[Freesurfer] FSGD error: class Input not defined

[Jarek Rokicki]

Dear Freesurfer experts,

I am trying to perform the resting state fMRI analysis as in:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough

I got stuck with the STEP8, when I tried to use my own fsgd file. I tried
to test for two group difference, no covariance as in:
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V

But I am getting this error:
mri_glmfit --y fc.lpccseed.surf.lh/L_PCC/ces.nii.gz  --wls
fc.lpccseed.surf.lh/L_PCC/cesvar.nii.gz --fsgd ../glm_file.fsgd --C
../group.diff.mtx --surface fsaverage lh --glmdir my-glm.wls --nii.gz
gdfRead(): reading ../glm_file.fsgd
Input line 1, subjid = HM-HR10-002Rest Group1, class Input not defined
FSGDF Format Error: file = ../glm_file.fsgd, tag=Input

I am testing the pipeline so just 8 subjects so far.
I've checked the ces.nii.gz and cesvar.nii.gz and both of them have correct
dimensions of 163842 x 1 x 1 x 8.

Thank you for your help in advance.


*fsdg_file is:*
GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
Input HM-HR10-002Rest Group1
Input HM-HR10-005Rest Group1
Input HM-HR10-007Rest Group1
Input HM-HR10-010Rest Group1
Input PD0001Rest Group2
Input PD0002Rest Group2
Input PD0004Rest Group2
Input PD0005Rest Group2

*mtx file is:*
1 -1



宜しくお願い致します。

Sincerely,
Jarek Rokicki, Ph.D.

Integrative Brain Imaging Center (IBIC)
National Center of Neurology and Psychiatry (NCNP)

*4-1-1 Ogawahigashi-chyo, Kodaira, Tokyo 187-8551 Japan*

TEL: +81-80-6628-5709

国立精神・神経医療研究センター
脳病態統合イメージングセンター(IBIC)
臨床脳画像研究部 画像情報解析研究室
*〒187-8551 東京都小平市小川東町4-1-1*


glm_file.fsgd
Description: Binary data
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Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

[Thomas Yeo]

Hi Bronwyn,

You raise a good point. You can consider creating a cortical mask using
aparc+aseg.mgz and use that to mask the networks.

However, another approach (which might be more accurate) is to take
cortical networks in fsaverage space and transform to your subject's
surface and then transform into your subject's volume:

# Transform from fsaverage to subject's surface
>> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh
--sval-annot *lh.Yeo2011_17Networks_N1000.annot*  --tval
$SUBJECTS_DIR/yoursubject/label/*lh.Yeo_17Network_native.annot*

# Transform from subject's surface into your subject's volume (I am not
super sure about this. You probably want to double check the output is
correct)
>> *mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot **--o
outfile.nii.gz --hemi lh --subject HS_001 **--regheader*

--Thomas

On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs  wrote:

> Hi Mailing List,
>
> I am attempting to apply the Yeo 2011 7-network fucntional parcellations
> to a set of fs MRIs processed with v5.1.0. Below are listed the first three
> steps I plan to take and I am seeking advice as to:
>
> A) Whether this approach is valid.
> B) Steps to take next.
>
>
>
> * Steps 1-3: *
>
> *1. Run MNI152 1mm template through recon-all*
> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
> Yeo2011_MNI152_FS
> recon-all -all -subjid Yeo2011_MNI152_FS
>
> *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space*
> mri_vol2vol --mov
> Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s
> Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
> talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest
>
> *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:*
> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
> Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz
> --nearest --inv-morph
>
>
> When previously mapping the Choi 2012 straital parcellations, steps 4 and
> 5 were:
>
> 4. *Creating a striatal mask in the native subject's space from
> freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens
> (26 & 58)*:
> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match
> 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz
>
> *5. **Using this mask to mask the choi striatal parcellations*
> fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz
> Yeo_atlas_subjID_mask.nii.gz
>
>
> Do I need to do a similar thing for the Yeo cortical parcellations and if
> so what regions should I include in the cortical mask?
> --
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
> [image: Neuroscience Research Australia]
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883
> neura.edu.au
>
> [image: Follow @neuraustralia on twitter]
> [image: Follow NeuRA on facebook]
> [image: Subscribe
> to the NeuRA Magazine] 
>
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[Freesurfer] patch error

[S.V.Shepherd [work]]

Hello all,

I'm trying to make a patch and have run into the 'bad vertex' error. It's
come up a few times on the listserv, but I never saw a public resolution.
One possible source of errors is that I had to do a manual correction in
FreeView, including a 'remove intersections' in FreeView. However, tksurfer
had no trouble mapping the curvature to the finished surface, so I assume
this was not likely to be the source of the error. Details below:

$mris_flatten -w 0 -distances 20 7 lh.cort.patch.3d lh.cort.patch.flat
using write iterations = 0
sampling 7 neighbors out to a distance of 20 mm
reading patch lh.cort.patch.3d with 1919246708 vertices (2846533.5% of
total)
MRISreadPatch: bad vertex # (1701060705) found in patch file
No such file or directory

stephen

*stephen v. shepherd   phd*
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7699
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Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

thanks Bruce - I had found that option for my fsaverage maps and it worked.

