Re: [Freesurfer] bbregister + mri_vol2vol different results

[Paul Glad Mihai]

Hello Experts,

Just to follow up on my previous posting, here is the information from
the headrs of the different nifti files after the steps performed.

  * First, the header of the mean original nifti after realignment:
qto_xyz:1  -1.099422  0.024665  0.025745  65.286888
qto_xyz:2  -0.021598  -1.092710  0.124570  38.997047
qto_xyz:3  0.028368  0.123999  1.092621  -26.324900
qto_xyz:4  0.00  0.00  0.00  1.00
qform_xorient  Right-to-Left
qform_yorient  Anterior-to-Posterior
qform_zorient  Inferior-to-Superior
sform_name Aligned Anat
sform_code 2
sto_xyz:1  -1.099422  0.024662  0.025746  65.286888
sto_xyz:2  -0.021594  -1.092710  0.124570  38.997047
sto_xyz:3  0.028368  0.123999  1.092621  -26.324900
sto_xyz:4  0.00  0.00  0.00  1.00
sform_xorient  Right-to-Left
sform_yorient  Anterior-to-Posterior
sform_zorient  Inferior-to-Superior

  * Second, the header of the nifti after bbregister with the write
output option enabled:
qto_xyz:1  -1.00  0.00  -0.00  126.995163
qto_xyz:2  0.00  0.00  1.00  -135.546768
qto_xyz:3  -0.00  -1.00  -0.00  109.658028
qto_xyz:4  0.00  0.00  0.00  1.00
qform_xorient  Right-to-Left
qform_yorient  Superior-to-Inferior
qform_zorient  Posterior-to-Anterior
sform_name Scanner Anat
sform_code 1
sto_xyz:1  -1.00  0.00  0.00  126.995163
sto_xyz:2  0.00  0.00  1.00  -135.546768
sto_xyz:3  0.00  -1.00  0.00  109.658028
sto_xyz:4  0.00  0.00  0.00  1.00
sform_xorient  Right-to-Left
sform_yorient  Superior-to-Inferior
sform_zorient  Posterior-to-Anterior

  * This is the matrix (.mat) resulting from the bbregister step:
  -0.69660.00760214   -0.00178158  192.10556030
   0.00103370   -0.09726234   -0.99525851  135.02107239
  -0.00773941   -0.995229780.09725130  173.68141174
   0.0.0.1.


  * Third, the header of the nifti after mri_vol2vol using the matrix
from the bbregister step:
qto_xyz:1  0.00  0.00  0.70  -85.004837
qto_xyz:2  -0.70  0.00  0.00  104.453209
qto_xyz:3  0.00  -0.70  0.00  93.658028
qto_xyz:4  0.00  0.00  0.00  1.00
qform_xorient  Anterior-to-Posterior
qform_yorient  Superior-to-Inferior
qform_zorient  Left-to-Right
sform_name Scanner Anat
sform_code 1
sto_xyz:1  0.00  0.00  0.70  -85.004837
sto_xyz:2  -0.70  0.00  0.00  104.453209
sto_xyz:3  0.00  -0.70  0.00  93.658028
sto_xyz:4  0.00  0.00  0.00  1.00
sform_xorient  Anterior-to-Posterior
sform_yorient  Superior-to-Inferior
sform_zorient  Left-to-Right

Regards,
Glad

On 07/13/2017 11:02 PM, Paul Glad Mihai wrote:
> Hello,
> 
> I'm getting two different results from the coregistration step. When I run 
> bbregister on the mean epi it coregisters properly and writes out _bbreg.nii. 
> The next step involves registering the realigned epi time series to the T1 
> image using the same transform matrix calculated from the mean image. But the 
> results fail miserably. I've attached some sample images. 
> 
> I came across the same result after transforming the matrix it to ITK space 
> and applying the transform using ANTs' applyTransform, which tells me that 
> the ITK conversion works, but this registration goes wrong. Or I may not 
> really understand what I'm doing, lol.
> 
> Here are the commands:
> 
> bbregister --t2 --epi-mask --init-header --fslmat 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>  --reg 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat
>  --o 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii
>  --mov 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii
>  --s sub-01
> 
> mri_vol2vol --fsl 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>  --mov 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold.nii
>  --targ 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/brainextract/sub-01_acq-T1w_brain.nii.gz
>  --o 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold_warped.nii
> 
> Regards,
> Glad
> 
> 
> 
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> 
> The information 

