Re: [Freesurfer] cannot allocate memory

[Bruce Fischl]

Hi Ehsan

We need the full command line and screen output and also what your hardware and 
software environments are to help you. Certainly sounds like you ran out of 
memory though

Cheers
Bruce

> On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon  wrote:
> 
> Ehsan

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[Freesurfer] cannot allocate memory

[Ehsan Tadayon]

Dear Freesurfer experts,

I'm trying to run mri_vol2vol on a functional mri to resample it onto
orig.mgz. I get this error:

```
mri_vol2vol(98217,0xa0ce01d4) malloc: *** mach_vm_map(size=262144) failed
(error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRIalloc(256, 256, 256): could not allocate 262144 bytes for 13664th slice

Cannot allocate memory
```
I was wondering if you have any suggestions. Thanks in advance for your
time.

Best,
Ehsan.
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Re: [Freesurfer] error while running dt-recon all

[Jasmin Alves]

Jasmins-MacBook-Pro:40 jasminalves$ dt_recon --i DTI.nii.gz --s 40 --o
/Users/jasminalves/Desktop/data/FREESURFER/40

INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER/

dt_recon logfile

Tue Mar 15 20:37:35 PDT 2016

VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $

setenv SUBJECTS_DIR /Users/jasminalves/Desktop/data/FREESURFER/

cd /Users/jasminalves/Desktop/data/40

/Applications/freesurfer/bin/dt_recon --i DTI.nii.gz --s 40 --o
/Users/jasminalves/Desktop/data/FREESURFER/40

Jasmins-MacBook-Pro.local

jasminalves

/Applications/Utilities/fsl/bin/eddy_correct

ECRefTP 0

#@#---

Converting input

Tue Mar 15 20:37:35 PDT 2016

cd /Users/jasminalves/Desktop/data/40

mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
/Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii

mri_convert /Users/jasminalves/Desktop/data/40/DTI.nii.gz
/Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /Users/jasminalves/Desktop/data/40/DTI.nii.gz...

TR=8100.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.29, 0.0116015, -0.00282784)

j_ras = (0.0115984, 0.32, 0.00109136)

k_ras = (-0.00284031, -0.00105848, 0.95)

writing to /Users/jasminalves/Desktop/data/FREESURFER/40/dwi.nii...

cd /Users/jasminalves/Desktop/data/40

mri_probedicom --i /Users/jasminalves/Desktop/data/40/DTI.nii.gz

Jasmins-MacBook-Pro:40 jasminalves$



On Tue, Mar 15, 2016 at 12:34 PM, Douglas N Greve  wrote:

> Can you send the full terminal output from when you run dt_recon with
> the nifti as input?
>
> On 03/15/2016 03:07 PM, Jasmin Alves wrote:
> > How was DTI.nii.gz created? DTI.nii.gz was converted from the raw
> > dicom data using dcm2nii.
> >
> > Response for: "What happens if you run mri_info DTI.nii.gz"
> >
> > Volume information for DTI.nii.gz
> >
> >   type: nii
> >
> > dimensions: 128 x 128 x 70 x 65
> >
> >voxel sizes: 2., 2., 2.
> >
> >   type: FLOAT (3)
> >
> >fov: 256.000
> >
> >dof: 0
> >
> > xstart: -128.0, xend: 128.0
> >
> > ystart: -128.0, yend: 128.0
> >
> > zstart: -70.0, zend: 70.0
> >
> > TR: 8100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
> > angle: 0.00 degrees
> >
> >nframes: 65
> >
> >PhEncDir: UNKNOWN
> >
> > ras xform present
> >
> > xform info: x_r =  -0., y_r =   0.0116, z_r =  -0.0028, c_r =
> >   -0.4290
> >
> >   : x_a =   0.0116, y_a =   0., z_a =  -0.0011, c_a =
> > 4.1548
> >
> >   : x_s =  -0.0028, y_s =   0.0011, z_s =   1., c_s =
> >   30.9622
> >
> > Orientation   : LAS
> >
> > Primary Slice Direction: axial
> >
> > voxel to ras transform:
> >
> >-1.   0.0232 -0.0057   126.2761
> >
> > 0.0232   1. -0.0021  -125.2474
> >
> >-0.0057   0.0022 2.   -38.8153
> >
> > 0.   0. 0. 1.
> >
> > voxel-to-ras determinant -8
> >
> > ras to voxel transform:
> >
> >-0.5000   0.0058 -0.001463.8052
> >
> > 0.0058   0.5000 0.000561.9083
> >
> >-0.0014  -0.0005 0.500019.5206
> >
> > 0.   0. 0. 1.
> >
> >
> > On Tue, Mar 15, 2016 at 11:25 AM, Douglas N Greve
> > > wrote:
> >
> >
> > How was DTI.nii.gz created? What happens if you run
> > mri_info DTI.nii.gz
> >
> > If the DICOM is a siemens dicom but has been stripped of special
> > siemens
> > info, then we cannot unpack it
> >
> >
> > On 03/15/2016 02:02 PM, Jasmin Alves wrote:
> > >
> > > Still get the same error:
> > >
> > > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
> > > contain a Siemens ASCII header
> > >
> > > has this file been anonymized?
> > >
> > > ERROR: cannot unpack mosiacs without ASCII header
> > >
> > >
> > > The error I get when running in nifti format is actually found
> > in the
> > > log file.
> > >
> > >  ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is not a
> dicom
> > > file or some other problem
> > >
> > >
> > >
> > >
> > > On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve
> > > 
> >  > >> wrote:
> > >
> > > if you run
> > > mri_convert 00010001 deleteme.nii
> > > what happens?
> > >
> > > what is the error when running with nifti?
> > >
> > >
> > > On 03/14/2016 05:59 PM, Jasmin Alves wrote:
> > > >
> > > > Dear Freesurfer experts,
> > > >
> > > > FREESURFER_HOME: /Applications/freesurfer
> > > >
> 

Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question

[Joseph Dien]

oh duh!  Sorry, wasn’t thinking clearly.
Okay, I see how to generate the betas now.  I don’t even need to mess with the 
mkcontrast-sess command.
I just run selxavg3-sess with the -no-con-ok flag.
With spmhrf 0 I generated a beta.nii.gz file with 85 betas in each vertex.
With spmhrf 1 I generated a beta.nii.gz file with 97 betas in each vertex.
With 12 conditions, 12 more betas is exactly right.
So how do I know which of the betas is which?
I looked through the files and couldn’t find any labels.
I’m guessing the first twelve are the condition betas for "spmhrf 0".
If so, for "spmhrf 1", is it arranged as:

1) c1 c2 c3…d1 d2 d3...

or

2) c1 d1 c2 d2...

 (where d is the first derivative term)

also, when I asked you earlier about implementing this procedure, I had 
suggested reading the betas, computing the Calhoun, then generating new 
beta.nii.gz files with the new betas replacing the original spmhrf0 betas and 
then continuing with the regular analysis stream but you said it would result 
in invalid p-values.  Instead, you suggested:

"I was just thinking you could load the beta into matlab, make the
Calhoun computations on each condition, then compute the contrasts, then
write out the new volume”

can you expand on how one might “compute the contrasts” and “write out the new 
volume”?

Thanks again for this help!

Joe


> On Mar 15, 2016, at 12:43, Douglas N Greve  wrote:
> 
> The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess)
> 
> On 03/13/2016 10:29 PM, Joseph Dien wrote:
>> After a long break, back to this…
>> 
>> My goal is still to get the betas for the first and maybe second spm 
>> hrf so I can calculate a Calhoun derivative boost measure.
>> 
>> As a first step I ran:
>> 
>> mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh 
>> -fwhm 5 -event-related  -paradigm RPA1fix.par -nconditions 12 -spmhrf 
>> 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg 
>> nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc
>> 
>> to use the SPM HRF with one derivative.
>> 
>> Then:
>> 
>> selxavg3-sess -sf sessidlistALL.dat -analysis RPA.sm05.lh
>> 
>> I got the following error:
>> 
>> ERROR: flac_evconw(): conVinc, Condition01 evrw dim mismatch
>> This condition has 2 regressors, but evrm has 1
>> Struct contents reference from a non-struct array object.
>> 
>> Error in flac_conmat (line 37)
>> if(nthcon > length(flac.con))
>> 
>> Error in flac_customize (line 369)
>>  flacnew = flac_conmat(flacnew,nthcon);
>> 
>> Error in fast_selxavg3 (line 65)
>> flac0 = flac_customize(flac0);
>> 
 --
>> ERROR: fast_selxavg3() failed\n
>> 
>> This ran fine with spmhrf 0
>> 
>> based on your prior response below that:
>> 
>> "This is what happens. If you want to use the derivatives,
>> then you need to spec -setwdelay. When you run the command, it will 
>> prompt you
>> for 3 values to use. If you spec 1 0 0, then it will be the same as the
>> default. If you want to test only the first derivative, then 
>> you would spec 0 1 0. Note that the 3rd regressor is the 2nd 
>> derivative wrt time, not the first derivative wrt the dispersion 
>> parameter. You
>> cannot get the Calhoun 2004 value using a contrast (it is non-linear).”
>> 
>> I tried:
>> 
>> mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh 
>> -fwhm 5 -event-related  -paradigm RPA1fix.par -nconditions 12 -spmhrf 
>> 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg 
>> nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc -setwdelay
>> 
>> but I just got the error:
>> 
>> ERROR: Flag -setwdelay unrecognized.
>> 
>> I also tried using the flag when setting up the contrasts but that 
>> didn’t work either.
>> 
>> so not quite sure what I’m doing wrong.  I had understood from your 
>> response below that the contrast weights didn’t need to be changed 
>> from the spmhrf 0 case but perhaps I misunderstood?
>> 
>> any help would be welcome!
>> 
>> Joe
>> 
>>> On Jul 10, 2013, at 13:58, Douglas N Greve >> >> 
>>> wrote:
>>> 
>>> 
>>> I was just thinking you could load the beta into matlab, make the
>>> Calhoun computations on each condition, then compute the contrasts, then
>>> write out the new volume
>>> 
>>> 
>>> On 07/10/2013 01:40 PM, Joseph Dien wrote:
 Sounds good!
 
 Regarding creating a new volume and computing contrasts from it, what
 do you mean?  I didn't follow that.
 
 Thanks!
 
 Joe
 
 
 On Jul 10, 2013, at 1:33 PM, Douglas N Greve
  
 >>> wrote:
 
> 
> On 07/10/2013 01:29 PM, Joseph Dien wrote:
>> Sorry, not following what you are suggesting?
>> 
>> 

Re: [Freesurfer] Editing Lesions in FreeSurfer 5.1

[Bruce Fischl]

Maybe you can draw the wm in? I wouldn't put control points there

> On Mar 15, 2016, at 9:13 AM, Allison Rainford 
>  wrote:
> 
> Hi Bruce,
> 
> I?ve attached a screen shot of a temporal pole of one of the brains that we
> have had issues with. Here the issue is that there is a lesion without a
> very clear boundary for the white matter and freesurfer was unresponsive to
> simply using white matter edits (placing 255s on the wm.mgz), and so we
> tried placing control points where we think the white matter boundary should
> lie. However, we know that control points should not be placed in these dark
> spots of a lesion. 
> 
> Thank you,
> 
> Allison
> 
> 
> ___
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Re: [Freesurfer] Recon Reprocessing Issues

[Bruce Fischl]

as long as you move the file into the tmp dir recon-all should find it 
and use it (search for control.dat in the recon-all.log after you have 
run it).


I'm not sure what's going on with your brainmask.mgz though. You are 
saying that there are voxels that are deleted (set to 1) in your 
brainmask.mgz, but still show up inside the surfaces? Are they 0 in the 
brain.finalsurfs.mgz? The brain.mgz?


On Tue, 15 Mar 2016, Champe Barton 
wrote:



Yes, the pial (and white, actually) surface is extending into an area where 
there is no brain tissue. I'm not sure the anatomical name for it, but it's two 
cavities, one in the lower half of either hemisphere, where there's no tissue 
at all. When I process the dicom files I get really erratic surfaces drawn in 
those areas.

