[Freesurfer] Error in qdec

[Mateus Aranha]

External Email - Use Caution

Hello,

Iḿ trying to perform a group analysis using qdec, but the analysis stops at
70% and the following error message is shown:

[image: Screenshot from 2020-06-29 13-03-27.png]

How should I proceed?

Thanks,
Mateus
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Re: [Freesurfer] Precise MNI152 space

[Douglas N. Greve]

We don't use MNI152 much. We have an affine matrix to convert from 305 
to 152, and that 152 is the one in FSL


On 6/25/2020 4:27 PM, Inês Pereira wrote:


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Dear FreeSurfer developers,

Which MNI152 space is used within FreeSurfer? Is it the MNI152 
nonlinear 6-th generation (as in, for example, FSL), or another one, 
like MNI152 nonlinear 2009a, 2009b or 2009c?


I wasn’t able to find this information in the fswiki.
I checked 
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems and the 
documentation of certain functions, such as mri_cvs_register.


Thank you for your help!

All the best,

Inês Pereira

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Re: [Freesurfer] Question regarding MRIread

[Douglas N. Greve]

There's a lot of stuff going on there, so it's hard to say withhout more 
detail. But it sounds like you might not be taking into account that the 
voxel coords in matlab are 1-based.


On 6/26/2020 12:04 PM, Franziska Klein wrote:


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Hello,


I am using the isosurface() function in order to create a mesh based 
on the T1.mgz and on the ribbon.mgz. I need those meshes for 
the coregistration of some channels.



After coregistration I do project the channels onto the cortex and 
extract the corresponding voxel coordinates. Until here, everything 
works fine.


Next, I am using MRIwrite in order to save the T1.mgz as *.nii.mgz 
which I am using to generate a deformation field with SPM12 to 
transform the voxel coordinates to normalized MNI coordinates. 
However, when I put the voxel coordinates (not normalized yet) 
into SPM12 while displaying my generated *.nii image it happens that 
the coordinates on the right hemisphere (MNI space) are slightly 
outside of the cortex which is of course not the case on my cortex 
mesh after projection.



Now I am wondering whether there is a mismatch between the mesh and 
the *.nii image (one voxel maybe)? And whether that is introduced by 
MRIwrite? If so, do I have to shift all points of the meshes by +1 in 
order to get correct results the way I want to? If not, any ideas on 
where that mismatch could come from?



Thank you and kind regards,

Franziska




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Re: [Freesurfer] FW: LGI and Global GI

[Douglas N. Greve]

I guess you could use something like

mri_segstats --i lh.lgi.mgz --slabel subject lh 
$SUBJECTS_DIR/subject/label/lh.cortex.label --excludeid 0 --o lh.lgi.sum



On 6/28/2020 11:08 AM, Alexopoulos, Dimitrios wrote:


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Is generating a Global hemispheric Gyrification Index possible?

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Alexopoulos, 
Dimitrios

*Sent:* Wednesday, May 27, 2020 3:39 PM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] LGI and Global GI

** External Email - Caution **

*External Email - Use Caution *

HI,

I have generated the LGI for a group of pediatric subjects. Is there a 
way to compute a single Global gyrification index measure  for each 
subject?


Jim,



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The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If 
you are not the intended recipient, be advised that any unauthorized 
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the contents of this information is strictly prohibited. If you have 
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Re: [Freesurfer] Error in qdec

[Douglas N. Greve]

Hard to say. We are not supporting QDEC anymore for these types of 
reasons. Can you cut and paste that mri_glmfit command into the terminal 
and see what happens?


On 6/29/2020 7:05 AM, Mateus Aranha wrote:


External Email - Use Caution

Hello,

Iḿ trying to perform a group analysis using qdec, but the analysis 
stops at 70% and the following error message is shown:


Screenshot from 2020-06-29 13-03-27.png

How should I proceed?

Thanks,
Mateus

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Re: [Freesurfer] Recon-all 5.3.0 failing and I can't see the error message

[Douglas N. Greve]

Not sure. Can you run this

cd /execute/freesurfer2016/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale 
--i orig.mgz --o orig_nu.mgz


and send the terminal output?


On 6/29/2020 7:01 AM, Ian wrote:


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I have attached the log - is there any chance you could tell me what 
the problem is?


Thanks,

Ian

--


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[Freesurfer] Recon-all 5.3.0 failing and I can't see the error message

[Ian]

   External Email - Use Caution

I have attached the log - is there any chance you could tell me what the 
problem is?


Thanks,

Ian

--

Mon Jun 29 10:53:22 UTC 2020
/execute/freesurfer2016
/usr/local/freesurfer/bin/recon-all
-all -subjid ./freesurfer2016
subjid freesurfer2016
setenv SUBJECTS_DIR /execute
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux 7d97b79d7546 5.3.0-59-generic #53~18.04.1-Ubuntu SMP Thu Jun 4 14:58:26 UTC 2020 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize unlimited
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1048576 
memorylocked 16384 kbytes
maxproc  unlimited
maxlocks unlimited
maxsignal63578 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   16390764 6474076  212720  304968 9703968 9295408
Swap:   2097148  818176 1278972


program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/06/29-10:53:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $  User: docker  Machine: 7d97b79d7546  Platform: Linux  PlatformVersion: 5.3.0-59-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/06/29-10:53:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: docker  Machine: 7d97b79d7546  Platform: Linux  PlatformVersion: 5.3.0-59-generic  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/06/29-10:53:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: docker  Machine: 7d97b79d7546  Platform: Linux  PlatformVersion: 5.3.0-59-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/06/29-10:53:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $  User: docker  Machine: 7d97b79d7546  Platform: Linux  PlatformVersion: 5.3.0-59-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/06/29-10:53:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $  User: docker  Machine: 7d97b79d7546  Platform: Linux  PlatformVersion: 5.3.0-59-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/06/29-10:53:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: docker  Machine: 7d97b79d7546  Platform: Linux  PlatformVersion: 5.3.0-59-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/06/29-10:53:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $  User: docker  Machine: 7d97b79d7546  Platform: Linux  PlatformVersion: 5.3.0-59-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/06/29-10:53:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $  User: docker  Machine: 7d97b79d7546  Platform: Linux  PlatformVersion: 5.3.0-59-generic  CompilerName: GCC  CompilerVersion: 40400 


 === NUMBER OF OPENMP THREADS = 1 === 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2020/06/29-10:53:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $  User: docker  Machine: 7d97b79d7546  Platform: Linux  PlatformVersion: 5.3.0-59-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  Prog

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

[Douglas N. Greve]

How did you generate 102.mgz? It looks like it was created by a pretty 
old version of FS.


On 6/28/2020 5:41 PM, Fischl, Bruce wrote:


And how did you generate the volumes? I wouldn’t name them 001.mgz, 
that will end up being confusing. Maybe something like sub.001.mgz 
might be better, since otherwise we might overwrite some of them


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Angela Favaro

*Sent:* Sunday, June 28, 2020 4:53 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

*External Email - Use Caution *

Yes, I am sure

Now I tried to use Freesurfer 6.0 again for that volume and both 
recon-all and mri_info  worked:


recon-all -all -s subj102

Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c

INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/prova

Actual FREESURFER_HOME /Applications/freesurfer

Darwin MacBookiAngela2 16.7.0 Darwin Kernel Version 16.7.0: Sun Jun  2 
20:26:31 PDT 2019; root:xnu-3789.73.50~1/RELEASE_X86_64 x86_64


#

#@# MotionCor Sun Jun 28 22:44:04 CEST 2020

Found 1 runs

/Users/angelafavaro/Desktop/prova/subj102/mri/orig/102.mgz

Checking for (invalid) multi-frame inputs...

