Re: [Freesurfer] FreeSurfer 7.1 Matlab error, GLIBC_PRIVATE not defined {Disarmed}

[fsbuild]

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Hello Alex,
I would try unseting LD_LIBRARY_PATH altogether or at least take the matlab 
paths out of it. My understanding is freesurfer commands don't need 
matlab paths in LD_LIBRARY_PATH to use matlab after you have setup the 
freesurfer environment (set FREESURFER_HOME, and source’d the freesurfer setup 
script).  It looks like the matlab libraries in LD_LIBRARY_PATH are 
overriding other binaries trying to find the system libc with the symbols they 
need (and are instead finding the matlab copy of the system libraries).
- R.

On May 27, 2020, at 23:22, Alexandru Hanganu 
hanganu.alexan...@gmail.com 
wrote:External Email - Use 
CautionHello FreeSurfer 
Developers,I attemtingto run brainstem/ hippocampus/ thalamus 
segmentation with FS 7.1 and there seems to be a problem with environment 
variables. Based on comments on other forums, I cannot install GlibC (if this 
isthe case) since it's a cluster. Are there any methods that can be used 
to avoid this limitation?FreeSurfer version: 
freesurfer-linux-centos7_x86_64-7.1.0Platform: CentOS Linux 7 (Core)uname 
-a:Linuxcedar5.cedar.computecanada.ca3.10.0-1062.12.1.el7.x86_64
 #1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 GNU/Linuxerror:Setting up 
environment variables---grep: relocation error: /lib64/libc.so.6: symbol 
_dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 
with link time referenceLD_LIBRARY_PATH is 
.:/lib64:/home/user/freesurfer/MCRv84//runtime/glnxa64:/home/user/freesurfer/MCRv84//bin/glnxa64:/home/user/freesurfer/MCRv84//sys/os/glnxa64:/home/user/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/home/user/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/home/userfreesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/home/userfreesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/opt/software/slurm/libod:
 relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version 
GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time 
referencetr: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, 
version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time 
referenceRegistering imageDump.mgz to mask from ASEGcp: relocation error: 
/lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in 
file ld-linux-x86-64.so.2 with link time referencegzip: relocation error: 
/lib64/libc.so.6: symbol _dl_starting_up, version GLIBC_PRIVATE not defined in 
file ld-linux-x86-64.so.2 with link time referenceERROR: problem reading 
fnameSWITCH expression must be a scalar or string constant.Error in 
myMRIreadload_mgh (line 550)Error in myMRIreadmyMRIread_aux (line 
92)Error in myMRIread (line 63)Error in SegmentThalamicNuclei (line 
278)MATLAB:badSwitchExpressionrm: relocation error: /lib64/libc.so.6: symbol 
_dl_starting_up, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 
with link time reference255Best 
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Re: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)

[Douglas N. Greve]

On 5/27/2020 11:10 PM, Elizabeth Haris wrote:


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Hi guys,

I’m wanting to run segmentHA_T1.sh on an MNI152 registered brain. On 
my subject, I have run recon-all, then run mri_cvs_register to obtain 
a brain image registered in MNI152 space. My questions are:


 1. In recon-all, is there a way to specify registration to MNI152
space, or is it necessary to first run recon-all and then to run
mri_cvs_register?


Yes, you must run recon-all first.


 1. Is it possible to run the segmentHA script on the brain registered
in MNI152 space? I’m unable to find where I would specify the use
the cvs/norm.mgz (instead of the mri/norm.mgz file). And from what
I can see in the script, the parameters set in lines 179/180/181
(below) point to fsaverage brain files, which don’t appear to be
the correct targets for the new MNI152 brain; however, there are
no corresponding output files in the cvs folder, so I am unsure
how to define these parameters.

Eugenio can answer better, but I think this will be hard. You'd have to 
make a "fake" subject using CVS to resample all the volumes segmentHA 
needs to do the segmentation. I think it would probably be a mess.


 1. Is there anything I have missed and would also need to do to run
the segmentHA script on an MNI152 brain? (I have previously run
the script on the average brain and all went well.)