What about if I am importing probability maps formed as .mnc and creating
overlays from them? The percentages seem to be very odd for min and max
threshold.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jun 22, 2016 at 9:32 PM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> if you are using mri_average you can give it -p as the first argument and
> it will compute a percent at the end
> Bruce
> On Wed, 22 Jun 2016, Trisanna Sprung-Much wrote:
>
> Hi Bruce
>>
>> Is there is a way to set the probability of an overlay between 0 and 1?
>> Would this have to be done when creating the overlay using mri_vol2surf?
>>
>> thanks
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Trisanna
>>
>>   the binaries that take mandatory command-line arguments (i.e.
>>   without a -- or - in front of them) require all options to be
>>   given before the mandatory arguments
>>
>>   cheers
>>   Bruce
>>
>>   On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> thanks, Bruce. Yes in the end through trial and
>> error I tried "mri_average -noconform input output"
>> and it worked. I was
>> surprised that I had to put the -noconform first as
>> normally one can put the argument anywhere in the
>> command.
>>
>> Best
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 20, 2016 at 9:27 AM, Bruce Fischl
>>  wrote:
>>   yes, your last file on the command line should
>> be the output file (the average)
>>
>>   cheers
>>   Bruce
>>
>>   On Mon, 20 Jun 2016, Trisanna Sprung-Much
>> wrote:
>>
>>   As a follow-up, here is the mri_info for one
>> of my overlays in the folder
>>   and the output file that mri_average seems to
>> create (if I don't specify an
>>   output and it re-writes my last file). The
>> dimensions are off:
>>   Any ideas?
>>
>>   Trisanna
>>
>>
>>  Tgtrisanna@kaplan
>> :/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_f
>> sa
>>   vee_left/aalf_lh$ mri_info
>> fsaverage_overlay_aalf_icbm-102_left.mgz
>>   Volume information for
>> fsaverage_overlay_aalf_icbm-102_left.mgz
>> type: MGH
>>   dimensions: 163842 x 1 x 1
>>  voxel sizes: 1., 1., 1.
>> type: FLOAT (3)
>>  fov: 163842.000
>>  dof: 0
>>   xstart: -81921.0, xend: 81921.0
>>   ystart: -0.5, yend: 0.5
>>   zstart: -0.5, zend: 0.5
>>   TR: 0.00 msec, TE: 0.00 msec, TI:
>> 0.00 msec, flip angle: 0.00
>>   degrees
>>  nframes: 1
>>  PhEncDir: UNKNOWN
>>   ras xform present
>>   xform info: x_r =   1., y_r =
>> 0., z_r =   0., c_r =
>>   0.5000
>> : x_a =   0., y_a =
>> 1., z_a =   0., c_a =
>>   -17.5000
>> : x_s =   0., y_s =
>> 0., z_s =   1., c_s =
>>18.5000
>>
>>   talairach xfm :
>>   Orientation   : RAS
>>   Primary Slice Direction: axial
>>
>>   voxel to ras transform:
>>   1.   0.   0.
>> -81920.5000
>>   0.   1.   0.
>> -18.
>>   0.   0.   1.
>>  18.
>>   0.   0.   0.
>> 1.
>>
>>   voxel-to-ras determinant 1
>>
>>   ras to voxel transform:
>>   1.  -0.  -0.
>> 81920.5000
>>  -0.   1.  -0.
>>  18.
>>  -0.  -0.   1.
>> -18.
>>   0.   0.   0.
>> 

Re: [Freesurfer] registering to fsaverage

[Bruce Fischl]

Hi Trisanna

if you are using mri_average you can give it -p as the first argument and 
it will compute a percent at the end

Bruce
On Wed, 22 Jun 2016, Trisanna 
Sprung-Much wrote:



Hi Bruce

Is there is a way to set the probability of an overlay between 0 and 1?
Would this have to be done when creating the overlay using mri_vol2surf?

thanks

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl 
wrote:
  Hi Trisanna

  the binaries that take mandatory command-line arguments (i.e.
  without a -- or - in front of them) require all options to be
  given before the mandatory arguments

  cheers
  Bruce

  On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:

thanks, Bruce. Yes in the end through trial and
error I tried "mri_average -noconform input output"
and it worked. I was
surprised that I had to put the -noconform first as
normally one can put the argument anywhere in the
command.

Best

Trisanna

--
Ph.D. CandidateMcGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 20, 2016 at 9:27 AM, Bruce Fischl
 wrote:
      yes, your last file on the command line should
be the output file (the average)

      cheers
      Bruce

      On Mon, 20 Jun 2016, Trisanna Sprung-Much
wrote:

      As a follow-up, here is the mri_info for one
of my overlays in the folder
      and the output file that mri_average seems to
create (if I don't specify an
      output and it re-writes my last file). The
dimensions are off:
      Any ideas?

      Trisanna


     
Tgtrisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_f
sa
      vee_left/aalf_lh$ mri_info
fsaverage_overlay_aalf_icbm-102_left.mgz 
      Volume information for
fsaverage_overlay_aalf_icbm-102_left.mgz
                type: MGH
          dimensions: 163842 x 1 x 1
         voxel sizes: 1., 1., 1.
                type: FLOAT (3)
                 fov: 163842.000
                 dof: 0
              xstart: -81921.0, xend: 81921.0
              ystart: -0.5, yend: 0.5
              zstart: -0.5, zend: 0.5
                  TR: 0.00 msec, TE: 0.00 msec, TI:
0.00 msec, flip angle: 0.00
      degrees
             nframes: 1
             PhEncDir: UNKNOWN
      ras xform present
          xform info: x_r =   1., y_r =  
0., z_r =   0., c_r =    
      0.5000
                    : x_a =   0., y_a =  
1., z_a =   0., c_a =  
      -17.5000
                    : x_s =   0., y_s =  
0., z_s =   1., c_s =  
       18.5000

      talairach xfm : 
      Orientation   : RAS
      Primary Slice Direction: axial

      voxel to ras transform:
                      1.   0.   0.
-81920.5000
                      0.   1.   0.  
-18.
                      0.   0.   1.  
 18.
                      0.   0.   0.    
1.

      voxel-to-ras determinant 1

      ras to voxel transform:
                      1.  -0.  -0.
81920.5000
                     -0.   1.  -0.  
 18.
                     -0.  -0.   1.  
-18.
                      0.   0.   0.    
1.


     
trisanna@kaplan:/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa

      verage_left/aalf_lh$ mri_info
fsaverage_overlay_aalf_icbm-350_left.mgz 
      Volume information for
fsaverage_overlay_aalf_icbm-350_left.mgz
                type: MGH
          dimensions: 256 x 256 x 256
         voxel sizes: 1., 1., 1.
                type: FLOAT (3)
                 fov: 256.000
                 dof: 0
              xstart: -128.0, xend: 128.0
              ystart: -128.0, yend: 128.0
              zstart: -128.0, zend: 128.0
  

Re: [Freesurfer] Any updates on recon-all GPU support?

