Re: [Freesurfer] Partial volume correction for aseg.mgz files

2019-03-29 Thread Bruce Fischl 

Hi Da-Yea

you would need to compute the jacobian of the warping and apply it at 
each voxel to scale the volumes (accounting for the warping).


cheers
Bruce
On Fri, 29 Mar 
2019, Song, Da-Yea wrote:




External Email - Use Caution

Hello,

 

I’m trying to extract regions (mri_extract_label) of interest from the aseg.mgz 
files and compare
them to our manual segmentations. I’ve warped these ROI masks onto our native 
space. I’ve noticed on
the forum that there were mentions of discrepancies in the volumes from 
aseg.mgz and aseg.stats due
to partial volume correction. If I were to calculate the volume using the ROI 
extracted masks (that
have been warped on to the native space), how can I calculate for partial 
volume correction? Any
suggestions would be greatly appreciated!

 

Thank you,

Da-Yea


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[Freesurfer] segmentHA_T1_long.sh HBT issue

2019-03-29 Thread Daniel Callow 
External Email - Use Caution

The issue was that I was using the freesurfer 6.0 version of freeview and
not the development version. Thanks for your help Eugenio!

Best,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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[Freesurfer] Partial volume correction for aseg.mgz files

2019-03-29 Thread Song, Da-Yea 
External Email - Use Caution

Hello,

I'm trying to extract regions (mri_extract_label) of interest from the aseg.mgz 
files and compare them to our manual segmentations. I've warped these ROI masks 
onto our native space. I've noticed on the forum that there were mentions of 
discrepancies in the volumes from aseg.mgz and aseg.stats due to partial volume 
correction. If I were to calculate the volume using the ROI extracted masks 
(that have been warped on to the native space), how can I calculate for partial 
volume correction? Any suggestions would be greatly appreciated!

Thank you,
Da-Yea

--
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Please note that e-mail communication is not encrypted by default. You have the 
right to request further emails be encrypted by notifying the sender. Your 
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recipient, be advised that any unauthorized use, disclosure, copying, 
distribution, or the taking of any action in reliance on the contents of this 
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Re: [Freesurfer] segmentHA_T1_long.sh HBT issue

2019-03-29 Thread Iglesias Gonzalez, Eugenio 
External Email - Use Caution

Dear Daniel,
This is weird. Can you please send us
lh.hippoAmygLabels-T1.long.v21.*.mgz
for a sample subject?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of Daniel Callow 

Reply-To: Freesurfer support list 
Date: Friday, 29 March 2019 at 11:56
To: Freesurfer support list 
Subject: [Freesurfer] segmentHA_T1_long.sh HBT issue


External Email - Use Caution
Hello,

I have run  segmentHA_T1_long.sh from the developer freesurfer version and am 
looking to segment and visualize the head body and tail of the left and right 
hippocampus.

However, when looking at the 
lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz and other files for each 
subject I see only amygdala and subfield segmentations. How do I use the 
outputs to create a head body and tail segmentation that I can visualize and 
extract values from?

Best,
Daniel Callow
PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298
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Re: [Freesurfer] petsurfer

2019-03-29 Thread Greve, Douglas N.,Ph.D. 
What is fICL161363_06_1_MRI_9746_series_2_MPRAGE_ADNI_P2.nii ? In general, 
you should not give mri_coreg a reference when using --s unless it is the same 
geometry as the orig.mgz

On 3/29/19 11:55 AM, ?? wrote:

External Email - Use Caution

Hi developers,
I am using the petsurfer now to do the PVC for my dynamic analysis, however 
there is something error happened.
Here is my commends:

mri_coreg --mov fICL161363_06_1_BU99008_9744_merged_00015.nii --ref 
fICL161363_06_1_MRI_9746_series_2_MPRAGE_ADNI_P2.nii --reg template.reg.lta 
--s subject6



mri_gtmpvc --i fICL161363_06_1_BU99008_9744_merged.nii --reg 
template.reg.lta --psf-col 9.2 --psf-row 10.5 --psf-slice 14.6  --seg 
subject6/mri/gtmseg.mgz --default-seg-merge --mgx .01 --o gtmpvc.output 
--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale





the coreg was ok, however the gtmpvc is not ok, here is the lines show my 
terminal, could you tell me what's the problem and how to fix it, Thanks so 
much for help me.