Also, how should I be saving my control points to get them in the tmp folder? I 
can manually move them there, but I assume it should be done automatically.

Thanks,
Champe

Sent from my iPhone


On Mar 15, 2016, at 2:43 PM, Bruce Fischl  wrote:

why are you deleting voxels from the brainmask.mgz? That is only used for 
masking out non-brain tissue. Is that what you are trying to do?


On Tue, 15 Mar 2016, Champe Barton wrote:

I used the recon editing tool—I explicitly followed the instructions from the 
tutorial (even on reprocessing the tutorial data it didn't work), so I had the 
brainmask.mgz highlighted, checked the recon editing box and held shift and 
clicked to remove the necessary voxels (they turned black). I removed them on 
all the necessary slices as well.

Champe

Sent from my iPhone


On Mar 15, 2016, at 1:43 PM, Bruce Fischl  wrote:

Hi Champe

it must be in the tmp subdirectory (that is /tmp/control.dat) 
otherwise we will not find it.

As for the deleted voxel issue - how did you delete them?

Bruce

On Tue, 15 Mar 2016, Champe Barton wrote:

I created them as instructed in the tutorial and called the file “control.dat” 
so there’s a control.dat file in my subjects directory. Should I have named it 
tmp/control.dat? Also, would resolving the control points issue also resolve 
the deleted voxels issue? Cause my it’s not redrawing the pial surface either.

Thanks
Champe

On Mar 15, 2016, at 1:22 PM, Bruce Fischl  wrote:

p.s. sorry, it should be tmp/control.dat

On Tue, 15 Mar 2016, Champe Barton wrote:

Hey Bruce,

I recently sent you a log file to look at to determine why reprocessing data 
wasn’t making any changes in freeview. Have you had a chance to go over it yet? 
Let me know.

Thanks,
Champe

On Mar 7, 2016, at 11:41 AM, Bruce Fischl  wrote:

I got it, thanks
Bruce

On Mon, 7 Mar 2016, Champe Barton wrote:


Hey Bruce,

I got a notification saying the email my recon-all.log file attachment was too 
large and had to await moderator approval to be posted to the support list. I 
was just wondering if you received it or if I should resend it.

Best,
Champe

Sent from my iPhone


On Mar 6, 2016, at 9:53 AM, Bruce Fischl  wrote:

Hi Champe

can you send us the recon-all.log file?

cheers
Bruce

On Sun, 6 Mar 2016, Champe Barton wrote:

Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X El Capitan version 
10.11.2 and I have System Integrity Protection disabled (though I hadn’t experienced 
any issues that could have been a result of that function). Everything in FreeSurfer 
works fine for me—I ran recon-all and successfully processed dicom files, I 
successfully viewed the T1.mgz and brainmask.mgz volumes and the pial and white 
surfaces, and I successfully deleted unnecessary voxels and added a set of control 
points (in both cases, being careful to make and save the changes on all necessary 
slices with the brainmask volume highlighted). My only issue is that when I reprocess 
the data using recon-all -autorecon2-cp -autorecon3 -subjid , it 
runs through the reconstruction without error and then shows no changes at all in 
freeview when I view the volumes/surfaces. The deleted voxels still appear deleted 
and I can still load the control points, so why wouldn’t it make the changes? And 
just to provide a little extra info: I encounter the same problem when I reprocess 
the tutorial data for the pial edits tutorial. I delete the voxels as instructed, 
save the file, reprocess it without error, and then nothing’s changed when I view it 
all again in freeview. Any help would be HUGELY appreciated—I’ve stressed over this 
for weeks trying to get my computer to function properly so that I can begin my work 
as a research assistant in a neuropsych lab editing and analyzing brain scans with 
FreeSurfer. Thanks, Champe

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Re: [Freesurfer] Recon Reprocessing Issues

[Champe Barton]

Yes, the pial (and white, actually) surface is extending into an area where 
there is no brain tissue. I'm not sure the anatomical name for it, but it's two 
cavities, one in the lower half of either hemisphere, where there's no tissue 
at all. When I process the dicom files I get really erratic surfaces drawn in 
those areas. 

Also, how should I be saving my control points to get them in the tmp folder? I 
can manually move them there, but I assume it should be done automatically.

Thanks,
Champe

Sent from my iPhone

> On Mar 15, 2016, at 2:43 PM, Bruce Fischl  wrote:
> 
> why are you deleting voxels from the brainmask.mgz? That is only used for 
> masking out non-brain tissue. Is that what you are trying to do?
> 
>> On Tue, 15 Mar 2016, Champe Barton wrote:
>> 
>> I used the recon editing tool—I explicitly followed the instructions from 
>> the tutorial (even on reprocessing the tutorial data it didn't work), so I 
>> had the brainmask.mgz highlighted, checked the recon editing box and held 
>> shift and clicked to remove the necessary voxels (they turned black). I 
>> removed them on all the necessary slices as well.
>> 
>> Champe
>> 
>> Sent from my iPhone
>> 
>>> On Mar 15, 2016, at 1:43 PM, Bruce Fischl  
>>> wrote:
>>> 
>>> Hi Champe
>>> 
>>> it must be in the tmp subdirectory (that is /tmp/control.dat) 
>>> otherwise we will not find it.
>>> 
>>> As for the deleted voxel issue - how did you delete them?
>>> 
>>> Bruce
 On Tue, 15 Mar 2016, Champe Barton wrote:
 
 I created them as instructed in the tutorial and called the file 
 “control.dat” so there’s a control.dat file in my subjects directory. 
 Should I have named it tmp/control.dat? Also, would resolving the control 
 points issue also resolve the deleted voxels issue? Cause my it’s not 
 redrawing the pial surface either.
 
 Thanks
 Champe
> On Mar 15, 2016, at 1:22 PM, Bruce Fischl  
> wrote:
> 
> p.s. sorry, it should be tmp/control.dat
>> On Tue, 15 Mar 2016, Champe Barton wrote:
>> 
>> Hey Bruce,
>> 
>> I recently sent you a log file to look at to determine why reprocessing 
>> data wasn’t making any changes in freeview. Have you had a chance to go 
>> over it yet? Let me know.
>> 
>> Thanks,
>> Champe
>>> On Mar 7, 2016, at 11:41 AM, Bruce Fischl  
>>> wrote:
>>> 
>>> I got it, thanks
>>> Bruce
 On Mon, 7 Mar 2016, Champe Barton wrote:
 
 
 Hey Bruce,
 
 I got a notification saying the email my recon-all.log file attachment 
 was too large and had to await moderator approval to be posted to the 
 support list. I was just wondering if you received it or if I should 
 resend it.
 
 Best,
 Champe
 
 Sent from my iPhone
 
> On Mar 6, 2016, at 9:53 AM, Bruce Fischl  
> wrote:
> 
> Hi Champe
> 
> can you send us the recon-all.log file?
> 
> cheers
> Bruce
>> On Sun, 6 Mar 2016, Champe Barton wrote:
>> 
>> Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X El 
>> Capitan version 10.11.2 and I have System Integrity Protection 
>> disabled (though I hadn’t experienced any issues that could have 
>> been a result of that function). Everything in FreeSurfer works fine 
>> for me—I ran recon-all and successfully processed dicom files, I 
>> successfully viewed the T1.mgz and brainmask.mgz volumes and the 
>> pial and white surfaces, and I successfully deleted unnecessary 
>> voxels and added a set of control points (in both cases, being 
>> careful to make and save the changes on all necessary slices with 
>> the brainmask volume highlighted). My only issue is that when I 
>> reprocess the data using recon-all -autorecon2-cp -autorecon3 
>> -subjid , it runs through the reconstruction without 
>> error and then shows no changes at all in freeview when I view the 
>> volumes/surfaces. The deleted voxels still appear deleted and I can 
>> still load the control points, so why wouldn’t it make the changes? 
>> And just to provide a little extra info: I encounter the same 
>> problem when I reprocess the tutorial data for the pial edits 
>> tutorial. I delete the voxels as instructed, save the file, 
>> reprocess it without error, and then nothing’s changed when I view 
>> it all again in freeview. Any help would be HUGELY appreciated—I’ve 
>> stressed over this for weeks trying to get my computer to function 
>> properly so that I can begin my work as a research assistant in a 
>> neuropsych lab 

Re: [Freesurfer] error while running dt-recon all

[Douglas N Greve]

Can you send the full terminal output from when you run dt_recon with 
the nifti as input?

On 03/15/2016 03:07 PM, Jasmin Alves wrote:
> How was DTI.nii.gz created? DTI.nii.gz was converted from the raw 
> dicom data using dcm2nii.
>
> Response for: "What happens if you run mri_info DTI.nii.gz"
>
> Volume information for DTI.nii.gz
>
>   type: nii
>
> dimensions: 128 x 128 x 70 x 65
>
>voxel sizes: 2., 2., 2.
>
>   type: FLOAT (3)
>
>fov: 256.000
>
>dof: 0
>
> xstart: -128.0, xend: 128.0
>
> ystart: -128.0, yend: 128.0
>
> zstart: -70.0, zend: 70.0
>
> TR: 8100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip 
> angle: 0.00 degrees
>
>nframes: 65
>
>PhEncDir: UNKNOWN
>
> ras xform present
>
> xform info: x_r =  -0., y_r =   0.0116, z_r =  -0.0028, c_r =  
>   -0.4290
>
>   : x_a =   0.0116, y_a =   0., z_a =  -0.0011, c_a = 
> 4.1548
>
>   : x_s =  -0.0028, y_s =   0.0011, z_s =   1., c_s =  
>   30.9622
>
> Orientation   : LAS
>
> Primary Slice Direction: axial
>
> voxel to ras transform:
>
>-1.   0.0232 -0.0057   126.2761
>
> 0.0232   1. -0.0021  -125.2474
>
>-0.0057   0.0022 2.   -38.8153
>
> 0.   0. 0. 1.
>
> voxel-to-ras determinant -8
>
> ras to voxel transform:
>
>-0.5000   0.0058 -0.001463.8052
>
> 0.0058   0.5000 0.000561.9083
>
>-0.0014  -0.0005 0.500019.5206
>
> 0.   0. 0. 1.
>
>
> On Tue, Mar 15, 2016 at 11:25 AM, Douglas N Greve 
> > wrote:
>
>
> How was DTI.nii.gz created? What happens if you run
> mri_info DTI.nii.gz
>
> If the DICOM is a siemens dicom but has been stripped of special
> siemens
> info, then we cannot unpack it
>
>
> On 03/15/2016 02:02 PM, Jasmin Alves wrote:
> >
> > Still get the same error:
> >
> > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
> > contain a Siemens ASCII header
> >
> > has this file been anonymized?
> >
> > ERROR: cannot unpack mosiacs without ASCII header
> >
> >
> > The error I get when running in nifti format is actually found
> in the
> > log file.
> >
> >  ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is not a dicom
> > file or some other problem
> >
> >
> >
> >
> > On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve
> > 
>  >> wrote:
> >
> > if you run
> > mri_convert 00010001 deleteme.nii
> > what happens?
> >
> > what is the error when running with nifti?
> >
> >
> > On 03/14/2016 05:59 PM, Jasmin Alves wrote:
> > >
> > > Dear Freesurfer experts,
> > >
> > > FREESURFER_HOME: /Applications/freesurfer
> > >
> > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> > >
> > > Kernel info: Darwin 14.5.0 x86_64
> > >
> > >
> > > I received the following error while running the dt_recon --i
> > 00010001
> > > --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40.
> > >
> > > The participant is 40.
> > >
> > > And I received the following error:
> > >
> > > WARNING: file /Users/jasminalves/Desktop/data/40/00010001
> does not
> > > contain a Siemens ASCII header has this file been anonymized?
> > >
> > > ERROR: cannot unpack mosiacs without ASCII header
> > >
> > >
> > > I did notice on previous threads this is a common error
> that occurs,
> > > but the files I have were directly exported from our
> siemens scanner
> > > via Osirix. I also tried running dt_recon using nifti
> format but
> > that
> > > resulted in an error as well. Is there anything else I can do?
> > >
> > > Thanks,
> > >
> > > Jasmin
> > >
> > >
> > > --
> > > Jasmin Alves
> > > Predoctoral Student
> > > Medical Biology Graduate Program
> > > University of Southern California
> > > jal...@usc.edu 
> >
> 
> > >>
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> 
>

Re: [Freesurfer] error while running dt-recon all

[Jasmin Alves]

 How was DTI.nii.gz created? DTI.nii.gz was converted from the raw dicom
data using dcm2nii.