[R Edgar]

On 22 June 2016 at 19:32, Derek Pisner  wrote:

> Thanks for the very quick reply.  Good to know that someone has successfully 
> compiled GPU binaries for newer CUDA versions.  I took a quick look at the 
> developer's guide for building the cuda binaries from source, but it seems 
> like a very involved process? Do your compiled binaries only work for CUDA 
> SDK 7.5 or have you tested them with other CUDA versions?

I only have one Linux box, running CentOS 7 (which isn't officially
supported by Freesurfer - I had to tweak CFLAGS quite a bit too) with
CUDA 7.5.

I wouldn't say the process is very involved to compile from source,
but I did have to tweak things a bit. Specifically, after running
./setup_configure, I had to open up the configure script, and find the
section which looks like:
#
# Nvidia CUDA enabling

CUDA_DIR=""
with_cuda=""

And comment out the with_cuda="" line. Then I run configure with
--enable-fermi-gpu --with-cuda="/usr/local/cuda"
(plus some other options for my machine). Note that for me:
$ which nvcc
/usr/local/cuda-7.5/bin/nvcc

> Also, would you mind sending me an example binary (e.g. mri_ca_register_cuda) 
> just so I cant test it myself and rule out whether this is just an issue with 
> the way our GPU is configured? (I can't even get cudadetect to acknowledge my 
> GPU as a cuda-enabled device (it just says 0 devices found), despite it 
> successfully acknowledging that the GPU "exists") Please let me know and I 
> cna send you a private email address.

I can do, but there's a lot of things which could go wrong.

Are you able to compile and run the sample CUDA programs which NVIDIA
supplies as part of the SDK? If you haven't tried that yet, it would
be a better place to start.

> Thanks again for your help! And hopefully this thread will help others 
> interested in updating their gpu-capabilities with Freesurfer.

Indeed - one Francis Thomas @arizona.edu was asking similar questions
a few months ago.

I'm afraid I'm not doing any extra GPU porting right now - I've been
getting concerned about potential drift between the CPU and GPU
pipelines, and trying to come up with a better way around the problem.

HTH,

Richard

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Re: [Freesurfer] Any updates on recon-all GPU support?

[Derek Pisner]

Hi Richards,

Thanks for the very quick reply.  Good to know that someone has successfully 
compiled GPU binaries for newer CUDA versions.  I took a quick look at the 
developer's guide for building the cuda binaries from source, but it seems like 
a very involved process? Do your compiled binaries only work for CUDA SDK 7.5 
or have you tested them with other CUDA versions? 

Also, would you mind sending me an example binary (e.g. mri_ca_register_cuda) 
just so I cant test it myself and rule out whether this is just an issue with 
the way our GPU is configured? (I can't even get cudadetect to acknowledge my 
GPU as a cuda-enabled device (it just says 0 devices found), despite it 
successfully acknowledging that the GPU "exists") Please let me know and I cna 
send you a private email address.

Thanks again for your help! And hopefully this thread will help others 
interested in updating their gpu-capabilities with Freesurfer.

-Derek

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of R Edgar 
[freesurfer@gmail.com]
Sent: Wednesday, June 22, 2016 3:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Any updates on recon-all GPU support?

On 22 June 2016 at 18:17, Derek Pisner  wrote:
> Anyone manage to successfully configure recon-all to run with -use-gpu for 
> recent cuda toolkit versions? I realize cuda support has ceased over the past 
> few years for Freesurfer, but have there been any successful builds for CUDA 
> toolkit versions 6 and up? I am currently looking to configure cuda support 
> on a Tesla K80 GPU, which is part of a small beowulf cluster, which is 
> working wonderfully with FSL's cuda support. Many moons ago, when gpu support 
> was working, I found the -use-gpu option with recon-all to be significantly 
> faster and more practical (for the user) than the -openmp option (which even 
> on a 150 core cluster has provided limited speedup during batch runs). 
> Curious to hear what others have been doing.

I've successfully compiled and run mri_ca_register_cuda with CUDA SDK
7.5 (and a K1200 Quadro). I've also made a few performance tweaks,
which have shaved another minute or so off mri_ca_register_cuda.

If you're having trouble compiling from source, I can try to help, if
you let me know where you're hitting trouble.