Loading input fICL161363_06_1_BU99008_9744_merged.nii

WARNING: niiRead(): unknown time units 0 in 
/Volumes/NIU20/analysis/volumetric_FS/trail/fICL161363_06_1_BU99008_9744_merged.nii

INFO: using NIfTI-1 qform

  done loading input 28 frames


$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $

setenv SUBJECTS_DIR /Volumes/NIU20/analysis/volumetric_FS/trail

cd /Volumes/NIU20/analysis/volumetric_FS/trail

mri_gtmpvc --i fICL161363_06_1_BU99008_9744_merged.nii --reg 
template.reg.lta --psf-col 9.2 --psf-row 10.5 --psf-slice 14.6 --seg 
subject6/mri/gtmseg.mgz --default-seg-merge --mgx .01 --o gtmpvc.output 
--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale

sysname  Darwin

hostname cengzhoudeMacBook-Air.local

machine  x86_64

user cengzhou

vgthresh   0.001000

nReplace   18

0. 0. 0. 0. 0. 0.

4 avail.processors, using 1

Creating output directory gtmpvc.output

Loading seg for gtm subject6/mri/gtmseg.mgz

Loading seg ctab subject6/mri/gtmseg.ctab

Reading subject6/mri/gtmseg.lta

ERROR: LTAconcat(): LTAs 0 and 1 do not match

LTA 0 ---

type  = 0 # LINEAR_VOX_TO_VOX

nxforms   = 1

mean  = 0. 0. 0.

sigma = 1.

1 4 4

5.000e-01 0.000e+00 0.000e+00 
4.875e+01

0.000e+00 5.000e-01 0.000e+00 
3.475e+01

0.000e+00 0.000e+00 5.000e-01 
1.775e+01

0.000e+00 0.000e+00 0.000e+00 
1.000e+00

src volume info

valid = 1  # volume info valid

filename = 
/Volumes/NIU20/analysis/volumetric_FS/trail/subject6/mri/apas+head.mgz

volume = 316 440 438

voxelsize = 5.000e-01 5.000e-01 5.000e-01

xras   = -1.000e+00 0.000e+00 0.000e+00

yras   = 0.000e+00 0.000e+00 -1.000e+00

zras   = 0.000e+00 1.000e+00 0.000e+00

cras   = 2.500e-01 -7.500e-01 -1.675e+01

dst volume info

valid = 1  # volume info valid

filename = 
/Volumes/NIU20/analysis/volumetric_FS/trail/subject6/mri/apas+head.mgz

volume = 256 256 256

voxelsize = 1.000e+00 1.000e+00 1.000e+00

xras   = -1.000e+00 0.000e+00 0.000e+00

yras   = 0.000e+00 0.000e+00 -1.000e+00

zras   = 0.000e+00 1.000e+00 0.000e+00

cras   = 0.000e+00 0.000e+00 0.000e+00

subject subject6

fscale 0.15

LTA 1 ---

type  = 0 # LINEAR_VOX_TO_VOX

nxforms   = 1

mean  = 0. 0. 0.

sigma = 1.

1 4 4

1.490079522132874e+00 -1.009208321571350e+00 -9.591113924980164e-01 
8.742171478271484e+01

9.481825828552246e-01 1.776931047439575e+00 -3.772042095661163e-01 
-4.950695037841797e+01

1.042477130889893e+00 -1.736743301153183e-01 1.714007139205933e+00 
2.799880599975586e+01

0.000e+00 0.000e+00 0.000e+00 
1.000e+00

src volume info

valid = 1  # volume info valid

filename = fICL161363_06_1_BU99008_9744_merged_00015.nii

volume = 128 128 82

voxelsize = 2.050889968872070e+00 2.050889968872070e+00 2.000e+00

xras   = -1.000e+00 0.000e+00 0.000e+00

yras   = 0.000e+00 1.000e+00 0.000e+00

zras   = 0.000e+00 0.000e+00 1.000e+00

cras   = 0.000e+00 0.000e+00 0.000e+00

dst volume info

valid = 1  # volume info valid

filename = fICL161363_06_1_MRI_9746_series_2_MPRAGE_ADNI_P2.nii

volume = 160 240 256

voxelsize = 1.00953674316e+00 1.000e+00 1.000e+00

xras   =

[Freesurfer] segmentHA_T1_long.sh HBT issue

2019-03-29 Thread Daniel Callow 
External Email - Use Caution

Hello,

To add to my original post it seems the issue is I am not able to look at
these merged images or that the HBT file write out seems to be wrong? I
don't know how to post a picture to the listserve so someone can determine
if I am just looking at it incorrectly in freeview?