WARNING: only one run found. This is OK, but motion

correction cannot be performed on one run, so I'll

copy the run to rawavg and continue.

….

…..



mri_info subj102/mri/orig/102.mgz

Volume information for subj102/mri/orig/102.mgz

        type: MGH

  dimensions: 256 x 256 x 256

voxel sizes: 1.00, 1.00, 1.00

        type: UCHAR (0)

        fov: 256.000

        dof: 0

      xstart: -128.0, xend: 128.0

      ystart: -128.0, yend: 128.0

      zstart: -128.0, zend: 128.0

          TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip 
angle: 9.00 degrees


    nframes: 1

    PhEncDir: UNKNOWN

    FieldStrength: 0.00

ras xform present

  xform info: x_r =  -1., y_r =   0., z_r = -0., c_r =    
-2.5219


            : x_a =   0., y_a =  -0., z_a = 1., c_a =    
10.8637


            : x_s =  -0., y_s =  -1., z_s = -0., c_s =   
-32.3759


talairach xfm : 
/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm


Orientation   : LIA

Primary Slice Direction: coronal

voxel to ras transform:

            -1.   0.  -0.   125.4781

              0.  -0.   1.  -117.1363

            -0.  -1.  -0.    95.6241

              0.   0.   0.     1.

voxel-to-ras determinant -1

ras to voxel transform:

            -1.  -0.  -0.   125.4781

              0.  -0.  -1.    95.6241

              0.   1.  -0.   117.1363

            -0.  -0.  -0.     1.

Il giorno 28 giu 2020, alle ore 20:45, Fischl, Bruce
mailto:bfis...@mgh.harvard.edu>> ha scritto:

Are you sure 102.mgz is from our analysis previously? We typically
name the volumes 001.mgz, 002.mgz, etc….

*From:*freesurfer-boun...@nmr.mgh.harvard.edu

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>*On Behalf
Of*Angela Favaro
*Sent:*Sunday, June 28, 2020 1:49 PM
*To:*Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:*Re: [Freesurfer] ERROR: input(s) cannot have multiple
frames!

*External Email - Use Caution *

Sure!

thank you for any help!

Angela

angelafavaro% recon-all -all -s subj102

Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b

Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b

INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/Aachen

Actual FREESURFER_HOME /Applications/freesurfer/7.1.0

-rw-rw-r-- 1 angelafavaro  staff  143379 Jun 28 13:46
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log

Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct
17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

#

#@# MotionCor Sun Jun 28 19:40:10 CEST 2020

Found 1 runs

/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz

Checking for (invalid) multi-frame inputs...

ERROR: input(s) cannot have multiple frames!

/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has 
frames

Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct
17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj102 exited with ERRORS at Sun Jun 28 19:40:11
CEST 2020

For more details, see the log file
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log

To report a problem,
seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Then I copied 102.mgz in a different folder. I also copied in t

[Freesurfer] Error in Trac-All Pre-Processing step

[Jocelyn Ra]

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Hi all,

After running the trac-all command in the pre-processing step in the
official TRACULA tutorial, I ran into the following error:

WARN: Could not find satisfactory control point fit - try 4718
Writing output files to
/home1/jr2359/diffusion_tutorial_april2018/diffusion_tutorial/elmo.2005/dlabel/mni/rh.cst_AS_avg33_mni_bbr_*
Writing spline volume to
/home1/jr2359/diffusion_tutorial_april2018/diffusion_tutorial/elmo.2005/dlabel/mni/rh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz
Segmentation fault

The "WARN" message repeated several times before this final message, making
me believe the issue is with the control points. For reference, I am using
the tutorial data set, "set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)"
for the control points, and LINUX.

Has anyone else run into this error, and could someone please help me with
this issue?

Thank you in advance!
Sincerely,
Jocelyn
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Re: [Freesurfer] Visualizing Talairach Registeration

[Douglas N. Greve]

We don't have a  replacement yet for tkregsiter2, but here is a work-around

cd $SUBJECTS_DIR/subject/mri/transforms

First, convert the xfm to an lta file

lta_convert --src ../orig.mgz --trg 
$FREESURFER_HOME/average/mni305.cor.mgz --inxfm talairach.xfm --outlta 
talairach.xfm2.lta --subject fsaverage --ltavox2vox


Next, check the registration with

 tkregisterfv --mov ../orig.mgz --reg talairach.xfm2.lta

If everything is ok, then just exit out of freeview and move on. If you 
need to make changes, then  save the changes back into talairach.xfm2.lta


Then convert the lta back to xfm:
lta_convert --inlta talairach.xfm2.lta --outmni talairach.xfm



On 6/28/2020 4:30 PM, Wakim, Kathryn-Mary wrote:


External Email - Use Caution

Hi all,

I’m a new FreeSurfer user, so I’d like to thank you all in advance for 
your patience!


After running recon-all to completion, I reviewed the log file and 
found the warning "#@# Talairach Failure Detection.” I am assuming 
that this is a warning and not a hard failure, because it seems that 
recon-all has run to completion “without error” (according to the log 
file).


I attempted to follow these instructions to verify my Tal 
registstration output: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview#:~:text=FreeSurfer%20computes%20a%20linear%20Talairach,via%20%2Dnotal%2Dcheck) 
 However, 
it seems based on archived Freesufer forum posts that the GUI for 
tkregister2 is no longer compatible with the current Mac OS, and I was 
therefore unable to use this tool.


I’m wondering if someone can provide me with some alternate 
instructions for how to view the output of the Tal registration so 
that I can verify whether or not there has been a registration error.



Warm regards,
Kamy Wakim

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Re: [Freesurfer] Error in Trac-All Pre-Processing step

[Yendiki, Anastasia]

Hi Jocelyn - It's strange to get this in the tutorial data, it's the kind of 
thing you might get if the FS recon was missing part of the brain or if the 
alignment between datasets was not good. So I'm surprised you're getting this 
in the tutorial data. Can you please send your entire trac-all.log file?

Thanks!
a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Jocelyn Ra 

Sent: Monday, June 29, 2020 11:08 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Error in Trac-All Pre-Processing step


External Email - Use Caution

Hi all,

After running the trac-all command in the pre-processing step in the official 
TRACULA tutorial, I ran into the following error:

WARN: Could not find satisfactory control point fit - try 4718
Writing output files to 
/home1/jr2359/diffusion_tutorial_april2018/diffusion_tutorial/elmo.2005/dlabel/mni/rh.cst_AS_avg33_mni_bbr_*
Writing spline volume to 
/home1/jr2359/diffusion_tutorial_april2018/diffusion_tutorial/elmo.2005/dlabel/mni/rh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz
Segmentation fault

The "WARN" message repeated several times before this final message, making me 
believe the issue is with the control points. For reference, I am using the 
tutorial data set, "set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)" for the 
control points, and LINUX.

Has anyone else run into this error, and could someone please help me with this 
issue?