Regards,

Richard

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Re: [Freesurfer] registering to fsaverage

[Trisanna Sprung-Much]

Hi Bruce

Is there is a way to set the probability of an overlay between 0 and 1?
Would this have to be done when creating the overlay using mri_vol2surf?

thanks

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Mon, Jun 20, 2016 at 12:11 PM, Bruce Fischl 
wrote:

> Hi Trisanna
>
> the binaries that take mandatory command-line arguments (i.e. without a --
> or - in front of them) require all options to be given before the mandatory
> arguments
>
> cheers
> Bruce
>
> On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:
>
> thanks, Bruce. Yes in the end through trial and error I tried "mri_average
>> -noconform input output" and it worked. I was
>> surprised that I had to put the -noconform first as normally one can put
>> the argument anywhere in the command.
>>
>> Best
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 20, 2016 at 9:27 AM, Bruce Fischl 
>> wrote:
>>   yes, your last file on the command line should be the output file
>> (the average)
>>
>>   cheers
>>   Bruce
>>
>>   On Mon, 20 Jun 2016, Trisanna Sprung-Much wrote:
>>
>>   As a follow-up, here is the mri_info for one of my overlays in the
>> folder
>>   and the output file that mri_average seems to create (if I don't
>> specify an
>>   output and it re-writes my last file). The dimensions are off:
>>   Any ideas?
>>
>>   Trisanna
>>
>>
>>   Tgtrisanna@kaplan
>> :/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
>>   vee_left/aalf_lh$ mri_info fsaverage_overlay_aalf_icbm-102_left.mgz
>>   Volume information for fsaverage_overlay_aalf_icbm-102_left.mgz
>> type: MGH
>>   dimensions: 163842 x 1 x 1
>>  voxel sizes: 1., 1., 1.
>> type: FLOAT (3)
>>  fov: 163842.000
>>  dof: 0
>>   xstart: -81921.0, xend: 81921.0
>>   ystart: -0.5, yend: 0.5
>>   zstart: -0.5, zend: 0.5
>>   TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
>> angle: 0.00
>>   degrees
>>  nframes: 1
>>  PhEncDir: UNKNOWN
>>   ras xform present
>>   xform info: x_r =   1., y_r =   0., z_r =   0., c_r
>> =
>>   0.5000
>> : x_a =   0., y_a =   1., z_a =   0., c_a
>> =
>>   -17.5000
>> : x_s =   0., y_s =   0., z_s =   1., c_s
>> =
>>18.5000
>>
>>   talairach xfm :
>>   Orientation   : RAS
>>   Primary Slice Direction: axial
>>
>>   voxel to ras transform:
>>   1.   0.   0. -81920.5000
>>   0.   1.   0.   -18.
>>   0.   0.   1.18.
>>   0.   0.   0. 1.
>>
>>   voxel-to-ras determinant 1
>>
>>   ras to voxel transform:
>>   1.  -0.  -0. 81920.5000
>>  -0.   1.  -0.18.
>>  -0.  -0.   1.   -18.
>>   0.   0.   0. 1.
>>
>>
>>   trisanna@kaplan
>> :/data-01/trisanna/freesurfer/fsaverage/DISPLAY_overlays_fsa
>>   verage_left/aalf_lh$ mri_info
>> fsaverage_overlay_aalf_icbm-350_left.mgz
>>   Volume information for fsaverage_overlay_aalf_icbm-350_left.mgz
>> type: MGH
>>   dimensions: 256 x 256 x 256
>>  voxel sizes: 1., 1., 1.
>> type: FLOAT (3)
>>  fov: 256.000
>>  dof: 0
>>   xstart: -128.0, xend: 128.0
>>   ystart: -128.0, yend: 128.0
>>   zstart: -128.0, zend: 128.0
>>   TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
>> angle: 0.00
>>   degrees
>>  nframes: 1
>>  PhEncDir: UNKNOWN
>>   ras xform present
>>   xform info: x_r =  -1., y_r =   0., z_r =   0., c_r
>> =
>>   0.5000
>> : x_a =   0., y_a =   0., z_a =   1., c_a
>> =
>>   -17.5000
>> : x_s =   0., y_s =  -1., z_s =   0., c_s
>> =
>>18.5000
>>
>>   talairach xfm :
>>   Orientation   : LIA
>>   Primary Slice Direction: coronal
>>
>>   --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 20, 2016 at 12:32 AM, Trisanna Sprung-Much
>>  wrote:
>>   Hi Dr. Fischl
>> I ran the following mri_average and consistently get this message. It
>> seems to be trying to read my output as one of the input volumes. If I
>> don't specify an output it re-writes my last file in the input folder
>> and when I try to open this it 

Re: [Freesurfer] Any updates on recon-all GPU support?

[R Edgar]

On 22 June 2016 at 18:17, Derek Pisner  wrote:
> Anyone manage to successfully configure recon-all to run with -use-gpu for 
> recent cuda toolkit versions? I realize cuda support has ceased over the past 
> few years for Freesurfer, but have there been any successful builds for CUDA 
> toolkit versions 6 and up? I am currently looking to configure cuda support 
> on a Tesla K80 GPU, which is part of a small beowulf cluster, which is 
> working wonderfully with FSL's cuda support. Many moons ago, when gpu support 
> was working, I found the -use-gpu option with recon-all to be significantly 
> faster and more practical (for the user) than the -openmp option (which even 
> on a 150 core cluster has provided limited speedup during batch runs). 
> Curious to hear what others have been doing.

I've successfully compiled and run mri_ca_register_cuda with CUDA SDK
7.5 (and a K1200 Quadro). I've also made a few performance tweaks,
which have shaved another minute or so off mri_ca_register_cuda.

If you're having trouble compiling from source, I can try to help, if
you let me know where you're hitting trouble.

Regards,

Richard

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[Freesurfer] Any updates on recon-all GPU support?

[Derek Pisner]

Anyone manage to successfully configure recon-all to run with -use-gpu for 
recent cuda toolkit versions? I realize cuda support has ceased over the past 
few years for Freesurfer, but have there been any successful builds for CUDA 
toolkit versions 6 and up? I am currently looking to configure cuda support on 
a Tesla K80 GPU, which is part of a small beowulf cluster, which is working 
wonderfully with FSL's cuda support. Many moons ago, when gpu support was 
working, I found the -use-gpu option with recon-all to be significantly faster 
and more practical (for the user) than the -openmp option (which even on a 150 
core cluster has provided limited speedup during batch runs). Curious to hear 
what others have been doing.