179 set 
ATLASMESH="$FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz";


180 set 
ATLASDUMP="$FREESURFER_HOME/average/HippoSF/atlas/AtlasDump.mgz";


181 set 
LUT="$FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt";


Thanks in advance,

Elizabeth


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[Freesurfer] FreeSurfer 7.1 Matlab error, GLIBC_PRIVATE not defined

[Alexandru Hanganu]

External Email - Use Caution

Hello FreeSurfer Developers,

I attemting to run brainstem/ hippocampus/ thalamus segmentation with FS
7.1 and there seems to be a problem with environment variables. Based on
comments on other forums, I cannot install GlibC (if this is the case)
since it's a cluster. Are there any methods that can be used to avoid this
limitation?

FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0
Platform: CentOS Linux 7 (Core)
uname -a: Linux cedar5.cedar.computecanada.ca 3.10.0-1062.12.1.el7.x86_64
#1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 GNU/Linux

error:
Setting up environment variables
---
grep: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version
GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time
reference
LD_LIBRARY_PATH is
.:/lib64:/home/user/freesurfer/MCRv84//runtime/glnxa64:/home/user/freesurfer/MCRv84//bin/glnxa64:/home/user/freesurfer/MCRv84//sys/os/glnxa64:/home/user/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/home/user/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/home/userfreesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/home/userfreesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/opt/software/slurm/lib
od: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version
GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time
reference
tr: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version
GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time
reference
Registering imageDump.mgz to mask from ASEG
cp: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version
GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time
reference
gzip: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version
GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time
reference
ERROR: problem reading fname
SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)



Error in myMRIread>myMRIread_aux (line 92)



Error in myMRIread (line 63)



Error in SegmentThalamicNuclei (line 278)



MATLAB:badSwitchExpression
rm: relocation error: /lib64/libc.so.6: symbol _dl_starting_up, version
GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time
reference
255


Best regards,
Alex
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[Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)

[Elizabeth Haris]

External Email - Use Caution

Hi guys,

I’m wanting to run segmentHA_T1.sh on an MNI152 registered brain. On my 
subject, I have run recon-all, then run mri_cvs_register to obtain a brain 
image registered in MNI152 space. My questions are:


  1.  In recon-all, is there a way to specify registration to MNI152 space, or 
is it necessary to first run recon-all and then to run mri_cvs_register?
  2.  Is it possible to run the segmentHA script on the brain registered in 
MNI152 space? I’m unable to find where I would specify the use the cvs/norm.mgz 
(instead of the mri/norm.mgz file). And from what I can see in the script, the 
parameters set in lines 179/180/181 (below) point to fsaverage brain files, 
which don’t appear to be the correct targets for the new MNI152 brain; however, 
there are no corresponding output files in the cvs folder, so I am unsure how 
to define these parameters.
  3.  Is there anything I have missed and would also need to do to run the 
segmentHA script on an MNI152 brain? (I have previously run the script on the 
average brain and all went well.)

179 set ATLASMESH="$FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz";
180 set 
ATLASDUMP="$FREESURFER_HOME/average/HippoSF/atlas/AtlasDump.mgz";
181 set 
LUT="$FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt";

Thanks in advance,

Elizabeth
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[Freesurfer] Circular/cyclic color map for polar data and threshold-ing question in freeview

[Devavrat Vartak]

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Hello freesurfer community,

I had asked this question before, however I am unable to reply to that
thread. The question still remains unsolved.

I am trying to setup a retinotopy pipeline. I have analysed population
receptive field data that generates polar angle and eccentricity maps which
I project onto an inflated surface / flattened surface in freeview
(Freesurfer 6).

MacOS 10.14.6
Freesurfer 6
Nipype (nipype version 1.5.0-rc1 (latest: 1.4.2)

I have two queries, which I think are connected.

1) Is there a way to display a circular/cyclic colour map (for the polar
angle data) in the overlay screen? The existing 'color wheel' option seems
linear(?) (i.e it doesn't not warp around).