Any help is greatly appreciated!

Best,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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[Freesurfer] petsurfer

2019-03-29 Thread ?? 
External Email - Use Caution

Hi developers,I am using the petsurfer now to do the PVC for my dynamic 
analysis, however there is something error happened.
Here is my commends:

mri_coreg --mov fICL161363_06_1_BU99008_9744_merged_00015.nii --ref 
fICL161363_06_1_MRI_9746_series_2_MPRAGE_ADNI_P2.nii --reg template.reg.lta 
--s subject6









mri_gtmpvc --i fICL161363_06_1_BU99008_9744_merged.nii --reg 
template.reg.lta --psf-col 9.2 --psf-row 10.5 --psf-slice 14.6  --seg 
subject6/mri/gtmseg.mgz --default-seg-merge --mgx .01 --o gtmpvc.output 
--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale

   







the coreg was ok, however the gtmpvc is not ok, here is the lines show my 
terminal, could you tell me what's the problem and how to fix it, Thanks so 
much for help me.

Loading input fICL161363_06_1_BU99008_9744_merged.nii

WARNING: niiRead(): unknown time units 0 in 
/Volumes/NIU20/analysis/volumetric_FS/trail/fICL161363_06_1_BU99008_9744_merged.nii

INFO: using NIfTI-1 qform 

  done loading input 28 frames




$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $

setenv SUBJECTS_DIR /Volumes/NIU20/analysis/volumetric_FS/trail

cd /Volumes/NIU20/analysis/volumetric_FS/trail

mri_gtmpvc --i fICL161363_06_1_BU99008_9744_merged.nii --reg 
template.reg.lta --psf-col 9.2 --psf-row 10.5 --psf-slice 14.6 --seg 
subject6/mri/gtmseg.mgz --default-seg-merge --mgx .01 --o gtmpvc.output 
--km-ref 8 47 --km-hb 11 12 13 50 51 52 --no-rescale 

sysname  Darwin

hostname cengzhoudeMacBook-Air.local

machine  x86_64

user cengzhou

vgthresh   0.001000

nReplace   18

0. 0. 0. 0. 0. 0. 

4 avail.processors, using 1

Creating output directory gtmpvc.output

Loading seg for gtm subject6/mri/gtmseg.mgz

Loading seg ctab subject6/mri/gtmseg.ctab

Reading subject6/mri/gtmseg.lta

ERROR: LTAconcat(): LTAs 0 and 1 do not match

LTA 0 ---

type  = 0 # LINEAR_VOX_TO_VOX

nxforms   = 1

mean  = 0. 0. 0.

sigma = 1.

1 4 4

5.000e-01 0.000e+00 0.000e+00 
4.875e+01 

0.000e+00 5.000e-01 0.000e+00 
3.475e+01 

0.000e+00 0.000e+00 5.000e-01 
1.775e+01 

0.000e+00 0.000e+00 0.000e+00 
1.000e+00 

src volume info

valid = 1  # volume info valid

filename = 
/Volumes/NIU20/analysis/volumetric_FS/trail/subject6/mri/apas+head.mgz

volume = 316 440 438

voxelsize = 5.000e-01 5.000e-01 5.000e-01

xras   = -1.000e+00 0.000e+00 0.000e+00

yras   = 0.000e+00 0.000e+00 -1.000e+00

zras   = 0.000e+00 1.000e+00 0.000e+00

cras   = 2.500e-01 -7.500e-01 -1.675e+01

dst volume info

valid = 1  # volume info valid

filename = 
/Volumes/NIU20/analysis/volumetric_FS/trail/subject6/mri/apas+head.mgz

volume = 256 256 256

voxelsize = 1.000e+00 1.000e+00 1.000e+00

xras   = -1.000e+00 0.000e+00 0.000e+00

yras   = 0.000e+00 0.000e+00 -1.000e+00

zras   = 0.000e+00 1.000e+00 0.000e+00

cras   = 0.000e+00 0.000e+00 0.000e+00

subject subject6

fscale 0.15

LTA 1 ---

type  = 0 # LINEAR_VOX_TO_VOX

nxforms   = 1

mean  = 0. 0. 0.

sigma = 1.