-Derek
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Re: [Freesurfer] X11 / mesa update broke tkmedit snapshots

[Flavin, John]

I should add that we're running tkmedit using xvfb since the process is 
automated and runs without a physical screen.

Flavin

> On Jun 22, 2016, at 4:15 PM, Flavin, John  wrote:
>
> Hi all,
>
> I run the pipelines for the CNDA and various other XNAT installations. We 
> recently updated some of our packages, and our Freesurfer snapshots 
> (generated with tkmedit using a tcl script) have broken.
>
> We're on Centos 6.8. The package that seems to cause the breakage is one of 
> the mesa packages, probably mesa-libGL, upgraded from 10.4.3 to 11.0.7. (But 
> it's hard to be sure that's the exact one because of the dependencies.) That 
> mesa package gets pulled in as a dependency to an X11 update, specifically 
> xorg-x11-server-Xorg upgraded from 1.15.0 to 1.17.4.
>
> We're working now on figuring out a strategy to downgrade these, and some 
> others. It's a little hairy because there are a lot of dependent packages and 
> a lot of affected machines.
>
> If anyone else has seen this, or knows how to fix it, I'd love to hear from 
> you.
>
> John Flavin
>
>
>
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
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>
>
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> dispose of the e-mail.
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[Freesurfer] X11 / mesa update broke tkmedit snapshots

[Flavin, John]

Hi all,

I run the pipelines for the CNDA and various other XNAT installations. We 
recently updated some of our packages, and our Freesurfer snapshots (generated 
with tkmedit using a tcl script) have broken.

We're on Centos 6.8. The package that seems to cause the breakage is one of the 
mesa packages, probably mesa-libGL, upgraded from 10.4.3 to 11.0.7. (But it's 
hard to be sure that's the exact one because of the dependencies.) That mesa 
package gets pulled in as a dependency to an X11 update, specifically 
xorg-x11-server-Xorg upgraded from 1.15.0 to 1.17.4.

We're working now on figuring out a strategy to downgrade these, and some 
others. It's a little hairy because there are a lot of dependent packages and a 
lot of affected machines.

If anyone else has seen this, or knows how to fix it, I'd love to hear from you.

John Flavin




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[Freesurfer] New Research Assistant Position in Neuroimaging Available at Washington University in St Louis

[Karl Friedrichsen]

NEW RESEARCH ASSISTANT POSITION IN NEUROIMAGING AVAILABLE

POSITION SUMMARY: Applications are invited for a research assistant
position in the Ances Laboratory at Washington University in St. Louis. The
primary focus of the lab is to understand how neurodegenerative diseases
(especially Alzheimer’s disease) disrupt brain organization and mediates
symptoms. Results are expected to have broad implications not only for
understanding the pathophysiology of neurodegenerative disorders but more
generally for understanding the relationship between brain physiology,
anatomy, and behavior. The laboratory utilizes state-of-the-art magnetic
resonance imaging (MRI) research facilities and has an outstanding record
of productivity. Funding is guaranteed for a minimum 2 year commitment

PRIMARY DUTIES AND RESPONSIBILITIES (Essential Functions): The primary
responsibility of the research assistant will be to archive/organize images
(large multi-modal imaging datasets) and process/analyze multi-modal
neuroimaging data. The research assistant will assist in various lab
maintenance and organizational duties including tracking project progress,
meet grant deadlines, and anticipate project needs.

QUALIFICATIONS: The qualified candidate will have at least a Bachelor's
degree in human biology, neurosciences, psychology, bioengineering,
computer sciences, or other related fields. The qualified candidate must
have computer skills and some basic knowledge of computer languages (e.g.
C, C++, Matlab, Python). The research assistant must be dependable, have
good attention to details, be well organized, self-motivated, and
comfortable working as part of a team. Previous experience with fMRI data
analysis programs is preferred but not necessary. Strong facility with
statistical analyses is also desired.

To apply, please send a letter of interest and CV to ban...@wustl.edu.
Please arrange for three confidential letters of reference to be sent to
the address below. Only applicants considered for employment will be
contacted.

Contact Information:

Beau Ances MD, PhD

Department of Neurology Washington University in Saint Louis Box 8111

660 South Euclid Ave

Saint Louis, MO 63110
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[Freesurfer] New Post Doctoral Position in Neuroimaging Available at Washington University in St Louis

[Karl Friedrichsen]

NEW POST DOCTORAL POSITION IN NEUROIMAGING AVAILABLE

POSITION SUMMARY: Applications are invited for a post doctoral position in
the Ances Laboratory at Washington University in St. Louis. The primary
focus of the lab is to understand how neurodegenerative diseases
(especially Alzheimer’s disease) disrupt brain organization and mediates
symptoms. Results are expected to have broad implications not only for
understanding the pathophysiology of neurodegenerative disorders but more
generally for understanding the relationship between brain physiology,
anatomy, and behavior. The laboratory utilizes state-of-the-art magnetic
resonance imaging (MRI) research facilities and has an outstanding record
of productivity. Writing manuscripts and applying for independent grants
will be strongly encouraged. Funding is guaranteed for a minimum 2 year
commitment.

