Re: [Freesurfer] mpr2mni305 talaraich transformation error

[Dijkshoorn, A.B.C. (Aicha)]

Dear Emma,

Thank you for your response!

Since I got this message I added the -cw256 flag:

The physical sizes are (512.00 mm, 512.00 mm, 110.00 mm), which cannot fit in 
256^3 mm^3 volume.
ERROR! FOV=512.000 > 256
Include the flag -cw256 with recon-all!

However, when inspecting the orig.mgz file the head is still not entirely 
visible any more (with -cw256 flag) ... Is is possible to link (-ln) the 
orig.mgz to the rawavg.mgz file to work around this problem? Or are there other 
options? I added screenshots for visualisation purposes.

Kind regards,
Aicha Dijkshoorn






From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Boyd, Emma 
[ebo...@mgh.harvard.edu]
Sent: Friday, February 02, 2018 5:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mpr2mni305 talaraich transformation error


Hi Aicha,


Have you visually inspected your input image, rawavg.mgz or orig.mgz to make 
sure they look ok?


Emma



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Dijkshoorn, A.B.C. 
(Aicha) 
Sent: Friday, February 2, 2018 7:37:25 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mpr2mni305 talaraich transformation error

Hello free surfer developers,


I am attempting to compute cortical thickness for anatomical ROIs in neonates, 
but for some of my subjects I get the following error when I run the 
auto-recon1 command:



\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n

ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

Darwin leia.ds.umcutrecht.nl 14.5.0 Darwin Kernel Version 14.5.0: Sun Jun  4 
21:40:08 PDT 2017; root:xnu-2782.70.3~1/RELEASE_X86_64 x86_64

recon-all -s N192_con_recon exited with ERRORS at Fri Feb  2 12:32:02 CET 2018



Is there any way I can work around this error?

I've also attached the recon-all.log and the talaraich_avi.log in case it's of 
any use.

Kind regards,
Aicha Dijkshoorn

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[Freesurfer] How to compile FreeSurfer with CUDA?

[Markus.Mertens]

Hello Freesurfer experts,

I am trying to compile FreeSurfer to make use of its CUDA capabilities. The 
precompiled version does not run on my system. But when I try to compile 
FreeSurfer I get the following error:

# ./configure --with-pkgs-dir=/usr/local/centos6-x86_64-packages 
--enable-fermi-gpu
...
configure: Getting OpenGL info...
checking GL directory... gl directory is /usr/include
checking windows.h usability... no
checking windows.h presence... no
checking for windows.h... no
checking for OpenGL library... no
configure: error: FATAL: GL not found, but needed for  tcltkapps XawPlusapps 
kwwapps wxwapps. Use --with-gl-dir=... to specify


But OpenGL is installed:

# ll /usr/lib64/libGL.so*
lrwxrwxrwx 1 root root 14 Jan 15 23:35 /usr/lib64/libGL.so -> 
libGL.so.1.2.0*
lrwxrwxrwx 1 root root 14 Jan 15 23:35 /usr/lib64/libGL.so.1 -> 
libGL.so.1.2.0*
-rwxr-xr-x 1 root root 452752 Jan 15 23:37 /usr/lib64/libGL.so.1.2.0*
# ll /usr/include/GL/gl.h
-rw-r--r-- 1 root root 80615 Jan 15 23:35 /usr/include/GL/gl.h
#


The configure script did not ask for CUDA, yet. But CUDA is also installed in 
/usr/lib64:

# ll /usr/lib64/libcuda*
-rw-r--r-- 1 root root 556000 Jan 13  2017 /usr/lib64/libcudadevrt.a
lrwxrwxrwx 1 root root 16 Jan 13  2017 /usr/lib64/libcudart.so -> 
libcudart.so.8.0*
lrwxrwxrwx 1 root root 19 Jan 13  2017 /usr/lib64/libcudart.so.8.0 -> 
libcudart.so.8.0.61*
-rwxr-xr-x 1 root root 415432 Jan 13  2017 /usr/lib64/libcudart.so.8.0.61*
-rw-r--r-- 1 root root 775162 Jan 13  2017 /usr/lib64/libcudart_static.a
#


Adding the option  "--with-gl-dir=/usr/lib64" to the configure script does not 
help. What else could I try?

Regards,

Markus



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Akademisches Lehrkrankenhaus der Universität Münster

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Geschäftsführer
Dr. Rainer Norden (Vorsitz)
Dr. Matthias Ernst
Dr. Maren Thäter

Vorsitzender des Aufsichtsrates
Pastor Ulrich Pohl


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Re: [Freesurfer] How to compile FreeSurfer with CUDA?

[Melvin Robinson]

Once upon a time I had many problems with OpenGL/GLU problems in my FreeSurfer 
build.  Ultimately the problem was that the version of GLU installed with Mesa 
package was not really compatible with the compiler that I was using.   After 
straightening this problem out using the configure option --with-cuda allowed 
me to build with CUDA 9.1 with no problems.


What is your setup?  Compilers?  GPU?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of markus.mert...@evkb.de 

Sent: Monday, February 5, 2018 7:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] How to compile FreeSurfer with CUDA?

Hello Freesurfer experts,

I am trying to compile FreeSurfer to make use of its CUDA capabilities. The 
precompiled version does not run on my system. But when I try to compile 
FreeSurfer I get the following error:

# ./configure --with-pkgs-dir=/usr/local/centos6-x86_64-packages 
--enable-fermi-gpu
...
configure: Getting OpenGL info...
checking GL directory... gl directory is /usr/include
checking windows.h usability... no
checking windows.h presence... no
checking for windows.h... no
checking for OpenGL library... no
configure: error: FATAL: GL not found, but needed for  tcltkapps XawPlusapps 
kwwapps wxwapps. Use --with-gl-dir=... to specify


But OpenGL is installed:

# ll /usr/lib64/libGL.so*
lrwxrwxrwx 1 root root 14 Jan 15 23:35 /usr/lib64/libGL.so -> 
libGL.so.1.2.0*
lrwxrwxrwx 1 root root 14 Jan 15 23:35 /usr/lib64/libGL.so.1 -> 
libGL.so.1.2.0*
-rwxr-xr-x 1 root root 452752 Jan 15 23:37 /usr/lib64/libGL.so.1.2.0*
# ll /usr/include/GL/gl.h
-rw-r--r-- 1 root root 80615 Jan 15 23:35 /usr/include/GL/gl.h
#


The configure script did not ask for CUDA, yet. But CUDA is also installed in 
/usr/lib64:

# ll /usr/lib64/libcuda*
-rw-r--r-- 1 root root 556000 Jan 13  2017 /usr/lib64/libcudadevrt.a
lrwxrwxrwx 1 root root 16 Jan 13  2017 /usr/lib64/libcudart.so -> 
libcudart.so.8.0*
lrwxrwxrwx 1 root root 19 Jan 13  2017 /usr/lib64/libcudart.so.8.0 -> 
libcudart.so.8.0.61*
-rwxr-xr-x 1 root root 415432 Jan 13  2017 /usr/lib64/libcudart.so.8.0.61*
-rw-r--r-- 1 root root 775162 Jan 13  2017 /usr/lib64/libcudart_static.a
#


Adding the option  "--with-gl-dir=/usr/lib64" to the configure script does not 
help. What else could I try?

Regards,

Markus


___

Evangelisches Klinikum Bethel gGmbH
Akademisches Lehrkrankenhaus der Universität Münster

Sitz der Gesellschaft
Kantensiek 11 | 33617 Bielefeld

Amtsgericht Bielefeld HRB 30169

Geschäftsführer
Dr. Rainer Norden (Vorsitz)
Dr. Matthias Ernst
Dr. Maren Thäter

Vorsitzender des Aufsichtsrates
Pastor Ulrich Pohl



[X]
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Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

[Douglas Greve]

I cannot replicate this. There must be some strange permission error. 
Can you try to make a new analysis with a different name and just see if 
fails?