2) The distribution of data overlayed changes/shifts compared to the RAW
data distribution.
I have linked the raw theta values generated from the pRF analysis (in
radians) as a histogram and a polarmap - (the figures depict values for
both hemispheres)
and the distribution when I overlay it on the LH (the distribution for RH
is similar)

See here for images: imgur[dot]com/a/Wo42DLd

This is my processing stream:

> The raw theta values based on their voxel coordinates are affined to the
functional image and saved as a NIFTI volume. The NIFTI volume in
functional space is transformed to the anatomical space and is converted to
a surface using
> > ! mri_vol2surf --src  (input_file_theta.nii.gz) --o theta.mgh --hemi lh
--regheader sub-03/freesurfer/recon_all --projfrac 0.5

Any help will be appreciated :-)

---
From the old thread, there was this comment:

"*Hi!*

*Jumping in on this, since it has come up many times but is without a
solution so far: the issue is that the color code is now mapped onto a
straight color bar, not a circle. At the same time, it is not
documented what color refers to which angle. That makes it very
difficult to work with this kind of color bar. It would be very
helpful to reintroduce the circle, and to explicitly document how
angles are mapped to colors.
Thank you! - Caspar (**Caspar M. Schwiedrzik)*

"

Thank you .

Cheers,
Dev
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[Freesurfer] LGI and Global GI

[Alexopoulos, Dimitrios]

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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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[Freesurfer] Problems with freesurfer 7.1.0

[Angela Favaro]

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Dear Freesurfer experts, 
I am re-analyzing my longitudinal dataset using Freesurfer 7.1.0 with a McOS 
Catalina. I found 2 main problems
1. About a 10% of cases failed at the segmentation stage during the recon-all 
processing (I uploaded one of these cases in one of my previous mails)
2. After the building of the template during the longitudinal processing, at 
the recon-all -long I found the following error:


> longmc Done
> /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri
> \n cp -f --preserve=timestamps 
> /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz 
> ./brainmask_template4.mgz \n
> cp: illegal option -- -
> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
>cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... 
> target_directory
> ERROR:
> Darwin iMac-di-Angela.local 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 subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 
> CEST 2020
> 


Can you please help me with this two issues?
Thank you so much!

Angela




> Inizio messaggio inoltrato:
> 
> Da: Angela Favaro 
> Oggetto: [Freesurfer] Longitudinal processing with freesurfer 7.1.0
> Data: 23 maggio 2020 10:41:02 CEST
> A: Freesurfer support list 
> Rispondi a: Freesurfer support list 
> 
> External Email - Use Caution
> 
> 
> Dear Freesurfer experts, 
> I am trying to process a dataset with a longitudinal design.
> However, after building the template, at the “recon-all -long” command I got 
> this error:
> 
> longmc Done
> /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri
> \n cp -f --preserve=timestamps 
> /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz 
> ./brainmask_template4.mgz \n
> cp: illegal option -- -
> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file
>cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... 
> target_directory
> ERROR:
> Darwin iMac-di-Angela.local 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 subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 
> CEST 2020
> 
> For more details, see the log file 
> /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log
> 
> 
> Thank you for any help!
> 
> Angela
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Re: [Freesurfer] Registering Mean Diffusivity to Anatomical Space {Disarmed}

[Douglas N. Greve]

Correct. Also make sure to set --projfrac 0.5 to sample in the middle of 
cortex (or set to some other value depending upon where you want to sample)


On 5/27/2020 3:12 PM, Nillo, Ryan Michael R wrote:

Thanks Doug!

When you say sample onto the mni152 surface, you mean to use 
mri_vol2surf, correct?


Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

On May 27, 2020, at 11:10 AM, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


I would probably run recon-all on the mni152, and then sample the MD 
map onto the mni152 surface, then use mris_apply_reg to map it to an 
individual.

Also, Thomas Yeo has some possibly-better tools to do this.

On 5/27/2020 2:02 PM, Nillo, Ryan Michael R wrote:

Hello FreeSurfer users,

I have a mean diffusivity map that exists in MNI152 space that I 
want to register to a subject’s anatomical space. In the end, I want 
to display the diffusivity on the subject’s surface. I want to ask 
if this is the correct way to do this:


1) bbregister --s sub-01 --mov ./MD.mni152.nii --reg 
$SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --init-fsl —dti 
#create registration matrix


2) mri_vol2vol --mov ./MD.mni152.nii --targ 
$SUBJECTS_DIR/sub-01/mri/brain.mgz --reg 
$SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --o ./MD.nii 
#register mean diffusivity map to subject space


Thanks in advance,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging


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Re: [Freesurfer] mris_register using manual label(s) as guides

[Bruce Fischl]

Hi Danny

yes, you can specify up to 100 labels. Make sure that the label name is 
exactly as it appears in the parcellation though


cheers
Bruce
On Wed, 27 May 2020, Danny 
Kim wrote:




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Hi FreeSurfer experts,


I'm currently working on a brain with a bit of atypical morphology and was
wanting to parcellate through the DKT labels, but by using manually drawn
labels as guides. The intent here is to fix specific labels to be where they
are on the surface by drawing them manually and then automatically classify
other labels around them (e.g. fix precentral and superiortemporal using
manual labels).


