Re: [Freesurfer] hemisphere analysis

[lanbo Wang]

Dr. Douglas,

I try #3 method, when I run mri_glmfit, get error.
The code I used:
[mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y
lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm
--surf fsaverage_sym lh
Reading source surface
/HD4/subjects_results_symptom//fsaverage_sym/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 61972.710938
AvgVtxArea   0.378247
AvgVtxDist   0.693419
StdVtxDist   0.190498

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness
cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir
glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
sysname  Linux
hostname localhost.localdomain
machine  x86_64
user mtobia
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 1
y
/HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.thickness.sm10.mgh
logyflag 0
usedti  0
labelmask
/HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex.label
maskinv 0
glmdir glm.lh.lh-rh.thickness.sm10
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory glm.lh.lh-rh.thickness.sm10
Loading y from
/HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.thickness.sm10.mgh
Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat
Normalized matrix condition is 1
Matrix condition is 1
Found 146902 points in label.
Pruning voxels by thr: 0.00
Found 146902 voxels in mask
Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh
Reshaping mriglm->mask...
search space = 79288.081914
DOF = 0
ERROR: DOF = 0

The code I used before this one is
How can I resolve this problem.

Thanks,
Lanbo


On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve 
wrote:

> which code. I gave 3 options below, which one did you use?
>
>
> On 11/07/2017 02:43 PM, lanbo Wang wrote:
> > I try to use this code to compare left and right hemisphere by paired
> > t-test  and add age as covariate.
> >
> > Thanks,
> > Lanbo
> >
> > On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > which method are you trying to implement? If #3, then you need to run
> > mris_preproc separately for each subject, and then run that fscalc
> > command
> >
> >
> > On 11/07/2017 11:33 AM, lanbo Wang wrote:
> > > Hi Douglas,
> > >
> > > Thanks for your reply.
> > > I created the fsgd file as you show me, and run code like this. Am
> I
> > > right?
> > > 1.
> > > mris_preproc --fsgd Subject.xhemi.dat \
> > >   --target fsaverage_sym --hemi lh \
> > >   --xhemi --paired-diff \
> > >   --srcsurfreg fsaverage_sym.sphere.reg \
> > >   --meas thickness \
> > >   --out lh.lh-rh.thickness.age.sm00.mgh \
> > >  --s subj_02_1  --s subj_04_1  --s subj_05_1  --s subj_06_1  --s
> > > subj_08_1  --s subj_09_1  --s subj_10_1 --s subj_11_1  --s
> > subj_12_1
> > > --s subj_13_1  --s subj_14_1  --s subj_15_1  --s subj_16_1  --s
> > > subj_17_1 --s subj_18_1  --s subj_20_1  --s subj_21_1  --s
> > subj_22_1
> > > --s subj_24_1  --s subj_25_1  --s subj_26_1 --s subj_27_1  --s
> > > subj_29_1  --s subj_32_1
> > >
> > > 2.
> > > mri_glmfit --y lh.lh-rh.thickness.age.sm10.mgh --glmdir
> > > glm.lh.lh-rh.thickness.age.sm10 \
> > > --fsgd Subject.xhemi.dat \
> > > --C Avg-thickness-age-Cor.mtx \
> > > --surf fsaverage_sym lh
> > >
> > > Attachment is fsgd and Avg-thickness-age-cor.mtx.
> > >
> > > All best,
> > > Lanbo Wang
> > >
> > >
> > > On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl
> > > mailto:fis...@nmr.mgh.harvard.edu>
> >  > >> wrote:
> > >
> > > Hi Danny
> > >
> > > you need to give us more information if you want us to help
> you.
> > > Please include the command you ran and the entire screen
> output.
> > >
> > > cheers
> > > Bruce
> > >
> > >
> > > On Tue, 7 Nov 2017, Danny Deng wrote:
> > >
> > > Dear FDs,
> > > I encountered an odd situation:
> > >
> > > My free surfer will always shut down when I run command.
> > >
> > > My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz
> Intel
> > > Core i5
> > >
> > > I don’t know if the compatibility is fine with my download
> > > version (MacOS Lion OS X 10.7 (64b
> > > intel)Stable v6.0.0)
> > >
> > > Please kindly suggest.
> > >
> > > Thanks ver much
> > >
> > > Best Regards,Danny Deng
> > >
> > >
> > >   On Nov 7, 2017, at 7:14 AM, Douglas N Greve
> > >  > 
> >  >>>
> > > wrote:
> > >
> > >
> >

[Freesurfer] localGI issues

[Nillo, Ryan Michael R]

Hello experts,


I am using FreeSurfer version 6 and am trying to run recon-all -localGI. Each 
time I run it, it fails on make_roi_paths. Below is an excerpt of the 
recon-all.log file. Any help is much appreciated.