Thank you in advance!
Sincerely,
Jocelyn
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Re: [Freesurfer] Error recon-all mri_cc

[Hoopes, Andrew]

Hi Yann (and anyone else with mri_cc failures on mac),
We have a fix that we'll include in an upcoming 7.1.1 patch release. If you'd 
like a quick local fix, you can update your distribution with the new version 
of mri_cc by running the following commands (this might require sudo):
cd $FREESURFER_HOME/bin
rm mri_cc
curl https://surfer.nmr.mgh.harvard.edu/pub/dist/tmp_patch/mri_cc -O mri_cc
chmod +x mri_cc
Please let us know if this does not solve your issue.
Andrew

From:  on behalf of Yann Quidé 

Reply-To: FS Help 
Date: Monday, June 29, 2020 at 2:35 AM
To: FS Help 
Subject: Re: [Freesurfer] Error recon-all mri_cc


External Email - Use Caution
Hi team,

I appreciate everyone is busy, but did anyone have time to look at my subject?
It was uploaded on June 18. It’s called yannquide.tar.gz

Thanks for your time.

Yann


On 22 Jun 2020, at 12:51 pm, Yann Quidé 
mailto:yannqu...@gmail.com>> wrote:

Hi team,

I was just wondering if you received my file and if you had time to look at it?

Thanks,

Yann


On 18 Jun 2020, at 7:08 am, Yann Quidé 
mailto:yannqu...@gmail.com>> wrote:

Hi Doug,

Thanks for this. I sent the file; it’s called yannquide.tar.gz.

Yann


On 16 Jun 2020, at 11:56 pm, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:

Can you upload the subject so I can take a look? Instructions below


From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.



On 6/15/2020 8:28 PM, Yann Quidé wrote:
External Email - Use Caution

Hi there,

I am using Freesurfer v7.1.0 and encounter an error for few of my subjects only.
Recon-all finishes with errors, and it seems this occurs during the 
segmentation.

What can I do to fix this?

I attached the recon-all log for one of my subject.

Thanks,

Yann
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Re: [Freesurfer] Visualizing Talairach Registeration

[Douglas N. Greve]

BTW, I just created a new version of tkregisterfv
https://gate.nmr.mgh.harvard.edu/safelinks/greve/tkregisterfv
Copy it to $FREESURFER_HOME/bin
Then run
tkregisterfv --s subject --fstal
If you have to edit the reg, save the lta in the pre-selected location 
(talairach.lta)
When done, exit out ot tkergisterfv (freeview), don't control-C from the 
command line

Let me know how it goes


On 6/29/2020 11:07 AM, Douglas N. Greve wrote:


We don't have a  replacement yet for tkregsiter2, but here is a 
work-around


cd $SUBJECTS_DIR/subject/mri/transforms

First, convert the xfm to an lta file

lta_convert --src ../orig.mgz --trg 
$FREESURFER_HOME/average/mni305.cor.mgz --inxfm talairach.xfm --outlta 
talairach.xfm2.lta --subject fsaverage --ltavox2vox


Next, check the registration with

 tkregisterfv --mov ../orig.mgz --reg talairach.xfm2.lta

If everything is ok, then just exit out of freeview and move on. If 
you need to make changes, then  save the changes back into 
talairach.xfm2.lta


Then convert the lta back to xfm:
lta_convert --inlta talairach.xfm2.lta --outmni talairach.xfm



On 6/28/2020 4:30 PM, Wakim, Kathryn-Mary wrote:


External Email - Use Caution

Hi all,

I’m a new FreeSurfer user, so I’d like to thank you all in advance 
for your patience!


After running recon-all to completion, I reviewed the log file and 
found the warning "#@# Talairach Failure Detection.” I am assuming 
that this is a warning and not a hard failure, because it seems that 
recon-all has run to completion “without error” (according to the log 
file).


I attempted to follow these instructions to verify my Tal 
registstration output: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview#:~:text=FreeSurfer%20computes%20a%20linear%20Talairach,via%20%2Dnotal%2Dcheck) 
 However, 
it seems based on archived Freesufer forum posts that the GUI for 
tkregister2 is no longer compatible with the current Mac OS, and I 
was therefore unable to use this tool.


I’m wondering if someone can provide me with some alternate 
instructions for how to view the output of the Tal registration so 
that I can verify whether or not there has been a registration error.



Warm regards,
Kamy Wakim

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Re: [Freesurfer] Question regarding MRIread

[Franziska Klein]

External Email - Use Caution

I know, a lot of steps.


1-based vs. 0-based, that is basically what I mean and what I think is the 
problem, but I need to be sure. When I load in the *.nii file generated from 
the mesh and display it in SPM, then the origin shown in the SPM Gui is the 
last column in vox2ras1. Oversimplified, when I want to compare a voxel from 
SPM with a voxel from freesurfer, I need to shift the coordinates of that voxel 
from freesurfer by +1, right? (or substract one from the SPM one).


Kind regards,

Franziska


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. Greve 

Gesendet: Montag, 29. Juni 2020 16:44:34
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Question regarding MRIread

There's a lot of stuff going on there, so it's hard to say withhout more 
detail. But it sounds like you might not be taking into account that the voxel 
coords in matlab are 1-based.

On 6/26/2020 12:04 PM, Franziska Klein wrote:

External Email - Use Caution

Hello,


I am using the isosurface() function in order to create a mesh based on the 
T1.mgz and on the ribbon.mgz. I need those meshes for the coregistration of 
some channels.


After coregistration I do project the channels onto the cortex and extract the 
corresponding voxel coordinates. Until here, everything works fine.

Next, I am using MRIwrite in order to save the T1.mgz as *.nii.mgz which I am 
using to generate a deformation field with SPM12 to transform the voxel 
coordinates to normalized MNI coordinates. However, when I put the voxel 
coordinates (not normalized yet) into SPM12 while displaying my generated *.nii 
image it happens that the coordinates on the right hemisphere (MNI space) are 
slightly outside of the cortex which is of course not the case on my cortex 
mesh after projection.


Now I am wondering whether there is a mismatch between the mesh and the *.nii 
image (one voxel maybe)? And whether that is introduced by MRIwrite? If so, do 
I have to shift all points of the meshes by +1 in order to get correct results 
the way I want to? If not, any ideas on where that mismatch could come from?


Thank you and kind regards,

Franziska








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[Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Mason Wells]

External Email - Use Caution

Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf files into .gii 
format (from FS format)

  *   e.g. mris_convert lh.pial lh.pial.surf.gii
I then applied the transformation to align the filtered_func to the T1

  *   mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta 
--fstarg --o movie_t1_space.nii.gz
I then tried to run the following wb command

  *   wb_command -volume-to-surface-mapping 
/home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.inflated.surf.gii
 /home/masontwells/Documents/Data/MovPPT_001/lh_movie.gii -ribbon-constrained 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.white.surf.gii
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.pial.surf.gii
Which resulted in this subsequent error.

ERROR: NAME OF FILE: movie_t1_space.nii.gz
PATH TO FILE: /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat

Unable to allocate memory for reading the file.

File Size: 3.24 Gigabytes

Note: The amount of memory required to read a data file may be substantially 
larger than the size of the file due to the way the file's data is organized in 
memory or compression of data within the file.

Any advice on how to convert NIFTI to GIFTI and then GIFTI to CIFTI whilst 
keeping the data in the subjects space would be really appreciated.