However, it seems like during the mris_register step, I'm able to use one of
my manual label to guide the registration to the sphere, but not more than
one.


e.g. mris_register -L label/manual_precentral.label DKTatlas40.gcs
precentral -curv sphere folding.atlas.acfb40.noaparc.tif surf/sphere.reg
(WORKS, after mris_ca_label, precentral is where the manual label was.
Superior temporal label is not where the manual label is)


e.g. mris_register -L label/manual_precentral.label DKTatlas40.gcs
precentral -L label/manual_superiortemporal.label DKTatlas40.gcs
superiortemporal -curv sphere folding.atlas.acfb40.noaparc.tif
surf/sphere.reg (Runs but output looks exactly the same as before, i.e.
superiortemporal label is not where the manual label was specified)


Is there a trick to specifying multiple manual labels in guiding
mris_register?
I am not sure if the -L flag can be specified multiple times and there's no
information on that on the mris_register manual.

I'm using the following FreeSurfer on my MAC:
freesurfer-i386-apple-darwin11.4.2-stable6-20170119

Thanks for your time in this experts!

Danny Kim





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[Freesurfer] mris_register using manual label(s) as guides

[Danny Kim]

External Email - Use Caution

Hi FreeSurfer experts,


I'm currently working on a brain with a bit of atypical morphology and was 
wanting to parcellate through the DKT labels, but by using manually drawn 
labels as guides. The intent here is to fix specific labels to be where they 
are on the surface by drawing them manually and then automatically classify 
other labels around them (e.g. fix precentral and superiortemporal using manual 
labels).


However, it seems like during the mris_register step, I'm able to use one of my 
manual label to guide the registration to the sphere, but not more than one.


e.g. mris_register -L label/manual_precentral.label DKTatlas40.gcs precentral 
-curv sphere folding.atlas.acfb40.noaparc.tif surf/sphere.reg (WORKS, after 
mris_ca_label, precentral is where the manual label was. Superior temporal 
label is not where the manual label is)


e.g. mris_register -L label/manual_precentral.label DKTatlas40.gcs precentral 
-L label/manual_superiortemporal.label DKTatlas40.gcs superiortemporal -curv 
sphere folding.atlas.acfb40.noaparc.tif surf/sphere.reg (Runs but output looks 
exactly the same as before, i.e. superiortemporal label is not where the manual 
label was specified)

Is there a trick to specifying multiple manual labels in guiding mris_register?
I am not sure if the -L flag can be specified multiple times and there's no 
information on that on the mris_register manual.

I'm using the following FreeSurfer on my MAC:
freesurfer-i386-apple-darwin11.4.2-stable6-20170119

Thanks for your time in this experts!

Danny Kim



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Re: [Freesurfer] Registering Mean Diffusivity to Anatomical Space {Disarmed}

[Nillo, Ryan Michael R]

Thanks Doug!

When you say sample onto the mni152 surface, you mean to use mri_vol2surf, 
correct?