Re: [Freesurfer] FS Version 6 Long Processing

[Martin Reuter]

Hi Allison,

seems like autorecon2-pial has been removed from FreeSurfer (also in the 
cross sectional stream). I don't know when, why and what would be the 
equivalent command, but someone on the list will know.



About brainmask edits, they are described here:

https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits

The brainmask in the base is the union of all mask from cross (after 
registration) and is fixed for all time points. If the mask is correct, 
this is usually OK. So it makes sense to edit the brainmask in the base 
and not in the individual time points. In the base you would re-run 
autorecon2 and autorecon3 as the edited brainmask affects not just the 
surfaces, but also aseg etc.


If edits are really needed in the long runs, then edit it there and also 
run autorecon2 and autorecon3.


Best, Martin



On 07/14/2017 07:28 PM, Allison Rainford wrote:

Hi FreeSurfer Team,

My lab has recently begun editing longitudinal data in version 6 and 
have found that we cannot use the same flags for –autorecon2 as we did 
when running longs in version 5.1. Typically, after making any 
necessary edits to a long, we run -autorecon2–pial –autorecon3. This 
flag hasn’t been successful in version 6, producing an error message 
that the flag is unrecognized. Because we still only require some 
brainmask edits on the longs, we would like to know how we can 
continue to run these to process only pial.


All help is greatly appreciated!

Allison


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[Freesurfer] qcache ERROR on longitudinal image processing with FreeSurfer v6.0

[Lisa Delalande]

Hello everyone,

I'm using the new version of FreeSurfer processing with longitudinal image
processing. And at the step -base after a recon-all processing i would like
to make a qcache processing but it doesn't work... "cannot find
[...]/template_1-01VALAL/surf/lh.w-g.pct.mgh" (See in attachment
longitudinal image processing withFSv6.0 first and FSv5.3).

Thanks in advance,
Best regards,

Lisa
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Re: [Freesurfer] ERROR: dimension mismatch between input volume and seg - VolumeROICorticalThickness

[M Janani]

Hi Douglas Greve,



Yes, I'm getting the same result as mentioned below.



Regards,

Janani







-



Did you get exactly the same error?



On 07/14/2017 02:05 AM, M Janani wrote:

>

> Hi Douglas Greve

> ,

>

>   Thanks for your support.

>

> I tried with the  --reshape-factor 6. But it didn't work for me.

>

>   The segmentation was created using the below mentioned data

>

> 1.SPM standard ROI

>

> 2..dat file generated using the T1.nii(available in SPM8 template) and

> fsaverage.

>

> Please help us to proceed further.

>

> Regards,

>

> Janani

>

> ---

>

> How did you create the segmentation? You can change the shape of the

> seg with mri_surf2surf --reshape 6 --s fsaverage --hemi lh --sval

> seg.mgh --tval seg.reshape.mgh

>

> On 7/7/17 10:15 AM, M Janani wrote:

> Hi Team,

>

> I'm attempting to extract cortical thickness values for a

> region-of-interest (ROI) defined in volume spacesubject for PiB MRI.

>

> I got the below mentioned error while computing the stats value

> cwd

>

> cmdline mri_segstats --seg

> freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh --in

> lh.thickness.fsaverage.mgh --sum segstats-CBLROI.txt

>

> sysname  Linux

> hostname teslak80

> machine  x86_64

> user lakshman

> UseRobust  0

> Loading /freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh

> Loading lh.thickness.fsaverage.mgh

> ERROR: dimension mismatch between input volume and seg

>   input 27307 1 6

>   seg   23406 1 7

>

> I tried with the solution provided in the below mail, but it didn't

> work for me

>

> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-January/027405.html

>

> 

>

> 

>

> Any help would be really helpful.