Response for: "What happens if you run mri_info DTI.nii.gz"

Volume information for DTI.nii.gz

  type: nii

dimensions: 128 x 128 x 70 x 65

   voxel sizes: 2., 2., 2.

  type: FLOAT (3)

   fov: 256.000

   dof: 0

xstart: -128.0, xend: 128.0

ystart: -128.0, yend: 128.0

zstart: -70.0, zend: 70.0

TR: 8100.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
0.00 degrees

   nframes: 65

   PhEncDir: UNKNOWN

ras xform present

xform info: x_r =  -0., y_r =   0.0116, z_r =  -0.0028, c_r =
-0.4290

  : x_a =   0.0116, y_a =   0., z_a =  -0.0011, c_a =
4.1548

  : x_s =  -0.0028, y_s =   0.0011, z_s =   1., c_s =
30.9622

Orientation   : LAS

Primary Slice Direction: axial

voxel to ras transform:

   -1.   0.0232  -0.0057   126.2761

0.0232   1.  -0.0021  -125.2474

   -0.0057   0.0022   2.   -38.8153

0.   0.   0. 1.

voxel-to-ras determinant -8

ras to voxel transform:

   -0.5000   0.0058  -0.001463.8052

0.0058   0.5000   0.000561.9083

   -0.0014  -0.0005   0.500019.5206

0.   0.   0. 1.

On Tue, Mar 15, 2016 at 11:25 AM, Douglas N Greve  wrote:

>
> How was DTI.nii.gz created? What happens if you run
> mri_info DTI.nii.gz
>
> If the DICOM is a siemens dicom but has been stripped of special siemens
> info, then we cannot unpack it
>
>
> On 03/15/2016 02:02 PM, Jasmin Alves wrote:
> >
> > Still get the same error:
> >
> > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
> > contain a Siemens ASCII header
> >
> > has this file been anonymized?
> >
> > ERROR: cannot unpack mosiacs without ASCII header
> >
> >
> > The error I get when running in nifti format is actually found in the
> > log file.
> >
> >  ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is not a dicom
> > file or some other problem
> >
> >
> >
> >
> > On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve
> > > wrote:
> >
> > if you run
> > mri_convert 00010001 deleteme.nii
> > what happens?
> >
> > what is the error when running with nifti?
> >
> >
> > On 03/14/2016 05:59 PM, Jasmin Alves wrote:
> > >
> > > Dear Freesurfer experts,
> > >
> > > FREESURFER_HOME: /Applications/freesurfer
> > >
> > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> > >
> > > Kernel info: Darwin 14.5.0 x86_64
> > >
> > >
> > > I received the following error while running the dt_recon --i
> > 00010001
> > > --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40.
> > >
> > > The participant is 40.
> > >
> > > And I received the following error:
> > >
> > > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
> > > contain a Siemens ASCII header has this file been anonymized?
> > >
> > > ERROR: cannot unpack mosiacs without ASCII header
> > >
> > >
> > > I did notice on previous threads this is a common error that
> occurs,
> > > but the files I have were directly exported from our siemens
> scanner
> > > via Osirix. I also tried running dt_recon using nifti format but
> > that
> > > resulted in an error as well. Is there anything else I can do?
> > >
> > > Thanks,
> > >
> > > Jasmin
> > >
> > >
> > > --
> > > Jasmin Alves
> > > Predoctoral Student
> > > Medical Biology Graduate Program
> > > University of Southern California
> > > jal...@usc.edu   > >
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=CwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs=369GPCb6aThxDDKHEPitpYUvNATIrFBISf_vC_ldmDs=
> >
> > --
> > 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
> > <
> https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting=CwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=Dg3E3_3nDK398YRIg5fpyFNMc_O6RObwIezN3fq92AQ=GpEEtkD1BnMJzWOlXkecPjAGlZyRbfpUD2D7FRdXC7o=
> >
> > 

Re: [Freesurfer] Recon Reprocessing Issues

[Bruce Fischl]

why are you deleting voxels from the brainmask.mgz? That is only used for 
masking out non-brain tissue. Is that what you are trying to do?


On Tue, 15 Mar 2016, Champe Barton wrote:


I used the recon editing tool—I explicitly followed the instructions from the 
tutorial (even on reprocessing the tutorial data it didn't work), so I had the 
brainmask.mgz highlighted, checked the recon editing box and held shift and 
clicked to remove the necessary voxels (they turned black). I removed them on 
all the necessary slices as well.

Champe

Sent from my iPhone


On Mar 15, 2016, at 1:43 PM, Bruce Fischl  wrote:

Hi Champe

it must be in the tmp subdirectory (that is /tmp/control.dat) 
otherwise we will not find it.

As for the deleted voxel issue - how did you delete them?

Bruce

On Tue, 15 Mar 2016, Champe Barton wrote:

I created them as instructed in the tutorial and called the file “control.dat” 
so there’s a control.dat file in my subjects directory. Should I have named it 
tmp/control.dat? Also, would resolving the control points issue also resolve 
the deleted voxels issue? Cause my it’s not redrawing the pial surface either.

Thanks
Champe

On Mar 15, 2016, at 1:22 PM, Bruce Fischl  wrote:

p.s. sorry, it should be tmp/control.dat

On Tue, 15 Mar 2016, Champe Barton wrote:

Hey Bruce,

I recently sent you a log file to look at to determine why reprocessing data 
wasn’t making any changes in freeview. Have you had a chance to go over it yet? 
Let me know.

Thanks,
Champe

On Mar 7, 2016, at 11:41 AM, Bruce Fischl  wrote:

I got it, thanks
Bruce

On Mon, 7 Mar 2016, Champe Barton wrote:


Hey Bruce,

I got a notification saying the email my recon-all.log file attachment was too 
large and had to await moderator approval to be posted to the support list. I 
was just wondering if you received it or if I should resend it.

Best,
Champe

Sent from my iPhone


On Mar 6, 2016, at 9:53 AM, Bruce Fischl  wrote:

Hi Champe

can you send us the recon-all.log file?

cheers
Bruce

On Sun, 6 Mar 2016, Champe Barton wrote:

Hi Freesurfer People, I’m working on a 2015 Macbook Pro with OS X 
El Capitan version 10.11.2 and I have System Integrity Protection 
disabled (though I hadn’t experienced any issues that could have 
been a result of that function). Everything in FreeSurfer works 
fine for me—I ran recon-all and successfully processed dicom 
files, I successfully viewed the T1.mgz and brainmask.mgz volumes 
and the pial and white surfaces, and I successfully deleted 
unnecessary voxels and added a set of control points (in both 
cases, being careful to make and save the changes on all 
necessary slices with the brainmask volume highlighted). My only 
issue is that when I reprocess the data using recon-all 
-autorecon2-cp -autorecon3 -subjid , it runs 
through the reconstruction without error and then shows no 
changes at all in freeview when I view the volumes/surfaces. The 
deleted voxels still appear deleted and I can still load the 
control points, so why wouldn’t it make the changes? And just to 
provide a little extra info: I encounter the same problem when I 
reprocess the tutorial data for the pial edits tutorial. I delete 
the voxels as instructed, save the file, reprocess it without 
error, and then nothing’s changed when I view it all again in 
freeview. Any help would be HUGELY appreciated—I’ve stressed over 
this for weeks trying to get my computer to function properly so 
that I can begin my work as a research assistant in a neuropsych 
lab editing and analyzing brain scans with FreeSurfer. Thanks, 
Champe

___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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



___
Freesurfer mailing list
Freesurfer@nmr.mgh.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
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 

Re: [Freesurfer] Recon Reprocessing Issues

[Champe Barton]

I used the recon editing tool—I explicitly followed the instructions from the 
tutorial (even on reprocessing the tutorial data it didn't work), so I had the 
brainmask.mgz highlighted, checked the recon editing box and held shift and 
clicked to remove the necessary voxels (they turned black). I removed them on 
all the necessary slices as well.

Champe 

Sent from my iPhone

> On Mar 15, 2016, at 1:43 PM, Bruce Fischl  wrote:
> 
> Hi Champe
> 
> it must be in the tmp subdirectory (that is /tmp/control.dat) 
> otherwise we will not find it.
> 
> As for the deleted voxel issue - how did you delete them?
> 
> Bruce
>> On Tue, 15 Mar 2016, Champe Barton wrote:
>> 
>> I created them as instructed in the tutorial and called the file 
>> “control.dat” so there’s a control.dat file in my subjects directory. Should 
>> I have named it tmp/control.dat? Also, would resolving the control points 
>> issue also resolve the deleted voxels issue? Cause my it’s not redrawing the 
>> pial surface either.
>> 
>> Thanks
>> Champe
>>> On Mar 15, 2016, at 1:22 PM, Bruce Fischl  
>>> wrote:
>>> 
>>> p.s. sorry, it should be tmp/control.dat
 On Tue, 15 Mar 2016, Champe Barton wrote:
 
 Hey Bruce,
 
 I recently sent you a log file to look at to determine why reprocessing 
 data wasn’t making any changes in freeview. Have you had a chance to go 
 over it yet? Let me know.
 
 Thanks,
 Champe
> On Mar 7, 2016, at 11:41 AM, Bruce Fischl  
> wrote:
> 
> I got it, thanks
> Bruce
>> On Mon, 7 Mar 2016, Champe Barton wrote:
>> 
>> 
>> Hey Bruce,
>> 
>> I got a notification saying the email my recon-all.log file attachment 
>> was too large and had to await moderator approval to be posted to the 
>> support list. I was just wondering if you received it or if I should 
>> resend it.
>> 
>> Best,
>> Champe
>> 
>> Sent from my iPhone
>> 
>>> On Mar 6, 2016, at 9:53 AM, Bruce Fischl  
>>> wrote:
>>> 
>>> Hi Champe
>>> 
>>> can you send us the recon-all.log file?
>>> 
>>> cheers
>>> Bruce
 On Sun, 6 Mar 2016, Champe Barton wrote:
 
 Hi Freesurfer People,
 I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 
 and I
 have System Integrity Protection disabled (though I hadn’t experienced 
 any
 issues that could have been a result of that function). Everything in
 FreeSurfer works fine for me—I ran recon-all and successfully processed
 dicom files, I successfully viewed the T1.mgz and brainmask.mgz 
 volumes and
 the pial and white surfaces, and I successfully deleted unnecessary 
 voxels
 and added a set of control points (in both cases, being careful to 
 make and
 save the changes on all necessary slices with the brainmask volume
 highlighted). My only issue is that when I reprocess the data using
 recon-all -autorecon2-cp -autorecon3 -subjid , it runs
 through the reconstruction without error and then shows no changes at 
 all in
 freeview when I view the volumes/surfaces. The deleted voxels still 
 appear
 deleted and I can still load the control points, so why wouldn’t it 
 make the
 changes?
 And just to provide a little extra info: I encounter the same problem 
 when I
 reprocess the tutorial data for the pial edits tutorial. I delete the 
 voxels
 as instructed, save the file, reprocess it without error, and then 
 nothing’s
 changed when I view it all again in freeview.
 Any help would be HUGELY appreciated—I’ve stressed over this for weeks
 trying to get my computer to function properly so that I can begin my 
 work
 as a research assistant in a neuropsych lab editing and analyzing brain
 scans with FreeSurfer.
 Thanks,
 Champe
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
>>> The information in this e-mail is intended only for the person to whom 
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you 
>>> in error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>> 
>> ___
>> Freesurfer mailing list
>> 