On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
> Hello Dr. Greve,
>
> The analysis.info file is below. I should also say that, when I am trying to 
> create new analysis and contrast files, while creating the .config file for 
> contrast, th system gives the same error saying that it cannot enter the file.
>
> # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $
> # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface self 
> lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 
> -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 1.25 
> -force
> # DATE Tue Jan 30 07:14:05 EST 2018
>
> analysis rtopyTR2.lh
> mcstem fmcpr
> fsd bold
> TR 2
> RegDOF 6
> PerSession 0
> RawSpace surface self lh
> mask brain
> RawFWHM 5
> RawSTC none
> nSliceGroups 1
> UseB0DC 0
> ApplySubCortMask 1
> inorm 100
> acfbins 30
> fixacf  1
> acffwhm 20
> acfsvd  0
> designtype event-related
> nskip 0
> polyfit 2
> HPFCutoffHz 0
> HeteroGCor 0
> nconditions 1
> parname rtopy.par
> RefEventDur 10
> timewindow 40.00
> prestim 0
> TER 0.05
> gamma 2.25 1.25 2 0
> stimulusdelay -1.
> Condition 1 Condition01
>
> Best,
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Saturday, February 03, 2018 9:21 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>
> Strange. Can you send me the analysis.info file?
>
>
> On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
>> Hello Dr. Greve,
>>
>> Yes it exists. The output below was with debug option.
>>
>> Best
>> Idil
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, January 30, 2018 8:40 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>
>> Does the file 
>> /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If 
>> so, can you run it with -debug as the first option and send the terminal 
>> output?
>>
>> On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
>>
>>
>> Hello FreeSurfer experts,
>>
>> I am getting this strange error when running selxavg3-sess. (in selxavg3 
>> command I am calling the analysis file with: -a rtopyTR2.rh) When the system 
>> enters fast_selxavg3, it cannot read analysis.info, thus produces the 
>> following output:
>>
>> #@# Sess05 ###
>> /home/vm01/local/freesurfer/Project_bold/Sess05
>> -
>> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
>> -
>> outtop = /home/vm01/local/freesurfer/Project_bold
>> Extension format = nii.gz
>> ERROR: could not open rtopyTR2.rh/analysis.info
>> else
>> else
>> echo "--" | tee -a $LF
>> echo --
>> tee -a 
>> /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
>> --
>> rm $MLF
>> rm /tmp/selxavg3-sess-10173.m
>> if ( ! -e $okfile ) then
>> if ( ! -e /tmp/selxavg3-sess-10173.ok ) then
>> echo "ERROR: fast_selxavg3() failed\n" ;
>> echo ERROR: fast_selxavg3() failed\n
>> ERROR: fast_selxavg3() failed\n
>> exit 1 ;
>> exit 1
>>
>> The analysis folder it is referring to( rtopyTR2.rh) is in the directory 
>> from which I am calling selxavg3-sess. It has the analysis.info file in 
>> which doesn't have any restrictions. To troubleshoot, I moved the folder to 
>> inside the session's functional directory and inside the session folder and 
>> these didn't create any changes. I looked at the script and tried to debug 
>> there but didn't give any results. It gave a similar error when trying to 
>> open the config file of contrast in mkcontrast-sess. (I also don't have root 
>> access)Any help is appreciated!
>>
>> Best,
>> Idil
>>
>>
>>
>>
>>
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Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[Douglas Greve]

The first frame in your input file is all 0s, so something is wrong with 
the fist subject



On 2/3/18 3:03 PM, miracle ozzoude wrote:

Hello Doug,

I have uploaded the files you requested. Thank you for your help.

Best,
Paul

On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


Can you upload the glmfit folders and the glmfit input (--y file)
to our filedrop?

https://gate.nmr.mgh.harvard.edu/filedrop2/



On 2/1/18 7:46 PM, miracle ozzoude wrote:

Hello Doug,

I have attached a screen shot of the mask.mgh for both right and
left hemispheres. Everything looks yellow. I followed the paired
t-test tutorial on the wiki page (included my scripts, fsgd
files, and matrix in email thread). How do i go about fixing it?
Thanks you

Best,
Paul

On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

that usually means that something has gone wrong with the
analysis. Do the maps look ok? In particular, look at the mask



On 1/20/18 1:56 PM, miracle ozzoude wrote:

Hello Doug,

I tried using the MC tables that FS distributed. However, i
got an error about " cannot find /fwhm00/pos/th30/mc-z.csd
". I checked and there's no fwhm00, the table starts from
fwhm01 to fwhm30. Below are my script and
cache.mri_glmfi-sim.log files. My FreeSurfer version is
stable version 5.3 on mac. Thank you.

Best,
Paul

mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex
--cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex
--cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite

On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

Why are you doing your own MC simulation? You can just
use the tables that we distribute ...


On 1/17/18 6:12 PM, miracle ozzoude wrote:

Hello Experts,

I am running a paired t-test cortical thickness
analysis based on the instruction on the wiki page
(https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
).
However, the monte carlo files weren't not created when
i corrected for multiple comparisons. Below are my
script, fsgd files, mc-z log file, and a screenshot of
contrast folder missing mc.z maps. Please can you help
me figure out why the error is happening. Thank you.

Best,
Paul

*Script*:
pairs=pairs.fsgd paired=paired_diff.fsgd
martrix1=mean.mtx martrix2=age.mtx
#resample each subjects's left and right hemisphere
data to fsavarage.
mris_preproc --target fsaverage --hemi lh --meas
thickness --out lh.paired-diff.thickness.mgh --fsgd
$pairs --paired-diff
mris_preproc --target fsaverage --hemi rh --meas
thickness --out rh.paired-diff.thickness.mgh --fsgd
$pairs --paired-diff
# #smoothen the concatenated file by 5mm FWHM. --cortex
means only smooth areas in the cortex. N:B. FWHM
changes based on study type.
mri_surf2surf --hemi lh --s fsaverage --sval
lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
lh.paired-diff.thickness.sm05.mgh
mri_surf2surf --hemi rh --s fsaverage --sval
rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
rh.paired-diff.thickness.sm05.mgh
# #Run GLM analysis
mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd
$paired --C $martrix1 --C $martrix2 --surf fsaverage lh
--cortex --glmdir lh.paired-diff.glmdirir
mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd
$paired --C $martrix1 --C $martrix2 --surf fsaverage rh
--cortex --glmdir rh.paired-diff.glmdir
# # #Run Clusterwise correction for multiple
comparisons using MONTE CARLO. First create a table for
of simulations
mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim
mc-z 1 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh
0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim
mc-z 1 2 mc-z.abs.2 --sim-sign abs --cwpvalthresh
0.05 --2spaces --overwrite
*Fsgd file 1:pairs.fsgd*

GroupDescriptorFile 1

Class ADEX

Input 1000_1 ADEX

Inp

Re: [Freesurfer] Fwd: Re: One Group (One Factor), Two Covariates

[Douglas Greve]

I guess you could make the contrast [1 1 0], but I have no idea what the 
interpretation would be. I'll leave that up to you



On 2/4/18 8:58 AM, std...@virgilio.it wrote:


Thanks.

what do I do if I would like to maintain the effect of "main" in the 
points 2 and 3.


Best regards


Stefano


Re:_[Freesurfer]_One_Group_(One_Factor),_Two_Covariates.eml

Subject:
Re: [Freesurfer] One Group (One Factor), Two Covariates
From:
Douglas Greve 
Date:
2/3/18, 1:57 PM

To:
freesurfer@nmr.mgh.harvard.edu




On 2/2/18 7:47 AM, std...@virgilio.it wrote:


Hi list,

in reference to One Group (One Factor), Two Covariates

https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx

that has been applied on FS-FAST fcMRI data

I obtain three folder, respectively, for "main", "covariate 1", 
"covariate 2".


What's meaning the sig.nii.gz that it is produced by mri_glmfit in 
each folder?

Please correct my conclusions if they are wrong.

1 - In the "Main" folder, the sig.nii.gz contains the results of 
One-sample t test regressing out the effect of the two covariates.



Correct


2 - In the "Covariate 1" folder, the sig.nii.gz contains the 
significant cluster that are associated with the covariate 1 
regressing out the effect for the covariate 2.



Yes (and the main)


3 - In the "Covariate 2" folder, the sig.nii.gz contains the 
significant cluster that are associated with the covariate 2 
regressing out the effect for the covariate 1.



Yes (and regressing out the main)


Thanks


Stefano

*
*

*
*



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Re: [Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

[Douglas Greve]

On 2/4/18 10:06 AM, std...@virgilio.it wrote:


I have run:

1)

mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh --meas 
thickness --out rh.GROUP1.thickness.00.mgh
mri_surf2surf --hemi rh --s fsaverage --sval 
rh.GROUP1.thickness.00.mgh --fwhm 10 --cortex --tval 
rh.GROUP1.thickness.10B.mgh



looks good


2)

mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh 
--glmdir Age.wls --nii.gz --fsgd g1v1_Age.fsgd --C intercept.mtx --C 
slope.mtx --pvr rh.GROUP1.thickness.10B.mgh


The command line is correct?

Yes, though I'm not sure about the effect of using --wls and --pvr. I 
guess it will be ok, I just have not used it.



My concern is on the fsgd file.

I have

GroupDescriptorFile 1
Title All
Class Main
Variables thickness
Input ADNI0XX_GROUP1 Main 
Input ADNI0XY_GROUP1 Main 
Input ADNI0YX.GROUP1 Main 
...

What I should add after Main if I would like to assess the vertex by 
vertex correlation between FC (between seed and target vertex) and 
thickness (in the target vertex)?


Don't represent the PVR in the FSGD file. You only need to include items 
in the contrast matrix. Eg, for intercept use [1 0] and for slope use [0 
1] eventhough you only have a single class.