> Regards,

> Janani

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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/Bug

Re: [Freesurfer] Pediatric Atlas/Template

[Lilla Zollei]

Hi Jess,

Yes, there are. But currently we are focusing on the 0-2yrs age range. 
Your age range of interest will come after that.


Lilla

On Thu, 13 Jul 2017, Jessica Reynolds wrote:



I am wondering whether there are still plans to implement a pediatric 
atlas/template? I’m working with children aged 3-6 years.

Thanks in advance,

Jess.

 


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Re: [Freesurfer] Freesurfer pipeline for infant

[Lilla Zollei]

Hi Gianluca,

For your younger ages, this is the wiki that I would check:

https://surfer.nmr.mgh.harvard.edu/fswiki/ChildBrainManualEdits

We will look into the stats file.

Best, Lilla

On Tue, 11 Jul 2017, Gianluca Sforza wrote:


Hi Lilla,is there a range of age I should possibly take more care of with the 
FS outputs?
Should I refer to the advices on this page 
http://freesurfer.net/fswiki/FsTutorial/TroubleshootingData

I take the opportunity to report a small issue in the format of the stat files 
rh.aparc.stats & lh.aparc.stats 
While parsing those files, I found that a comma is missing after the field 
`CortexVol’ on the Measure Cortex row.
Please double check it; I am using last ver. 6 of FS.


sincerely
gianluca
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[Freesurfer] SPMPainting

[Geng Shuang]

I am confused that how to align the brain.img with my functional data in
spm...

https://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting

Best wishes!

1. Convert the brain.mgz volume to analyze:

mri_convert $SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img

2. Align brain.img with your functional data in spm (eg, func.img)



Irene Geng

Institute of Cognitive Neuroscience

East China Normal University
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Re: [Freesurfer] SPMPainting

[Geng Shuang]

I am confused that how to align the brain.img with my functional data in
spm...

https://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting

Best wishes!

1. Convert the brain.mgz volume to analyze:

mri_convert $SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img

2. Align brain.img with your functional data in spm (eg, func.img)



Shuang Geng

Master Candidate

Institute of Cognitive Neuroscience

East China Normal University

No.3663, Zhongshan North Road, Po District

Shanghai 200062, P. R. China



2017-07-17 22:33 GMT+08:00 Geng Shuang :

> I am confused that how to align the brain.img with my functional data in
> spm...
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting
>
> Best wishes!
>
> 1. Convert the brain.mgz volume to analyze:
>
> mri_convert $SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img
>
> 2. Align brain.img with your functional data in spm (eg, func.img)
>
> 
> 
>
> Irene Geng
>
> Institute of Cognitive Neuroscience
>
> East China Normal University
>
>
>
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Re: [Freesurfer] bbregister + mri_vol2vol different results

[Paul Glad Mihai]

Hello again,

I've found my mistake! Instead of using the brainmask from reconall for
the target, I used the brain from the fsl ouput of BET. This is a
mistake, since the two brains aren't aligned. I've corrected the mistake
and now it works.

Regards,
Glad

On 07/13/2017 11:02 PM, Paul Glad Mihai wrote:
> Hello,
> 
> I'm getting two different results from the coregistration step. When I run 
> bbregister on the mean epi it coregisters properly and writes out _bbreg.nii. 
> The next step involves registering the realigned epi time series to the T1 
> image using the same transform matrix calculated from the mean image. But the 
> results fail miserably. I've attached some sample images. 
> 
> I came across the same result after transforming the matrix it to ITK space 
> and applying the transform using ANTs' applyTransform, which tells me that 
> the ITK conversion works, but this registration goes wrong. Or I may not 
> really understand what I'm doing, lol.
> 
> Here are the commands:
> 
> bbregister --t2 --epi-mask --init-header --fslmat 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>  --reg 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat
>  --o 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii
>  --mov 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii
>  --s sub-01
> 
> mri_vol2vol --fsl 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>  --mov 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold.nii
>  --targ 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/brainextract/sub-01_acq-T1w_brain.nii.gz
>  --o 
> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold_warped.nii
> 
> Regards,
> Glad
> 
> 
> 
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> properly
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-- 
Paul Glad Mihai, PhD