#@# Local Gyrification Index lh Thu Nov  9 14:06:42 PST 2017

 mris_compute_lgi --i lh.pial

=
rm -Rf /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial
=
=
mkdir -p /data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial
=
=
mris_fill -c -r 1 lh.pial 
/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=
reading surface from lh.pial...
writing filled volume to 
/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.
=
make_outer_surface('/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
 exit
=

< M A T L A B (R) >
  Copyright 1984-2015 The MathWorks, Inc.
   R2015b (8.6.0.267246) 64-bit (glnxa64)
  August 20, 2015


For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.


Academic License

>> reading filled volume...
closing volume...
morphological closing done.
writing outer surface...

=
mris_extract_main_component 
/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer 
/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main
=

counting number of connected components...
   76848 voxel in cpt #1: X=2 [v=76848,e=230538,f=153692] located at 
(-26.925182, 5.953999, 4.185574)
For the whole surface: X=2 [v=76848,e=230538,f=153692]
One single component has been found
nothing to do
done

=
mris_smooth -nw -n 30 
/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main
 ./lh.pial-outer-smoothed
=
smoothing for 30 iterations
smoothing surface tessellation for 30 iterations...
smoothing complete - recomputing first and second fundamental forms...
=
mris_euler_number ./lh.pial-outer-smoothed
=
euler # = v-e+f = 2g-2: 76848 - 230538 + 153692 = 2 --> 0 holes
  F =2V-4:  153692 = 153696-4 (0)
  2E=3F:461076 = 461076 (0)

total defect index = 0
=
mris_convert -n lh.pial-outer-smoothed 
/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc
=
=
find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_8510_.m');
 exit
=

< M A T L A B (R) >
  Copyright 1984-2015 The MathWorks, Inc.
   R2015b (8.6.0.267246) 64-bit (glnxa64)
  August 20, 2015


For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.


Academic License

>> FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.07 sec)

FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial-outer-smoothed
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.01 sec)


deltaT =

   10.1400


=
make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/data/sugrue2/NF1_qdec/sub_0015/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_8510_.m');
 exit
=

< M A T L A B (R) >
  Copyright 1984-2015 The MathWorks, Inc.
   R2015b (8.6.0.267246) 64-bit (glnxa64)
  August 20, 2015


For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.


Academic License

>> loading datas ...
FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.07 sec)

FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial-outer-smoothed
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.02 sec)

preparing outer mesh structure ...
face 5000 / 153692
face 1 / 153692
face 15000 / 153692
face 2 / 153692
face 25000 / 153692
face 3 / 153692
face 35000 / 153692
face 4 / 153692
face 45000 / 153692
face 5 / 153692
face 55000 / 153692
face 6 / 153692
face 65000 / 153692
face 7 / 153692
face 75000 / 15

Re: [Freesurfer] Getting aparc.a2009s.annot in MNI

[Bruce Fischl]

Hi Daiana

run mri_vol2vol --help. It has a bunch of examples and quite extensive help 
(thank you Doug!)
Bruce

On Thu, 9 Nov 2017, Daya P wrote:

> Hi Bruce,
> Can you give me some example code? I am not sure where the talairach would go?
> 
> 
> On Thu, Nov 9, 2017 at 1:21 PM, Bruce Fischl  
> wrote:
>   Hi Daiana
>
>   You should be able to use mri_vol2vol on the aparc+aseg.mgz and the
>   talairach.xfm in the subject's mri/transforms dir.
>
>   cheers
>   Bruce
>
>   On Thu, 9 Nov 2017, Daya P wrote:
>
>   > Hi All,
>   > I processed a bunch of subjects using recon-all, but now I would like 
> to get labels
>   from
>   > aparc.a2009s.annot from each subject in MNI space in nii from, the 
> problem is that the
>   annotation
>   > file (lh and rh) is in subject native space. I have a grey matter 
> mask in MNI from
>   each subject and
>   > my goal is to have each label from aparc.a2009s.annot to fit that 
> mask.
>   > How can I do this?
>   >
>   > Thank you,
>   > Daiana
>   >
>   >
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> 
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Re: [Freesurfer] Getting aparc.a2009s.annot in MNI

[Daya P]

Hi Bruce,

Can you give me some example code? I am not sure where the talairach would
go?


On Thu, Nov 9, 2017 at 1:21 PM, Bruce Fischl 
wrote:

> Hi Daiana
>
> You should be able to use mri_vol2vol on the aparc+aseg.mgz and the
> talairach.xfm in the subject's mri/transforms dir.
>
> cheers
> Bruce
>
> On Thu, 9 Nov 2017, Daya P wrote:
>
> > Hi All,
> > I processed a bunch of subjects using recon-all, but now I would like to
> get labels from
> > aparc.a2009s.annot from each subject in MNI space in nii from, the
> problem is that the annotation
> > file (lh and rh) is in subject native space. I have a grey matter mask
> in MNI from each subject and
> > my goal is to have each label from aparc.a2009s.annot to fit that mask.
> > How can I do this?
> >
> > Thank you,
> > Daiana
> >
> >
> ___
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>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] comparing sphere and sphere.reg

[Bruce Fischl]

Hi Tony

you can do that but it won't measure the distortion induced by the sphere 
mapping itself.


cheers
Bruce

On Thu, 9 Nov 2017, tony han wrote:



Hi,


I'm trying evaluating the distortion for each subject from their native space 
to fsaverage atlas
space. Is it a appropriate measure to compare ?h.sphere and ?h.sphere.reg? I 
assume that by
comparison, I may get the how each vertex warped during the registration? 
Thanks!