Re: [Freesurfer] error while running dt-recon all

[Douglas N Greve]

How was DTI.nii.gz created? What happens if you run
mri_info DTI.nii.gz

If the DICOM is a siemens dicom but has been stripped of special siemens 
info, then we cannot unpack it


On 03/15/2016 02:02 PM, Jasmin Alves wrote:
>
> Still get the same error:
>
> WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not 
> contain a Siemens ASCII header
>
> has this file been anonymized?
>
> ERROR: cannot unpack mosiacs without ASCII header
>
>
> The error I get when running in nifti format is actually found in the 
> log file.
>
>  ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is not a dicom 
> file or some other problem
>
>
>
>
> On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve 
> > wrote:
>
> if you run
> mri_convert 00010001 deleteme.nii
> what happens?
>
> what is the error when running with nifti?
>
>
> On 03/14/2016 05:59 PM, Jasmin Alves wrote:
> >
> > Dear Freesurfer experts,
> >
> > FREESURFER_HOME: /Applications/freesurfer
> >
> > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> >
> > Kernel info: Darwin 14.5.0 x86_64
> >
> >
> > I received the following error while running the dt_recon --i
> 00010001
> > --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40.
> >
> > The participant is 40.
> >
> > And I received the following error:
> >
> > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
> > contain a Siemens ASCII header has this file been anonymized?
> >
> > ERROR: cannot unpack mosiacs without ASCII header
> >
> >
> > I did notice on previous threads this is a common error that occurs,
> > but the files I have were directly exported from our siemens scanner
> > via Osirix. I also tried running dt_recon using nifti format but
> that
> > resulted in an error as well. Is there anything else I can do?
> >
> > Thanks,
> >
> > Jasmin
> >
> >
> > --
> > Jasmin Alves
> > Predoctoral Student
> > Medical Biology Graduate Program
> > University of Southern California
> > jal...@usc.edu   >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> >
> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=CwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs=369GPCb6aThxDDKHEPitpYUvNATIrFBISf_vC_ldmDs=
>
> --
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2=CwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs=K5-xLMTkmvO4akwQ1yNQhCyFkQ3yeGkg4bIrAd6xArI=
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> 
> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_=CwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs=XP0Fok4OAHAC7DYzCOyUrPu9PLDR_RULGfbnE8c0hNs=
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=CwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs=369GPCb6aThxDDKHEPitpYUvNATIrFBISf_vC_ldmDs=
>
>
> 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
> 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline=CwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs=kr8DioqB8ZA30rJ-OJWi601znNchJg-CCjnpQKvHYhI=
> . 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.
>
>
>
>
> -- 
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate 

Re: [Freesurfer] group analysis all measures same results

[Kaiming Yin]

Dear Douglas,

Does it also affect the individual data analysis or the volumetric group
analysis, e.g. the files in the stats/ folder? So could I use the results
of these surface group analyses after running the "-qcache" on V5.3 then?

Thanks,
Kaiming


On 15 March 2016 at 18:00, Douglas N Greve 
wrote:

>
> this only has to do with the qcache part of recon-all, so you could use
> version 5.3 recon-all -qcache and it should be fine. However, it is not a
> good idea to try to publish using the analysis from the version of FS that
> you used. That was a beta version of version 6 and things will change.
>
>
> On 03/15/2016 01:56 PM, Kaiming Yin wrote:
>
>> Dear Douglas,
>>
>> Is there anything I can do now to fix this now? I don't want to re-run
>> all the data again.
>>
>> Thanks,
>> Kaiming
>>
>>
>> On 15 March 2016 at 16:53, Douglas N Greve > > wrote:
>>
>>
>> OK, this is a bug that I found and fixed in early Nov. Sorry,
>> that's part of the danger of using a beta version.
>>
>> On 03/14/2016 12:22 PM, Kaiming Yin wrote:
>>
>> Dear Douglas,
>>
>> I re-run the "-qcache" on one data and it took 8 mins to
>> finish. Still the files are the same, all in 668.6kB size.
>>
>>
>> Kaiming
>>
>> On 14 March 2016 at 15:56, Douglas Greve
>> 
>> > >> wrote:
>>
>> I don't know what happened. I cannot replicate it here.
>> Can you
>> re-run the recon-all -s -qcache command and verify that
>> the files
>> are still the same?
>>
>>
>> On 3/14/16 11:11 AM, Kaiming Yin wrote:
>>
>> Dear Douglas,
>>
>> Yes, both of the two pairs of files are the same. i.e.
>>
>> mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh
>>
>> diffcount 0
>>
>>
>> mri_diff rh.thickness.fwhm10.fsaverage.mgh
>> rh.area.fwhm10.fsaverage.mgh
>>
>> diffcount 0
>>
>>
>> Does this mean I run the "-qcache" wrongly? I just run
>> "recon-all
>> -s XX -qcache" on each subject.
>>
>> Thanks,
>> Kaiming
>>
>>
>> On 14 March 2016 at 14:58, Douglas Greve
>> > 
>> >
>> >> wrote:
>>
>> Check whether rh.ad_hv.thick.10.mgh and
>> rh.ad_hv.area.10.mgh
>> are the same, ie,
>> mri_diff  rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh
>>
>> If those are the same, then check whether
>> thickness.fwhm10.fsaverage and
>> area.fwhm10.fsaverage  are the
>> same in each subject
>>
>>
>> On 3/14/16 10:53 AM, Kaiming Yin wrote:
>>
>> Dear Douglas,
>>
>> My command lines were, e.g. right thickness
>> and right white
>> surface (using the same ad_hv.fsgd and
>> group_diff.mtx files
>> in the command lines):
>>
>>
>> ad_hv.fsgd
>>
>> GroupDescriptorFile 1
>> Title AD_HV_GroupAnalysis
>> Class AD
>> Class HV
>> InputAD_003AD
>> InputAD_005AD
>> ...
>> InputHV_ABHV
>> InputHV_AEHV
>>
>>
>> group_diff.mtx
>>
>> 1 -1
>>
>>
>> right thickness
>>
>> mris_preproc --fsgd ad_hv.fsgd --cache-in
>> thickness.fwhm10.fsaverage --target fsaverage
>> --hemi rh
>> --out rh.ad_hv.thick.10.mgh
>>
>> mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd
>> ad_hv.fsgd dods
>> --C group_diff.mtx --surf fsaverage rh
>> --cortex --glmdir
>> rh.ad_hv.thick.glmdir
>>
>> mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir
>> --cache 4 neg
>> --cwp 0.05 --2spaces
>>
>>
>> right white surface
>>
>> mris_preproc --fsgd ad_hv.fsgd --cache-in
>> area.fwhm10.fsaverage --target fsaverage
>> --hemi rh --out
>> rh.ad_hv.area.10.mgh
>>
>>   

Re: [Freesurfer] error while running dt-recon all

[Jasmin Alves]

Still get the same error:

WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not contain
a Siemens ASCII header

has this file been anonymized?

ERROR: cannot unpack mosiacs without ASCII header


The error I get when running in nifti format is actually found in the log
file.

 ERROR: /Users/jasminalves/Desktop/data/40/DTI.nii.gz is not a dicom file
or some other problem




On Tue, Mar 15, 2016 at 9:01 AM, Douglas N Greve 
wrote:

> if you run
> mri_convert 00010001 deleteme.nii
> what happens?
>
> what is the error when running with nifti?
>
>
> On 03/14/2016 05:59 PM, Jasmin Alves wrote:
> >
> > Dear Freesurfer experts,
> >
> > FREESURFER_HOME: /Applications/freesurfer
> >
> > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> >
> > Kernel info: Darwin 14.5.0 x86_64
> >
> >
> > I received the following error while running the dt_recon --i 00010001
> > --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40.
> >
> > The participant is 40.
> >
> > And I received the following error:
> >
> > WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not
> > contain a Siemens ASCII header has this file been anonymized?
> >
> > ERROR: cannot unpack mosiacs without ASCII header
> >
> >
> > I did notice on previous threads this is a common error that occurs,
> > but the files I have were directly exported from our siemens scanner
> > via Osirix. I also tried running dt_recon using nifti format but that
> > resulted in an error as well. Is there anything else I can do?
> >
> > Thanks,
> >
> > Jasmin
> >
> >
> > --
> > Jasmin Alves
> > Predoctoral Student
> > Medical Biology Graduate Program
> > University of Southern California
> > jal...@usc.edu 
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=CwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs=369GPCb6aThxDDKHEPitpYUvNATIrFBISf_vC_ldmDs=
>
> --
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2=CwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs=K5-xLMTkmvO4akwQ1yNQhCyFkQ3yeGkg4bIrAd6xArI=
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing:
> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_transfer_outgoing_flat_greve_=CwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs=XP0Fok4OAHAC7DYzCOyUrPu9PLDR_RULGfbnE8c0hNs=
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=CwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs=369GPCb6aThxDDKHEPitpYUvNATIrFBISf_vC_ldmDs=
>
>
> 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
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline=CwIBAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=v9tFPBwUhooWQdua1MFl4G-WkZdqs5b-a3SFZRYSRDs=kr8DioqB8ZA30rJ-OJWi601znNchJg-CCjnpQKvHYhI=
> . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and
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> dispose of the e-mail.
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>


-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
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Re: [Freesurfer] group analysis all measures same results

[Douglas N Greve]

this only has to do with the qcache part of recon-all, so you could use 
version 5.3 recon-all -qcache and it should be fine. However, it is not 
a good idea to try to publish using the analysis from the version of FS 
that you used. That was a beta version of version 6 and things will change.


On 03/15/2016 01:56 PM, Kaiming Yin wrote:
> Dear Douglas,
>
> Is there anything I can do now to fix this now? I don't want to re-run 
> all the data again.
>
> Thanks,
> Kaiming
>
>
> On 15 March 2016 at 16:53, Douglas N Greve  > wrote:
>
>
> OK, this is a bug that I found and fixed in early Nov. Sorry,
> that's part of the danger of using a beta version.
>
> On 03/14/2016 12:22 PM, Kaiming Yin wrote:
>
> Dear Douglas,
>
> I re-run the "-qcache" on one data and it took 8 mins to
> finish. Still the files are the same, all in 668.6kB size.
>
>
> Kaiming
>
> On 14 March 2016 at 15:56, Douglas Greve
> 
>  >> wrote:
>
> I don't know what happened. I cannot replicate it here.
> Can you
> re-run the recon-all -s -qcache command and verify that
> the files
> are still the same?
>
>
> On 3/14/16 11:11 AM, Kaiming Yin wrote:
>
> Dear Douglas,
>
> Yes, both of the two pairs of files are the same. i.e.
>
> mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh
>
> diffcount 0
>
>
> mri_diff rh.thickness.fwhm10.fsaverage.mgh
> rh.area.fwhm10.fsaverage.mgh
>
> diffcount 0
>
>
> Does this mean I run the "-qcache" wrongly? I just run
> "recon-all
> -s XX -qcache" on each subject.
>
> Thanks,
> Kaiming
>
>
> On 14 March 2016 at 14:58, Douglas Greve
>  
>  >> wrote:
>
> Check whether rh.ad_hv.thick.10.mgh and
> rh.ad_hv.area.10.mgh
> are the same, ie,
> mri_diff  rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh
>
> If those are the same, then check whether
> thickness.fwhm10.fsaverage and
> area.fwhm10.fsaverage  are the
> same in each subject
>
>
> On 3/14/16 10:53 AM, Kaiming Yin wrote:
>
> Dear Douglas,
>
> My command lines were, e.g. right thickness
> and right white
> surface (using the same ad_hv.fsgd and
> group_diff.mtx files
> in the command lines):
>
>
> ad_hv.fsgd
>
> GroupDescriptorFile 1
> Title AD_HV_GroupAnalysis
> Class AD
> Class HV
> InputAD_003AD
> InputAD_005AD
> ...
> InputHV_ABHV
> InputHV_AEHV
>
>
> group_diff.mtx
>
> 1 -1
>
>
> right thickness
>
> mris_preproc --fsgd ad_hv.fsgd --cache-in
> thickness.fwhm10.fsaverage --target fsaverage
> --hemi rh
> --out rh.ad_hv.thick.10.mgh
>
> mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd
> ad_hv.fsgd dods
> --C group_diff.mtx --surf fsaverage rh
> --cortex --glmdir
> rh.ad_hv.thick.glmdir
>
> mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir
> --cache 4 neg
> --cwp 0.05 --2spaces
>
>
> right white surface
>
> mris_preproc --fsgd ad_hv.fsgd --cache-in
> area.fwhm10.fsaverage --target fsaverage
> --hemi rh --out
> rh.ad_hv.area.10.mgh
>
> mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd
> ad_hv.fsgd dods
> --C group_diff.mtx --surf fsaverage rh
> --cortex --glmdir
> rh.ad_hv.area.glmdir
>
> mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir
> --cache 4 neg
> --cwp 0.05 --2spaces
>
>
> Their results were all the same.
>
> 

Re: [Freesurfer] Upgrading to OS X EL Capitan

[Z K]

That would be fine. The idea is to simply process (recon) all your 
subjetcs under the same OS version. Once that is complete, viewing the 
data, and post processing statistical analysis is perfectly fine on an 
upgraded/updated system.