Should I add the path where is contained rh.thickness.mgh of each subject?


No


Please give me an help because I did not find these information using 
--help or mail list.


Thanks


Stefano



Il 3 febbraio 2018 alle 19.55 Douglas Greve 
 ha scritto:


Yes, use the --pvr option to mri_glmfit (per-voxel regressor). Search 
through the mail archives for an example on how to use it



On 2/3/18 12:10 PM, std...@virgilio.it  wrote:


Hi list,

Is there a way to obtain a map that report the "vertex by vertex" 
correlation between the FC (obtained by FS-FAST) and cortical thickness?


Thanks


Stefano



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Re: [Freesurfer] One Group (One Factor), Two Covariates

[Douglas Greve]

If you have one class and two variables, then [0 1 0] and [0 0 1]


On 2/4/18 10:23 AM, std...@virgilio.it wrote:


I would like to find where the functional connectivity is correlated 
to VARIABLE 1 regressing out the VARIABLE 2.


How I should set my contrast.mtx?

Thanks


Stefano

Il 3 febbraio 2018 alle 19.57 Douglas Greve 
 ha scritto:




On 2/2/18 7:47 AM, std...@virgilio.it  wrote:


Hi list,

in reference to One Group (One Factor), Two Covariates

https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx

that has been applied on FS-FAST fcMRI data

I obtain three folder, respectively, for "main", "covariate 1", 
"covariate 2".


What's meaning the sig.nii.gz that it is produced by mri_glmfit in 
each folder?

Please correct my conclusions if they are wrong.

1 - In the "Main" folder, the sig.nii.gz contains the results of 
One-sample t test regressing out the effect of the two covariates.



Correct


2 - In the "Covariate 1" folder, the sig.nii.gz contains the 
significant cluster that are associated with the covariate 1 
regressing out the effect for the covariate 2.



Yes (and the main)


3 - In the "Covariate 2" folder, the sig.nii.gz contains the 
significant cluster that are associated with the covariate 2 
regressing out the effect for the covariate 1.



Yes (and regressing out the main)


Thanks


Stefano

*
*

*
*



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Re: [Freesurfer] Removing labels after extending parcellation into white matter

[Douglas Greve]

You mean you want to remove everything but the WM labels? You can do it 
in two steps:


1. Create a mask of the wm labels:

mri_binarize --i aparc+aseg+2mm.nii.gz --min 2999.5 --max 4035.5 --o 
wm.mask.nii.gz


2. Mask the wmparc:

mri_mask aparc+aseg+2mm.nii.gz wm.mask.nii.gz aparc+aseg+2mm.masked.nii.gz




On 2/4/18 5:28 PM, Michiko H. wrote:

Hi Freesurfer experts,

I am wondering if it is possible to remove the original labels after 
extending the parcellation by 2mm into the WM for tractography? I 
don't wish to have tractography run on both sets of labels considering 
the algorithm would take into account the streamlines terminating at 
nodes defined by the labels so it doesn't quite make sense to count 
streamlines terminating at both the original label separately from the 
new label extending into the WM.


I used the following command for growing the parcellation into WM:

mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 --labelwm 
--hypo-as-wm --o $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz



Would appreciate help and suggestions!


Thanks,

Michiko.



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Re: [Freesurfer] One Group (One Factor), Two Covariates

[stdp82]

Thanks.

Only for I quick check of my understanding, if I'm using:


FSGD File (g1v1.fsgd)

GroupDescriptorFile 1

Title OSGM

Class Main

Variables Age

Input subject1 Main 30

Input subject2 Main 40

.


A) Contrast 1 (intercept.mtx) 1 0

B) Contrast 2 (slope.mtx) 0 1

Considering that my goal is to obtain a map reporting the significant clusters 
where the FC is positively/negatively associated with Age, is this contrast 
exact? Or it shows the clusters where la FC between seed and target regions is 
significant, regressing out the Age? This second case in not of my interest.
Please suggest a way to reach the first case.

Thanks


Stefano



> Il 5 febbraio 2018 alle 18.27 Douglas Greve  ha 
> scritto:
> 
> 
> If you have one class and two variables, then [0 1 0] and [0 0 1]
> 
> 
> On 2/4/18 10:23 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > I would like to find where the functional connectivity is 
> > correlated to VARIABLE 1 regressing out the VARIABLE 2.
> > 
> > How I should set my contrast.mtx?
> > 
> > Thanks
> > 
> > 
> > Stefano
> > 
> > > > > Il 3 febbraio 2018 alle 19.57 Douglas Greve 
> >  mailto:gr...@nmr.mgh.harvard.edu ha scritto:
> > > 
> > > 
> > > 
> > > 
> > > On 2/2/18 7:47 AM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > Hi list,
> > > > 
> > > > in reference to One Group (One Factor), Two Covariates
> > > > 
> > > > 
> > > > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx
> > > > 
> > > > that has been applied on FS-FAST fcMRI data
> > > > 
> > > > I obtain three folder, respectively, for "main", 
> > > > "covariate 1", "covariate 2".
> > > > 
> > > > What's meaning the sig.nii.gz that it is produced by 
> > > > mri_glmfit in each folder?
> > > > Please correct my conclusions if they are wrong.
> > > > 
> > > > 1 - In the "Main" folder, the sig.nii.gz contains the 
> > > > results of One-sample t test regressing out the effect of the two 
> > > > covariates.
> > > > 
> > > > > > > Correct
> > > 
> > > > > > > 
> > > > 2 - In the "Covariate 1" folder, the sig.nii.gz 
> > > > contains the significant cluster that are associated with the covariate 
> > > > 1 regressing out the effect for the covariate 2.
> > > > 
> > > > > > > Yes (and the main)
> > > 
> > > > > > > 
> > > > 3 - In the "Covariate 2" folder, the sig.nii.gz 
> > > > contains the significant cluster that are associated with the covariate 
> > > > 2 regressing out the effect for the covariate 1.
> > > > 
> > > > > > > Yes (and regressing out the main)
> > > 
> > > > > > > 
> > > > Thanks
> > > > 
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > ___
> > > > Freesurfer mailing list
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> > > > 
> > > > > > > 
> > > > > 
> > 
> >  
> > 
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> > > 
> > > 
> > > The information in this e-mail is intended only for the 
> > > person to whom it is
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> > > contains patient information, please contact the Partners 
> > > Compliance HelpLine at
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> > > sent to you in error
> > > but does not contain patient information, please contact the 
> > > sender and properly
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> > > 
> > > > > 
> > > 


 

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Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm

[Sims, Sara A]

This is the whole process output from a rerun on a subject that didn’t work the 
first time or with the rerun:
Reading ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab
Number of ctab entries 2

$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
cwd /data/user/snolin/Scripts/Labelmaker
cmdline mris_label2annot --ctab 
/data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab --s 211215 
--h lh --l 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/8_LH_V1.label
 --a 8V1
sysname  Linux
hostname c0039
machine  x86_64
user snolin

subject 211215
hemilh
SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon
ColorTable /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab
AnnotName  8V1
nlables 1
LabelThresh 0 0.00
ERROR: 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/lh.8V1.annot
 already exists
Reading ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab
Number of ctab entries 2

$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
cwd /data/user/snolin/Scripts/Labelmaker
cmdline mris_label2annot --ctab 
/data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab --s 211215 
--h rh --l 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/8_RH_V1.label
 --a 8V1
sysname  Linux
hostname c0039
machine  x86_64
user snolin

subject 211215
hemirh
SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon
ColorTable /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab
AnnotName  8V1
nlables 1
LabelThresh 0 0.00
ERROR: 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/rh.8V1.annot
 already exists
SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon
subject 211215
outvol 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz
useribbon 0
baseoffset 0
labeling wm
dmaxctx 5.00
RipUnknown 0

Reading lh white surface
 /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/lh.white

Reading lh pial surface
 /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/lh.pial

Loading lh annotations from 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/lh.8V1.annot

Reading rh white surface
 /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/rh.white

Reading rh pial surface
 /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/rh.pial

Loading rh annotations from 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/rh.8V1.annot
Loading ribbon segmentation from 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/aseg.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
0.0   0.0   1.0  -128.0;
0.0  -1.0   0.0   128.0;
0.0   0.0   0.0   1.0;
-

Labeling Slice
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1124316
Used brute-force search on 0 voxels
Fixing Parahip LH WM
  Found 0 clusters
Fixing Parahip RH WM
  Found 0 clusters
Writing output aseg to 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /data/user/snolin/Scripts/Labelmaker
cmdline mri_binarize.bin --i 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz
 --o 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz
 --match 4001 3001
sysname  Linux
hostname c0039
machine  x86_64
user snolin

input  
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz
frame  0
nErode3d   0
nErode2d   0
output 
/d

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

[Yagmur Ozdemir 19]

Dr. Greve,

Yes I have tried making new files. (I also gave the previous files and folders 
full permission with chmod which again didn't work) Mkanalysis-sess did not 
have any problems as expected, but mkcontrast-sess failed for the same reason 
of not being able to open the .config file that it should be creating under the 
analysis folder. 