Best,

Tony



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[Freesurfer] comparing sphere and sphere.reg

[tony han]

Hi,


I'm trying evaluating the distortion for each subject from their native space 
to fsaverage atlas space. Is it a appropriate measure to compare ?h.sphere and 
?h.sphere.reg? I assume that by comparison, I may get the how each vertex 
warped during the registration? Thanks!


Best,

Tony

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Re: [Freesurfer] Getting aparc.a2009s.annot in MNI

[Bruce Fischl]

Hi Daiana

You should be able to use mri_vol2vol on the aparc+aseg.mgz and the 
talairach.xfm in the subject's mri/transforms dir.

cheers
Bruce

On Thu, 9 Nov 2017, Daya P wrote:

> Hi All,
> I processed a bunch of subjects using recon-all, but now I would like to get 
> labels from
> aparc.a2009s.annot from each subject in MNI space in nii from, the problem is 
> that the annotation
> file (lh and rh) is in subject native space. I have a grey matter mask in MNI 
> from each subject and
> my goal is to have each label from aparc.a2009s.annot to fit that mask.
> How can I do this?
> 
> Thank you,
> Daiana
> 
>
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[Freesurfer] Getting aparc.a2009s.annot in MNI

[Daya P]

Hi All,

I processed a bunch of subjects using recon-all, but now I would like to
get labels from aparc.a2009s.annot from each subject in MNI space in nii
from, the problem is that the annotation file (lh and rh) is in subject
native space. I have a grey matter mask in MNI from each subject and my
goal is to have each label from aparc.a2009s.annot to fit that mask.
How can I do this?

Thank you,
Daiana
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Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[Mehta, Chintan]

Thank you for the insight; that is very interesting. I'm performing tests of 
continuous independent variables over a single sample of normally developing 
children (ages uniformly distributed from 8 to 15 along with 50/50 gender 
split). The IV is, for example, age-normed cognitive scores falling in a normal 
distribution. Since there is only one group, I suppose creating my own template 
from all samples could introduce significant bias; especially if there are 
hidden sources of heterogeneity I'm unaware of.

Thank you.

Best,
Chintan


On 11/09/2017 07:07 AM, Greve, Douglas wrote:



> It might capture specific anatomical features that are unique to your
> data set. It can be tricky though as you need to make sure to include an
> equal mix of all your groups. Eg, if you have 20 ADs and 10 controls,
> you'd need to make an atlas with 10 ADs and 10 controls.


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Re: [Freesurfer] QDEC

[Kinzel, Phillipp]

Hi Doug,

do you have any other ideas why I can´t open the project file?

Best, Philipp

Von:  im Auftrag von "Kinzel, Phillipp" 

Antworten an: Freesurfer support list 
Datum: Mittwoch, 8. November 2017 um 14:33
An: Freesurfer support list 
Betreff: Re: [Freesurfer] QDEC

Hi Douglas, thank you for your quick response. Yes, I have permission to read 
and write for the file. I modified the permission to be able to execute the 
file as well, but that didn´t change anything. I created the file through the 
qdec- GUI and didn´t have any problems while running the GLM.

Von:  im Auftrag von Douglas Greve 

Antworten an: Freesurfer support list 
Datum: Mittwoch, 8. November 2017 um 09:51
An: "freesurfer@nmr.mgh.harvard.edu" 
Betreff: Re: [Freesurfer] QDEC


Do you have permission to read it? How was it created?

On 11/8/17 1:18 AM, Kinzel, Phillipp wrote:
Hi, I have problems loading project  files in QDEC.

I get the following error:

Loading data table /tmp/qdec_project_archive/qdec.table.dat...
ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat
Error loading the project file.

I would be greatful for any advice.

Best, Philipp







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Re: [Freesurfer] surface based fMRI gorup analysis from spm

[Elisa Castaldi]

Thank you very much for your help,
that almost fixed the problem.. Indeed it seems like it worked well for the
first subject, but then it crashed for the second one..
this is the last part of what it typed on the command window:

%
Cleaning up
---
rm -r ./tmp.mris_preproc.2277
mardi 7 novembre 2017, 17:12:21 (UTC+0100)
mris_preproc done
SUBJECTS_DIR$ --iv ${SUBJECTS_DIR}/sub02/stats/con_0001.nii
${SUBJECTS_DIR}/sub02/fmri/bbrumeanSBref_sess1_mb1.dat\
> --projfrac 0.5 \
>
--iv : commande introuvable


For the first subject it correctly created the lh.con.mris_preproc.log file
Any idea?
Thanks


On 7 November 2017 at 17:00, Douglas N Greve 
wrote:

> looks like you did not create the lta file properly. You can just pass
> mris_preproc the .dat file instead of the lta.
>
>
> On 11/07/2017 10:51 AM, Elisa Castaldi wrote:
> > Yes, the output is in native functional space.
> >
> > On 7 November 2017 at 16:40, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Did you keep the spm output in native functional space?
> >
> >
> > On 11/07/2017 09:23 AM, Elisa Castaldi wrote:
> > > Yes,
> > > this is what I have already done: I moved both the fsaverage and
> the
> > > subjects into SUBJECTS_DIR and the error I get is ERROR: source
> > volume
> > > is neither source nor target of the registration.
> > >
> > > On 7 November 2017 at 15:11, Douglas Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
> > >  > >> wrote:
> > >
> > > When you look in SUBJECTS_DIR,  you should see fsaverage and
> all
> > > the subjects being passed to mris_preproc. If not, you need to
> > > move them (or sym link them) into that folder.
> > >
> > >
> > > On 11/7/17 6:07 AM, Elisa Castaldi wrote:
> > >> Thanks for your answer.
> > >> If I don't specify the directory I get the following error
> > >> ERROR: cannot find fsaverage in SUBJECTS_DIR
> > >>
> > >> and if I move fsaverage to SUBJECTS_DIR it says that it cannot
> > >> find manat_mp1 which is the name of the folder containing the
> > >> results of recon all for the subject sub01 (contained in the
> > >> SUBJECTS_DIR/surfaces folder). If then I move the manat_mp1
> > >> folder into SUBJECTS_DIR it starts running, but then gives the
> > >> following error ERROR: source volume is neither source nor
> > target
> > >> of the registration.
> > >> Below the entire list of output printed before the error
> > >>
> > >> mris_preproc --out lh.con.mgh --target fsaverage --hemi lh \
> > >> > --iv ${SUBJECTS_DIR}/sub01/stats/con_0001.nii
> > >> ${SUBJECTS_DIR}/sub01/fmri/mp1reg.lta\
> > >> nsubjects = 1
> > >> tmpdir is ./tmp.mris_preproc.30824
> > >> SUBJECTS_DIR
> > >> Log file is lh.con.mris_preproc.log
> > >>
> > >> setenv SUBJECTS_DIR
> > >> cd /SUBJECTS_DIR
> > >> /i2bm/local/freesurfer/bin/mris_preproc --out lh.con.mgh
> > --target
> > >> fsaverage --hemi lh --iv /SUBJECTS_DIR/sub01/stats/con_
> 0001.nii
> > >> /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
> > >>
> > >> $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp
> $
> > >> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> > >> tmpdir is ./tmp.mris_preproc.30824
> > >> Src lh sphere.reg
> > >> Trg lh sphere.reg
> > >>
> > >> ---
> > >> #@# 1/1 manat_mp1  --
> > >> ---
> > >> mri_vol2surf --src /SUBJECTS_DIR/sub01/stats/con_0001.nii
> > >> --srcreg /SUBJECTS_DIR/sub01/fmri/mp1reg.lta --hemi lh --out
> > >> ./tmp.mris_preproc.30824/subjsurfvals.mgh --cortex
> --noreshape
> > >> srcvol = SUBJECTS_DIR/sub01/stats/con_0001.nii
> > >> srcreg = /SUBJECTS_DIR/sub01/fmri/mp1reg.lta
> > >> srcregold = 0
> > >> srcwarp unspecified
> > >> surf = white
> > >> hemi = lh
> > >> reshape = 0
> > >> interp = nearest
> > >> float2int = round
> > >> GetProjMax = 0
> > >> INFO: float2int code = 0
> > >> Done loading volume
> > >> Input reg is LTA
> > >>
> > >> type  = 0 # LINEAR_VOX_TO_VOX
> > >> nxforms   = 1
> > >> mean  = 0. 0. 0.
> > >> sigma = 1.
> > >> 1 4 4
> > >> 9.66621398926e-01 2.551120938733220e-03
> > 5.084594013169408e-04
> > >> -5.48828125000e-01
> > >> 4.461563366930932e-04 2.438484877347946e-02
> > >> -9.997024536132812e-01 2.180384216308594e+02
> > >> -2.562706125900149e-03 9.996992945671082e-01
> > >> 2.438353188

Re: [Freesurfer] Creating cached versions of Xhemi registrations

[Mehta, Chintan]

Dear Doug,

I think that is essentially what I figured. Based on remarks in other posts, my 
steps for evaluating laterality index entail applying:


(1). Apply mri_preproc for each subject $SUB and $meas (area or thickness) 
individually using -xhemi flag but without any paired differences via:
> mris_preproc --target fsaverage_sym --hemi lh --xhemi --srcsurfreg 
> fsaverage_sym.sphere.reg --meas $meas --out  ${SUB}_out.mgh --s $SUB
Result is a surface file with two volumes (lh and xhemi-lh) called 
${SUB}_out.mgh for each subject.