PRIMARY DUTIES AND RESPONSIBILITIES (Essential Functions): The primary
responsibility of the post-doctoral fellow will be to conceive, design, and
analyze studies pertaining to the effect of neurodegenerative disease on
structural (e.g., volumetric imaging and diffusion tensor imaging [DTI])
and functional (e.g., blood oxygen level dependent [BOLD] imaging and
arterial spin labeling [ASL]) brain organization. Anticipated activities
entail development and implementation of new analytic strategies to
facilitate understanding of disease in the human brain, integration of
large multi-modal imaging datasets, and analysis of the relationship
between brain imaging markers and cognition or clinical status. Strong
written communication skills are required. Attention to detail,
organizational capability, and the ability to handle multiple concurrent
tasks are essential. The post-doctoral fellow is expected to be able to
work independently as well as part of a team in a fast paced environment.

PREFERRED EDUCATION/EXPERIENCE: A PhD in neuroscience, computer science,
physics, engineering, mathematics, psychology, or related fields is
requested. Previous experience is preferred in computational methods,
scientific programming, and/or neuroimaging data analysis. Experience in
computer programming (e.g. Matlab, shell scripting, Python, C), image
processing (e.g. custom routines, FSL, AFNI, Freesurfer), and statistical
analyses (R, SPSS) is beneficial.

CRITICAL SKILLS AND EXPERTISE: The successful applicant will have a strong
background in scientific computing (e.g., Unix/Linux experience). Academic
proficiency in statistics is strongly desired. The applicant should have
experience designing or adopting statistical approaches to address
neurobiological questions. Preference will be given to applicants with a
strong publication record or experience with writing grant applications.
The successful candidate should be highly motivated with excellent
analytical and interpersonal skills.

To apply, please send a letter of interest and CV to ban...@wustl.edu.
Please arrange for three confidential letters of reference to be sent to
the address below. Only applicants considered for employment will be
contacted.

Contact Information:

Beau Ances MD, PhD

Department of Neurology Washington University in Saint Louis Box 8111

660 South Euclid Ave

Saint Louis, MO 63110

ban...@wustl.edu
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[Freesurfer] doubts

[Elias Vergílio Da Cás]

Hi,

*After the command: *

asegstats2table  --subjects AntonioMagnani -- meas volume --tablefile
TESTE.txt

This message:

[image: Imagem inline 1]


Thanks.

elias.



-- 
Atte.

Elias Vergílio Da Cás - Físico
UFES/HUCAM/EBSERH
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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

[Fernando Pasquini Santos]

Hi all,

I'll give some feedback about the two methods you've mentioned. I also
tried using a 0.5 T1 image and then:

*Changing the headers of the T1 and T2 images:*
It worked for the 0.7mm T1, however, in the 0.5mm the tailarach aligment
failed.

In both cases I had the warning "MRIsetRas2VoxFromMatrix(): voxels sizes
are inconsistent"

Output:

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0434, pval=0.0034 < threshold=0.0050)

Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach



*Using the -hires flag:*Although it is not sure if this is handling the
original resolution, it also worked only for the 0.7mm, and for the 0.5mm
it had a segmentation fault in the topology correction step.


Em sex, 10 de jun de 2016 às 03:37, Iglesias, Eugenio 
escreveu:

> Hi Matt,
> Bruce actually mentioned this possibility yesterday. Good to hear it
> doesn’t crash when you run it! That said, I need to go through the code,
> and make sure that data are handled the way they are supposed to: the fact
> that it doesn’t crash doesn’t directly imply that it is working properly.
> Hopefully I’ll find time to do this next week…
> Cheers,
> Eugenio
>
>
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 9 Jun 2016, at 21:51, Hibert, Matthew Louis 
> wrote:
>
> Hi Eugenio,
> Would it also be possible to use the -hires flag in the initial recon-all
> command to prevent the T1 from being downsampled and maintain the voxel
> size that the T1 was acquired at, and use that resulting recon for the
> hippocampal subfield segmentation?  I've tested this with MEMPRAGE scans
> acquired at 0.75mm isotropic and coronal T2 anisotropic scans acquired at
> 0.33mm in plane with 1mm thick slices, and the results look reasonable.
> The "1mm" label files are correctly downsampled to 0.75mm instead of 1mm,
> and the higher resolution label files remain at 0.33mm resolution.
>
> Thanks,
> Matt
>
> Stufflebeam Lab
> Athinoula A. Martinos Center
> Massachusetts General Hospital
> 149 13th Street, Room 1115S
> Charlestown, MA 02129
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias, Eugenio [
> e.igles...@ucl.ac.uk]
> *Sent:* Thursday, June 09, 2016 2:36 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Hippocampal subfields segmentation - what is
> the voxel size of the input?
>
> Hi Fernando,
>
> Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield
> code assumes that the T1 comes from FreeSurfer… For the paper, I hacked the
> code to take advantage of multiple images with higher resolution, but it
> hasn’t been thoroughly tested and it’s not publicly available at this
> point.
> That said, there are different things you can do at this point:
> 1. Use the T1+T2 as is (disadvantage: T1 will be resampled to 1 mm).
> 2. Use only the T2.
> 3. Use only the T1. To do this, you would use the T1 as additional scan on
> its own (i.e., the main and additional scans are the same, but the
> additional one won’t be resampled).
> 4. There might be a way (hack) of using both scans at full resolution. If
> you change the header of the T1 scan and specify that the voxel size is
> 1mm, no resampling will happen; FreeSurfer will believe that you’re dealing
> with a subject with a very large head. If you do this, you’ll also have to
> enlarge the voxel size of the T2 by a factor 1/0.7. Also, the resulting
> volumes will have to be divided by (1/0.7)^3 in order to correct for the
> “wrong” voxel size.
>
> I hope this helps!
>
> Cheers,
>
> Eugenio
>
> Juan Eugenio Iglesias
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 9 Jun 2016, at 19:23, Fernando Pasquini Santos 
> wrote:
>
> Dear,
>
> I have a doubt regarding the input T1 image used for the Hippocampal
> Subfield segmentation in Freesurfer 6.0 -
> https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
>
> In this documentation it says that I can use a standard 1mm T1 image or
> the same standard 1mm T1 image with an additional scan. However, I want to
> use a 0.7mm T1 image as input, with an additional T2 scan. When I run the
> program with it, the output images (nu.mgz and orig.mgz) are downsampled to
> 1mm voxel size. So, I don't know if this happens just because of the
> recon-all program or if the segmentation is being done in the downsampled
> T1 image or in the original 0.7mm.
>
> By reading the article "A computational atlas of the 

Re: [Freesurfer] Quality control with different pipelines

[Kirstie Whitaker]

Brilliant - many thanks.

