A-reum Min

hello experts


i have some question to you

What method do you use when measuring the cortical thickness?

(ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal
equation?)

plz answer me.

2016-01-17 0:53 GMT+09:00 A-reum Min :

> Thank you for u r answer.
>
> I have some question to you.
>
> i compared two groups(patients VS control)
>
> How can i extract the total vertices(ex.#1 vertex : cortical thickness
> value) to 1 subject(patient) and average of patients ?
> I want to compared asymmetry of brain (lateralization). So, i really
> necessary above value(cortical thickness value of vertex).
>
> plz answer me.
>
> Thank you.
>
>
> 2016-01-17 0:22 GMT+09:00 Bruce Fischl :
>
>> Hi Areum
>>
>> every brain will have a somewhat different number of vertices depending
>> on size and geometry. If you want them to be comparable you need to map
>> them into the fsaverage space using e.g. the -qcache switch to recon-all
>> (or mri_surf2surf directly if you prefer).
>>
>> cheers
>> Bruce
>>
>>
>> On Sat, 16 Jan 2016, A-reum Min wrote:
>>
>> Hello expert.
>>> I'm Areum.
>>>
>>> I have some question to you.
>>>
>>> A weeks ago, i compared two groups (OSA patients VS control) and then the
>>> number of vertices were confirmed.
>>>
>>> Each group has the same number of vertices.(176416) -experiment 1.
>>>
>>> And yesterday, i compared two groups(partial sleep deprivation:PSD VS
>>> control) and then the number of vertices were confirmed.
>>>
>>> Each group has the same number of vertices(169548) -experiment 2.
>>>
>>>
>>> 1) Why isn't the same number of total vertices? is it related rain size?
>>>
>>>
>>> 2) How can i extract the number of total vertices(ex.#1 vertex : cortical
>>> thickness value) to 1 subject(PSD) and average of PSD ?
>>> I want to compared asymmetry of brain (lateralization). So, i really
>>> necessary above value(cortical thickness value of vertex).
>>>
>>> plz answer me.
>>>
>>> Thank you.
>>>
>>>
>>> 2016-01-07 3:52 GMT+09:00 Bruce Fischl :
>>>   Hi A-reum
>>>
>>>   did you talk to the Wash U group? If you have nifti files they
>>>   can be processed using recon-all (i.e. recon-all -i >>   to nifti file> -s  -sd >>   subjects> -all)
>>>
>>>   cheers
>>>   Bruce
>>>
>>>
>>>   On Tue, 29 Dec 2015, A-reum Min wrote:
>>>
>>> hello experts!my name is areum.
>>> i have some question to you.i have never seen before
>>> these NIFTI
>>> format(fig.1.png)
>>> I want to see these data subjects's cortical
>>> thickness using qdec.
>>> how can i to do? plz answer me
>>>
>>> 2015-12-25 2:16 GMT+09:00 Bruce Fischl
>>> :
>>>   Hi A-reum
>>>
>>>   you should probably ask the Wash U HCP group.
>>> I'll cc Matt
>>>   Glasser who might be able to answer your
>>> question
>>>   cheers
>>>   Bruce
>>>
>>>   On Thu, 24 Dec 2015, A-reum Min wrote:
>>>
>>> hello experts!my name is areum.
>>> i have some question to you.
>>> a few days ago i was down load HCP(human
>>> connectom
>>> project) data.
>>> but.. how can i use these HCP format.
>>> i have never seen before these
>>> format(fig.1.png)
>>> I want to see HCP data subjects's
>>> cortical thickness
>>> using qdec.
>>> how can i to do?
>>> plz answer me
>>>
>>> 2015-11-10 7:49 GMT+09:00 A-reum Min
>>> :
>>>   Hello experts!
>>> I have some question to you..
>>>
>>> I don't need to show up so small blue
>>> regions(fig.1
>>> blue region)
>>>
>>> How can i control these?
>>>
>>> 2015-11-10 7:41 GMT+09:00 Douglas N
>>> Greve
>>> :
>>>   Hi, please create a new thread
>>> since this is a
>>> new topic.
>>>   Also, I don't
>>>   understand your question so please
>>> elaborate.
>>>
>>>   On 11/09/2015 05:34 AM, A-reum Min
>>> wrote:
>>>   > Hello experts!
>>>   >
>>>   > i have some question to you..
>>>   >
>>>   > How can i control the

Re: [Freesurfer] seq.info

2016-02-05 Thread Douglas Greve


you don't need an seq.info file anymore with fsfast

On 2/5/16 2:54 PM, Ji Won Bang wrote:

Dear. Freesurfer team

I used dcmunpack to convert DCM to nii.