(2). Smooth the two volumes in ${SUB}_out.mgh at a given $fwhm (5, 10, 15...):
> mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm $fwhm  
> --i ${SUB}_out.mgh --o ${SUB}_out-sm${fwhm}.mgh
to create a surface file with two volumes whose values are smoothed at fwhm = 
$fwhm.

(3). Compute laterality index over the surface for each subject via 
paired-diff-norm:
> mri_concat ${SUB}_out-sm${fwhm}.mgh --paired-diff-norm --o 
> ${SUB}_latIndex-sm${fwhm}.mgh
where ${SUB}_latIndex-sm${fwhm}.mgh is the surface file with laterality index 
for subject $SUB (after smoothing measures over left and right hemispheres).

(4). Stack laterality indices for each subject in sample G  (of n subjects) 
into a single mgh,
> mri_concat --i  SUB1_latIndex-sm${fwhm}.mgh --i  SUB2_latIndex-sm${fwhm}.mgh 
> ... --i  SUBn_latIndex-sm${fwhm}.mgh --out --i  
> sampleG_latIndex-sm${fwhm}.mgh.

(5) Run glm with designed matrix sampleG_design.txt containing n rows of 
covariates for SUB1, SUB2, ..., SUBn (in order) via:
> mri_glmfit --y sampleG_latIndex-sm${fwhm}.mgh --X $sampleG_design.txt 
> --no-rescale-x --glmdir glm_sampleG --C con1.mat --surf fsaverage_sym lh

The whole purpose of this exercise + question was that I need to fit the GLM 
over subsets of the sample for sensitivity analysis to determine whether 
significance for the contrast in con1.mat (say slope of an IV, such as age) 
depends on patterns of based on demographics groups (such as gender). I suppose 
alternatively, I could just as well fit another GLMs with a design matrix 
modeling interactions between age and gender to make my evaluation, over the 
same set of stacked surfaces for the full sample.

Thank you.

Best,
Chintan


  1.
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Re: [Freesurfer] longitudinal base error. (not a netCDF file)

[miracle ozzoude]

Hello Martin,

I tried your first suggestion (removing the flags) and I got the same
errors. Yes, I do have enough space on the disk and nu1.mnc file does
exist. Do you think my script is the problem? I have attached the new recon
log file and my script. Thanks.

Best,
Paul

On Thu, Nov 9, 2017 at 11:13 AM, Martin Reuter 
wrote:

> Hi Paul,
>
> you can try to re-run from scratch (ensure there is enough space on the
> disk) and if you can replicate the problem start dropping some of the flags
> (like the parallel and the bigventricles etc, to find out if this is caused
> by one of the flags.)
>
> Anyway it looks more like an IO problem
> ncopen: filename "./tmp.mri_nu_correct.mni.53099/nu1.mnc": Not a netCDF
> file
> miopen: MINC package entry point
> Error opening ./tmp.mri_nu_correct.mni.53099/nu1.mnc
> mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.
> 53099/nu1.mnc
>
> is that file even there?
>
> Best, Martin
>
>
> > On 8. Nov 2017, at 19:56, miracle ozzoude  wrote:
> >
> > Hello FreeSurfer,
> >
> > While running base step of the longitudinal pipeline, i got the
> following error (please see the rec-all.log file for more details). How do
> i solve this problem? Thank you
> >
> > Best,
> > Paul
> > ___
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>
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recon-all.error
Description: Binary data


recon-all.log
Description: Binary data


FreeSurferLongitudinal.sh
Description: Bourne shell script
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Re: [Freesurfer] longitudinal base error. (not a netCDF file)

[Martin Reuter]

Hi Paul,

you can try to re-run from scratch (ensure there is enough space on the disk) 
and if you can replicate the problem start dropping some of the flags (like the 
parallel and the bigventricles etc, to find out if this is caused by one of the 
flags.) 

Anyway it looks more like an IO problem 
ncopen: filename "./tmp.mri_nu_correct.mni.53099/nu1.mnc": Not a netCDF file
miopen: MINC package entry point
Error opening ./tmp.mri_nu_correct.mni.53099/nu1.mnc
mincRead(): error reading volume from file 
./tmp.mri_nu_correct.mni.53099/nu1.mnc

is that file even there?

Best, Martin


> On 8. Nov 2017, at 19:56, miracle ozzoude  wrote:
> 
> Hello FreeSurfer, 
> 
> While running base step of the longitudinal pipeline, i got the following 
> error (please see the rec-all.log file for more details). How do i solve this 
> problem? Thank you
> 
> Best, 
> Paul
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[Freesurfer] Creating functional ROI

[a a]

Dear FreeSurfer community,

I am new to FreeSurfer and I apologize in advance if my questions are too
naiive.

I have some nii files for both a localizer and an experiment. I would like
to find some ROIs in the localizer, get their coordinates, create a mask,
and then find those regions on the experiment data and run MVPA.

My main goal is to keep everything in the native space. Also, I am looking
for percent signal change in selected ROIs.