I am not the root user of the system, but maybe getting sudo access would be 
helpful? I can look into this. 

Best
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 05, 2018 6:53 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

I cannot replicate this. There must be some strange permission error.
Can you try to make a new analysis with a different name and just see if
fails?


On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
> Hello Dr. Greve,
>
> The analysis.info file is below. I should also say that, when I am trying to 
> create new analysis and contrast files, while creating the .config file for 
> contrast, th system gives the same error saying that it cannot enter the file.
>
> # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $
> # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface self 
> lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 
> -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 1.25 
> -force
> # DATE Tue Jan 30 07:14:05 EST 2018
>
> analysis rtopyTR2.lh
> mcstem fmcpr
> fsd bold
> TR 2
> RegDOF 6
> PerSession 0
> RawSpace surface self lh
> mask brain
> RawFWHM 5
> RawSTC none
> nSliceGroups 1
> UseB0DC 0
> ApplySubCortMask 1
> inorm 100
> acfbins 30
> fixacf  1
> acffwhm 20
> acfsvd  0
> designtype event-related
> nskip 0
> polyfit 2
> HPFCutoffHz 0
> HeteroGCor 0
> nconditions 1
> parname rtopy.par
> RefEventDur 10
> timewindow 40.00
> prestim 0
> TER 0.05
> gamma 2.25 1.25 2 0
> stimulusdelay -1.
> Condition 1 Condition01
>
> Best,
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Saturday, February 03, 2018 9:21 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>
> Strange. Can you send me the analysis.info file?
>
>
> On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
>> Hello Dr. Greve,
>>
>> Yes it exists. The output below was with debug option.
>>
>> Best
>> Idil
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, January 30, 2018 8:40 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>
>> Does the file 
>> /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? If 
>> so, can you run it with -debug as the first option and send the terminal 
>> output?
>>
>> On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
>>
>>
>> Hello FreeSurfer experts,
>>
>> I am getting this strange error when running selxavg3-sess. (in selxavg3 
>> command I am calling the analysis file with: -a rtopyTR2.rh) When the system 
>> enters fast_selxavg3, it cannot read analysis.info, thus produces the 
>> following output:
>>
>> #@# Sess05 ###
>> /home/vm01/local/freesurfer/Project_bold/Sess05
>> -
>> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
>> -
>> outtop = /home/vm01/local/freesurfer/Project_bold
>> Extension format = nii.gz
>> ERROR: could not open rtopyTR2.rh/analysis.info
>> else
>> else
>> echo "--" | tee -a $LF
>> echo --
>> tee -a 
>> /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
>> --
>> rm $MLF
>> rm /tmp/selxavg3-sess-10173.m
>> if ( ! -e $okfile ) then
>> if ( ! -e /tmp/selxavg3-sess-10173.ok ) then
>> echo "ERROR: fast_selxavg3() failed\n" ;
>> echo ERROR: fast_selxavg3() failed\n
>> ERROR: fast_selxavg3() failed\n
>> exit 1 ;
>> exit 1
>>
>> The analysis folder it is referring to( rtopyTR2.rh) is in the directory 
>> from which I am calling selxavg3-sess. It has the analysis.info file in 
>> which doesn't have any restrictions. To troubleshoot, I moved the folder to 
>> inside the session's functional directory and inside the session folder and 
>> these didn't create any changes. I looked at the script and tried to debug 
>> there but didn't give any results. It gave

Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm

[Douglas N Greve]

Sorry, is this related to the earlier question about how to remove 
non-wm labels or is this a new submission? If a new subj, can you 
describe the problem you are having?


On 02/05/2018 01:23 PM, Sims, Sara A wrote:
>
> This is the whole process output from a rerun on a subject that didn’t 
> work the first time or with the rerun:
>
> Reading ctab 
> /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab
>
> Number of ctab entries 2
>
> $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
>
> cwd /data/user/snolin/Scripts/Labelmaker
>
> cmdline mris_label2annot --ctab 
> /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab --s 
> 211215 --h lh --l 
> /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/8_LH_V1.label
>  
> --a 8V1
>
> sysname Linux
>
> hostname c0039
>
> machine x86_64
>
> user snolin
>
> subject 211215
>
> hemi    lh
>
> SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon
>
> ColorTable 
> /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab
>
> AnnotName 8V1
>
> nlables 1
>
> LabelThresh 0 0.00
>
> ERROR: 
> /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/lh.8V1.annot
>  
> already exists
>
> Reading ctab 
> /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab
>
> Number of ctab entries 2
>
> $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
>
> cwd /data/user/snolin/Scripts/Labelmaker
>
> cmdline mris_label2annot --ctab 
> /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab --s 
> 211215 --h rh --l 
> /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/8_RH_V1.label
>  
> --a 8V1
>
> sysname Linux
>
> hostname c0039
>
> machine x86_64
>
> user snolin
>
> subject 211215
>
> hemi    rh
>
> SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon
>
> ColorTable 
> /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab
>
> AnnotName 8V1
>
> nlables 1
>
> LabelThresh 0 0.00
>
> ERROR: 
> /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/rh.8V1.annot
>  
> already exists
>
> SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon
>
> subject 211215
>
> outvol 
> /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz
>
> useribbon 0
>
> baseoffset 0
>
> labeling wm
>
> dmaxctx 5.00
>
> RipUnknown 0
>
> Reading lh white surface
>
>  
> /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/lh.white
>
> Reading lh pial surface
>
>  
> /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/lh.pial
>
> Loading lh annotations from 
> /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/lh.8V1.annot
>
> Reading rh white surface
>
>  
> /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/rh.white
>
> Reading rh pial surface
>
>  
> /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/rh.pial
>
> Loading rh annotations from 
> /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/rh.8V1.annot
>
> Loading ribbon segmentation from 
> /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/ribbon.mgz
>
> Building hash of lh white
>
> Building hash of lh pial
>
> Building hash of rh white
>
> Building hash of rh pial
>
> Loading aseg from 
> /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/aseg.mgz
>
> ASeg Vox2RAS: ---
>
> -1.0 0.0   0.0   128.0;
>
> 0.0 0.0   1.0  -128.0;
>
> 0.0 -1.0   0.0   128.0;
>
> 0.0 0.0   0.0   1.0;
>
> -
>
> Labeling Slice
>
>   0   1 2   3   4   5   6   7   8   9  10  11  12  13  14  15  16 17  
> 18  19
>
>  20  21  22 23  24  25  26  27  28  29  30  31  32  33  34  35  36  37 
> 38  39
>
>  40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  
> 57 58  59
>
>  60  61  62 63  64  65  66  67  68  69  70  71  72  73  74  75  76  77 
> 78  79
>
>  80  81  82 83  84  85  86  87  88  89  90  91  92  93  94  95  96  97 
> 98  99
>
> 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 
> 117 118 119
>
> 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 
> 137 138 139
>
> 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 
> 157 158 159
>
> 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 
> 177 178 179
>
> 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 
> 197 198 199
>
> 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 
> 217 218 219
>
> 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 
> 237 238 239
>
> 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 
> 1124316
>
> Used brute-force search on 0 voxels
>
> Fixing Parahip LH WM
>
>   Found 0 clusters
>
> Fixing Parahip RH WM
>
>   Found 0 clusters
>
> Writing output as

Re: [Freesurfer] One Group (One Factor), Two Covariates

[Douglas N Greve]

The 2nd contrast (slope) is the one you want.