1 4 4

1.490079522132874e+00 -1.009208321571350e+00 -9.591113924980164e-01 
8.742171478271484e+01 

9.481825828552246e-01 1.776931047439575e+00 -3.772042095661163e-01 
-4.950695037841797e+01 

1.042477130889893e+00 -1.736743301153183e-01 1.714007139205933e+00 
2.799880599975586e+01 

0.000e+00 0.000e+00 0.000e+00 
1.000e+00 

src volume info

valid = 1  # volume info valid

filename = fICL161363_06_1_BU99008_9744_merged_00015.nii

volume = 128 128 82

voxelsize = 2.050889968872070e+00 2.050889968872070e+00 2.000e+00

xras   = -1.000e+00 0.000e+00 0.000e+00

yras   = 0.000e+00 1.000e+00 0.000e+00

zras   = 0.000e+00 0.000e+00 1.000e+00

cras   = 0.000e+00 0.000e+00 0.000e+00

dst volume info

valid = 1  # volume info valid

filename = fICL161363_06_1_MRI_9746_series_2_MPRAGE_ADNI_P2.nii

volume = 160 240 256

voxelsize = 1.00953674316e+00 1.000e+00 1.000e+00

xras   = -1.000e+00 0.000e+00 0.000e+00

yras   = 0.000e+00 1.000e+00 0.000e+00

zras   = -0.000e+00

[Freesurfer] segmentHA_T1_long.sh HBT issue

2019-03-29 Thread Daniel Callow 
External Email - Use Caution

Hello,

I have run  *segmentHA_T1_long.sh from the developer freesurfer version and
am looking to segment and visualize the head body and tail of the left and
right hippocampus.*

*However, when looking at the
lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelSpace.mgz and other files for
each subject I see only amygdala and subfield segmentations. How do I use
the outputs to create a head body and tail segmentation that I can
visualize and extract values from?*


*Best,*
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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Re: [Freesurfer] VT images from pmod to freesurfer

2019-03-29 Thread Donatienne Van Weehaeghe 
External Email - Use Caution

#mri_glmfit --glmdir
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/concatenate/PVC_proj0.5_lh
--y
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/concatenate/all.lh.mgx.ctxgm.fsaverage.pvc.VT.sm06.proj-0.5.nii.gz
--surface fsaverage lh --fsgd
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/FSGD/fsgd_all_VT
--C
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/FSGD/group.diff.mtx
#mri_glmfit --glmdir
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/concatenate/PVC_proj0.5_rh
--y
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/concatenate/all.rh.mgx.ctxgm.fsaverage.pvc.VT.sm06.proj-0.5.nii.gz
--surface fsaverage lh --fsgd
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/FSGD/fsgd_all_VT
--C
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/FSGD/group.diff.mtx


#mri_glmfit-sim --glmdir
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/concatenate/PVC_proj0.5_lh
--cache 2.0 pos --cwp 0.05 --2spaces
#mri_glmfit-sim --glmdir
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/concatenate/PVC_proj0.5_rh
--cache 1.3 pos --cwp 0.05 --2spaces


Op vr 29 mrt. 2019 om 11:08 schreef Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> What is the full command line for that program?
>
> On 3/29/19 11:01 AM, Donatienne Van Weehaeghe wrote:
>
> External Email - Use Caution
> Dear,
>
> The Freesurfer program generated the error after multiple comparison
> corerction.
>
> Thank you for your help.
>
> Kind regards
> Donatienne
>
> Op vr 29 mrt. 2019 om 10:58 schreef Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu>:
>
>> what program generated the error? What is the full command line for that
>> program?
>>
>> On 3/21/19 12:49 PM, Donatienne Van Weehaeghe wrote:
>>
>> External Email - Use Caution
>>
>> Dear,
>>
>>
>> I encountered a problem when going from pmod to freesurfer.
>>
>>
>> I made Vt images in pmod using the logan plot, then I used the following
>> commands to convert them to freesurfer space:
>>
>>
>>
>> #flirt -noresample -in
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
>> -ref
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/T1-2mm_skullstripped.nii.gz
>> -applyxfm -init
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUV.lrrev_lin_T1.mat
>> -out
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
>>
>> #3dresample -master
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/occipital.nii.gz
>> -inset
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
>> -prefix
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
>>
>>
>>
>> Then I did partial volume correction using this command:
>>
>> #mri_gtmpvc --i
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
>> --reg Vt.reg.lta --psf 5 --seg
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz
>> --default-seg-merge --auto-mask 5 0.01 --rbv --o
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg
>> --no-rescale --threads 8
>>
>>
>>
>>
>>
>> Then I did surface projection:
>>
>> #mri_vol2surf --mov
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
>> --reg
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
>> --hemi lh --projfrac 0.5 --o
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/lh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
>> --cortex --trgsubject fsaverage
>>
>> #mri_vol2surf --mov
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
>> --reg
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
>> --hemi rh --projfrac 0.5 --o
>> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
>> --cortex --trgsubject fsaverage
>>
>>
>>
>> followed by smoothing, concatening and then a group comparison. However
>> then I obtained the following error:
>>
>> ERROR: cannot find
>> /usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd
>>
>>
>> Kind regards
>>
>>