-Zeke


On 03/15/2016 01:47 PM, Elissa Ash wrote:
> What if all of the data have already been processed (recon -all) and I
> am now just looking at the data and doing statistical analyses (QDEC,
> ROI generation, etc)?
>
> Thanks
>
> On Tue, Mar 15, 2016 at 10:24 AM, Z K  > wrote:
>
> v5.3 is compatible with El Capitan. In general, we dissuade people from
> performing group studies or performing comparisons on subjects processed
> under different version operating system. In reality the difference
> would be quite small (if it exists at all), but it is still highly
> discouraged.
>
> -Zeke
>
> On 03/15/2016 12:53 PM, Elissa Ash wrote:
>  > Dear Freesurfer experts,
>  >
>  > I have been working with freesurfer V5.3 on the Mac OS 10.8.5. My
>  > institution is requesting that I upgrade the OS on my computer to
> OS X
>  > El Capitan (10.11). Will this change my ability to look at or process
>  > freesurfer data? Will the recons that I have done be compatible?
> If I do
>  > more recons then can I still compare the data to those done on OS X
>  > 10.8.5? Is it recommended that I upgrade to OS or should I not do it?
>  >
>  > Thank you kindly for your help,
>  >
>  > Elissa
>  >
>  > --
>  > Elissa Ash, MD, PhD
>  > Director, Center for Memory and Attention Disorders
>  > Department of Neurology
>  > Tel Aviv Sourasky Medical Center
>  >
>  > 6 Weizmann St.
>  > Tel Aviv 64239, Israel
>  > 972-3-6973698
>  > fax: 972-3-695-0365
>  >
>  >
>  > ___
>  > Freesurfer mailing list
>  > Freesurfer@nmr.mgh.harvard.edu
> 
>  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>  >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>
>
>
>
> --
> Elissa Ash, MD, PhD
> Director, Center for Memory and Attention Disorders
> Department of Neurology
> Tel Aviv Sourasky Medical Center
>
> 6 Weizmann St.
> Tel Aviv 64239, Israel
> 972-3-6973698
> fax: 972-3-695-0365
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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[Freesurfer] Cortical thickness analysis -- Qdec

[Alshikho, Mohamad J.]

Hi Doug,
I have two groups of subjects and I want to study the difference in cortical 
thickness between the groups. I used Qdec to run the analysis and I got 
significant difference between the groups in areas support what I am looking 
for.
I repeated the analysis as mentioned in Wiki 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis


1.   My data is previously cached so I ran the command : mris_preproc 
--fsgd gender_age.fsgd  --cache-in thickness.fwhm10.fsaverage  --target 
fsaverage --hemi lh  --out lh.gender_age.thickness.10.mgh

2.   GLM analysis: mri_glmfit  --y lh.gender_age.thickness.10.mgh  --fsgd 
gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx  --surf fsaverage lh  
--cortex  --glmdir lh.gender_age.glmdir

3.   Correction for multiple comparison  mri_glmfit-sim  --glmdir 
lh.gender_age.glmdir  --cache 4 neg  --cwp  0.05  --2spaces

Surprisingly, the results are totally different from what I get in Qdec.
I checked Qdec's commands generated in Terminal and I noticed that it uses the 
command "mri_surfcluster" instead of " mri_glmfit-sim "

Kindly,

1.   What is the difference between "mri_surfcluster" and " mri_glmfit-sim "

2.   Is it expected that we get different results as an output of the 
previous two different methods

3.   In order to run statistical analysis regarding volumetrics and 
cortical thickness. Which method is more advisable, Qdec or the previous 
command lines (1-3)

Best,
Mohamad

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Re: [Freesurfer] Upgrading to OS X EL Capitan

[Elissa Ash]

Thanks!!

On Tue, Mar 15, 2016 at 10:50 AM, Z K  wrote:

> That would be fine. The idea is to simply process (recon) all your
> subjetcs under the same OS version. Once that is complete, viewing the
> data, and post processing statistical analysis is perfectly fine on an
> upgraded/updated system.
>
> -Zeke
>
>
> On 03/15/2016 01:47 PM, Elissa Ash wrote:
> > What if all of the data have already been processed (recon -all) and I
> > am now just looking at the data and doing statistical analyses (QDEC,
> > ROI generation, etc)?
> >
> > Thanks
> >
> > On Tue, Mar 15, 2016 at 10:24 AM, Z K  > > wrote:
> >
> > v5.3 is compatible with El Capitan. In general, we dissuade people
> from
> > performing group studies or performing comparisons on subjects
> processed
> > under different version operating system. In reality the difference
> > would be quite small (if it exists at all), but it is still highly
> > discouraged.
> >
> > -Zeke
> >
> > On 03/15/2016 12:53 PM, Elissa Ash wrote:
> >  > Dear Freesurfer experts,
> >  >
> >  > I have been working with freesurfer V5.3 on the Mac OS 10.8.5. My
> >  > institution is requesting that I upgrade the OS on my computer to
> > OS X
> >  > El Capitan (10.11). Will this change my ability to look at or
> process
> >  > freesurfer data? Will the recons that I have done be compatible?
> > If I do
> >  > more recons then can I still compare the data to those done on OS
> X
> >  > 10.8.5? Is it recommended that I upgrade to OS or should I not do
> it?
> >  >
> >  > Thank you kindly for your help,
> >  >
> >  > Elissa
> >  >
> >  > --
> >  > Elissa Ash, MD, PhD
> >  > Director, Center for Memory and Attention Disorders
> >  > Department of Neurology
> >  > Tel Aviv Sourasky Medical Center
> >  >
> >  > 6 Weizmann St.
> >  > Tel Aviv 64239, Israel
> >  > 972-3-6973698
> >  > fax: 972-3-695-0365
> >  >
> >  >
> >  > ___
> >  > Freesurfer mailing list
> >  > Freesurfer@nmr.mgh.harvard.edu
> > 
> >  > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >  >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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.
> >
> >
> >
> >
> > --
> > Elissa Ash, MD, PhD
> > Director, Center for Memory and Attention Disorders
> > Department of Neurology
> > Tel Aviv Sourasky Medical Center
> >
> > 6 Weizmann St.
> > Tel Aviv 64239, Israel
> > 972-3-6973698
> > fax: 972-3-695-0365
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>



-- 
Elissa Ash, MD, PhD
Director, Center for Memory and Attention Disorders
Department of Neurology
Tel Aviv Sourasky Medical Center

6 Weizmann St.
Tel Aviv 64239, Israel
972-3-6973698
fax: 972-3-695-0365
___
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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.

Re: [Freesurfer] Upgrading to OS X EL Capitan

[Elissa Ash]

What if all of the data have already been processed (recon -all) and I am
now just looking at the data and doing statistical analyses (QDEC, ROI
generation, etc)?

Thanks

On Tue, Mar 15, 2016 at 10:24 AM, Z K  wrote:

> v5.3 is compatible with El Capitan. In general, we dissuade people from
> performing group studies or performing comparisons on subjects processed
> under different version operating system. In reality the difference
> would be quite small (if it exists at all), but it is still highly
> discouraged.
>
> -Zeke
>
> On 03/15/2016 12:53 PM, Elissa Ash wrote:
> > Dear Freesurfer experts,
> >
> > I have been working with freesurfer V5.3 on the Mac OS 10.8.5. My
> > institution is requesting that I upgrade the OS on my computer to OS X
> > El Capitan (10.11). Will this change my ability to look at or process
> > freesurfer data? Will the recons that I have done be compatible? If I do
> > more recons then can I still compare the data to those done on OS X
> > 10.8.5? Is it recommended that I upgrade to OS or should I not do it?
> >
> > Thank you kindly for your help,
> >
> > Elissa
> >
> > --
> > Elissa Ash, MD, PhD
> > Director, Center for Memory and Attention Disorders
> > Department of Neurology
> > Tel Aviv Sourasky Medical Center
> >
> > 6 Weizmann St.
> > Tel Aviv 64239, Israel
> > 972-3-6973698
> > fax: 972-3-695-0365
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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>


-- 
Elissa Ash, MD, PhD
Director, Center for Memory and Attention Disorders
Department of Neurology
Tel Aviv Sourasky Medical Center

6 Weizmann St.
Tel Aviv 64239, Israel
972-3-6973698
fax: 972-3-695-0365
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Re: [Freesurfer] Recon Reprocessing Issues

[Bruce Fischl]

Hi Champe

it must be in the tmp subdirectory (that is name>/tmp/control.dat) otherwise we will not find it.


As for the deleted voxel issue - how did you delete them?

Bruce
On Tue, 15 Mar 2016, 
Champe Barton wrote:



I created them as instructed in the tutorial and called the file “control.dat” 
so there’s a control.dat file in my subjects directory. Should I have named it 
tmp/control.dat? Also, would resolving the control points issue also resolve 
the deleted voxels issue? Cause my it’s not redrawing the pial surface either.

Thanks
Champe

On Mar 15, 2016, at 1:22 PM, Bruce Fischl  wrote:

p.s. sorry, it should be tmp/control.dat
On Tue, 15 Mar 2016, Champe Barton wrote:


Hey Bruce,

I recently sent you a log file to look at to determine why reprocessing data 
wasn’t making any changes in freeview. Have you had a chance to go over it yet? 
Let me know.

Thanks,
Champe

On Mar 7, 2016, at 11:41 AM, Bruce Fischl  wrote:

I got it, thanks
Bruce
On Mon, 7 Mar 2016, Champe Barton wrote:



Hey Bruce,

I got a notification saying the email my recon-all.log file attachment was too 
large and had to await moderator approval to be posted to the support list. I 
was just wondering if you received it or if I should resend it.

Best,
Champe

Sent from my iPhone


On Mar 6, 2016, at 9:53 AM, Bruce Fischl  wrote:

Hi Champe

can you send us the recon-all.log file?

cheers
Bruce

On Sun, 6 Mar 2016, Champe Barton wrote:

Hi Freesurfer People,
I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I
have System Integrity Protection disabled (though I hadn’t experienced any
issues that could have been a result of that function). Everything in
FreeSurfer works fine for me—I ran recon-all and successfully processed
dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and
the pial and white surfaces, and I successfully deleted unnecessary voxels
and added a set of control points (in both cases, being careful to make and
save the changes on all necessary slices with the brainmask volume
highlighted). My only issue is that when I reprocess the data using
recon-all -autorecon2-cp -autorecon3 -subjid , it runs
through the reconstruction without error and then shows no changes at all in
freeview when I view the volumes/surfaces. The deleted voxels still appear
deleted and I can still load the control points, so why wouldn’t it make the
changes?
And just to provide a little extra info: I encounter the same problem when I
reprocess the tutorial data for the pial edits tutorial. I delete the voxels
as instructed, save the file, reprocess it without error, and then nothing’s
changed when I view it all again in freeview.
Any help would be HUGELY appreciated—I’ve stressed over this for weeks
trying to get my computer to function properly so that I can begin my work
as a research assistant in a neuropsych lab editing and analyzing brain
scans with FreeSurfer.
Thanks,
Champe

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Re: [Freesurfer] Recon Reprocessing Issues

[Champe Barton]

I created them as instructed in the tutorial and called the file “control.dat” 
so there’s a control.dat file in my subjects directory. Should I have named it 
tmp/control.dat? Also, would resolving the control points issue also resolve 
the deleted voxels issue? Cause my it’s not redrawing the pial surface either.