Best wishes,
Mason


Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University 
webpage
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628

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[Freesurfer] Position open: Research Engineer in Neuroimaging at BBRC - Barcelona

[Juan Domingo Gispert López]

External Email - Use Caution

The Alzheimer's Prevention Program of the Barcelonabeta Brain Research
center is seeking a  Research Engineer in Neuroimaging. For further
information on the position, please visit the following link:

https://fpmaragall.org/wp-content/uploads/2020/06/Research-Engineer-in-Neuroimaging_Job-description.pdf


To apply, please submit a single PDF file containing the following: 1)
Cover letter describing research interests and relevant background; 2) CV
3) The names of up to three individuals who could provide reference
letters. All files or inquiries should be submitted electronically to:
r...@barcelonabeta.org Subject: Research Engineer in Neuroimaging

Deadline: 10th of July
-- 

*Juan Domingo Gispert*Group Leader - Neuroimaging
*BarcelonaBeta*
* Brain Research Center (BBRC) *jdgisp...@barcelonabeta.org
T. (+34) 93 326 31 67
C/ Wellington, 30

08005 Barcelona

www.barcelonabeta.org
www.fpmaragall.org
--

Confidencialitat correu electrònic BBRC
. Confidencialidad
correo electrónico BBRC
. E-mail
confidentiality BBRC .
Gràcies per estalviar paper. *Gracias por ahorrar papel. *Thanks for saving
paper.
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Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Glasser, Matthew]

External Email - Use Caution

Your command below is missing the  argument:

   wb_command -volume-to-surface-mapping
   - the volume to map data from
   - the surface to map the data onto
   - output - the output metric file
  [-ribbon-constrained] - use ribbon constrained mapping algorithm
  - the inner surface of the ribbon
  - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically 
use the midthickness surface here.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion



External Email - Use Caution
Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf files into .gii 
format (from FS format)

  *   e.g. mris_convert lh.pial lh.pial.surf.gii
I then applied the transformation to align the filtered_func to the T1

  *   mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta 
--fstarg --o movie_t1_space.nii.gz
I then tried to run the following wb command

  *   wb_command -volume-to-surface-mapping 
/home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.inflated.surf.gii
 /home/masontwells/Documents/Data/MovPPT_001/lh_movie.gii -ribbon-constrained 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.white.surf.gii
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.pial.surf.gii
Which resulted in this subsequent error.

ERROR: NAME OF FILE: movie_t1_space.nii.gz
PATH TO FILE: /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat

Unable to allocate memory for reading the file.

File Size: 3.24 Gigabytes

Note: The amount of memory required to read a data file may be substantially 
larger than the size of the file due to the way the file's data is organized in 
memory or compression of data within the file.

Any advice on how to convert NIFTI to GIFTI and then GIFTI to CIFTI whilst 
keeping the data in the subjects space would be really appreciated.

Best wishes,
Mason


Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University 
webpage
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Glasser, Matthew]

External Email - Use Caution

Scratch that, I guess you did include a surface.  How much RAM do you have 
available and are you on a 64bit OS?  As I mentioned last week, what you are 
trying to do is not computationally efficient and not really the best approach 
to go about things.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:24 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Your command below is missing the  argument:

   wb_command -volume-to-surface-mapping
   - the volume to map data from
   - the surface to map the data onto
   - output - the output metric file
  [-ribbon-constrained] - use ribbon constrained mapping algorithm
  - the inner surface of the ribbon
  - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically 
use the midthickness surface here.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion



External Email - Use Caution
Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf files into .gii 
format (from FS format)

  *   e.g. mris_convert lh.pial lh.pial.surf.gii
I then applied the transformation to align the filtered_func to the T1

  *   mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta 
--fstarg --o movie_t1_space.nii.gz
I then tried to run the following wb command

  *   wb_command -volume-to-surface-mapping 
/home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.inflated.surf.gii
 /home/masontwells/Documents/Data/MovPPT_001/lh_movie.gii -ribbon-constrained 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.white.surf.gii
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.pial.surf.gii
Which resulted in this subsequent error.

ERROR: NAME OF FILE: movie_t1_space.nii.gz
PATH TO FILE: /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat

Unable to allocate memory for reading the file.

File Size: 3.24 Gigabytes

Note: The amount of memory required to read a data file may be substantially 
larger than the size of the file due to the way the file's data is organized in 
memory or compression of data within the file.

Any advice on how to convert NIFTI to GIFTI and then GIFTI to CIFTI whilst 
keeping the data in the subjects space would be really appreciated.

Best wishes,
Mason


Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University 
webpage
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action

Re: [Freesurfer] Question regarding MRIread

[Douglas N. Greve]

How did you generate the nii file from the mesh?

On 6/29/2020 12:21 PM, Franziska Klein wrote:


External Email - Use Caution

I know, a lot of steps.


1-based vs. 0-based, that is basically what I mean and what I think is 
the problem, but I need to be sure. When I load in the *.nii file 
generated from the mesh and display it in SPM, then the origin shown 
in the SPM Gui is the last column in vox2ras1. Oversimplified, when I 
want to compare a voxel from SPM with a voxel from freesurfer, I need 
to shift the coordinates of that voxel from freesurfer by +1, right? 
(or substract one from the SPM one).



Kind regards,

Franziska


*Von:* freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. 
Greve 

*Gesendet:* Montag, 29. Juni 2020 16:44:34
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] Question regarding MRIread
There's a lot of stuff going on there, so it's hard to say withhout 
more detail. But it sounds like you might not be taking into account 
that the voxel coords in matlab are 1-based.


On 6/26/2020 12:04 PM, Franziska Klein wrote:


External Email - Use Caution

Hello,


I am using the isosurface() function in order to create a mesh based 
on the T1.mgz and on the ribbon.mgz. I need those meshes for 
the coregistration of some channels.



After coregistration I do project the channels onto the cortex and 
extract the corresponding voxel coordinates. Until here, everything 
works fine.


Next, I am using MRIwrite in order to save the T1.mgz as *.nii.mgz 
which I am using to generate a deformation field with SPM12 to 
transform the voxel coordinates to normalized MNI coordinates. 
However, when I put the voxel coordinates (not normalized yet) 
into SPM12 while displaying my generated *.nii image it happens that 
the coordinates on the right hemisphere (MNI space) are slightly 
outside of the cortex which is of course not the case on my cortex 
mesh after projection.



Now I am wondering whether there is a mismatch between the mesh and 
the *.nii image (one voxel maybe)? And whether that is introduced by 
MRIwrite? If so, do I have to shift all points of the meshes by +1 in 
order to get correct results the way I want to? If not, any ideas on 
where that mismatch could come from?



Thank you and kind regards,

Franziska




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Re: [Freesurfer] freesurfer 7.1.0 mris_sphere failure, "singular matrix in quadratic form"

[Douglas N. Greve]

Not sure what is going on there. Can you take a look at lh.inflated and 
lh.white.preaparc to make sure that they don't look crazy?