Independent Research Group "Neural Mechanisms of Human Communication"
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstraße 1A, 04103 Leipzig, Germany

Phone:   +49 (0) 341-9940-2478
E-mail:  mi...@cbs.mpg.de

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Re: [Freesurfer] SPMPainting

[Douglas Greve]

use bbregister


On 7/17/17 10:35 AM, Geng Shuang wrote:


I am confused that how to align the brain.img with my functional data 
in spm...


https://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting 



Best wishes!

1. Convert the brain.mgz volume to analyze:

mri_convert $SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img

2. Align brain.img with your functional data in spm (eg, func.img)



Shuang Geng

Master Candidate

Institute of Cognitive Neuroscience

East China Normal University

No.3663, Zhongshan North Road, Po District

Shanghai 200062, P. R. China

2017-07-17 22:33 GMT+08:00 Geng Shuang >:


I am confused that how to align the brain.img with my functional
data in spm...

https://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting


Best wishes!

1. Convert the brain.mgz volume to analyze:

mri_convert $SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img

2. Align brain.img with your functional data in spm (eg, func.img)



Irene Geng

Institute of Cognitive Neuroscience

East China Normal University

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Re: [Freesurfer] FS Version 6 Long Processing

[Bruce Fischl]

Hi Martin

I believe it has been replaced with -autorecon-pial (since some of the 
pial surface generation has moved to autorecon3)


cheers
Bruce
On Mon, 17 Jul 2017, Martin 
Reuter wrote:




Hi Allison,

seems like autorecon2-pial has been removed from FreeSurfer (also in the cross 
sectional stream). I don't know when, why and what would be the equivalent
command, but someone on the list will know.


About brainmask edits, they are described here:

https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits

The brainmask in the base is the union of all mask from cross (after 
registration) and is fixed for all time points. If the mask is correct, this is 
usually OK.
So it makes sense to edit the brainmask in the base and not in the individual 
time points. In the base you would re-run autorecon2 and autorecon3 as the 
edited
brainmask affects not just the surfaces, but also aseg etc.

If edits are really needed in the long runs, then edit it there and also run 
autorecon2 and autorecon3.

Best, Martin



On 07/14/2017 07:28 PM, Allison Rainford wrote:
  Hi FreeSurfer Team,

My lab has recently begun editing longitudinal data in version 6 and have found 
that we cannot use the same flags for –autorecon2 as we did when running
longs in version 5.1. Typically, after making any necessary edits to a long, we 
run -autorecon2–pial –autorecon3. This flag hasn’t been successful in
version 6, producing an error message that the flag is unrecognized. Because we 
still only require some brainmask edits on the longs, we would like to
know how we can continue to run these to process only pial.

All help is greatly appreciated!

Allison


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Re: [Freesurfer] bbregister + mri_vol2vol different results

[Bruce Fischl]

glad it worked out
Bruce
On Mon, 17 Jul 2017, Paul Glad Mihai wrote:

> Hello again,
>
> I've found my mistake! Instead of using the brainmask from reconall for
> the target, I used the brain from the fsl ouput of BET. This is a
> mistake, since the two brains aren't aligned. I've corrected the mistake
> and now it works.
>
> Regards,
> Glad
>
> On 07/13/2017 11:02 PM, Paul Glad Mihai wrote:
>> Hello,
>>
>> I'm getting two different results from the coregistration step. When I run 
>> bbregister on the mean epi it coregisters properly and writes out 
>> _bbreg.nii. The next step involves registering the realigned epi time series 
>> to the T1 image using the same transform matrix calculated from the mean 
>> image. But the results fail miserably. I've attached some sample images.
>>
>> I came across the same result after transforming the matrix it to ITK space 
>> and applying the transform using ANTs' applyTransform, which tells me that 
>> the ITK conversion works, but this registration goes wrong. Or I may not 
>> really understand what I'm doing, lol.
>>
>> Here are the commands:
>>
>> bbregister --t2 --epi-mask --init-header --fslmat 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>>  --reg 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat
>>  --o 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii
>>  --mov 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii
>>  --s sub-01
>>
>> mri_vol2vol --fsl 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat
>>  --mov 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold.nii
>>  --targ 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/brainextract/sub-01_acq-T1w_brain.nii.gz
>>  --o 
>> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold_warped.nii
>>
>> Regards,
>> Glad
>>
>>
>>
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Re: [Freesurfer] Custom Annotation: 1st Annot Visible in TKSurfer but not Freeview

[Ruopeng Wang]

Hi Ursula,

Since FS 6.0, freeview stopped displaying index 0 in the annotation look 
up table which is usually reserved as "unknown 0 0 0 0", so that it 
doesn't show a black region on the surface. Would it be possible for you 
change your indices starting from 1? I will also update freeview so that 
it can check the color of index 0 and handle it more smartly.


Best,
Ruopeng

On 07/14/2017 06:10 PM, Ursula Tooley wrote:

Hi FreeSurfer Experts,

I’ve created a custom annotation file in MATLAB, using 
read_annotation.m and write_annotation.m, relabeling the Glasser 
parcellation regions. It seems to display as expected in tksurfer and 
tkmedit, but in freeview the first annotation is completely 
transparent (see images below), although if I hover my mouse over the 
area, it’s labeled with the correct struct_name. I’ve changed the 
alpha value in the annotation file and see no difference in freeview, 
and also given some previous listserv posts tried changing the RGB 
values for that first annotation in colortable.table.


View in tksurfer:
tksurfer fsaverage lh inflated -annotation my_annotation.annot

View in freeview:
freeview 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=my_annotation.annot


Any help would be greatly appreciated. I’m running FS 6.0, Freeview 
V2, this occurs both locally on my OSX El Capitan and on an HPC 
running Linux Centos.


Thanks in advance,
Ursula






---
Ursula Tooley
Ph.D. Student
Neuroscience Graduate Group
University of Pennsylvania
utoo...@gmail.com 
202.413.5627





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Re: [Freesurfer] qcache ERROR on longitudinal image processing with FreeSurfer v6.0

[Douglas N Greve]

you can run

pctsurfcon --s subject


On 07/17/2017 06:32 AM, Lisa Delalande wrote:
> Hello everyone,
>
> I'm using the new version of FreeSurfer processing with longitudinal 
> image processing. And at the step -base after a recon-all processing i 
> would like to make a qcache processing but it doesn't work... "cannot 
> find [...]/template_1-01VALAL/surf/lh.w-g.pct.mgh" (See in attachment 
> longitudinal image processing withFSv6.0 first and FSv5.3).
>
> Thanks in advance,
> Best regards,
>
> Lisa
>
>
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Re: [Freesurfer] Fw: spmregister

[Douglas N Greve]