Thanks 
Champe
> On Mar 15, 2016, at 1:22 PM, Bruce Fischl  wrote:
> 
> p.s. sorry, it should be tmp/control.dat
> On Tue, 15 Mar 2016, Champe Barton wrote:
> 
>> Hey Bruce,
>> 
>> I recently sent you a log file to look at to determine why reprocessing data 
>> wasn’t making any changes in freeview. Have you had a chance to go over it 
>> yet? Let me know.
>> 
>> Thanks,
>> Champe
>>> On Mar 7, 2016, at 11:41 AM, Bruce Fischl  
>>> wrote:
>>> 
>>> I got it, thanks
>>> Bruce
>>> On Mon, 7 Mar 2016, Champe Barton wrote:
>>> 
 
 Hey Bruce,
 
 I got a notification saying the email my recon-all.log file attachment was 
 too large and had to await moderator approval to be posted to the support 
 list. I was just wondering if you received it or if I should resend it.
 
 Best,
 Champe
 
 Sent from my iPhone
 
> On Mar 6, 2016, at 9:53 AM, Bruce Fischl  
> wrote:
> 
> Hi Champe
> 
> can you send us the recon-all.log file?
> 
> cheers
> Bruce
>> On Sun, 6 Mar 2016, Champe Barton wrote:
>> 
>> Hi Freesurfer People,
>> I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 
>> and I
>> have System Integrity Protection disabled (though I hadn’t experienced 
>> any
>> issues that could have been a result of that function). Everything in
>> FreeSurfer works fine for me—I ran recon-all and successfully processed
>> dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes 
>> and
>> the pial and white surfaces, and I successfully deleted unnecessary 
>> voxels
>> and added a set of control points (in both cases, being careful to make 
>> and
>> save the changes on all necessary slices with the brainmask volume
>> highlighted). My only issue is that when I reprocess the data using
>> recon-all -autorecon2-cp -autorecon3 -subjid , it runs
>> through the reconstruction without error and then shows no changes at 
>> all in
>> freeview when I view the volumes/surfaces. The deleted voxels still 
>> appear
>> deleted and I can still load the control points, so why wouldn’t it make 
>> the
>> changes?
>> And just to provide a little extra info: I encounter the same problem 
>> when I
>> reprocess the tutorial data for the pial edits tutorial. I delete the 
>> voxels
>> as instructed, save the file, reprocess it without error, and then 
>> nothing’s
>> changed when I view it all again in freeview.
>> Any help would be HUGELY appreciated—I’ve stressed over this for weeks
>> trying to get my computer to function properly so that I can begin my 
>> work
>> as a research assistant in a neuropsych lab editing and analyzing brain
>> scans with FreeSurfer.
>> Thanks,
>> Champe
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it 
> is
> addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
> contains patient information, please contact the Partners Compliance 
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Upgrading to OS X EL Capitan

[Z K]

v5.3 is compatible with El Capitan. In general, we dissuade people from 
performing group studies or performing comparisons on subjects processed 
under different version operating system. In reality the difference 
would be quite small (if it exists at all), but it is still highly 
discouraged.

-Zeke

On 03/15/2016 12:53 PM, Elissa Ash wrote:
> Dear Freesurfer experts,
>
> I have been working with freesurfer V5.3 on the Mac OS 10.8.5. My
> institution is requesting that I upgrade the OS on my computer to OS X
> El Capitan (10.11). Will this change my ability to look at or process
> freesurfer data? Will the recons that I have done be compatible? If I do
> more recons then can I still compare the data to those done on OS X
> 10.8.5? Is it recommended that I upgrade to OS or should I not do it?
>
> Thank you kindly for your help,
>
> Elissa
>
> --
> Elissa Ash, MD, PhD
> Director, Center for Memory and Attention Disorders
> Department of Neurology
> Tel Aviv Sourasky Medical Center
>
> 6 Weizmann St.
> Tel Aviv 64239, Israel
> 972-3-6973698
> fax: 972-3-695-0365
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Recon Reprocessing Issues

[Bruce Fischl]

Hi Champe

it looks like it is not using the control points. How did you create 
them? They should be stored in a file under in tmp/edit.dat within the 
subject directory. Does that file exist?


cheers
Bruce


On Tue, 15 Mar 2016, Champe Barton 
wrote:



Hey Bruce,

I recently sent you a log file to look at to determine why reprocessing data 
wasn’t making any changes in freeview. Have you had a chance to go over it yet? 
Let me know.

Thanks,
Champe

On Mar 7, 2016, at 11:41 AM, Bruce Fischl  wrote:

I got it, thanks
Bruce
On Mon, 7 Mar 2016, Champe Barton wrote:



Hey Bruce,

I got a notification saying the email my recon-all.log file attachment was too 
large and had to await moderator approval to be posted to the support list. I 
was just wondering if you received it or if I should resend it.

Best,
Champe

Sent from my iPhone


On Mar 6, 2016, at 9:53 AM, Bruce Fischl  wrote:

Hi Champe

can you send us the recon-all.log file?

cheers
Bruce

On Sun, 6 Mar 2016, Champe Barton wrote:

Hi Freesurfer People,
I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I
have System Integrity Protection disabled (though I hadn’t experienced any
issues that could have been a result of that function). Everything in
FreeSurfer works fine for me—I ran recon-all and successfully processed
dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and
the pial and white surfaces, and I successfully deleted unnecessary voxels
and added a set of control points (in both cases, being careful to make and
save the changes on all necessary slices with the brainmask volume
highlighted). My only issue is that when I reprocess the data using
recon-all -autorecon2-cp -autorecon3 -subjid , it runs
through the reconstruction without error and then shows no changes at all in
freeview when I view the volumes/surfaces. The deleted voxels still appear
deleted and I can still load the control points, so why wouldn’t it make the
changes?
And just to provide a little extra info: I encounter the same problem when I
reprocess the tutorial data for the pial edits tutorial. I delete the voxels
as instructed, save the file, reprocess it without error, and then nothing’s
changed when I view it all again in freeview.
Any help would be HUGELY appreciated—I’ve stressed over this for weeks
trying to get my computer to function properly so that I can begin my work
as a research assistant in a neuropsych lab editing and analyzing brain
scans with FreeSurfer.
Thanks,
Champe

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


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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



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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] Recon Reprocessing Issues

[Bruce Fischl]

p.s. sorry, it should be tmp/control.dat
On Tue, 15 Mar 2016, Champe Barton 
wrote:



Hey Bruce,

I recently sent you a log file to look at to determine why reprocessing data 
wasn’t making any changes in freeview. Have you had a chance to go over it yet? 
Let me know.

Thanks,
Champe

On Mar 7, 2016, at 11:41 AM, Bruce Fischl  wrote:

I got it, thanks
Bruce
On Mon, 7 Mar 2016, Champe Barton wrote:



Hey Bruce,

I got a notification saying the email my recon-all.log file attachment was too 
large and had to await moderator approval to be posted to the support list. I 
was just wondering if you received it or if I should resend it.

Best,
Champe

Sent from my iPhone


On Mar 6, 2016, at 9:53 AM, Bruce Fischl  wrote:

Hi Champe

can you send us the recon-all.log file?

cheers
Bruce

On Sun, 6 Mar 2016, Champe Barton wrote:

Hi Freesurfer People,
I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I
have System Integrity Protection disabled (though I hadn’t experienced any
issues that could have been a result of that function). Everything in
FreeSurfer works fine for me—I ran recon-all and successfully processed
dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and
the pial and white surfaces, and I successfully deleted unnecessary voxels
and added a set of control points (in both cases, being careful to make and
save the changes on all necessary slices with the brainmask volume
highlighted). My only issue is that when I reprocess the data using
recon-all -autorecon2-cp -autorecon3 -subjid , it runs
through the reconstruction without error and then shows no changes at all in
freeview when I view the volumes/surfaces. The deleted voxels still appear
deleted and I can still load the control points, so why wouldn’t it make the
changes?
And just to provide a little extra info: I encounter the same problem when I
reprocess the tutorial data for the pial edits tutorial. I delete the voxels
as instructed, save the file, reprocess it without error, and then nothing’s
changed when I view it all again in freeview.
Any help would be HUGELY appreciated—I’ve stressed over this for weeks
trying to get my computer to function properly so that I can begin my work
as a research assistant in a neuropsych lab editing and analyzing brain
scans with FreeSurfer.
Thanks,
Champe

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


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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] adapt Monte Carlo correction for specific sample

[Clara Kühn]

Thanks a lot! I will do that then :)

Cheers, Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 15. März 2016 17:40:08
Betreff: Re: [Freesurfer] adapt Monte Carlo correction for specific sample

You can just store it in a different directory, then use the --cache-dir 
option when running mri_glmfit-sim to specify the new folder, eg, if you 
use --o /path/to/myspace/yoursubject/lh/cortex, then specify 
/path/to/myspace

On 03/15/2016 12:36 PM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I have a question regarding the Monte Carlo correction.
> To create a Monte Carlo correction for my specific sample (4year old kids) 
> the wiki suggests this command:
> mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/lh/cortex 
> --base mc-z --surface yoursubject lh --nreps 1
>
> I have run this command, however I get an error message that I have no rights 
> to write into the $FREESURFER_HOME directory. I work at an institute where 
> that directory is stored on a server to which many people have access but no 
> writing rights (which is definitely a good thing), so getting the rights is 
> not really an option. I was wondering now whether I could just specify a 
> different directory or whether it absolutely has to be the $FREESURFER_HOME 
> directory? If the latter is the case, would you suggest I install a local 
> copy or do you have any other suggestions?
>
> Thanks in advance!
> Clara
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] voxel vs surface based morphometric analysis

[Douglas N Greve]

There are a lot of things you mention (vbm, pet, surface-based, and 
dti). You'll have to explain in more detail what you did.

On 03/14/2016 01:10 PM, John Anderson wrote:
> Hi Doug,
> I ran voxel based analysis in FSL to check the differnce in PET signal 
> between two groups. The results are totally differnt than surface 
> based analysis in Freesurfer.  I this real or I am doing something 
> wrong? I tried to do the same but using FA maps and also I got totally 
> differnt results.
> I have special interest in understanding why these two methods leads 
> to differnt results?!
> I have read this 
> refernce 
> http://cds.ismrm.org/protected/11MProceedings/files/ISMRM2011-8410.pdf 
> and actually I was unable to reach the point that can explain this 
> differnce in th results. I highly appreciate if you clarify that to me.
> Bests,
> John
>
>
> ___
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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
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Re: [Freesurfer] aparc stats volume outputting area instead

[Douglas N Greve]

Can you send the terminal output? Also, what version are you using?