On 6/23/2020 11:17 AM, Malone, Ian wrote:


External Email - Use Caution

Hello,

We've run into an issue with 
freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b (on Rocks 
release 7.0, kernel 3.10.0-957.12.2.el7.x86_64). It appears some runs 
are failing at the mris_sphere stage, but not producing any very 
informative errors, just repeated "singular matrix in quadratic form" 
at the end of mris_sphere as below. I was wondering if anyone had any 
suggestions for further troubleshooting please?


recon-all is being invoked in two stages, with a manual brain mask 
replacing 
/scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/brainmask.mgz 
in between them. This is being managed by a python script, but I think 
the sequence being executed is the following:


$ recon-all -i 
/SAN/medic/insight46/analysis/gradwarp/sub-11233210/ses-followup/anat/sub-11233210_ses-followup_T1w_run-1_desc-gradwarp.nii.gz 
-T2 
/SAN/medic/insight46/analysis/gradwarp/sub-11233210/ses-followup/anat/sub-11233210_ses-followup_T2w_run-1_desc-gradwarp.nii.gz 
-autorecon1 -noskullstrip -noT2pial -cw256 -cubic -3T -openmp 4 -s 
sub-11233210_ses-followup -status 
/SAN/medic/insight46/analysis/freesurfer7/status/sub-11233210_ses-followup_recon_all_status.log 
-log 
/SAN/medic/insight46/analysis/freesurfer7/log/sub-11233210_ses-followup_recon_all.log


$ mri_convert 
/SAN/medic/insight46/analysis/drc_brain/sub-11233210/ses-followup/anat/sub-11233210_ses-followup_T1w_run-1_space-orig_desc-drc-brain-mask.nii.gz 
/scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/drcmask.mgz 
--cw256 --conform -rt nearest


$ mri_mask -T 1 
/scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/T1.mgz 
/scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/drcmask.mgz 
/scratch0/wcoath/2217885.100/sub-11233210_ses-followup/mri/brainmask.mgz


$ recon-all -autorecon2, -autorecon3 -cw256 -cubic -T2pial -openmp 4 
-s sub-11233210_ses-followup -status 
/SAN/medic/insight46/analysis/freesurfer7/status/sub-11233210_ses-followup_recon_all_status.log 
-log 
/SAN/medic/insight46/analysis/freesurfer7/log/sub-11233210_ses-followup_recon_all.log


The first recon-all (autorecon1) completes okay, the autorecon2,3 
stage fails on occasion (this works for most scans). Its last output 
looks like this (full copy attached):


@#@FSLOADPOST 2020:06:17:02:37:18 mris_curvature N 12 1.14 1.51 1.48
#
#@# Sphere lh Wed Jun 17 02:37:18 BST 2020
/state/partition1/scratch0/wcoath/2217885.100/sub-11233210_ses-followup/scripts

 mris_sphere -rusage 
/state/partition1/scratch0/wcoath/2217885.100/sub-11233210_ses-followup/touch/rusage.mris_sphere.lh.dat 
-seed 1234 ../surf/lh.inflated ../surf/lh.sphere


setting seed for random number genererator to 1234
7.1.0
  7.1.0

== Number of threads available to mris_sphere for OpenMP = 4 ==
reading original vertex positions...
scaling brain by 0.309...
projecting onto sphere...
surface projected - minimizing metric distortion...
MRISunfold() max_passes = 1 ---
tol=5.0e-01, sigma=0.0, host=fry-6, nav=1024, nbrs=2, l_area=1.000, 
l_dist=1.000

using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.00
nfields 0
scale 1.00
desired_rms_height -1.00
momentum 0.90
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
singular matrix in quadratic form
@#@FSTIME  2020:06:17:02:37:18 mris_sphere N 6 e 256.90 S 2.38 U 
723.85 P 282% M 2286104 F 0 R 931286 W 0 c 79152 w 33537 I 0 O 0 L 
1.14 1.51 1.48

@#@FSLOADPOST 2020:06:17:02:41:35 mris_sphere N 6 2.62 2.15 1.75
Linux fry-611-142.local 3.10.0-1062.9.1.el7.x86_64 #1 SMP Fri Dec 6 
15:49:49 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s sub-11233210_ses-followup exited with ERRORS at Wed Jun 
17 02:41:35 BST 2020


For more details, see the log file 
/SAN/medic/insight46/analysis/freesurfer7/log/sub-11233210_ses-followup_recon_all.log
To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 



Thanks for your time,
Ian

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Re: [Freesurfer] Question regarding MRIread

[Franziska Klein]

External Email - Use Caution

I've used the MRIwrite function.


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. Greve 

Gesendet: Montag, 29. Juni 2020 18:55:01
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Question regarding MRIread

How did you generate the nii file from the mesh?

On 6/29/2020 12:21 PM, Franziska Klein wrote:

External Email - Use Caution

I know, a lot of steps.


1-based vs. 0-based, that is basically what I mean and what I think is the 
problem, but I need to be sure. When I load in the *.nii file generated from 
the mesh and display it in SPM, then the origin shown in the SPM Gui is the 
last column in vox2ras1. Oversimplified, when I want to compare a voxel from 
SPM with a voxel from freesurfer, I need to shift the coordinates of that voxel 
from freesurfer by +1, right? (or substract one from the SPM one).


Kind regards,

Franziska


Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 im Auftrag von Douglas N. Greve 

Gesendet: Montag, 29. Juni 2020 16:44:34
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Question regarding MRIread

There's a lot of stuff going on there, so it's hard to say withhout more 
detail. But it sounds like you might not be taking into account that the voxel 
coords in matlab are 1-based.

On 6/26/2020 12:04 PM, Franziska Klein wrote:

External Email - Use Caution

Hello,


I am using the isosurface() function in order to create a mesh based on the 
T1.mgz and on the ribbon.mgz. I need those meshes for the coregistration of 
some channels.


After coregistration I do project the channels onto the cortex and extract the 
corresponding voxel coordinates. Until here, everything works fine.

Next, I am using MRIwrite in order to save the T1.mgz as *.nii.mgz which I am 
using to generate a deformation field with SPM12 to transform the voxel 
coordinates to normalized MNI coordinates. However, when I put the voxel 
coordinates (not normalized yet) into SPM12 while displaying my generated *.nii 
image it happens that the coordinates on the right hemisphere (MNI space) are 
slightly outside of the cortex which is of course not the case on my cortex 
mesh after projection.


Now I am wondering whether there is a mismatch between the mesh and the *.nii 
image (one voxel maybe)? And whether that is introduced by MRIwrite? If so, do 
I have to shift all points of the meshes by +1 in order to get correct results 
the way I want to? If not, any ideas on where that mismatch could come from?


Thank you and kind regards,

Franziska





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Re: [Freesurfer] Question regarding MRIread

[Franziska Klein]

External Email - Use Caution

Sorry. I am not using the mesh for this, but the volume.


Von: Franziska Klein
Gesendet: Montag, 29. Juni 2020 19:15:01
An: freesurfer@nmr.mgh.harvard.edu
Betreff: AW: [Freesurfer] Question regarding MRIread


I've used the MRIwrite function.


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. Greve 

Gesendet: Montag, 29. Juni 2020 18:55:01
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Question regarding MRIread

How did you generate the nii file from the mesh?

On 6/29/2020 12:21 PM, Franziska Klein wrote:

External Email - Use Caution

I know, a lot of steps.


1-based vs. 0-based, that is basically what I mean and what I think is the 
problem, but I need to be sure. When I load in the *.nii file generated from 
the mesh and display it in SPM, then the origin shown in the SPM Gui is the 
last column in vox2ras1. Oversimplified, when I want to compare a voxel from 
SPM with a voxel from freesurfer, I need to shift the coordinates of that voxel 
from freesurfer by +1, right? (or substract one from the SPM one).


Kind regards,

Franziska


Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 im Auftrag von Douglas N. Greve 

Gesendet: Montag, 29. Juni 2020 16:44:34
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Question regarding MRIread

There's a lot of stuff going on there, so it's hard to say withhout more 
detail. But it sounds like you might not be taking into account that the voxel 
coords in matlab are 1-based.

On 6/26/2020 12:04 PM, Franziska Klein wrote:

External Email - Use Caution

Hello,


I am using the isosurface() function in order to create a mesh based on the 
T1.mgz and on the ribbon.mgz. I need those meshes for the coregistration of 
some channels.


After coregistration I do project the channels onto the cortex and extract the 
corresponding voxel coordinates. Until here, everything works fine.