Re: [Freesurfer] VT images from pmod to freesurfer

2019-03-29 Thread Greve, Douglas N.,Ph.D. 
What is the full command line for that program?

On 3/29/19 11:01 AM, Donatienne Van Weehaeghe wrote:

External Email - Use Caution

Dear,

The Freesurfer program generated the error after multiple comparison corerction.

Thank you for your help.

Kind regards
Donatienne

Op vr 29 mrt. 2019 om 10:58 schreef Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>>:
what program generated the error? What is the full command line for that 
program?

On 3/21/19 12:49 PM, Donatienne Van Weehaeghe wrote:

External Email - Use Caution
Dear,

I encountered a problem when going from pmod to freesurfer.

I made Vt images in pmod using the logan plot, then I used the following 
commands to convert them to freesurfer space:

#flirt -noresample -in 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
 -ref 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/T1-2mm_skullstripped.nii.gz
 -applyxfm -init 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUV.lrrev_lin_T1.mat
 -out 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
#3dresample -master 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/occipital.nii.gz
  -inset 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
 -prefix 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii

Then I did partial volume correction using this command:
#mri_gtmpvc --i 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
 --reg Vt.reg.lta --psf 5 --seg 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz
 --default-seg-merge --auto-mask 5 0.01 --rbv --o 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg
 --no-rescale --threads 8


Then I did surface projection:
#mri_vol2surf --mov 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
 --reg 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
 --hemi lh --projfrac 0.5 --o 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/lh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
 --cortex --trgsubject fsaverage
#mri_vol2surf --mov 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
 --reg 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
 --hemi rh --projfrac 0.5 --o 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
 --cortex --trgsubject fsaverage

followed by smoothing, concatening and then a group comparison. However then I 
obtained the following error:
ERROR: cannot find 
/usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd

Kind regards
Donatienne



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Re: [Freesurfer] mris_preproc not running

2019-03-29 Thread Greve, Douglas N.,Ph.D. 
Can you send your full command line and the full terminal output? Are 
you sure you're using the new command?