Kx

On 22 June 2016 at 14:57, Harms, Michael  wrote:

>
> Yes on all fronts.
>
> --
> 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 Kirstie
> Whitaker 
> Reply-To: Freesurfer support list 
> Date: Wednesday, June 22, 2016 at 8:55 AM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Quality control with different pipelines
>
> Thank you Michael!
>
> So - just to be super sure I'm on the same page here. If I've run a
> subject using 5.3 I take that same subject directory (after backing it up
> somewhere) and then run the dev version of recon-all with the -all flag.
> After it's completed I (should - contingent on checking again as you
> recommend) have a well edited subject who can now be reported as having
> been processed with the dev version, right?
>
> Thanks again
> Kx
>
> On 22 June 2016 at 14:48, Harms, Michael  wrote:
>
>>
>> Hi,
>> You can simply rerun 'recon-all -all’ on top of your already
>> processed/edited subject, and it will respect your previous edits.  Of
>> course, it is a good idea to still review/QC the results afterwards, to
>> make sure that the outcome of those edits is satisfactory under the new FS
>> version.
>>
>> And, if you want to preserve your results under FS 5.3, then you should
>> make a copy of those results before rerunning recon-all.
>>
>> 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 Kirstie
>> Whitaker 
>> Reply-To: Freesurfer support list 
>> Date: Wednesday, June 22, 2016 at 1:28 AM
>> To: Freesurfer support list 
>> Subject: [Freesurfer] Quality control with different pipelines
>>
>> Hi everyone,
>>
>> I processed and edited 300 participants for our study using Freesurfer
>> 5.3 and I'd like to move to using the dev version that's currently
>> available because we have a bunch more data that's been collected and I
>> think it does a better job. (This question also applies to moving to v 6
>> when it is released).
>>
>> If I run the dev version of recon-all and then copy over the control
>> points and wm.mgz files that we edited in the original run, and run
>> recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very
>> good approximation for the edits we conducted? Or does this "shortcut" not
>> do what I think it does?
>>
>> Does anyone have any experience moving from one version of freesurfer to
>> another without having to start from square one with the edits?
>>
>> Thank you again for the fantastic tools!
>>
>> Kx
>>
>>
>> --
>> Kirstie Whitaker, PhD
>> Research Associate
>>
>> Department of Psychiatry
>> University of Cambridge
>>
>> *Mailing Address*
>> Brain Mapping Unit
>> Department of Psychiatry
>> Sir William Hardy Building
>> Downing Street
>> Cambridge CB2 3EB
>>
>> *Phone: *+44 7583 535 307
>> *Website:* www.kirstiewhitaker.com
>>
>>
>> --
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the contents
>> of this information is strictly prohibited. If you have received this email
>> in error, please immediately notify the sender via telephone or return mail.
>>
>> ___
>> 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.
>>
>>
>
>
> --
> Kirstie Whitaker, PhD
> Research Associate
>
> Department of Psychiatry
> University of Cambridge
>
> *Mailing Address*
> Brain Mapping Unit
> Department of Psychiatry
> Sir 

Re: [Freesurfer] Quality control with different pipelines

[Harms, Michael]

Yes on all fronts.




-- 
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 Kirstie Whitaker 
Reply-To: Freesurfer support list 
Date: Wednesday, June 22, 2016 at 8:55 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Quality control with different pipelines







Thank you Michael!

So - just to be super sure I'm on the same page here. If I've run a subject using 5.3 I take that same subject directory (after backing it up somewhere) and then run the dev version of recon-all with the -all flag. After it's completed I (should - contingent
 on checking again as you recommend) have a well edited subject who can now be reported as having been processed with the dev version, right?


Thanks again

Kx


On 22 June 2016 at 14:48, Harms, Michael 
 wrote:





Hi,
You can simply rerun 'recon-all -all’ on top of your already processed/edited subject, and it will respect your previous edits.  Of course, it is a good idea to still review/QC the results afterwards, to make sure that the outcome of those edits is satisfactory
 under the new FS version.


And, if you want to preserve your results under FS 5.3, then you should make a copy of those results before rerunning recon-all.


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 Kirstie Whitaker 
Reply-To: Freesurfer support list 
Date: Wednesday, June 22, 2016 at 1:28 AM
To: Freesurfer support list 
Subject: [Freesurfer] Quality control with different pipelines












Hi everyone,


I processed and edited 300 participants for our study using Freesurfer 5.3 and I'd like to move to using the dev version that's currently available because we have a bunch more data that's been collected and I think it does a better job. (This question also
 applies to moving to v 6 when it is released).


If I run the dev version of recon-all and then copy over the control points and wm.mgz files that we edited in the original run, and run recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very good approximation for the edits we conducted?
 Or does this "shortcut" not do what I think it does?


Does anyone have any experience moving from one version of freesurfer to another without having to start from square one with the edits?


Thank you again for the fantastic tools!