On 02/05/2018 01:21 PM, std...@virgilio.it wrote:
>
> Thanks.
>
> Only for I quick check of my understanding, if I'm using:
>
>
> FSGD File (g1v1.fsgd)
>
> GroupDescriptorFile 1
>
> Title OSGM
>
> Class Main
>
> Variables Age
>
> Input subject1 Main 30
>
> Input subject2 Main 40
>
> .
>
>
> A) Contrast 1 (intercept.mtx) 1 0
>
> B) Contrast 2 (slope.mtx) 0 1
>
> Considering that my goal is to obtain a map reporting the significant 
> clusters where the FC is positively/negatively associated with Age, is 
> this contrast exact? Or it shows the clusters where la FC between seed 
> and target regions is significant, regressing out the Age? This second 
> case in not of my interest.
> Please suggest a way to reach the first case.
>
> Thanks
>
>
> Stefano
>
>
>
>> Il 5 febbraio 2018 alle 18.27 Douglas Greve 
>>  ha scritto:
>>
>> If you have one class and two variables, then [0 1 0] and [0 0 1]
>>
>>
>> On 2/4/18 10:23 AM, std...@virgilio.it  wrote:
>>>
>>> I would like to find where the functional connectivity is correlated 
>>> to VARIABLE 1 regressing out the VARIABLE 2.
>>>
>>> How I should set my contrast.mtx?
>>>
>>> Thanks
>>>
>>>
>>> Stefano
>>>
 Il 3 febbraio 2018 alle 19.57 Douglas Greve 
   ha 
 scritto:



 On 2/2/18 7:47 AM, std...@virgilio.it  
 wrote:
>
> Hi list,
>
> in reference to One Group (One Factor), Two Covariates
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx
>
> that has been applied on FS-FAST fcMRI data
>
> I obtain three folder, respectively, for "main", "covariate 1", 
> "covariate 2".
>
> What's meaning the sig.nii.gz that it is produced by mri_glmfit in 
> each folder?
> Please correct my conclusions if they are wrong.
>
> 1 - In the "Main" folder, the sig.nii.gz contains the results of 
> One-sample t test regressing out the effect of the two covariates.
>
 Correct
>
> 2 - In the "Covariate 1" folder, the sig.nii.gz contains the 
> significant cluster that are associated with the covariate 1 
> regressing out the effect for the covariate 2.
>
 Yes (and the main)
>
> 3 - In the "Covariate 2" folder, the sig.nii.gz contains the 
> significant cluster that are associated with the covariate 2 
> regressing out the effect for the covariate 1.
>
 Yes (and regressing out the main)
>
> Thanks
>
>
> Stefano
>
> *
> *
>
> *
> *
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

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Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

[Douglas N Greve]

I don't know, it is all very weird. What platform are you using?


On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote:
> Dr. Greve,
>
> Yes I have tried making new files. (I also gave the previous files and 
> folders full permission with chmod which again didn't work) Mkanalysis-sess 
> did not have any problems as expected, but mkcontrast-sess failed for the 
> same reason of not being able to open the .config file that it should be 
> creating under the analysis folder.
>
> I am not the root user of the system, but maybe getting sudo access would be 
> helpful? I can look into this.
>
> Best
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, February 05, 2018 6:53 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>
> I cannot replicate this. There must be some strange permission error.
> Can you try to make a new analysis with a different name and just see if
> fails?
>
>
> On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
>> Hello Dr. Greve,
>>
>> The analysis.info file is below. I should also say that, when I am trying to 
>> create new analysis and contrast files, while creating the .config file for 
>> contrast, th system gives the same error saying that it cannot enter the 
>> file.
>>
>> # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>> # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $
>> # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface 
>> self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 
>> -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 
>> 1.25 -force
>> # DATE Tue Jan 30 07:14:05 EST 2018
>>
>> analysis rtopyTR2.lh
>> mcstem fmcpr
>> fsd bold
>> TR 2
>> RegDOF 6
>> PerSession 0
>> RawSpace surface self lh
>> mask brain
>> RawFWHM 5
>> RawSTC none
>> nSliceGroups 1
>> UseB0DC 0
>> ApplySubCortMask 1
>> inorm 100
>> acfbins 30
>> fixacf  1
>> acffwhm 20
>> acfsvd  0
>> designtype event-related
>> nskip 0
>> polyfit 2
>> HPFCutoffHz 0
>> HeteroGCor 0
>> nconditions 1
>> parname rtopy.par
>> RefEventDur 10
>> timewindow 40.00
>> prestim 0
>> TER 0.05
>> gamma 2.25 1.25 2 0
>> stimulusdelay -1.
>> Condition 1 Condition01
>>
>> Best,
>> Idil
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Saturday, February 03, 2018 9:21 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>
>> Strange. Can you send me the analysis.info file?
>>
>>
>> On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
>>> Hello Dr. Greve,
>>>
>>> Yes it exists. The output below was with debug option.
>>>
>>> Best
>>> Idil
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Tuesday, January 30, 2018 8:40 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>>
>>> Does the file 
>>> /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? 
>>> If so, can you run it with -debug as the first option and send the terminal 
>>> output?
>>>
>>> On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
>>>
>>>
>>> Hello FreeSurfer experts,
>>>
>>> I am getting this strange error when running selxavg3-sess. (in selxavg3 
>>> command I am calling the analysis file with: -a rtopyTR2.rh) When the 
>>> system enters fast_selxavg3, it cannot read analysis.info, thus produces 
>>> the following output:
>>>
>>> #@# Sess05 ###
>>> /home/vm01/local/freesurfer/Project_bold/Sess05
>>> -
>>> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
>>> -
>>> outtop = /home/vm01/local/freesurfer/Project_bold
>>> Extension format = nii.gz
>>> ERROR: could not open rtopyTR2.rh/analysis.info
>>> else
>>> else
>>> echo "--" | tee -a $LF
>>> echo --
>>> tee -a 
>>> /home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
>>> --
>>> rm $MLF
>>> rm /tmp/selxavg3-sess-10173.m
>>> if ( ! -e $okfile ) then
>>> if ( ! -e /tmp/selxavg3-sess-10173.ok ) then
>>> echo "ERROR: fast_selxavg3() failed\n" ;
>>> echo ERROR: fast_selxavg3() failed\n
>>> ERROR: fast_selxavg3() failed\n
>>> exit 1 ;
>>> exit 1
>>>
>>> The analysis folder it is referring to( rtopyTR2.rh) is in the directory 
>>> from which I am calling selxavg3-sess. It has the analysis.info file in 
>>

Re: [Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

[stdp82]

I obtain this error: 

mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir 
Thickness.wls --nii.gz --fsgd g1v1_thickness.fsgd --C intercept.mtx --C 
slope.mtx --pvr $SUBJECTS_DIR/rh.MCI.thickness.10B.mgh

Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/rh.white

gdfRead(): reading g1v1_thickness.fsgd

ERROR: fio_FileHasCarriageReturn(): cannot open g1v1_thickness.fsgd


> Il 5 febbraio 2018 alle 18.26 Douglas Greve  ha 
> scritto:
> 
> 
> 
> 
> On 2/4/18 10:06 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:
> 
> > > 
> > I have run:
> > 
> > 1)
> > 
> > mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh --meas 
> > thickness --out rh.GROUP1.thickness.00.mgh
> > mri_surf2surf --hemi rh --s fsaverage --sval 
> > rh.GROUP1.thickness.00.mgh --fwhm 10 --cortex --tval 
> > rh.GROUP1.thickness.10B.mgh
> > 
> > > looks good
> 
> > > 
> > 2)
> > 
> > mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage 
> > rh --glmdir Age.wls --nii.gz --fsgd g1v1_Age.fsgd --C intercept.mtx --C 
> > slope.mtx --pvr rh.GROUP1.thickness.10B.mgh
> > 
> > The command line is correct?
> > 
> > > Yes, though I'm not sure about the effect of using --wls and --pvr. I 
> > guess it will be ok, I just have not used it.
> 
> > > 
> > 
> > My concern is on the fsgd file.
> > 
> > I have 
> > 
> > GroupDescriptorFile 1
> > Title All
> > Class Main
> > Variables thickness
> > Input ADNI0XX_GROUP1 Main 
> > Input ADNI0XY_GROUP1 Main 
> > Input ADNI0YX.GROUP1 Main 
> > ...
> > 
> > What I should add after Main if I would like to assess the vertex 
> > by vertex correlation between FC (between seed and target vertex) and 
> > thickness (in the target vertex)?
> > 
> > > Don't represent the PVR in the FSGD file. You only need to include 
> > items in the contrast matrix. Eg, for intercept use [1 0] and for slope use 
> > [0 1] eventhough you only have a single class.
> 
> > > 
> > Should I add the path where is contained rh.thickness.mgh of each 
> > subject?
> > 
> > > No
> 
> > > 
> > Please give me an help because I did not find these information 
> > using --help or mail list.
> > 
> > Thanks
> > 
> > 
> > Stefano
> > 
> > 
> > 
> > Il 3 febbraio 2018 alle 19.55 Douglas Greve 
> >  mailto:gr...@nmr.mgh.harvard.edu ha scritto:
> > 
> > 
> > Yes, use the --pvr option to mri_glmfit (per-voxel regressor). 
> > Search through the mail archives for an example on how to use it
> > 
> > 
> > On 2/3/18 12:10 PM, std...@virgilio.it mailto:std...@virgilio.it 
> > wrote:
> > 
> > > > > 
> > > Hi list,
> > > 
> > > Is there a way to obtain a map that report the "vertex by 
> > > vertex" correlation between the FC (obtained by FS-FAST) and cortical 
> > > thickness?
> > > 
> > > Thanks
> > > 
> > > 
> > > Stefano
> > > 
> > > 
> > > 
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu 
> > > mailto:Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > 
> > > > > 
> > 
> >  
> > 
> > > > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu 
> > > mailto:Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > 
> > > 
> > > The information in this e-mail is intended only for the 
> > > person to whom it is
> > > addressed. If you believe this e-mail was sent to you in 
> > > error and the e-mail
> > > contains patient information, please contact the Partners 
> > > Compliance HelpLine at
> > > http://www.partners.org/complianceline . If the e-mail was 
> > > sent to you in error
> > > but does not contain patient information, please contact the 
> > > sender and properly
> > > dispose of the e-mail.
> > > 
> > > > > 
> > > 
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

[Yagmur Ozdemir 19]

Dr. Greve,

I tried with root access and it still gave the same error. I am using a virtual 
machine from our server that I connect with VCN, and it has freesurfer and 
matlab installed and setup in its shell. The VM has Ubuntu 16.04 (Xenial), 
Freesurfer v.6, and Matlab R2016b. I appreciate your help.