On 3/27/19 10:33 PM, Sims, Sara A (Campus) wrote:
>  External Email - Use Caution
>
> Doug,
> I have implemented the new version of the command. I am getting this error 
> when I add the no-prune flag to my script.
> ERROR: could not find volume --no-prune.  Does it exist?
> ERROR: reading --no-prune
> Are there specifics with where in the command line it should go? I have tried 
> it near the beginning and near the end and still get this error.
>
> Sara Sims
> Graduate Research Fellow
> University of Alabama at Birmingham
> Department of Psychology
> 205-975-4060
> sno...@uab.edu
>
> On 3/19/19, 3:30 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Greve, Douglas N.,Ph.D."  dgr...@mgh.harvard.edu> wrote:
>
>  I think the problem is that one or more of the subjects has all 0s. The
>  way mris_preproc works is that if any subject has a 0 in a vertex, that
>  vertex is set to 0 for all subjects. So, if one subject has all 0s or if
>  tp1=tp2, then everything can get set to 0. At the end of the terminal
>  output you'll see "Found 0 voxels in prune mask" indicating that this is
>  the case. I've created a version of mris_preproc that allows you to turn
>  this function off using --no-prune. You can get it from here:
>  https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc
>  I would run it with --no-prune and without --paired-diff to give you a
>  stack of all data. You can load this as an overlay in freeview. At the
>  top of the freeview window is a little box with waveform in it. If you
>  click on that and then click on a point in the surface, you should be
>  able to see a waveform of the measurements for all inputs. See if there
>  is one that is always 0. If you don't find any, then repeat with
>  --paired-diff
>  
>  
>  
>  
>  On 3/19/19 3:30 PM, Sims, Sara A (Campus) wrote:
>  >
>  > External Email - Use Caution
>  >
>  > I uploaded them to the Filedrop here:
>  > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=65zt2jk45ll
>  >
>  > Thanks!
>  >
>  > Sara Sims
>  >
>  > Graduate Research Fellow
>  >
>  > University of Alabama at Birmingham
>  >
>  > Department of Psychology
>  >
>  > 205-975-4060
>  >
>  > sno...@uab.edu
>  >
>  > *From: * on behalf of "Greve,
>  > Douglas N.,Ph.D." 
>  > *Reply-To: *Freesurfer support list 
>  > *Date: *Monday, March 18, 2019 at 10:24 AM
>  > *To: *"freesurfer@nmr.mgh.harvard.edu" 
>  > *Subject: *Re: [Freesurfer] mris_preproc not running
>  >
>  >
>  > can you send the terminal output? I realize it might be quite big. You
>  > can ftp it to here: 
> /autofs/space/nihilus_001/CICS/ACRsoftware/ACRcurrent
>  >
>  >
>  > On 3/18/19 11:12 AM, Sims, Sara A (Campus) wrote:
>  >
>  > *External Email - Use Caution *
>  >
>  > Hello!
>  >
>  > I have 786 subjects that I am trying to do a paired difference
>  > analysis using mri_glm. I am getting stuck at the mris_preproc
>  > stage. I have tried running it on a handful of subjects and it
>  > works wonderfully. However, when I run it on all the subjects it
>  > outputs an empty file.
>  >
>  > I think part of my problem is that I am having to do 1572 flags to
>  > enter all the subjects files (which I made a script to create, I
>  > did not hand type them). Is there a better way to do this? Do I
>  > just have too many subjects?
>  >
>  > This is what I have that isn’t working:
>  >
>  > *mris_preproc --target fsaverage --hemi lh --isp
>  > $in/${network}/100206.${run1}/lhsurf.mgh --isp
>  > $in/${network}/100206.${run2}/lhsurf.mgh --isp
>  > $in/${network}/100307.${run1}/lhsurf.mgh --isp
>  > $in/${network}/100307.${run2}/lhsurf.mgh ……. --out
>  > 
> $out/preproc_${network}_${pair}/lh.paired-diff.${network}_${pair}.mgh
>  > --f $sublist --paired-diff --no-cortex-only*
>  >
>  > **
>  >
>  > Thanks for the help!
>  >
>  > Sara Sims
>  >
>  >
>  >
>  > ___
>  >
>  > 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
>  
>  
>  ___
>

Re: [Freesurfer] VT images from pmod to freesurfer

2019-03-29 Thread Donatienne Van Weehaeghe 
External Email - Use Caution

Dear,

The Freesurfer program generated the error after multiple comparison
corerction.

Thank you for your help.

Kind regards
Donatienne

Op vr 29 mrt. 2019 om 10:58 schreef Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> what program generated the error? What is the full command line for that
> program?
>
> On 3/21/19 12:49 PM, Donatienne Van Weehaeghe wrote:
>
> External Email - Use Caution
>
> Dear,
>
>
> I encountered a problem when going from pmod to freesurfer.
>
>
> I made Vt images in pmod using the logan plot, then I used the following
> commands to convert them to freesurfer space:
>
>
>
> #flirt -noresample -in
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
> -ref
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/T1-2mm_skullstripped.nii.gz
> -applyxfm -init
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUV.lrrev_lin_T1.mat
> -out
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
>
> #3dresample -master
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/occipital.nii.gz
> -inset
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
> -prefix
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
>
>
>
> Then I did partial volume correction using this command:
>
> #mri_gtmpvc --i
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
> --reg Vt.reg.lta --psf 5 --seg
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz
> --default-seg-merge --auto-mask 5 0.01 --rbv --o
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg
> --no-rescale --threads 8
>
>
>
>
>
> Then I did surface projection:
>
> #mri_vol2surf --mov
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
> --reg
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
> --hemi lh --projfrac 0.5 --o
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/lh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
> --cortex --trgsubject fsaverage
>
> #mri_vol2surf --mov
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
> --reg
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
> --hemi rh --projfrac 0.5 --o
> /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
> --cortex --trgsubject fsaverage
>
>
>
> followed by smoothing, concatening and then a group comparison. However
> then I obtained the following error:
>
> ERROR: cannot find
> /usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd
>
>
> Kind regards
>
> Donatienne
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] VT images from pmod to freesurfer