On 03/14/2016 09:56 AM, Clare Loane wrote:
> Hi,
>
> I am trying to pull out the volumes from the aparc stats file but when 
> I input the following (below) it produces a file identical to the area 
> instead:
>
> aparcstats2table --subjects 001 002 003 --hemi rh --meas volume 
> --tablefile aparc_stats_volume_rh.txt
>
> It works fine for thickness and area as well aseg_stats.
>
> I would appreciate any help with this.
>
> Thank you!
>
> Clare
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Difficulty correcting Pial surfaces

[pablo najt]

Dear experts and FS users,I came across the following problem it would be 
useful help if anyone is able to advice.ThanksPablo
I am having issues when trying to remove non cortical tissue (mostly skull). I 
load my images as follow:







freeview -v mri/T1.mgz mri/brainmask.mgz -f surf/lh.white:edgecolor=yellow 
surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow 
surf/rh.pial:edgecolor=r
"invalid drawable" error is displayed.
  Then I have tried to follow the guide in the tutorial 'Correcting 
Pial Surfaces'Selected Recon edit free hand option, selected brain mask.mgz 
hold down the Shift key and left click. This does not change the surface.I am 
wondering if there is a different key shortcut with O SX. Or if there is 
anything else I could try. I also tried older instructions with tkmedik and I 
have the same problem.Any advice will be greatly appreciated.Thanks,
Pablo 

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[Freesurfer] Upgrading to OS X EL Capitan

[Elissa Ash]

Dear Freesurfer experts,

I have been working with freesurfer V5.3 on the Mac OS 10.8.5. My
institution is requesting that I upgrade the OS on my computer to OS X El
Capitan (10.11). Will this change my ability to look at or process
freesurfer data? Will the recons that I have done be compatible? If I do
more recons then can I still compare the data to those done on OS X 10.8.5?
Is it recommended that I upgrade to OS or should I not do it?

Thank you kindly for your help,

Elissa

-- 
Elissa Ash, MD, PhD
Director, Center for Memory and Attention Disorders
Department of Neurology
Tel Aviv Sourasky Medical Center

6 Weizmann St.
Tel Aviv 64239, Israel
972-3-6973698
fax: 972-3-695-0365
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Re: [Freesurfer] FSFAST mkcontrast-sess with spmhrf 2 question

[Douglas N Greve]

The setwdelay is an option for mkcontrast-sess (not mkanalysis-sess)

On 03/13/2016 10:29 PM, Joseph Dien wrote:
> After a long break, back to this…
>
> My goal is still to get the betas for the first and maybe second spm 
> hrf so I can calculate a Calhoun derivative boost measure.
>
> As a first step I ran:
>
> mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh 
> -fwhm 5 -event-related  -paradigm RPA1fix.par -nconditions 12 -spmhrf 
> 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg 
> nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc
>
> to use the SPM HRF with one derivative.
>
> Then:
>
> selxavg3-sess -sf sessidlistALL.dat -analysis RPA.sm05.lh
>
> I got the following error:
>
> ERROR: flac_evconw(): conVinc, Condition01 evrw dim mismatch
> This condition has 2 regressors, but evrm has 1
> Struct contents reference from a non-struct array object.
>
> Error in flac_conmat (line 37)
> if(nthcon > length(flac.con))
>
> Error in flac_customize (line 369)
>   flacnew = flac_conmat(flacnew,nthcon);
>
> Error in fast_selxavg3 (line 65)
> flac0 = flac_customize(flac0);
>
> >> --
> ERROR: fast_selxavg3() failed\n
>
> This ran fine with spmhrf 0
>
> based on your prior response below that:
>
> "This is what happens. If you want to use the derivatives,
> then you need to spec -setwdelay. When you run the command, it will 
> prompt you
> for 3 values to use. If you spec 1 0 0, then it will be the same as the
> default. If you want to test only the first derivative, then 
> you would spec 0 1 0. Note that the 3rd regressor is the 2nd 
> derivative wrt time, not the first derivative wrt the dispersion 
> parameter. You
> cannot get the Calhoun 2004 value using a contrast (it is non-linear).”
>
> I tried:
>
> mkanalysis-sess -fsd bold -analysis RPA.sm05.lh -surface fsaverage lh 
> -fwhm 5 -event-related  -paradigm RPA1fix.par -nconditions 12 -spmhrf 
> 1 -TR 2 -refeventdur .25 -polyfit 2 -per-run -force -nuisreg 
> nuisreg.dat 6 -tpexclude tpexclude.dat -b0dc -setwdelay
>
> but I just got the error:
>
> ERROR: Flag -setwdelay unrecognized.
>
> I also tried using the flag when setting up the contrasts but that 
> didn’t work either.
>
> so not quite sure what I’m doing wrong.  I had understood from your 
> response below that the contrast weights didn’t need to be changed 
> from the spmhrf 0 case but perhaps I misunderstood?
>
> any help would be welcome!
>
> Joe
>
>> On Jul 10, 2013, at 13:58, Douglas N Greve > > wrote:
>>
>>
>> I was just thinking you could load the beta into matlab, make the
>> Calhoun computations on each condition, then compute the contrasts, then
>> write out the new volume
>>
>>
>> On 07/10/2013 01:40 PM, Joseph Dien wrote:
>>> Sounds good!
>>>
>>> Regarding creating a new volume and computing contrasts from it, what
>>> do you mean?  I didn't follow that.
>>>
>>> Thanks!
>>>
>>> Joe
>>>
>>>
>>> On Jul 10, 2013, at 1:33 PM, Douglas N Greve
>>> >> > wrote:
>>>

 On 07/10/2013 01:29 PM, Joseph Dien wrote:
> Sorry, not following what you are suggesting?
>
> I want the second derivative for calculating the Calhoun et al 2004
> derivative boost measure.
> My understanding is that to the extent that the BOLD signal deviates
> from the canonical hrf, the amplitude of the primary regressor will be
> attenuated and the variance will instead end up in the first and
> second derivatives (to the extent that they are able to accommodate
> the divergence).  By using a Calhoun measure that incorporates both
> the first and second derivatives, in principle I'll have a BOLD
> measure that is more robust to deviations from the canonical hrf.
 Sorry, it had been a while since I read that paper. I did not know that
 they had a formulation that included the 2nd derivative.
>
> However, if the way FSFAST is calculating the second derivative
> regressor is resulting in loss of statistical power due to shared
> variance with the primary regressor, then it would be best to just not
> include it at all in the estimation step.
 I don't know how much it will hurt the power. You'd have to look at the
 efficiency.
 doug

>
>
> On Jul 10, 2013, at 1:21 PM, Douglas N Greve
>  
> > wrote:
>
>>
>> Why not just create a new volume and then compute contrasts from
>> the new
>> volume? What you are suggesting will work I think, but it leaves me a
>> little nervous. The p-values will be meaningless.
>>
>>
>> As for the 2nd derivative, I think it must be a numerical issue 
>> (it is
>> not computed analytically). Why 

Re: [Freesurfer] adapt Monte Carlo correction for specific sample

[Douglas N Greve]

You can just store it in a different directory, then use the --cache-dir 
option when running mri_glmfit-sim to specify the new folder, eg, if you 
use --o /path/to/myspace/yoursubject/lh/cortex, then specify 
/path/to/myspace

On 03/15/2016 12:36 PM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I have a question regarding the Monte Carlo correction.
> To create a Monte Carlo correction for my specific sample (4year old kids) 
> the wiki suggests this command:
> mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/lh/cortex 
> --base mc-z --surface yoursubject lh --nreps 1
>
> I have run this command, however I get an error message that I have no rights 
> to write into the $FREESURFER_HOME directory. I work at an institute where 
> that directory is stored on a server to which many people have access but no 
> writing rights (which is definitely a good thing), so getting the rights is 
> not really an option. I was wondering now whether I could just specify a 
> different directory or whether it absolutely has to be the $FREESURFER_HOME 
> directory? If the latter is the case, would you suggest I install a local 
> copy or do you have any other suggestions?
>
> Thanks in advance!
> Clara
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] adapt Monte Carlo correction for specific sample

[Clara Kühn]

Dear FreeSurfer experts,

I have a question regarding the Monte Carlo correction.
To create a Monte Carlo correction for my specific sample (4year old kids) the 
wiki suggests this command:
mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/lh/cortex 
--base mc-z --surface yoursubject lh --nreps 1

I have run this command, however I get an error message that I have no rights 
to write into the $FREESURFER_HOME directory. I work at an institute where that 
directory is stored on a server to which many people have access but no writing 
rights (which is definitely a good thing), so getting the rights is not really 
an option. I was wondering now whether I could just specify a different 
directory or whether it absolutely has to be the $FREESURFER_HOME directory? If 
the latter is the case, would you suggest I install a local copy or do you have 
any other suggestions? 

Thanks in advance!
Clara___
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Re: [Freesurfer] Recon Reprocessing Issues

[Champe Barton]

Hey Bruce, 

I recently sent you a log file to look at to determine why reprocessing data 
wasn’t making any changes in freeview. Have you had a chance to go over it yet? 
Let me know.

Thanks, 
Champe
> On Mar 7, 2016, at 11:41 AM, Bruce Fischl  wrote:
> 
> I got it, thanks
> Bruce
> On Mon, 7 Mar 2016, Champe Barton wrote:
> 
>> 
>> Hey Bruce,
>> 
>> I got a notification saying the email my recon-all.log file attachment was 
>> too large and had to await moderator approval to be posted to the support 
>> list. I was just wondering if you received it or if I should resend it.
>> 
>> Best,
>> Champe
>> 
>> Sent from my iPhone
>> 
>>> On Mar 6, 2016, at 9:53 AM, Bruce Fischl  wrote:
>>> 
>>> Hi Champe
>>> 
>>> can you send us the recon-all.log file?
>>> 
>>> cheers
>>> Bruce
 On Sun, 6 Mar 2016, Champe Barton wrote:
 
 Hi Freesurfer People,
 I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and 
 I
 have System Integrity Protection disabled (though I hadn’t experienced any
 issues that could have been a result of that function). Everything in
 FreeSurfer works fine for me—I ran recon-all and successfully processed
 dicom files, I successfully viewed the T1.mgz and brainmask.mgz volumes and
 the pial and white surfaces, and I successfully deleted unnecessary voxels
 and added a set of control points (in both cases, being careful to make and
 save the changes on all necessary slices with the brainmask volume
 highlighted). My only issue is that when I reprocess the data using
 recon-all -autorecon2-cp -autorecon3 -subjid , it runs
 through the reconstruction without error and then shows no changes at all 
 in
 freeview when I view the volumes/surfaces. The deleted voxels still appear
 deleted and I can still load the control points, so why wouldn’t it make 
 the
 changes?
 And just to provide a little extra info: I encounter the same problem when 
 I
 reprocess the tutorial data for the pial edits tutorial. I delete the 
 voxels
 as instructed, save the file, reprocess it without error, and then 
 nothing’s
 changed when I view it all again in freeview.
 Any help would be HUGELY appreciated—I’ve stressed over this for weeks
 trying to get my computer to function properly so that I can begin my work
 as a research assistant in a neuropsych lab editing and analyzing brain
 scans with FreeSurfer.
 Thanks,
 Champe
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>>> 
>>> 
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>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
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>>> HelpLine 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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> 
> 
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Re: [Freesurfer] Problems with file un qdec analysis

[Douglas N Greve]

you cannot have more than two levels of a factor in qdec. You can use 
the "command line" stream. See the wiki

On 03/14/2016 06:52 AM, Lisa Delalande wrote:
> Hello everyone,
>
> I've got some problems with qdec. I have .levels with more than 2 
> factors. For example a "grpe.levels" with three factors : children 
> (enfant), adults (adultes) and nothing (rien). But if I want to 
> exclude some subjects like children qdec doesn't work anymore 
> (attachment : error message). Is that possible a .levels can not have 
> more than two factors ? Or the problem came from anything else ?
>
> Thanks in advance for your help !
> Best regards,
>
> Lisa
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] error - mri_nu_correct.mni

[Douglas N Greve]

It should all be on one line

  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale 
--i orig.mgz --o orig_nu.mgz