Best
Idil 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, February 05, 2018 8:34 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

I don't know, it is all very weird. What platform are you using?


On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote:
> Dr. Greve,
>
> Yes I have tried making new files. (I also gave the previous files and 
> folders full permission with chmod which again didn't work) Mkanalysis-sess 
> did not have any problems as expected, but mkcontrast-sess failed for the 
> same reason of not being able to open the .config file that it should be 
> creating under the analysis folder.
>
> I am not the root user of the system, but maybe getting sudo access would be 
> helpful? I can look into this.
>
> Best
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, February 05, 2018 6:53 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>
> I cannot replicate this. There must be some strange permission error.
> Can you try to make a new analysis with a different name and just see if
> fails?
>
>
> On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
>> Hello Dr. Greve,
>>
>> The analysis.info file is below. I should also say that, when I am trying to 
>> create new analysis and contrast files, while creating the .config file for 
>> contrast, th system gives the same error saying that it cannot enter the 
>> file.
>>
>> # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>> # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $
>> # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface 
>> self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 
>> -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 
>> 1.25 -force
>> # DATE Tue Jan 30 07:14:05 EST 2018
>>
>> analysis rtopyTR2.lh
>> mcstem fmcpr
>> fsd bold
>> TR 2
>> RegDOF 6
>> PerSession 0
>> RawSpace surface self lh
>> mask brain
>> RawFWHM 5
>> RawSTC none
>> nSliceGroups 1
>> UseB0DC 0
>> ApplySubCortMask 1
>> inorm 100
>> acfbins 30
>> fixacf  1
>> acffwhm 20
>> acfsvd  0
>> designtype event-related
>> nskip 0
>> polyfit 2
>> HPFCutoffHz 0
>> HeteroGCor 0
>> nconditions 1
>> parname rtopy.par
>> RefEventDur 10
>> timewindow 40.00
>> prestim 0
>> TER 0.05
>> gamma 2.25 1.25 2 0
>> stimulusdelay -1.
>> Condition 1 Condition01
>>
>> Best,
>> Idil
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Saturday, February 03, 2018 9:21 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>
>> Strange. Can you send me the analysis.info file?
>>
>>
>> On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
>>> Hello Dr. Greve,
>>>
>>> Yes it exists. The output below was with debug option.
>>>
>>> Best
>>> Idil
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Tuesday, January 30, 2018 8:40 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>>
>>> Does the file 
>>> /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? 
>>> If so, can you run it with -debug as the first option and send the terminal 
>>> output?
>>>
>>> On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:
>>>
>>>
>>> Hello FreeSurfer experts,
>>>
>>> I am getting this strange error when running selxavg3-sess. (in selxavg3 
>>> command I am calling the analysis file with: -a rtopyTR2.rh) When the 
>>> system enters fast_selxavg3, it cannot read analysis.info, thus produces 
>>> the following output:
>>>
>>> #@# Sess05 ###
>>> /home/vm01/local/freesurfer/Project_bold/Sess05
>>> -
>>> $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
>>> -
>>> outtop = /home/vm01/local/freesurfer/Project_bold
>>> Extension format = nii.gz
>>> ERROR: could not open rtopyTR2.rh/analysis.info
>>> else
>>> else
>>> echo "--" | tee -

Re: [Freesurfer] FSFAST

[Ashley Cole]

Only fmc.odd.sm5.nii.gz is in the same dimensions as the f.nii.gz. However,
I found a flag in the selxavg3 (-no-con-ok)that I do not need to specify a
contrast. If I am not mistaken, all is good now. Thank you for your
response.


On Sat, Feb 3, 2018 at 2:03 PM, Douglas Greve 
wrote:

> That file should be in the same dimensions, no?
>
> On 1/30/18 12:19 AM, Ashley Cole wrote:
>
> I just noticed that that file "fmc.odd.sm5.nii.gz" is created after
> selxavg3-sess. I was wondering how can I preprocess the functional image
> and have the output with the same dimension as the f.nii.gz without
> performing any contrasts. I just need to look at the signal in some ROIs
> without performing any contrasts. I hope this makes sense.
>
> Thanks,
> Ash
>
> On Mon, Jan 29, 2018 at 10:54 PM, Ashley Cole 
> wrote:
>
>> Hello,
>>
>> I have several nifti files. I have preprocessed some of them before. I
>> used this command:
>> preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305
>> -fwhm 5 -per-session -force
>>
>> The output files contained fmc.odd.sm5.self.lh.nii.gz,
>> fmc.odd.sm5.self.rh.nii.gz, fmc.odd.sm5.mni305.2mm.nii.gz, and
>> *fmc.odd.sm5.nii.gz*. Which this last one (fmc.odd.sm5.nii.gz) was the
>> file that I needed for my further analyses. However, when I run the same
>> command on another nifti file which was obtained from the same scanner and
>> the same session, the output doesn't have the fmc.odd.sm5.nii.gz.
>>
>> I ran it several times but it never gave me that file. Also, it doesn't
>> give me any errors.
>>
>> I appreciate any help.
>>
>> Ash
>>
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
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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
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Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

[Douglas N Greve]

Try running selxavg3-sess with -monly sxa3.m

Then start matlab and run sxa3.m


On 02/05/2018 02:02 PM, Yagmur Ozdemir 19 wrote:
> Dr. Greve,
>
> I tried with root access and it still gave the same error. I am using a 
> virtual machine from our server that I connect with VCN, and it has 
> freesurfer and matlab installed and setup in its shell. The VM has Ubuntu 
> 16.04 (Xenial), Freesurfer v.6, and Matlab R2016b. I appreciate your help.
>
> Best
> Idil
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, February 05, 2018 8:34 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>
> I don't know, it is all very weird. What platform are you using?
>
>
> On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote:
>> Dr. Greve,
>>
>> Yes I have tried making new files. (I also gave the previous files and 
>> folders full permission with chmod which again didn't work) Mkanalysis-sess 
>> did not have any problems as expected, but mkcontrast-sess failed for the 
>> same reason of not being able to open the .config file that it should be 
>> creating under the analysis folder.
>>
>> I am not the root user of the system, but maybe getting sudo access would be 
>> helpful? I can look into this.
>>
>> Best
>> Idil
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, February 05, 2018 6:53 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>
>> I cannot replicate this. There must be some strange permission error.
>> Can you try to make a new analysis with a different name and just see if
>> fails?
>>
>>
>> On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
>>> Hello Dr. Greve,
>>>
>>> The analysis.info file is below. I should also say that, when I am trying 
>>> to create new analysis and contrast files, while creating the .config file 
>>> for contrast, th system gives the same error saying that it cannot enter 
>>> the file.
>>>
>>> # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>>> # MKAVERSION $Id: mkanalysis-sess,v 1.78 2015/12/10 22:51:30 zkaufman Exp $
>>> # MKACMD /home/vm01/local/freesurfer/fsfast/bin/mkanalysis-sess -surface 
>>> self lh -analysis rtopyTR2.lh -paradigm rtopy.par -TR 2 -nconditions 1 
>>> -event-related -fwhm 5 -per-run -fsd bold -refeventdur 10 -gammafit 2.25 
>>> 1.25 -force
>>> # DATE Tue Jan 30 07:14:05 EST 2018
>>>
>>> analysis rtopyTR2.lh
>>> mcstem fmcpr
>>> fsd bold
>>> TR 2
>>> RegDOF 6
>>> PerSession 0
>>> RawSpace surface self lh
>>> mask brain
>>> RawFWHM 5
>>> RawSTC none
>>> nSliceGroups 1
>>> UseB0DC 0
>>> ApplySubCortMask 1
>>> inorm 100
>>> acfbins 30
>>> fixacf  1
>>> acffwhm 20
>>> acfsvd  0
>>> designtype event-related
>>> nskip 0
>>> polyfit 2
>>> HPFCutoffHz 0
>>> HeteroGCor 0
>>> nconditions 1
>>> parname rtopy.par
>>> RefEventDur 10
>>> timewindow 40.00
>>> prestim 0
>>> TER 0.05
>>> gamma 2.25 1.25 2 0
>>> stimulusdelay -1.
>>> Condition 1 Condition01
>>>
>>> Best,
>>> Idil
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Saturday, February 03, 2018 9:21 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file
>>>
>>> Strange. Can you send me the analysis.info file?
>>>
>>>
>>> On 1/31/18 9:26 AM, Yagmur Ozdemir 19 wrote:
 Hello Dr. Greve,

 Yes it exists. The output below was with debug option.