This command didn't generate seq.info  (I couldn't 
find it).


I'd like to create one by myself

Do you know how I can check the scan parameters:
sequencename
nrows
ncols
nslcs
rowpixelsize
colpixelsize
slcpixelsize
ntrs
TR

I know that when I use: unpacksdcmdir -src dicomdir -targ targetdir 
-scanonly targetdir /scan.info 


I can get sequencename, nrows, ncols... but then from where can I 
check the others?


Thank you very much.

Best,
Ji Won


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[Freesurfer] spot checking results

2016-02-05 Thread Krieger, Donald N.

Dear List,

I have run recon-all -all on the same scan on two different machines likely 
running two different versions of Linux but in any case the runs were done with 
different numbers of cores.
I  haven't done anything fancy to compare that the results are identical except 
for some spot checks of individual files with md5sum.
label/lh.BA4a.label shows up the same on both.
mri/wmparc.mgz does not.
Your comments would be welcome.
Is there something about the non-ascii files, e.g. wmparc.mgz, which would make 
them show different checksums, e.g. inclusion of a processing time or some such?
Do you have experience or suggestions for convincing ourselves that we are 
getting the same answers on different machines?
???

Thanks - Don

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Re: [Freesurfer] spot checking results

2016-02-05 Thread dgw

Don,

Running FreeSurfer on two different versions of any operating system 
will not produce the same results. If you want the same results, you 
must use exactly the same version of an operating system for all of an 
analysis.

hth
d

On 2/5/16 8:29 PM, Krieger, Donald N. wrote:
> Dear List,
>
> I have run recon-all –all on the same scan on two different machines
> likely running two different versions of Linux but in any case the runs
> were done with different numbers of cores.
>
> I  haven’t done anything fancy to compare that the results are identical
> except for some spot checks of individual files with md5sum.
>
> label/lh.BA4a.label shows up the same on both.
>
> mri/wmparc.mgz does not.
>
> Your comments would be welcome.
>
> Is there something about the non-ascii files, e.g. wmparc.mgz, which
> would make them show different checksums, e.g. inclusion of a processing
> time or some such?
>
> Do you have experience or suggestions for convincing ourselves that we
> are getting the same answers on different machines?
>
> ???
>
> Thanks - Don
>
>
>
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> at
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Re: [Freesurfer] DTI - Tracula question

Re: [Freesurfer] DTI - Tracula question

Re: [Freesurfer] DTI - Tracula question

Re: [Freesurfer] Volume analysis in native space vs. mni305 space

Re: [Freesurfer] DTI - Tracula question

Re: [Freesurfer] hello freesurfer developer~

Re: [Freesurfer] (no subject)

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[Freesurfer] tkregister2 - horizontal and coronal inverted in the functional only

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Re: [Freesurfer] DTI - Tracula question

Re: [Freesurfer] TRACULA Longitudinal can't find subject folder

[Freesurfer] use as seed a ROI.label as seed in FS-FAST

Re: [Freesurfer] seq.info

Re: [Freesurfer] seq.info

[Freesurfer] seq.info

Re: [Freesurfer] tracula preproc complains about missing bvec-file

[Freesurfer] problem mri_convert

Re: [Freesurfer] Brain stem segmentation-- FS6

[Freesurfer] Combining lh. and rh. surfaces

[Freesurfer] FreeSurfer group analysis: mri_glmfit-sim

Re: [Freesurfer] TRACULA Longitudinal can't find subject folder

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

Re: [Freesurfer] Combining lh. and rh. surfaces

Re: [Freesurfer] hello freesurfer developer~

Re: [Freesurfer] seq.info

[Freesurfer] spot checking results

Re: [Freesurfer] spot checking results

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