Here is my approach to analyze the localizer data:

First, I ran the recon-all command. Then, I preprocessed the data in native
space. The command that I ran was:

preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm
5 -per-session -force



Then, I configured my analyses and contrasts in each hemisphere, as well as
the volume.

Finally, I ran the analyses for each hemispheres and the volume. I ran this
command:


selxavg3-sess -s sess01 -analysis ffa.native.rh



Lastly, I visualized the results by running these commands:

tksurfer-sess -s sess01 -hemi rh -analysis ffa.native.rh -c faces-vs-bodies
-self



tkmedit-sess -s sess01 -analysis ffa.native.mni -c faces-vs-bodies -self



So far, I think I have done everything correctly as am seeing the
activation map where I am supposed to.



Now, I would like to be able to select some of these ROIs/clusters, take
their voxel coordinates/numbers and create a mask. Then, use this mask on
the main experiment (non localizer) nii files and get the signal value for
only those voxels. Is this possible?


I have found this tutorial to create a functional ROI
https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs but unfortunately I
am not following it. I don't see these options in tksurfer.


Also is it possible to create an ROI on the surface?


I appreciate any help.



Thank you so much



Ashley Cole
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Re: [Freesurfer] preproc-sess with symbolic links

[Douglas N Greve]

Why do you think this has to do with sym links? Can you run the 
preproc-sess command with -debug as the first option and send the results?


On 11/08/2017 11:50 AM, Tuominen, Lauri Johannes wrote:
> Hi all,
> I’m trying to run preproc-sess using symbolic links in my SUBJECTS_DIR but 
> the program exists with error message: could not find session .
>
> Symbolic links work fine when I run recon-all for instance.
>
> Suggestion for a fix would be greatly appreaciated.
>
> Cheers!
> Laurio
>   
>
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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
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Re: [Freesurfer] Creating cached versions of Xhemi registrations

[Douglas N Greve]

Sorry, caching is not possible with xhemi. You can just run the 
mris_preproc command multiple times, one for each subject, specifing a 
subject-specific output file for each. This is all  that the -qcache 
flag does anyway


On 11/08/2017 02:10 PM, Mehta, Chintan wrote:
>
> Dear FreeSurfer Users,
>
> I'm using FreeSurfer version 6.0. I've processing subjects with 
> recon-all and performed surface-based interhemispheric registration 
> (via Xhemi at https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi).
>
>
> I want to run a GLM on the subjects Area and Thickness from the 
> differences (Left minus Right). When stacking subjects asymmetry maps, 
> I wanted to use a "--cache-only".
>
> The post at 
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27657.html 
> seems to imply this requires running
> > recon-all -qcache -measure area -target fsaverage_sym -fwhm 10 
> -no-isrunning -s subjid -hemi lh
> for area at FWHM = 10.
>
> This would create files with the left hemisphere area registered to 
> fsaverage_sym at smoothing FWHM = 10:
> $subjid/surf/lh.area.fwhm10.fsaverage_sym.mgh
>
> However, how do I do this also for the xhemi registration? I.e. create 
> a file like $subjid/xhemi/surf/lh.area.fwhm10.fsaverage_sym.mgh
>
>
> Then, if I do this, can I stack the subjects using something like:
> > mris_preproc --target fsaverage_sym --hemi lh
>   --xhemi --paired-diff \
>   --srcsurfreg fsaverage_sym.sphere.reg \
>   --cache-in area.fwhm10.fsaverage_sym \
>   --out lh.lh-rh.area.sm10.mgh \
>   --s subj1 --s subj2 ...
>
> Thank you.
>
> Best,
> Chintan
>
>
>
> mris_preproc --target fsaverage_sym --hemi lh
>--xhemi --paired-diff \
>--srcsurfreg fsaverage_sym.sphere.reg \
>--meas thickness \
>--out lh.lh-rh.thickness.sm00.mgh \
>--s subj1 --s subj2 ...
>
>
>
>
>
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Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[Douglas N Greve]

It might capture specific anatomical features that are unique to your 
data set. It can be tricky though as you need to make sure to include an 
equal mix of all your groups. Eg, if you have 20 ADs and 10 controls, 
you'd need to make an atlas with 10 ADs and 10 controls.


On 11/08/2017 03:57 PM, Mehta, Chintan wrote:
> Dear Doug,
> Are there reasons why registering to my_subject_average 
> (template defined from, say, average in a cross-sectional sample) can 
> be better than registering to fsaverage?
> Thank you.
> Best,
> Chintan
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[Douglas N Greve]

no, sorry


On 11/09/2017 03:50 AM, M del Mar Velasco wrote:
>
> Thanks you for your reply.
>
> I have used surfreg script and now it runs correctly. However, my 
> subject list is very long, I have 100 subjects and running surfreg 
> with all subject takes 13 hours (using all my cpus in a parallel way). 
> Is there any option to reduce this long time? Any cuda file?
>
>
> Thanks in advance,
>
>
> M del Mar
>
>
>
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Re: [Freesurfer] Local gyrification index - vertex-wise analysis values

[Douglas N Greve]

Don't know what you mean by "extract lGI values from surface data" if 
not using mri_segstats as we've discussed. I think you can do the 
comparison you want  in the GLM using a "two group" analysis where one 
group only has one subject.