 Best
 Idil
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
 [gr...@nmr.mgh.harvard.edu]
 Sent: Tuesday, January 30, 2018 8:40 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

 Does the file 
 /home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info exist? 
 If so, can you run it with -debug as the first option and send the 
 terminal output?

 On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:


 Hello FreeSurfer experts,

 I am getting this strange error when running selxavg3-sess. (in selxavg3 
 command I am calling the analysis file with: -a rtopyTR2.rh) When the 
 system enters fast_selxavg3, it cannot read analysis.info, thus produces 
 the following output:

 #@# Sess05 ###
 /home/vm01/local/freesurfer/Project_bold/Sess05
 -
 $Id: fast_selxavg

[Freesurfer] Curvature Index and Folding Index

[Ting Li]

Dear FreeSurfer Expert,

Could you explain me what does the curvature index and folding index mean in 
the Parcellation Stats File? In which way they are calculated? or you can give 
me some related documents. Thanks a lot.

Ting
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Re: [Freesurfer] correlation between the FC (obtained by FS-FAST) and cortical thickness

[stdp82]

I have resolve the previous error (there was a typo in the fsdg file) but 
re-running I obtain this error:


Normalized matrix condition is 1

Matrix condition is 1

mghRead(/Applications/freesurfer/subjects/rh.GROUP.thickness.10B.mgh, -1): 
could not open file



fsgd file is:

GroupDescriptorFile 1 
Title All
Class Main
Input 032_XX Main
Input 047_XX Main
Input 049_XX Main
Input 060_XX Main


and I have two contrast (intercept 1 0; slope 0 1)


command line that runs:

mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir 
Thickness.wls --nii.gz --fsgd g1v1_thickness.fsgd --C intercept.mtx --C 
slope.mtx --pvr $SUBJECTS_DIR/rh.GROUP1.thickness.10B.mgh


> Il 5 febbraio 2018 alle 19.36 std...@virgilio.it ha scritto:
> 
> 
>  
> 
> I obtain this error: 
> 
> mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh 
> --glmdir Thickness.wls --nii.gz --fsgd g1v1_thickness.fsgd --C intercept.mtx 
> --C slope.mtx --pvr $SUBJECTS_DIR/rh.MCI.thickness.10B.mgh
> 
> Reading source surface 
> /Applications/freesurfer/subjects/fsaverage/surf/rh.white
> 
> gdfRead(): reading g1v1_thickness.fsgd
> 
> ERROR: fio_FileHasCarriageReturn(): cannot open g1v1_thickness.fsgd
> 
> 
> > > Il 5 febbraio 2018 alle 18.26 Douglas Greve 
>  ha scritto:
> > 
> > 
> > 
> > 
> > On 2/4/18 10:06 AM, std...@virgilio.it mailto:std...@virgilio.it 
> > wrote:
> > 
> > > > > 
> > > I have run:
> > > 
> > > 1)
> > > 
> > > mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh 
> > > --meas thickness --out rh.GROUP1.thickness.00.mgh
> > > mri_surf2surf --hemi rh --s fsaverage --sval 
> > > rh.GROUP1.thickness.00.mgh --fwhm 10 --cortex --tval 
> > > rh.GROUP1.thickness.10B.mgh
> > > 
> > > > > looks good
> > 
> > > > > 
> > > 2)
> > > 
> > > mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface 
> > > fsaverage rh --glmdir Age.wls --nii.gz --fsgd g1v1_Age.fsgd --C 
> > > intercept.mtx --C slope.mtx --pvr rh.GROUP1.thickness.10B.mgh
> > > 
> > > The command line is correct?
> > > 
> > > > > Yes, though I'm not sure about the effect of using --wls and 
> > > --pvr. I guess it will be ok, I just have not used it.
> > 
> > > > > 
> > > 
> > > My concern is on the fsgd file.
> > > 
> > > I have 
> > > 
> > > GroupDescriptorFile 1
> > > Title All
> > > Class Main
> > > Variables thickness
> > > Input ADNI0XX_GROUP1 Main 
> > > Input ADNI0XY_GROUP1 Main 
> > > Input ADNI0YX.GROUP1 Main 
> > > ...
> > > 
> > > What I should add after Main if I would like to assess the 
> > > vertex by vertex correlation between FC (between seed and target vertex) 
> > > and thickness (in the target vertex)?
> > > 
> > > > > Don't represent the PVR in the FSGD file. You only need to 
> > > include items in the contrast matrix. Eg, for intercept use [1 0] and for 
> > > slope use [0 1] eventhough you only have a single class.
> > 
> > > > > 
> > > Should I add the path where is contained rh.thickness.mgh of 
> > > each subject?
> > > 
> > > > > No
> > 
> > > > > 
> > > Please give me an help because I did not find these 
> > > information using --help or mail list.
> > > 
> > > Thanks
> > > 
> > > 
> > > Stefano
> > > 
> > > 
> > > 
> > > Il 3 febbraio 2018 alle 19.55 Douglas Greve 
> > >  mailto:gr...@nmr.mgh.harvard.edu ha scritto:
> > > 
> > > 
> > > Yes, use the --pvr option to mri_glmfit (per-voxel 
> > > regressor). Search through the mail archives for an example on how to use 
> > > it
> > > 
> > > 
> > > On 2/3/18 12:10 PM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > Hi list,
> > > > 
> > > > Is there a way to obtain a map that report the "vertex 
> > > > by vertex" correlation between the FC (obtained by FS-FAST) and 
> > > > cortical thickness?
> > > > 
> > > > Thanks
> > > > 
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > 
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu 
> > > > mailto:Freesurfer@nmr.mgh.harvard.edu
> > > > 
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > > 
> > > > > > > 
> > > 
> > >  
> > > 
> > > > > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu 
> > > > mailto:Freesurfer@nmr.mgh.harvard.edu
> > > > 
> > 

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[miracle ozzoude]

Hello Doug,

Thank you. How do i got about fixing? Do you think it's a good idea to
start afresh on this subject (i.e. recon-all and longitudinal pipeline)?

Best,
Paul

On Mon, Feb 5, 2018 at 12:20 PM, Douglas Greve 
wrote:

> The first frame in your input file is all 0s, so something is wrong with
> the fist subject
>
> On 2/3/18 3:03 PM, miracle ozzoude wrote:
>
> Hello Doug,
>
> I have uploaded the files you requested. Thank you for your help.
>
> Best,
> Paul
>
> On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve 
> wrote:
>
>> Can you upload the glmfit folders and the glmfit input (--y file) to our
>> filedrop?
>>
>> https://gate.nmr.mgh.harvard.edu/filedrop2/
>>
>> On 2/1/18 7:46 PM, miracle ozzoude wrote:
>>
>> Hello Doug,
>>
>> I have attached a screen shot of the mask.mgh for both right and left
>> hemispheres. Everything looks yellow. I followed the paired t-test tutorial
>> on the wiki page (included my scripts, fsgd files, and matrix in email
>> thread). How do i go about fixing it? Thanks you
>>
>> Best,
>> Paul
>>
>> On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve > > wrote:
>>
>>> that usually means that something has gone wrong with the analysis. Do
>>> the maps look ok? In particular, look at the mask
>>>
>>>
>>>
>>> On 1/20/18 1:56 PM, miracle ozzoude wrote:
>>>
>>> Hello Doug,
>>>
>>> I tried using the MC tables that FS distributed. However, i got an error
>>> about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and there's no
>>> fwhm00, the table starts from fwhm01 to fwhm30. Below are my script and
>>> cache.mri_glmfi-sim.log files. My FreeSurfer version is stable version 5.3
>>> on mac. Thank you.
>>>
>>> Best,
>>> Paul
>>>
>>> mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir
>>> $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos
>>> --cwpvalthresh 0.05 --2spaces --overwrite
>>> mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir
>>> $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos
>>> --cwpvalthresh 0.05 --2spaces --overwrite
>>>
>>> On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve <
>>> gr...@nmr.mgh.harvard.edu> wrote:
>>>
 Why are you doing your own MC simulation? You can just use the tables
 that we distribute ...

 On 1/17/18 6:12 PM, miracle ozzoude wrote:

 Hello Experts,

 I am running a paired t-test cortical thickness analysis based on the
 instruction on the wiki page (https://surfer.nmr.mgh.harvar
 d.edu/fswiki/PairedAnalysis). However, the monte carlo files weren't
 not created when i corrected for multiple comparisons. Below are my script,
 fsgd files, mc-z log file, and a screenshot of contrast folder missing mc.z
 maps. Please can you help me figure out why the error is happening. Thank
 you.