Next, I am using MRIwrite in order to save the T1.mgz as *.nii.mgz which I am 
using to generate a deformation field with SPM12 to transform the voxel 
coordinates to normalized MNI coordinates. However, when I put the voxel 
coordinates (not normalized yet) into SPM12 while displaying my generated *.nii 
image it happens that the coordinates on the right hemisphere (MNI space) are 
slightly outside of the cortex which is of course not the case on my cortex 
mesh after projection.


Now I am wondering whether there is a mismatch between the mesh and the *.nii 
image (one voxel maybe)? And whether that is introduced by MRIwrite? If so, do 
I have to shift all points of the meshes by +1 in order to get correct results 
the way I want to? If not, any ideas on where that mismatch could come from?


Thank you and kind regards,

Franziska





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Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Mason Wells]

External Email - Use Caution

Hi Matt,

I have 3.5GB free on my 64 bit linux machine, do you think the wb_command issue 
is due to memory alone then? Perhaps I misunderstood your previous emails about 
this, I thought that using the workbench commands was the best way. E.g. 
running volume-to-surface to get the functional data resampled to the subjects 
lh and rh surface, and then cifti-create-dense-timerseries to create a a single 
cifti file with the functional data on the subjects surface? Then I was going 
to use the matlab code you suggest to get an estimation of dimensionality and 
finally run melodic. Is this not the best route to go down with my aims in 
mind? This was also why I asked the FS list whether the same thing can be done 
with mri_vol2surf or other FS commands.

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University 
webpage
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628


From:  on behalf of "Glasser, Matthew" 

Reply to: Freesurfer support list 
Date: Monday, 29 June 2020 at 17:28
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion


External Email - Use Caution
Scratch that, I guess you did include a surface.  How much RAM do you have 
available and are you on a 64bit OS?  As I mentioned last week, what you are 
trying to do is not computationally efficient and not really the best approach 
to go about things.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:24 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Your command below is missing the  argument:

   wb_command -volume-to-surface-mapping
   - the volume to map data from
   - the surface to map the data onto
   - output - the output metric file
  [-ribbon-constrained] - use ribbon constrained mapping algorithm
  - the inner surface of the ribbon
  - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically 
use the midthickness surface here.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion



External Email - Use Caution
Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf files into .gii 
format (from FS format)

  *   e.g. mris_convert lh.pial lh.pial.surf.gii
I then applied the transformation to align the filtered_func to the T1

  *   mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta 
--fstarg --o movie_t1_space.nii.gz
I then tried to run the following wb command

  *   wb_command -volume-to-surface-mapping 
/home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.inflated.surf.gii
 /home/masontwells/Documents/Data/MovPPT_001/lh_movie.gii -ribbon-constrained 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.white.surf.gii
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.pial.surf.gii
Which resulted in this subsequent error.

ERROR: NAME OF FILE: movie_t1_space.nii.gz
PATH TO FILE: /home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat

Unable to allocate memory for reading the file.

File Size: 3.24 Gigabytes

Note: The amount of memory required to read a data file may be substantially 

Re: [Freesurfer] Question regarding MRIread

[Douglas N. Greve]

what volume? how did you create it? please give some details

On 6/29/2020 1:19 PM, Franziska Klein wrote:


External Email - Use Caution

Sorry. I am not using the mesh for this, but the volume.


*Von:* Franziska Klein
*Gesendet:* Montag, 29. Juni 2020 19:15:01
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* AW: [Freesurfer] Question regarding MRIread

I've used the MRIwrite function.


*Von:* freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. 
Greve 

*Gesendet:* Montag, 29. Juni 2020 18:55:01
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] Question regarding MRIread
How did you generate the nii file from the mesh?

On 6/29/2020 12:21 PM, Franziska Klein wrote:


External Email - Use Caution

I know, a lot of steps.


1-based vs. 0-based, that is basically what I mean and what I think 
is the problem, but I need to be sure. When I load in the *.nii file 
generated from the mesh and display it in SPM, then the origin shown 
in the SPM Gui is the last column in vox2ras1. Oversimplified, when I 
want to compare a voxel from SPM with a voxel from freesurfer, I need 
to shift the coordinates of that voxel from freesurfer by +1, right? 
(or substract one from the SPM one).



Kind regards,

Franziska


*Von:* freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. 
Greve 

*Gesendet:* Montag, 29. Juni 2020 16:44:34
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] Question regarding MRIread
There's a lot of stuff going on there, so it's hard to say withhout 
more detail. But it sounds like you might not be taking into account 
that the voxel coords in matlab are 1-based.


On 6/26/2020 12:04 PM, Franziska Klein wrote:


External Email - Use Caution

Hello,


I am using the isosurface() function in order to create a mesh based 
on the T1.mgz and on the ribbon.mgz. I need those meshes for 
the coregistration of some channels.



After coregistration I do project the channels onto the cortex and 
extract the corresponding voxel coordinates. Until here, everything 
works fine.


Next, I am using MRIwrite in order to save the T1.mgz as *.nii.mgz 
which I am using to generate a deformation field with SPM12 to 
transform the voxel coordinates to normalized MNI coordinates. 
However, when I put the voxel coordinates (not normalized yet) 
into SPM12 while displaying my generated *.nii image it happens that 
the coordinates on the right hemisphere (MNI space) are slightly 
outside of the cortex which is of course not the case on my cortex 
mesh after projection.



Now I am wondering whether there is a mismatch between the mesh and 
the *.nii image (one voxel maybe)? And whether that is introduced by 
MRIwrite? If so, do I have to shift all points of the meshes by +1 
in order to get correct results the way I want to? If not, any ideas 
on where that mismatch could come from?



Thank you and kind regards,

Franziska




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



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Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Glasser, Matthew]

External Email - Use Caution

Yes you are probably low on memory (3.5GB is really low for brain imaging these 
days).  Like I said, probably best to use the ciftify outputs if you have them 
and then resample the ICA maps back to the native mesh.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 12:50 PM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Hi Matt,

I have 3.5GB free on my 64 bit linux machine, do you think the wb_command issue 
is due to memory alone then? Perhaps I misunderstood your previous emails about 
this, I thought that using the workbench commands was the best way. E.g. 
running volume-to-surface to get the functional data resampled to the subjects 
lh and rh surface, and then cifti-create-dense-timerseries to create a a single 
cifti file with the functional data on the subjects surface? Then I was going 
to use the matlab code you suggest to get an estimation of dimensionality and 
finally run melodic. Is this not the best route to go down with my aims in 
mind? This was also why I asked the FS list whether the same thing can be done 
with mri_vol2surf or other FS commands.