Kx






-- 


Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building 
Downing Street
Cambridge CB2 3EB

Phone: +44 7583 535 307

Website: www.kirstiewhitaker.com
















 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


___
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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.






-- 


Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building 
Downing Street
Cambridge CB2 3EB

Phone: +44 7583 535 307

Website: www.kirstiewhitaker.com








 



The materials in this message are 

Re: [Freesurfer] Quality control with different pipelines

[Kirstie Whitaker]

Thank you Michael!

So - just to be super sure I'm on the same page here. If I've run a subject
using 5.3 I take that same subject directory (after backing it up
somewhere) and then run the dev version of recon-all with the -all flag.
After it's completed I (should - contingent on checking again as you
recommend) have a well edited subject who can now be reported as having
been processed with the dev version, right?

Thanks again
Kx

On 22 June 2016 at 14:48, Harms, Michael  wrote:

>
> Hi,
> You can simply rerun 'recon-all -all’ on top of your already
> processed/edited subject, and it will respect your previous edits.  Of
> course, it is a good idea to still review/QC the results afterwards, to
> make sure that the outcome of those edits is satisfactory under the new FS
> version.
>
> And, if you want to preserve your results under FS 5.3, then you should
> make a copy of those results before rerunning recon-all.
>
> 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 Kirstie
> Whitaker 
> Reply-To: Freesurfer support list 
> Date: Wednesday, June 22, 2016 at 1:28 AM
> To: Freesurfer support list 
> Subject: [Freesurfer] Quality control with different pipelines
>
> Hi everyone,
>
> I processed and edited 300 participants for our study using Freesurfer 5.3
> and I'd like to move to using the dev version that's currently available
> because we have a bunch more data that's been collected and I think it does
> a better job. (This question also applies to moving to v 6 when it is
> released).
>
> If I run the dev version of recon-all and then copy over the control
> points and wm.mgz files that we edited in the original run, and run
> recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very
> good approximation for the edits we conducted? Or does this "shortcut" not
> do what I think it does?
>
> Does anyone have any experience moving from one version of freesurfer to
> another without having to start from square one with the edits?
>
> Thank you again for the fantastic tools!
>
> Kx
>
>
> --
> Kirstie Whitaker, PhD
> Research Associate
>
> Department of Psychiatry
> University of Cambridge
>
> *Mailing Address*
> Brain Mapping Unit
> Department of Psychiatry
> Sir William Hardy Building
> Downing Street
> Cambridge CB2 3EB
>
> *Phone: *+44 7583 535 307
> *Website:* www.kirstiewhitaker.com
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
> ___
> 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.
>
>


-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
___
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.

Re: [Freesurfer] Quality control with different pipelines

[Harms, Michael]

Hi,
You can simply rerun 'recon-all -all’ on top of your already processed/edited subject, and it will respect your previous edits.  Of course, it is a good idea to still review/QC the results afterwards, to make sure that the outcome of those edits is satisfactory
 under the new FS version.


And, if you want to preserve your results under FS 5.3, then you should make a copy of those results before rerunning recon-all.


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 Kirstie Whitaker 
Reply-To: Freesurfer support list 
Date: Wednesday, June 22, 2016 at 1:28 AM
To: Freesurfer support list 
Subject: [Freesurfer] Quality control with different pipelines










Hi everyone,


I processed and edited 300 participants for our study using Freesurfer 5.3 and I'd like to move to using the dev version that's currently available because we have a bunch more data that's been collected and I think it does a better job. (This question also
 applies to moving to v 6 when it is released).


If I run the dev version of recon-all and then copy over the control points and wm.mgz files that we edited in the original run, and run recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very good approximation for the edits we conducted?
 Or does this "shortcut" not do what I think it does?


Does anyone have any experience moving from one version of freesurfer to another without having to start from square one with the edits?


Thank you again for the fantastic tools!


Kx






-- 


Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building 
Downing Street
Cambridge CB2 3EB

Phone: +44 7583 535 307

Website: www.kirstiewhitaker.com














 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Quality control with different pipelines

[Kirstie Whitaker]

Hi everyone,

I processed and edited 300 participants for our study using Freesurfer 5.3
and I'd like to move to using the dev version that's currently available
because we have a bunch more data that's been collected and I think it does
a better job. (This question also applies to moving to v 6 when it is
released).

If I run the dev version of recon-all and then copy over the control points
and wm.mgz files that we edited in the original run, and run recon-all with
the "-autorecon2-cp -autorecon3" flags will that be a very good
approximation for the edits we conducted? Or does this "shortcut" not do
what I think it does?

Does anyone have any experience moving from one version of freesurfer to
another without having to start from square one with the edits?

Thank you again for the fantastic tools!

Kx


-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] LGI

[Walid Yassin]

*Hello,*

*I’m trying to run recon-all -lgi - s Subjectname  on my data but i am
getting this error!*

***

Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);


Error in reorganize_verticeslist (line 28)

[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));


Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
verticeslist, step);


>>
ERROR:  make_roi_paths did not complete successfully!


***


*I checked the archives and saw a reply by Marie to someone who had the
same problem.*
*She recommended changing the info inside “SearchProjectionByPial.m" in the
~/Application/freesurfer/matlab directory to:*



***

function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim,
step)

% step is typically set between 5 and 10. Default is 7, increasing it will
% limit redundancies in the resulting path file.

verticeslist=[];
si=max(size(perim));
for t=1:step:si

[nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:));
verticeslist= [verticeslist nearestIndexMT];
end
verticeslist=unique(vertices list);

***


*Which i did, but i am still getting this error!*
*Any recommendations on what to do next? I am running MATLAB_R2016.*

*Thank you in advance,*

*WY*
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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