Can you try

tkregister --mov perfusion_calib.nii.gz --reg reg.dat


On 07/14/2017 06:56 PM, John Anderson wrote:
>
> Hi Doug,
>
> It is the same command left by spmregister
> freeview orig.mgz pcals.nii
>
> Just i excluded the flag -f /surf/?h.orig
>
> what is your freeview command?
>
>
>
> On 07/14/2017 08:46 AM, John Anderson wrote:
>
> >
>
> >> Dear Freesurfer experts,
>
> >> I want to derive registration matrix between pcasl image and the
>
> >> structural space in Freesurfer (i.e. orig.mgz) If I open orig.mgz and
>
> >> the pcasl image in Freesurefr I see overlap between the images
>
> >> (attached Figure1).
>
> >> When I use "spmregister" as follow:
>
> >> spmregister --mov perfusion_calib.nii.gz --s SUBJ --reg reg.dat
>
> >> --fsvol orig --o CBF_T1.nii
>
> >>
>
> >> Then visualize "CBF_T1" using freeview I see mis-registration
>
> >> (attached Figure2)
>
> >>
>
> >> Please what I am doing wrong?
>
> >> Thank you for any guidance
>
> >> Jon
>
> >>
>
> >
>
> >
>
> >
>
> > ___
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>
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>
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>
> --
>
> Douglas N. Greve, Ph.D.
>
> MGH-NMR Center
>
> gr...@nmr.mgh.harvard.edu 
>
> Phone Number: 617-724-2358
>
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Re: [Freesurfer] TalAviQA and mris_jacobian

[Douglas N Greve]

cc'ing Avi who is the best person to shed light on TalAviQA. Not sure 
about the jacobian answer


On 07/15/2017 03:25 PM, Helfand, Alexander I wrote:
> Hi FreeSurfer Team,
>
> I was hoping I might be able to get some information about TalAviQA. I have 
> read that this number is a spatial correlation between the input image and 
> the image transformed to the Talairach atlas. Is that correct? Can you tell 
> me any more about how this correlation is calculated?
>
> I hope this isn't a silly question, but besides the Euler numbers and the 
> mris_jacobian command, are there any other quantitative metrics of how much 
> warping was necessary for a particular subject's recon-all? Also, are there 
> multiple ways to run mris_jacobian such that you can get information beyond 
> lh/rh.white.preaparc? Might you be able to offer any hints as to other files 
> to feed the mris_jacobian command besides 'mris_jacobian 
> ../surf/l(r)h.white.preaparc ../surf/l(r)h.sphere.reg 
> ../surf/l(r)h.jacobian_white'
>
> Finally, is there a complete set of documentation somewhere for the QA Tools 
> package of scripts? Are these scripts up to date and compatible with 
> Freesurfer 6? https://surfer.nmr.mgh.harvard.edu/fswiki/QATools suggests that 
> v1.1 came out in 2012 and the current release for download is v1.2...
>
> Thanks for your time, thanks for your efforts creating and maintaining 
> Freesurfer!
> Alex
>
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[Freesurfer] dev -FLAIRpial bug?

[Hibert, Matthew Louis]

Hi FS Devs,
We're running some reconstructions of 7T MPRAGEs with the -FLAIRpial flag 
turned on using the Martinos install of the dev version.  Recently we 
encountered the error in the attached recon-all log in which it appears that 
recon-all is trying to use the aseg.mgz before it has been created.  According 
to the dev table online, the mris_make_surfaces command as part of the 
-FLAIRpial processing should use aseg.presurf.mgz, but it crashes with an error 
that it was unable to open aseg.mgz.

Thanks,
Matt
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[Freesurfer] Monte-Carlo in LME

[Jordi Pegueroles]

Dear FS experts,

I was wondering if someone had performed multiple comparisons (ie 
monte-carlo) with the LME analyses. I have found a thread 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40195.html) 
where Doug recommends to run a GLM fit with the same data and then 
overwrite the sig.mgh file with the LME one.

My question is if is not more accurate to estimate the residuals from 
the LME model, then compute the relative smooth of the data with the 
mris_fwhm command and pass it as an argument in the mri_surfcluster 
command (mri_surfcluster --in $direct1/sig.mgh --csd 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/${hemi}/cortex/fwhm${rfwhm}/abs/th13/mc-z.csd
 
--cwsig $direct1/mc.abs.th13.sig.cluster.mgh --vwsig 
$direct1/abs.th13.sig.vertex.mgh --cwpvalthresh 0.05 --surf white).

Thanks in advance.

-- 
Jordi.
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