On 03/14/2016 05:43 AM, Flavia Niccolini new wrote:
> Hi Douglas,
>
> I have done this and I got the following message:
>
> “cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
> hwilson@nig05 mri]$   mri_nu_correct.mni --n 1 --proto-iters 1000 
> --distance 50 --no-rescale
> ERROR: must specify an input volume
> hwilson@nig05 mri]$ --i orig.mgz --o orig_nu.mgz “
>
>
> Many Thanks
>
> With Best Wishes
>
> Flavia
>
>
>
>
>> On 7 Mar 2016, at 23:51, Douglas N Greve > > wrote:
>>
>> what happens when you run the following?
>>
>> cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
>>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
>> --i orig.mgz --o orig_nu.mgz
>>
>>
>>
>> On 03/07/2016 04:09 PM, Flavia Niccolini new wrote:
>>> Hello,
>>>
>>> I was wondering whether you could help with this error:
>>>
>>> #
>>> #@# MotionCor Thu Mar  3 11:35:51 GMT 2016
>>> Found 1 runs
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz
>>> Checking for (invalid) multi-frame inputs...
>>> WARNING: only one run found. This is OK, but motion
>>> correction cannot be performed on one run, so I'll
>>> copy the run to rawavg and continue.
>>>
>>> cp
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig/001.mgz
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz
>>>
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1
>>>
>>> mri_convert
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
>>> --conform
>>>
>>> mri_convert
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
>>> --conform
>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>> reading from
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/rawavg.mgz...
>>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>>> i_ras = (-1, 0, 0)
>>> j_ras = (0, 1, 0)
>>> k_ras = (-0, -0, 1)
>>> Original Data has (1, 1, 1) mm size and (160, 240, 256) voxels.
>>> Data is conformed to 1 mm size and 256 voxels for all directions
>>> changing data type from float to uchar (noscale = 0)...
>>> MRIchangeType: Building histogram
>>> Reslicing using trilinear interpolation
>>> writing to
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz...
>>>
>>> mri_add_xform_to_header -c
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/transforms/talairach.xfm
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri/orig.mgz
>>>
>>> INFO: extension is mgz
>>> #
>>> #@# Talairach Thu Mar  3 11:35:59 GMT 2016
>>> /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri
>>>
>>> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
>>> --no-rescale --i orig.mgz --o orig_nu.mgz
>>>
>>> Linux nig05.nig.ioppn.kcl.ac.uk 
>>> >> >
>>> 3.10.0-327.3.1.el7.x86_64 #1 SMP Wed Dec 9 14:09:15 UTC 2015 x86_64
>>> x86_64 x86_64 GNU/Linux
>>>
>>> recon-all -s PD1 exited with ERRORS at Thu Mar  3 11:36:02 GMT 2016
>>>
>>>
>>> Many Thanks
>>>
>>> With Best Wishes
>>>
>>> Flavia
>>>
>>>
>>>
>>>
>>>
>>>
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>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
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Re: [Freesurfer] mri_glmfit-sim

[Douglas N Greve]

The problem is that the smoothness of the data (35mm) is beyond that 
computed for the simulation. 35mm is very smooth. What kind of data is 
this? How much did you smooth it by?


On 03/13/2016 07:10 PM, John Anderson wrote:
> Hi experts,
> I am trying to correct the results of groups analysis using mri_glmfit-sim
> the command is :
> mri_glmfit-sim --glmdir lh_10mm --cache 3 pos --cwpvalthresh .0166
> I receive the follwoing error :
> ERROR: cannot find 
> /usr/local/freesurfer/stable6/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/pos/th30/mc-z.csd
> Thanks you for any suggestion!
> Bests,
> John
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] mri_binarize

[Douglas N Greve]

Hi Mohamad, I don't know why that would be. Note that the aseg does not 
have individual cortical labels. You should use aparc+aseg.mgz



On 03/12/2016 04:19 PM, Alshikho, Mohamad J. wrote:
>
> Hi Doug,
>
> I would like to inquire about the command “ mri_binarize”. In the 
> past, this command was able to create a _binarized nifti_ mask from 
> aseg.mgz, wmparc.mgz …. etc without the need to convert the output 
> “mgz” files to nifti. In other words If I want to create a mask for 
> the precentral gyrus I was using the following:
>
> mri_binarize --i aseg.mgz  --o precentral.nii --match 1024
>
> The command was able to create the mask and convert it to nifti file 
> at once, but right now if the output is nifti file, it returns empty 
> so I need to make the output “mgz” then convert it to nifti!!
>
> Is this real or I am missing something? Thanks for any advice!
>
> By the way I see this issue came up recently and in both freesurfer V 
> 5.3 and V6
>
> Best,
>
> Mohamad
>
>
>
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-- 
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] error while running dt-recon all

[Douglas N Greve]

if you run
mri_convert 00010001 deleteme.nii
what happens?

what is the error when running with nifti?


On 03/14/2016 05:59 PM, Jasmin Alves wrote:
>
> Dear Freesurfer experts,
>
> FREESURFER_HOME: /Applications/freesurfer
>
> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> Kernel info: Darwin 14.5.0 x86_64
>
>
> I received the following error while running the dt_recon --i 00010001 
> --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40.
>
> The participant is 40.
>
> And I received the following error:
>
> WARNING: file /Users/jasminalves/Desktop/data/40/00010001 does not 
> contain a Siemens ASCII header has this file been anonymized?
>
> ERROR: cannot unpack mosiacs without ASCII header
>
>
> I did notice on previous threads this is a common error that occurs, 
> but the files I have were directly exported from our siemens scanner 
> via Osirix. I also tried running dt_recon using nifti format but that 
> resulted in an error as well. Is there anything else I can do?
>
> Thanks,
>
> Jasmin
>
>
> -- 
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jal...@usc.edu 
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Extremely small numbers of extracted pial surface area

[Karl Liu]

Thank you for your comment, Bruce.


Regardless of technical issues, I am still troubled by the
small magnitude of extracted value of pial surface area. Following group
comparison and correction in QDEC, there is a significant cluster (size: 760
mm^2). In order to make a bar group of group means, I use numbers from the 
"cache.th20.neg.y.ocn.dat"
file, but the average is less than 1. Did I use the right file to plot group
mean of pial surface area, but why the magnitude is so small ?


Thank you for your help!


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[Freesurfer] TRACULA and NIFTI images

[Jacek Manko]

Dear Anastasia,

Thank you very much. 
This time I attach motion-corrected NIFTI-data (plus bval and bvec tables) that 
I have been unsuccessfully trying to process with Tracula. I also attach log 
file with error message. I suspect there must be something wrong with the 
tables again, but I am clueless on what that might be.

http://gate.nmr.mgh.harvard.edu/filedrop2/?p=3xql45jb18z

Is there anything you could advise me on? Thanks in advance.


Best,
Jacek Manko


Dnia 7-03-2016 o godz. 21:17 Anastasia Yendiki napisał(a):
> Hi Jacek - I'm attaching the files.
> 
> a.y
> 
> On Mon, 7 Mar 2016, Jacek Manko wrote:
> 
> > Dear Anastasia,
> >
> > Thank you! Wouldn't you mind for example sending me these tables? As far 
> as I am concerned I need only one table for all my subjects, so that 
> would help me a lot. The issue with flipped coordinates in the gradient 
> table is, as I mentioned before, due to the fact that I obtained these 
> values from motion corrected nifti data (which I was futilely trying to 
> preprocess as well). Anyway, I would like to get back to to you with 
> that issue later on.
> >
> > Best,
> > Jacek
> >
> > Dnia 7-03-2016 o godz. 17:58 Anastasia Yendiki napisał(a):
> >> Hi Jacek - I looked at the data that you uploaded. The problem is that
> >> both the b-value table and the gradient table that you were using were
> >> assuming that the b=0 images were interspersed throughout your scan, when
> >> in fact based on your dicoms they are all in the begining of the scan. So
> >> the 10 entries of 0.000 need to be in the beginning of the b-value table,
> >> not one every 7th image. Same with the gradient table. The gradient table
> >> also had some flipped coordinates that would cause a different problem
> >> down the line.
> >>
> >> I was able to get the right tables by using mri_convert from the
> >> development version of freesurfer. The 5.3 version doesn't have the
> >> capability to read these tables from the dicoms but the 6.0 version will.
> >> In the meantime you can download the dev version and use mri_convert from
> >> that version.
> >>
> >> Best,
> >>
> >> a.y
> >>
> >> On Sun, 14 Feb 2016, Jacek Manko wrote:
> >>
> >>>
> >>> Dear Freesurfer experts,
> >>>
> >>>  
> >>>
> >>> I have also noticed something wrong with the tracts I reconctructed.
> >> There were no erroors during the processing, but when I visualized all
> >> tracts in
> >>> Freeview according to your command "freeview -tv
> >> my-subject/dpath/merged_avg33_mni_bbr.mgz", but the results seem a bit
> >> odd to say the least. Please
> >>> have a look at the attached image.
> >>>
> >>>  
> >>>
> >>> I have also notice abnormal volumes of these tracts in comparison to
> >> your elmo-subjects. For example the volume of left uncinate for your
> >> tutorial
> >>> subject elmo.2012 is 393 and for my subject it is 5459. This discrepancy
> >> seems to coincide with with what you can spot in my screen, because it
> >> was my
> >>> first impression that these tracts are extremely large.
> >>>
> >>>  
> >>>
> >>> I run tracula with default commands as you stated in your tutorial, no
> >> major changes were made. If there is anything you could advise me, I
> >> will very
> >>> grateful. Are these results ok or I should udertake some steps? If you
> >> perhaps need some additional information I will be pleased to provide
> >> you with
> >>> that as well.
> >>>
> >>>  
> >>>
> >>> Cheers,
> >>>
> >>> Jacek
> >>>
> >>>  
> >>>
> >>>  
> >>>
> >>> Dnia 10-02-2016 o godz. 11:41 denizzgursel napisał(a):
> >>>
> >>>   Dear Anastasia and Tracula users,
> >>>  
> >>> I succesfully ran the longitudinal Tracula procedure for one subject.
> >> However, when I visualized the tracts, they look a bit weird (not
> >> smooth).
> >>> Even if I played with the threshold on freeview, I couldn't make them
> >> look nice as in the wiki page. I checked the registration and it looks
> >>> accurate, so I am not sure what could be wrong. I am attaching the messy
> >> looking tracts for your reference.
> >>>  
> >>> Could you tell me if I should run again with reinit=1 for these tracts?
> >>>  
> >>> Thank you very much for your time.
> >>> Best regards,
> >>>  
> >>>  
> >>> --
> >>> D.
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >
> >
> >
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> >
> >
> >
> 
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trac-all.log
Description: Binary data

Re: [Freesurfer] Editing Lesions in FreeSurfer 5.1

[Allison Rainford]

Hi Bruce,

I?ve attached a screen shot of a temporal pole of one of the brains that we
have had issues with. Here the issue is that there is a lesion without a
very clear boundary for the white matter and freesurfer was unresponsive to
simply using white matter edits (placing 255s on the wm.mgz), and so we
tried placing control points where we think the white matter boundary should
lie. However, we know that control points should not be placed in these dark
spots of a lesion.

Thank you,

Allison

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Re: [Freesurfer] Extremely small numbers of extracted pial surace area

[Bruce Fischl]

Hi Karl

differences in surface area are a bit harder to interpret. There are also 
some technical issues that perhaps Doug and/or Anderson Winkler can comment 
on. Anderson had a recent article on this that you might want to look at:


http://www.ncbi.nlm.nih.gov/pubmed/22446492

cheers
Bruce

On Mon, 14 Mar 2016, Karl Liu wrote:



Dear FS team:


I want to ask for some advice on how to extract the values of pial surface
area. I use QDEC to perform a surface-based F-test. The measurement is
area.pial and the smoothing is 10 in QDEC. After correction, there is one
significant cluster  with size of ~760 mm^2. The problem comes when I want
to extract the measure from each participant, so that I can plot the group
means. Currently I used the values from the "cache.th20.neg.y.ocn.dat" file,
but all the group means varies between 0.7-1.0 in magnitude. I believe the
unit is mm^2, because this is pial surface area. But is 0.7-1.0 mm^2 too
small? What is the correct way to extract surface area from this signficant
cluster, so I can plot the pattern of group differences in a bar graph?


Another question is  the validity of  surface-based analysis on pial or WM
surface area. I found most FS publications focus on the thickness, but not
the surface area. From your perspective, is  the surface area as valid as
the thickness measure?


Many thanks in advance


Karl


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