On 11/09/2017 01:46 AM, Buse Merve Ürgen wrote:
> Thank you so much! Can I also learn whether running vertex-wise analysis 
> without GLM analysis in Qdec is possible or not? As I said, I will compare a 
> single patient with a group of healthy controls, so GLM would not work. What 
> would you suggest for this? Is it possible to extract lGI values from surface 
> data?
>
> Thank you for your help,
> Buse
>
> —
>
> Douglas N Greve  şunları yazdı (7 Kas 2017 21:12):
>
>> Intensity Mean will be the mean value of the input (lGI) averaged over
>> the ROI.
>>
>> STD, Max, Min, and Range are the intensity stddev maximimum mininum
>> andrange=max-min over the ROI
>>
>>
>>> On 11/07/2017 12:57 PM, Buse Merve Ürgen wrote:
>>> Dear Freesurfers,
>>>
>>> I have two questions:
>>>
>>> 1) In the last stage of the recon-all -s  -localGI analysis,
>>> local gyrification index values are calculated at each pial vertices.
>>> Is there any way (command?) to extract /vertex-wise local gyrification
>>> index values/ (of individual subjects) /before running GLM analysis in
>>> Qdec/? GLM analysis is not suitable for my study (single-case), so I
>>> need to extract values for each subject and use them for my own
>>> statistical analysis.
>>>
>>> 2) As far as I know we can extract /parcel-wise lGI/ values using the
>>> following command:
>>>
>>> mri_segstats --annot /subjID/ lh aparc \
>>>
>>>--i $SUBJECTS_DIR//subjID//surf/lh.pial_lgi \
>>>
>>>--sum lh.aparc.pial_lgi.stats
>>>
>>>
>>> Running this command provides "Intensity Mean, Intensity STD,
>>> Intensity Max, Intensity Min, Intensity Range" values for each
>>> parcellated area. Can you explain these values and what they mean?
>>>
>>>
>>> Thanks,
>>>
>>> -Buse
>>>
>>>
>>>
>>>
>>> On 5 November 2017 at 19:54, Buse Merve Ürgen >> > wrote:
>>>
>>> Dear Freesurfer developers,
>>>
>>> I would like to run Local Gyrification Index analysis for a group
>>> of healthy controls and a single patient. After running recon-all
>>> -s  -localGI command, we get lh.pial_lgi and rh.pial_lgi
>>> surf files. In the last stage of this analysis, local gyrification
>>> index values are calculated at each pial vertices.
>>>
>>> In the wiki, it is said that the next process should be done in
>>> qdec, but since I have only one patient, GLM analysis would not be
>>> suitable. Thus, I would like to get the LGI values of each subject
>>> as e.g. text files (like stats files for curvature, thickness, gm
>>> volume), and use them for my own analysis (not in qdec). I know
>>> that we can get parcel-wise anaysis values using this command:
>>> mri_segstats --annot CASE lh aparc \
>>>
>>>   --i $SUBJECTS_DIR/CASE/surf/lh.pial_lgi \
>>>
>>>   --sum lh.aparc.pial_lgi.stats
>>>
>>> But I would like to use vertex-wise analysis values for my won
>>> analysis. Is it possible? Can I learn the command I need to use to
>>> get these values for each subject?
>>>
>>> Thank you,
>>> Buse
>>>
>>> --
>>>
>>> Buse
>>>
>>> ​ Urgen
>>>
>>>
>>>
>>>
>>> -- 
>>>
>>> Buse M. Ürgen
>>>
>>> Ph.D. Candidate Neuroscience Graduate Program National Magnetic
>>> Resonance Research Center (UMRAM) & Aysel Sabuncu Brain Research
>>> Center Bilkent University Ankara, 06800 Turkey
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
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>>
>>
>> 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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> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center

Re: [Freesurfer] Repeated amygdala dev7-segmentation volumes do not correspond

[Iglesias Gonzalez, Eugenio]

Dear Reetta-Liina,
After discussion with Koen Van Leemput, I believe I know what the source for 
these differences it, and it should be fixed soon. 
Having said that, I wouldn’t worry too much about a 2 cubic mm difference 
between two runs. 
Cheers,
/Eugenio

-- 
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
 

On 09/11/2017, 09:01, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Reetta-Liina Armio"  wrote:

Yes, all the specs are absolutely the same, same machine, same platform 
etc. No parallelization. 

Thank you for the help!

Best,

Reetta-Liina

Lähettäjä: freesurfer-boun...@nmr.mgh.harvard.edu 
 käyttäjän  puolestaIglesias Gonzalez, 
Eugenio 
Lähetetty: 9. marraskuuta 2017 10:26
Vastaanottaja: Freesurfer support list
Aihe: Re: [Freesurfer] Repeated amygdala dev7-segmentation volumes do not 
correspond

Dear Reetta-Liina,
Is this on the same machine, platform, etc?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 08/11/2017, 20:45, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Reetta-Liina Armio"  wrote:


Hi!