 Best,
 Paul

 *Script*:
 pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx
 martrix2=age.mtx
 #resample each subjects's left and right hemisphere data to fsavarage.
 mris_preproc --target fsaverage --hemi lh --meas thickness --out
 lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
 mris_preproc --target fsaverage --hemi rh --meas thickness --out
 rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
 # #smoothen the concatenated file by 5mm FWHM. --cortex means only
 smooth areas in the cortex. N:B. FWHM changes based on study type.
 mri_surf2surf --hemi lh --s fsaverage --sval
 lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
 lh.paired-diff.thickness.sm05.mgh
 mri_surf2surf --hemi rh --s fsaverage --sval
 rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
 rh.paired-diff.thickness.sm05.mgh
 # #Run GLM analysis
 mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
 $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
 lh.paired-diff.glmdirir
 mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired --C
 $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
 rh.paired-diff.glmdir
 # # #Run Clusterwise correction for multiple comparisons using MONTE
 CARLO. First create a table for of simulations
 mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2
 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
 mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2
 mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
 *Fsgd file 1:pairs.fsgd*

 GroupDescriptorFile 1

 Class ADEX

 Input 1000_1 ADEX

 Input 1000_2 ADEX

 Input 1001_1 ADEX

 Input 1001_2 ADEX

 Input 1003_1 ADEX

 Input 1003_2 ADEX

 Input 1005_1 ADEX

 Input 1005_2 ADEX

 Input 1008_1 ADEX

 Input 1008_2 ADEX

 Input 1013_1 ADEX

 Input 1013_2 ADEX

 Input 1014_1 ADEX

 Input 1014_2 ADEX
 *Fsgd file 2: paired_diff.fsgd*

 Gr

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[Douglas N Greve]

I don't know, you'll have to look at how you computed the first frame. 
Maybe the 1st and 2nd time point for that subject are the same


On 02/05/2018 04:27 PM, miracle ozzoude wrote:
> Hello Doug,
>
> Thank you. How do i got about fixing? Do you think it's a good idea to 
> start afresh on this subject (i.e. recon-all and longitudinal pipeline)?
>
> Best,
> Paul
>
> On Mon, Feb 5, 2018 at 12:20 PM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> The first frame in your input file is all 0s, so something is
> wrong with the fist subject
>
>
> On 2/3/18 3:03 PM, miracle ozzoude wrote:
>> Hello Doug,
>>
>> I have uploaded the files you requested. Thank you for your help.
>>
>> Best,
>> Paul
>>
>> On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>> Can you upload the glmfit folders and the glmfit input (--y
>> file) to our filedrop?
>>
>> https://gate.nmr.mgh.harvard.edu/filedrop2/
>> 
>>
>>
>> On 2/1/18 7:46 PM, miracle ozzoude wrote:
>>> Hello Doug,
>>>
>>> I have attached a screen shot of the mask.mgh for both right
>>> and left hemispheres. Everything looks yellow. I followed
>>> the paired t-test tutorial on the wiki page (included my
>>> scripts, fsgd files, and matrix in email thread). How do i
>>> go about fixing it? Thanks you
>>>
>>> Best,
>>> Paul
>>>
>>> On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve
>>> >> > wrote:
>>>
>>> that usually means that something has gone wrong with
>>> the analysis. Do the maps look ok? In particular, look
>>> at the mask
>>>
>>>
>>>
>>> On 1/20/18 1:56 PM, miracle ozzoude wrote:
 Hello Doug,

 I tried using the MC tables that FS distributed.
 However, i got an error about " cannot find
 /fwhm00/pos/th30/mc-z.csd ". I checked and there's no
 fwhm00, the table starts from fwhm01 to fwhm30. Below
 are my script and cache.mri_glmfi-sim.log files. My
 FreeSurfer version is stable version 5.3 on mac. Thank
 you.

 Best,
 Paul

 mri_glmfit-sim --glmdir lh.paired.diff.glmdir
 --cache-dir
 $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex
 --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite
 mri_glmfit-sim --glmdir rh.paired.diff.glmdir
 --cache-dir
 $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex
 --cache 3 pos --cwpvalthresh 0.05 --2spaces --overwrite

 On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve
 >>> > wrote:

 Why are you doing your own MC simulation? You can
 just use the tables that we distribute ...


 On 1/17/18 6:12 PM, miracle ozzoude wrote:
> Hello Experts,
>
> I am running a paired t-test cortical thickness
> analysis based on the instruction on the wiki page
> (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
> 
> ).
> However, the monte carlo files weren't not created
> when i corrected for multiple comparisons. Below
> are my script, fsgd files, mc-z log file, and a
> screenshot of contrast folder missing mc.z maps.
> Please can you help me figure out why the error is
> happening. Thank you.
>
> Best,
> Paul
>
> *Script*:
> pairs=pairs.fsgd paired=paired_diff.fsgd
> martrix1=mean.mtx martrix2=age.mtx
> #resample each subjects's left and right
> hemisphere data to fsavarage.
> mris_preproc --target fsaverage --hemi lh --meas
> thickness --out lh.paired-diff.thickness.mgh
> --fsgd $pairs --paired-diff
> mris_preproc --target fsaverage --hemi rh --meas
> thickness --out rh.paired-diff.thickness.mgh
> --fsgd $pairs --paired-diff
> # #smoothen the concatenated file by 5mm FWHM.
> --cortex means only smooth areas in the cortex.
> N:B. FWHM changes based on study type.
> mri_surf2surf --hemi lh --s fsaverage --sval
> 

Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm

[Sims, Sara A]

Doug,

This is a new problem. I figured out my earlier issue. This makes a 
8V1+aseg.mgz file there are just no 4001 and 3001's in the file so when I 
binarize there is nothing there. So my question is why is it not identifying 
the wm next to my label? This is happening in multiple subjects on varying 
labels.

Sara Sims 
Graduate Research Fellow
University of Alabama at Birmingham
Department of Psychology
205-975-4060
sno...@uab.edu
On 2/5/18, 12:31 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Douglas N Greve"  wrote:

Sorry, is this related to the earlier question about how to remove 
non-wm labels or is this a new submission? If a new subj, can you 
describe the problem you are having?


On 02/05/2018 01:23 PM, Sims, Sara A wrote:
>
> This is the whole process output from a rerun on a subject that didn’t 
> work the first time or with the rerun:
>
> Reading ctab 
> /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab
>
> Number of ctab entries 2
>
> $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
>
> cwd /data/user/snolin/Scripts/Labelmaker
>
> cmdline mris_label2annot --ctab 
> /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab --s 
> 211215 --h lh --l 
> 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/8_LH_V1.label
 
> --a 8V1
>
> sysname Linux
>
> hostname c0039
>
> machine x86_64
>
> user snolin
>
> subject 211215
>
> hemilh
>
> SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon
>
> ColorTable 
> /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab
>
> AnnotName 8V1
>
> nlables 1
>
> LabelThresh 0 0.00
>
> ERROR: 
> 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/lh.8V1.annot
 
> already exists
>
> Reading ctab 
> /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab
>
> Number of ctab entries 2
>
> $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
>
> cwd /data/user/snolin/Scripts/Labelmaker
>
> cmdline mris_label2annot --ctab 
> /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab --s 
> 211215 --h rh --l 
> 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/8_RH_V1.label
 
> --a 8V1
>
> sysname Linux
>
> hostname c0039
>
> machine x86_64
>
> user snolin
>
> subject 211215
>
> hemirh
>
> SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon
>
> ColorTable 
> /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab
>
> AnnotName 8V1
>
> nlables 1
>
> LabelThresh 0 0.00
>
> ERROR: 
> 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/rh.8V1.annot
 
> already exists
>
> SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon
>
> subject 211215
>
> outvol 
> 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz
>
> useribbon 0
>
> baseoffset 0
>
> labeling wm
>
> dmaxctx 5.00
>
> RipUnknown 0
>
> Reading lh white surface
>
>  
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/lh.white
>
> Reading lh pial surface
>
>  
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/lh.pial
>
> Loading lh annotations from 
> 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/lh.8V1.annot
>
> Reading rh white surface
>
>  
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/rh.white
>
> Reading rh pial surface
>
>  
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/rh.pial
>
> Loading rh annotations from 
> 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/rh.8V1.annot
>
> Loading ribbon segmentation from 
> 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/ribbon.mgz
>
> Building hash of lh white
>
> Building hash of lh pial
>
> Building hash of rh white
>
> Building hash of rh pial
>
> Loading aseg from 
> 
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/aseg.mgz
>
> ASeg Vox2RAS: ---
>
> -1.0 0.0   0.0   128.0;
>
> 0.0 0.0   1.0  -128.0;
>
> 0.0 -1.0   0.0   128.0;
>
> 0.0 0.0   0.0   1.0;
>
> -
>
> Labeling Slice
>
>   0   1 2   3   4   5   6   7   8   9  10  11  12  13  14  15  16 17  
> 18  19
>