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University 
webpage
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628


From:  on behalf of "Glasser, Matthew" 

Reply to: Freesurfer support list 
Date: Monday, 29 June 2020 at 17:28
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion


External Email - Use Caution
Scratch that, I guess you did include a surface.  How much RAM do you have 
available and are you on a 64bit OS?  As I mentioned last week, what you are 
trying to do is not computationally efficient and not really the best approach 
to go about things.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:24 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

External Email - Use Caution
Your command below is missing the  argument:

   wb_command -volume-to-surface-mapping
   - the volume to map data from
   - the surface to map the data onto
   - output - the output metric file
  [-ribbon-constrained] - use ribbon constrained mapping algorithm
  - the inner surface of the ribbon
  - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically 
use the midthickness surface here.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion



External Email - Use Caution
Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf files into .gii 
format (from FS format)

  *   e.g. mris_convert lh.pial lh.pial.surf.gii
I then applied the transformation to align the filtered_func to the T1

  *   mri_vol2vol --mov filtered_func_data.nii.gz --reg partial-to-struct.lta 
--fstarg --o movie_t1_space.nii.gz
I then tried to run the following wb command

  *   wb_command -volume-to-surface-mapping 
/home/masontwells/Documents/Data/MovPPT_001/MovPPT_001.feat/movie_t1_space.nii.gz
 
/home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/surf/lh.inflated.surf.gii
 /home/masontwells/Documents/Data/MovPPT_001/lh_movi

Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

[Glasser, Matthew]

External Email - Use Caution

Also I missed that you upsampled the volume fMRI file massively as well.  
Indeed, this is not how I would recommend going about things, particularly in a 
memory limited environment.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 1:11 PM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

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Yes you are probably low on memory (3.5GB is really low for brain imaging these 
days).  Like I said, probably best to use the ciftify outputs if you have them 
and then resample the ICA maps back to the native mesh.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 12:50 PM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

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Hi Matt,

I have 3.5GB free on my 64 bit linux machine, do you think the wb_command issue 
is due to memory alone then? Perhaps I misunderstood your previous emails about 
this, I thought that using the workbench commands was the best way. E.g. 
running volume-to-surface to get the functional data resampled to the subjects 
lh and rh surface, and then cifti-create-dense-timerseries to create a a single 
cifti file with the functional data on the subjects surface? Then I was going 
to use the matlab code you suggest to get an estimation of dimensionality and 
finally run melodic. Is this not the best route to go down with my aims in 
mind? This was also why I asked the FS list whether the same thing can be done 
with mri_vol2surf or other FS commands.

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University 
webpage
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628


From:  on behalf of "Glasser, Matthew" 

Reply to: Freesurfer support list 
Date: Monday, 29 June 2020 at 17:28
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion


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Scratch that, I guess you did include a surface.  How much RAM do you have 
available and are you on a 64bit OS?  As I mentioned last week, what you are 
trying to do is not computationally efficient and not really the best approach 
to go about things.

Matt.

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:24 AM
To: Freesurfer support list , 
"freesurfer-boun...@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion

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Your command below is missing the  argument:

   wb_command -volume-to-surface-mapping
   - the volume to map data from
   - the surface to map the data onto
   - output - the output metric file
  [-ribbon-constrained] - use ribbon constrained mapping algorithm
  - the inner surface of the ribbon
  - the outer surface of the ribbon

Which can be a repeat of one of the other surfaces I think, though we typically 
use the midthickness surface here.

Matt.

From:  on behalf of Mason Wells 

Reply-To: Freesurfer support list 
Date: Monday, June 29, 2020 at 11:20 AM
To: "freesurfer-boun...@nmr.mgh.harvard.edu" 
, Freesurfer support list 

Subject: [Freesurfer] mri_vol2surf for NIFTI to GIFTI conversion



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Dear experts,

I posted a message last week about converting NIFTI files into GIFTI format, 
then GIFTI to CIFTI, whilst keeping these functional data in the same space as 
the subjects FS surface. I got some information RE usign the HCP workbench, but 
I wondered if running mri_vol2surf could achieve the same thing as running the 
wb_command? For example, is it advisable to run the following command for each 
hemisphere and then merge them into a single GIFTI/CIFTI in the next steps?

  *   mri_vol2surf --src filtered_func_data.nii.gz --out movie_surface.gii 
--srcreg partial-to-struct.lta --hemi lh --projfrac 0.5 --out_type gii
I have also tried the wb_command option but this has been unsuccesful:

I first ran the mris_convert to convert the relevant surf files into .gii 
format (from FS format)

  *   e.g. mris_convert lh.pial lh.pial.surf.gii
I then applied 

Re: [Freesurfer] Question regarding MRIread

[Franziska Klein]

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Okay. I'll try.

The basic steps are, loading in a slightly adapted and I guess repaired version 
of the T1.mgz file called hseg.mgz (this is created by the AtlasViewer toolbox 
because I need to set the fiducials and some other reference points and this 
toolbox also calculates all other 10-20 points based on those reference points) 
and the ribbon.mgz file

head = load_mgh(fullfile(DIR, 'mri/hseg.mgz'));
brain = load_mgh(fullfile(DIR, 'mri/ribbon.mgz'));

for both I am creating a mesh with isosurface function

mesh_head = isosurface(head, .9);
mesh_brain = isosurface(brain, .9);

v = mesh_head .vertices(:, [2 1 3]); % isosurface flips x- and y-axes
f = mesh_head .faces;

Then I am doing the coregistration based on the meshes, resulting in some mesh 
voxel coordinates.

In order to get a *.nii.gz file I simply use

MRIwrite(head, filename)

I checked already: hseg.vol and T1.vol (when loading T1.mgz instead of 
hseg.mgz) are identical.

I want to use the new .nii file to generate a deformations field in SPM12 in 
order to normalize my mesh voxel coordinates to the normalized T1 generated in 
SPM12 for some specific analyses. Therefore the mesh coordinates (freesurfer 
0-based) should be identical with those in the .nii file (SPM Matlab 1-based).

I hope this is detailed enough.



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. Greve 

Gesendet: Montag, 29. Juni 2020 20:08:04
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Question regarding MRIread

what volume? how did you create it? please give some details

On 6/29/2020 1:19 PM, Franziska Klein wrote:

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Sorry. I am not using the mesh for this, but the volume.


Von: Franziska Klein
Gesendet: Montag, 29. Juni 2020 19:15:01
An: freesurfer@nmr.mgh.harvard.edu
Betreff: AW: [Freesurfer] Question regarding MRIread


I've used the MRIwrite function.


Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 im Auftrag von Douglas N. Greve 

Gesendet: Montag, 29. Juni 2020 18:55:01
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Question regarding MRIread

How did you generate the nii file from the mesh?

On 6/29/2020 12:21 PM, Franziska Klein wrote:

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I know, a lot of steps.


1-based vs. 0-based, that is basically what I mean and what I think is the 
problem, but I need to be sure. When I load in the *.nii file generated from 
the mesh and display it in SPM, then the origin shown in the SPM Gui is the 
last column in vox2ras1. Oversimplified, when I want to compare a voxel from 
SPM with a voxel from freesurfer, I need to shift the coordinates of that voxel 
from freesurfer by +1, right? (or substract one from the SPM one).


Kind regards,

Franziska


Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 im Auftrag von Douglas N. Greve 

Gesendet: Montag, 29. Juni 2020 16:44:34
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Question regarding MRIread

There's a lot of stuff going on there, so it's hard to say withhout more 
detail. But it sounds like you might not be taking into account that the voxel 
coords in matlab are 1-based.

On 6/26/2020 12:04 PM, Franziska Klein wrote:

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Hello,


I am using the isosurface() function in order to create a mesh based on the 
T1.mgz and on the ribbon.mgz. I need those meshes for the coregistration of 
some channels.


After coregistration I do project the channels onto the cortex and extract the 
corresponding voxel coordinates. Until here, everything works fine.

Next, I am using MRIwrite in order to save the T1.mgz as *.nii.mgz which I am 
using to generate a deformation field with SPM12 to transform the voxel 
coordinates to normalized MNI coordinates. However, when I put the voxel 
coordinates (not normalized yet) into SPM12 while displaying my generated *.nii 
image it happens that the coordinates on the right hemisphere (MNI space) are 
slightly outside of the cortex which is of course not the case on my cortex 
mesh after projection.