2019-03-29 Thread Greve, Douglas N.,Ph.D. 
what program generated the error? What is the full command line for that 
program?

On 3/21/19 12:49 PM, Donatienne Van Weehaeghe wrote:

External Email - Use Caution
Dear,

I encountered a problem when going from pmod to freesurfer.

I made Vt images in pmod using the logan plot, then I used the following 
commands to convert them to freesurfer space:

#flirt -noresample -in 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
 -ref 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/T1-2mm_skullstripped.nii.gz
 -applyxfm -init 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/SUVR/SUV.lrrev_lin_T1.mat
 -out 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
#3dresample -master 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/occipital.nii.gz
  -inset 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.nii
 -prefix 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii

Then I did partial volume correction using this command:
#mri_gtmpvc --i 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}_Vt.fsl.nii
 --reg Vt.reg.lta --psf 5 --seg 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/$word/mri/gtmseg.mgz
 --default-seg-merge --auto-mask 5 0.01 --rbv --o 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg
 --no-rescale --threads 8


Then I did surface projection:
#mri_vol2surf --mov 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
 --reg 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
 --hemi lh --projfrac 0.5 --o 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/lh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
 --cortex --trgsubject fsaverage
#mri_vol2surf --mov 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rbv.nii.gz
 --reg 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/aux/rbv2anat.lta
 --hemi rh --projfrac 0.5 --o 
/autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/${word}gtmpvc.output.spmreg/rh.mgx.ctxgm.fsaverage.pvc.VT.sm00.proj-0.5.nii.gz
 --cortex --trgsubject fsaverage

followed by smoothing, concatening and then a group comparison. However then I 
obtained the following error:
ERROR: cannot find 
/usr/local/freesurfer/stable6_0_0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/pos/th13/mc-z.csd

Kind regards
Donatienne



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Re: [Freesurfer] (no subject)

2019-03-29 Thread Greve, Douglas N.,Ph.D. 
What threshold are you using in tksurfer? It should be the same as -log10(cwp), 
where cwp is the --cwp threshold you used in mri_glmfit-sim. If it is 
different, then it might not show all the cluster

On 3/29/19 6:48 AM, Giuliana Klencklen wrote:

External Email - Use Caution

Hi FS experts,

I use tksurfer (e.g., tksurfer fsaverage/ lh inflated -gray) to open the 
overlays (i.e., something.sig.cluster.mgh) I generated with the permutation 
simulation correction. It goes perfectly well for most of them expect for some, 
where the overlay does not show at all the significant clusters summarized in 
the something.sig.cluster.summary.

I run the mri_glmfit-sim command again but the problem persists.

Does anyone have a clue about what is going wrong?

Many thanks,
Giuliana Klencklen


--
Giuliana Klencklen, Ph.D.

Helen Wills Neuroscience Institute
University of California, Berkeley
118 Barker Hall
Berkeley, CA 94720-3190
510-395-0040
giuliana.klenck...@berkeley.edu



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Re: [Freesurfer] Group X Time Interaction in Qdec

2019-03-29 Thread Greve, Douglas N.,Ph.D. 
There is not a way to do this. Instead, try a paired analysis
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis

On 3/28/19 8:08 PM, brain health wrote:

External Email - Use Caution

What is the best way to run a whole- brain Group (intervention group, control 
group) x Time (Pre, post) interaction via QDEC? 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview)

Thanks!