I have done twice the analysis of amygdala segmentation (dev 7 version) 
with exactly same way. The volumes do not correspond each other and there is 
approximately 2mm3 difference in volumes randomly in either direction.

Is this normal or is it something to do with the dev 7 version? Should 
I be worried?

Thank you!

Best, Reetta-Liina Armio



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Re: [Freesurfer] Repeated amygdala dev7-segmentation volumes do not correspond

[Reetta-Liina Armio]

Yes, all the specs are absolutely the same, same machine, same platform etc. No 
parallelization. 

Thank you for the help!

Best,

Reetta-Liina

Lähettäjä: freesurfer-boun...@nmr.mgh.harvard.edu 
 käyttäjän  puolestaIglesias Gonzalez, 
Eugenio 
Lähetetty: 9. marraskuuta 2017 10:26
Vastaanottaja: Freesurfer support list
Aihe: Re: [Freesurfer] Repeated amygdala dev7-segmentation volumes do not 
correspond

Dear Reetta-Liina,
Is this on the same machine, platform, etc?
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 08/11/2017, 20:45, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Reetta-Liina Armio"  wrote:


Hi!

I have done twice the analysis of amygdala segmentation (dev 7 version) 
with exactly same way. The volumes do not correspond each other and there is 
approximately 2mm3 difference in volumes randomly in either direction.

Is this normal or is it something to do with the dev 7 version? Should I be 
worried?

Thank you!

Best, Reetta-Liina Armio



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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.




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Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

[M del Mar Velasco]

Thanks you for your reply.

I have used surfreg script and now it runs correctly. However, my subject list 
is very long, I have 100 subjects and running surfreg with all subject takes 13 
hours (using all my cpus in a parallel way). Is there any option to reduce this 
long time? Any cuda file?


Thanks in advance,


M del Mar
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[Freesurfer] Where is the result of mris_pmake ?

[Hyungjun Kim]

Dear surfers,

I am trying to measure the distance between two activated vertices...

Now, I run "mris_pmake --optionsFile=options.txt"
and here is the options.txt file below ,
But I did not get any result on the window or ./ores.log file...

How can I get the result from mris_pmake ?

Thanks in advance.

Hyungjun Kim (Korea Institute of Oriental Medicine)

***


#
# auto-generated optionsFile
#


# Input surfaces and curvature functions
surfaceFile  =
/mnt/data1/subjects/csm0928/surf/lh.inflated
auxSurfaceFile   =
/mnt/data1/subjects/csm0928/surf/lh.smoothwm
curvatureFile=
/mnt/data1/subjects/csm0928/surf/lh.smoothwm.H.crv
sulcalHeightFile =
/mnt/data1/subjects/csm0928/surf/lh.sulc

# Start and End vertices

startVertex  =
1803
endVertex=
44765

# Control flags and settings
controlPort  =
1701
timeoutSec   =
60
b_transitionPenalties=
0
b_syslogPrepend  =
1
b_patchFile_save =
0
b_labelFile_save =
1
b_useAbsCurvs=
0
b_exitOnDone =
1
b_costPathSave   =
0

# Output file names and file stems
costFile =
cost.txt
patchFile=
dijk
labelFile=
dijk
labelFileAuxSurface  =
dijkAuxSurface

# Messaging channels
userMessages =
./user_msg.log
sysMessages  = ./osys.log
resultMessages   = ./ores.log

# Weights
wd   =
1.00
wc   =
0.00
wh   =
0.00
wdc  =
0.00
wdh  =
0.00
wch  =
0.00
wdch =
0.00
wdir =
0.00

# Transitional penality weights
Dwd  =
1.00
Dwc  =
1.00
Dwh  =
1.00
Dwdc =
1.00
Dwdh =
1.00
Dwch =
1.00
Dwdch=
1.00
Dwdir=
1.00

# mpmProg
mpmProgID=
2
mpmArgs  =
startVertex:1803,endVertex:44765
costCurvFile =
lh.autodijk.crv

# mpmOverlay
mpmOverlayID =
3

# Debugging -- change at your own risk!
b_mpmProgUse =
1
b_mpmOverlayUse  = 0
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Re: [Freesurfer] Repeated amygdala dev7-segmentation volumes do not correspond

[Iglesias Gonzalez, Eugenio]

Dear Reetta-Liina,
Is this on the same machine, platform, etc?
Cheers,
/Eugenio

-- 
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
 

On 08/11/2017, 20:45, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Reetta-Liina Armio"  wrote:


Hi!

I have done twice the analysis of amygdala segmentation (dev 7 version) 
with exactly same way. The volumes do not correspond each other and there is 
approximately 2mm3 difference in volumes randomly in either direction.

Is this normal or is it something to do with the dev 7 version? Should I be 
worried?

Thank you!

Best, Reetta-Liina Armio



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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
dispose of the e-mail.




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