Now I am wondering whether there is a mismatch between the mesh and the *.nii 
image (one voxel maybe)? And whether that is introduced by MRIwrite? If so, do 
I have to shift all points of the meshes by +1 in order to get correct results 
the way I want to? If not, any ideas on where that mismatch could come from?


Thank you and kind regards,

Franziska





___

[Freesurfer] Discrepancy in volume calculated for thalamic nuclei in FreeSurfer

[Corinna Bauer]

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Hello all,

We are working on calculating the volume of thalamic nuclei in our
participants and noticed that there is often a discrepancy in measured
volume in the ThalamicNuclei.v12.T1.volumes.txt and the volume calculated
for the same thalamic nucleus using fslstats -V. (Note that the nuclei are
all created in FreeSurfer, just extracted to individual .nii files
afterwards).

For example: in one control subject, the volume of the right VPL was
measured in FreeSurfer as 264.650938 mm^3, but the same extracted label in
fslstats shows a volume of 242 mm^3. What could be causing this discrepancy?

Thanks

Corinna
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Re: [Freesurfer] Error recon-all mri_cc

[Yann Quidé]

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Hi Andrew,

Thanks for this.
Just a quick follow up question: does that mean I will have to recon all all 
the other scans that did not show this error with v7.1.1 for consistency, or 
will it be fine to keep them processed with v7.1.0?

Thanks,

Yann


> On 30 Jun 2020, at 2:04 am, Hoopes, Andrew  wrote:
> 
> Hi Yann (and anyone else with mri_cc failures on mac),
> We have a fix that we'll include in an upcoming 7.1.1 patch release. If you'd 
> like a quick local fix, you can update your distribution with the new version 
> of mri_cc by running the following commands (this might require sudo):
> cd $FREESURFER_HOME/bin
> rm mri_cc
> curl https://surfer.nmr.mgh.harvard.edu/pub/dist/tmp_patch/mri_cc 
>  -O mri_cc
> chmod +x mri_cc
> Please let us know if this does not solve your issue.
> Andrew
>  
> From:  > on behalf of Yann Quidé 
> mailto:yannqu...@gmail.com>>
> Reply-To: FS Help  >
> Date: Monday, June 29, 2020 at 2:35 AM
> To: FS Help  >
> Subject: Re: [Freesurfer] Error recon-all mri_cc
>  
> External Email - Use Caution
> Hi team,
>  
> I appreciate everyone is busy, but did anyone have time to look at my subject?
> It was uploaded on June 18. It’s called yannquide.tar.gz
>  
> Thanks for your time.
>  
> Yann
> 
> 
>> On 22 Jun 2020, at 12:51 pm, Yann Quidé > > wrote:
>>  
>> Hi team,
>>  
>> I was just wondering if you received my file and if you had time to look at 
>> it?
>>  
>> Thanks,
>>  
>> Yann
>> 
>> 
>>> On 18 Jun 2020, at 7:08 am, Yann Quidé >> > wrote:
>>>  
>>> Hi Doug,
>>>  
>>> Thanks for this. I sent the file; it’s called yannquide.tar.gz.
>>>  
>>> Yann
>>> 
>>> 
 On 16 Jun 2020, at 11:56 pm, Douglas N. Greve >>> > wrote:
  
 Can you upload the subject so I can take a look? Instructions below
 
 
 From the linux command line,
 Create the file you want to upload, eg, 
 cd $SUBJECTS_DIR
 tar cvfz subject.tar.gz ./subject
 Now log  into our anonymous FTP site:
 ftp surfer.nmr.mgh.harvard.edu 
 It will ask you for a user name: use "anonymous" (no quotes)
 It will ask you for a password: use "anonymous" (no quotes)
 cd transfer/incoming
 binary
 put subject.tar.gz
 Send an email that the file has been and the name of the file.
 
 
 
 On 6/15/2020 8:28 PM, Yann Quidé wrote:
> External Email - Use Caution
> 
> Hi there,
> 
> I am using Freesurfer v7.1.0 and encounter an error for few of my 
> subjects only.
> Recon-all finishes with errors, and it seems this occurs during the 
> segmentation.
> 
> What can I do to fix this?
> 
> I attached the recon-all log for one of my subject.
> 
> Thanks,
> 
> Yann
> 
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu 
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
 
>>>  
>> 
>>  
> 
>  
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> 
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Re: [Freesurfer] Error recon-all mri_cc

[Douglas N. Greve]

I think they should give the same result, but try one or two to confirm

On 6/29/2020 6:12 PM, Yann Quidé wrote:


External Email - Use Caution

Hi Andrew,

Thanks for this.
Just a quick follow up question: does that mean I will have to recon 
all all the other scans that did not show this error with v7.1.1 for 
consistency, or will it be fine to keep them processed with v7.1.0?


Thanks,

Yann


On 30 Jun 2020, at 2:04 am, Hoopes, Andrew > wrote:


Hi Yann (and anyone else with mri_cc failures on mac),
We have a fix that we'll include in an upcoming 7.1.1 patch release. 
If you'd like a quick local fix, you can update your distribution 
with the new version of mri_cc by running the following commands 
(this might require sudo):

cd $FREESURFER_HOME/bin
rm mri_cc
curlhttps://surfer.nmr.mgh.harvard.edu/pub/dist/tmp_patch/mri_cc-O mri_cc
chmod +x mri_cc
Please let us know if this does not solve your issue.
Andrew
*From:*> on behalf of Yann 
Quidé mailto:yannqu...@gmail.com>>
*Reply-To:*FS Help >

*Date:*Monday, June 29, 2020 at 2:35 AM
*To:*FS Help >

*Subject:*Re: [Freesurfer] Error recon-all mri_cc
*External Email - Use Caution *
Hi team,
I appreciate everyone is busy, but did anyone have time to look at my 
subject?

It was uploaded on June 18. It’s called yannquide.tar.gz
Thanks for your time.
Yann


On 22 Jun 2020, at 12:51 pm, Yann Quidé > wrote:

Hi team,
I was just wondering if you received my file and if you had time to 
look at it?

Thanks,
Yann


On 18 Jun 2020, at 7:08 am, Yann Quidé > wrote:

Hi Doug,
Thanks for this. I sent the file; it’s called yannquide.tar.gz.
Yann


On 16 Jun 2020, at 11:56 pm, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:

Can you upload the subject so I can take a look? Instructions below


From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftpsurfer.nmr.mgh.harvard.edu 
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.



On 6/15/2020 8:28 PM, Yann Quidé wrote:


External Email - Use Caution

Hi there,

I am using Freesurfer v7.1.0 and encounter an error for few of my 
subjects only.
Recon-all finishes with errors, and it seems this occurs during 
the segmentation.


What can I do to fix this?

I attached the recon-all log for one of my subject.

Thanks,

Yann

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[Freesurfer] Sub-cortical areas and other atlases

[Martin Juneja]

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Hello experts,

I am following these instructions
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis to
analyze the association between IQ and whole brain cortical thickness of
brain areas (which by default uses Desikan atlas of 34 regions).

I was wondering how:
(1). To do the similar analysis to identify sub-cortical regions which show
significant association between thickness and IQ.
(2). To use other atlases here i.e., replace Desikan atlas with 7 or 17
network Yeo atlas to identify which network shows the association with IQ.

I know how to extract thickness etc from sub-cortical areas (i.e., aseg
stats) and use Yeo atlas outside these instructions, but I am not sure how
to do this in above described instructions i.e., replace Desikan with
sub-cortical and Yeo atlases etc.

Any help would be really appreciated.

Thanks !
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