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Re: [Freesurfer] nu_correct: Command not found

2019-03-29 Thread Tim Schäfer 
External Email - Use Caution

Could you replace this line:

  export PATH=/usr/local/freesurfer/bin:PATH=/usr/local/freesurfer/mni/bin:$PATH

with this one and try again:

  export PATH=/usr/local/freesurfer/bin:/usr/local/freesurfer/mni/bin:$PATH

Please also paste the output of the following command:

  echo $PATH

Best,

Tim

> On March 28, 2019 at 4:00 PM Ian Hardingham  wrote:
> 
> 
> External Email - Use Caution
> 
> Hello all.
> 
> I am attempting to run recon-all in a docker container.  I have a set of 
> commands to set up the system, and on my local machine (Ubuntu) it works 
> fine.  However on the docker container (also Ubuntu) I get
> 
> nu_correct: Command not found.
> 
> I imagine there is some software that is required that I haven't 
> installed on the container image - does anyone have any idea what it 
> might be?
> 
> 1. I have run these commands:
> 
> source /usr/local/freesurfer/SetUpFreeSurfer.sh
> export 
> PATH=/usr/local/freesurfer/bin:PATH=/usr/local/freesurfer/mni/bin:$PATH
> 
> 2. I have set FREESURFER_HOME
> 
> Attached at the end is some output from both failing and successful runs.
> 
> 3. nu_correct exists in freesurfer/mni/bin
> 
> 4. Perl is present and correct on both systems.
> 
> Thank you in advance,
> Ian
> 
> 
> FAILING OUTPUT:
> 
> #
> #@# Talairach Thu Mar 28 14:12:31 UTC 2019
> /subjects/FS_subj_001/mri
> 
>   mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 
> --proto-iters 1000 --distance 50
> 
> /subjects/FS_subj_001/mri
> /usr/local/freesurfer/bin/mri_nu_correct.mni
> --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 
> --distance 50
> nIters 1
> $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
> Linux 40ed7e79aa5d 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 
> UTC 2019 x86_64 GNU/Linux
> Thu Mar 28 14:12:32 UTC 2019
> nu_correct: Command not found.
> 
> 
> SUCCESSFUL OUTPUT:
> 
> #
> #@# Talairach Thu Mar 28 14:33:45 GMT 2019
> /home/ian/subjects/FS_subj_001/mri
> 
>   mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 
> --proto-iters 1000 --distance 50
> 
> /home/ian/subjects/FS_subj_001/mri
> /usr/local/freesurfer/bin/mri_nu_correct.mni
> --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 
> --distance 50
> nIters 1
> $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
> Linux ian-Sabre-17WV8 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 
> 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
> Thu Mar 28 14:33:45 GMT 2019
> Program nu_correct, built from:
> 
> 
> 
> -- 
> Ian Hardingham
> 
> 
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> Freesurfer@nmr.mgh.harvard.edu
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Best,


Tim


--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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[Freesurfer] (no subject)

2019-03-29 Thread Giuliana Klencklen 
External Email - Use Caution

 Hi FS experts,

I use tksurfer (e.g., tksurfer fsaverage/ lh inflated -gray) to open the
overlays (i.e., something.sig.cluster.mgh) I generated with the permutation
simulation correction. It goes perfectly well for most of them expect for
some, where the overlay does not show at all the significant clusters
summarized in the something.sig.cluster.summary.

I run the mri_glmfit-sim command again but the problem persists.

Does anyone have a clue about what is going wrong?

Many thanks,
Giuliana Klencklen


-- 
Giuliana Klencklen, Ph.D.

Helen Wills Neuroscience Institute
University of California, Berkeley
118 Barker Hall
Berkeley, CA 94720-3190
510-395-0040
giuliana.klenck...@berkeley.edu
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[Freesurfer] Error with "recon-all -make all" following multiple manual editing

2019-03-29 Thread Matthieu VANHOUTTE 
   External Email - Use Caution


Dear Freesurfer's experts,

Havng done multiple types of manual editing in two subjects, I 
relaunched the recon-all process (Freesurfer 6.0.1) with the flag "-make 
all".


However, during the process, I goth for both subjects the following 
error message: /

/

/make: *** 
[/netapp/vol2_agewell/pro/IMAP/imap_mvh/FS6.0.1/awellv1s097/mri/aseg.presurf.mgz] 
Error 1/


/recon-all -s /netapp/vol2_agewell/pro/IMAP/imap_mvh/FS6.0.1/awellv3s024 
-ccseg

ERROR: Flag -ccseg unrecognized./

Following the troubleshooting site 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.0) 
I have over-writed the "recon-all.makefile" file since I use the 6.0.1 
version of Freesurfer.


Thanks for helping.

Best,

Matthieu

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