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging

> On May 27, 2020, at 11:10 AM, Douglas N. Greve  wrote:
> 
> I would probably run recon-all on the mni152, and then sample the MD map onto 
> the mni152 surface, then use mris_apply_reg to map it to an individual. 
> Also, Thomas Yeo has some possibly-better tools to do this. 
> 
> On 5/27/2020 2:02 PM, Nillo, Ryan Michael R wrote:
>> Hello FreeSurfer users,
>> 
>> I have a mean diffusivity map that exists in MNI152 space that I want to 
>> register to a subject’s anatomical space. In the end, I want to display the 
>> diffusivity on the subject’s surface. I want to ask if this is the correct 
>> way to do this:
>> 
>> 1) bbregister --s sub-01 --mov ./MD.mni152.nii --reg 
>> $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --init-fsl —dti #create 
>> registration matrix
>> 
>> 2) mri_vol2vol --mov ./MD.mni152.nii --targ 
>> $SUBJECTS_DIR/sub-01/mri/brain.mgz --reg 
>> $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --o ./MD.nii #register 
>> mean diffusivity map to subject space
>> 
>> Thanks in advance,
>> 
>> Ryan Michael Nillo
>> Staff Research Associate I
>> University of California San Francisco
>> Department of Radiology and Biomedical Imaging
>> 
>> 
>> 
>> External Email - Use Caution
>> 
>> 
>> 
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>> 
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Re: [Freesurfer] Registering Mean Diffusivity to Anatomical Space

[Douglas N. Greve]

I would probably run recon-all on the mni152, and then sample the MD map 
onto the mni152 surface, then use mris_apply_reg to map it to an 
individual.

Also, Thomas Yeo has some possibly-better tools to do this.

On 5/27/2020 2:02 PM, Nillo, Ryan Michael R wrote:

Hello FreeSurfer users,

I have a mean diffusivity map that exists in MNI152 space that I want 
to register to a subject’s anatomical space. In the end, I want to 
display the diffusivity on the subject’s surface. I want to ask if 
this is the correct way to do this:


1) bbregister --s sub-01 --mov ./MD.mni152.nii --reg 
$SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --init-fsl —dti 
#create registration matrix


2) mri_vol2vol --mov ./MD.mni152.nii --targ 
$SUBJECTS_DIR/sub-01/mri/brain.mgz --reg 
$SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --o ./MD.nii 
#register mean diffusivity map to subject space


Thanks in advance,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging


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Re: [Freesurfer] Citation of hard and soft failures

[Douglas N. Greve]

Not that I know of, but I think most programmers would know what you mean

On 5/27/2020 1:59 PM, Monereo Sanchez, Jennifer (RAD) wrote:


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Dear all,


I am writing a paper for which I need to introduce the concepts of 
“hard” and “soft failures”, and I am wondering what is the proper way 
of citing them. I am aware there is plenty of material online (see for 
example 
https://fscph.nru.dk/slides/Allison/freesurfer.failure_modes.pdf) but 
I am wondering if there is a citable paper in which these are 
described or discussed.



Best wishes,

​Jennifer Monereo


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[Freesurfer] Registering Mean Diffusivity to Anatomical Space

[Nillo, Ryan Michael R]

Hello FreeSurfer users,

I have a mean diffusivity map that exists in MNI152 space that I want to 
register to a subject’s anatomical space. In the end, I want to display the 
diffusivity on the subject’s surface. I want to ask if this is the correct way 
to do this:

1) bbregister --s sub-01 --mov ./MD.mni152.nii --reg 
$SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --init-fsl —dti #create 
registration matrix

2) mri_vol2vol --mov ./MD.mni152.nii --targ $SUBJECTS_DIR/sub-01/mri/brain.mgz 
--reg $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --o ./MD.nii #register 
mean diffusivity map to subject space

Thanks in advance,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging



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[Freesurfer] Citation of hard and soft failures

[Monereo Sanchez, Jennifer (RAD)]

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Dear all,


I am writing a paper for which I need to introduce the concepts of "hard" and 
"soft failures", and I am wondering what is the proper way of citing them. I am 
aware there is plenty of material online (see for example 
https://fscph.nru.dk/slides/Allison/freesurfer.failure_modes.pdf) but I am 
wondering if there is a citable paper in which these are described or discussed.


Best wishes,

?Jennifer Monereo
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Re: [Freesurfer] recon-all misses part of occipital cortex

[Douglas N. Greve]

my guess is that it is a topological defect that was fixed incorrectly. 
Try looking at this tutorial

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview

You can also run defect-seg to create a segmenttation of the defects and 
see whether a defect is in that area. run it with --help to get more info


One more thing: just check the skull strip to make sure it was not too 
aggressive.


On 5/27/2020 12:34 PM, Isaac Adanyeguh wrote:


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Dear Freesurfer Development Team,

I am having some issues with recon-all where it misses a huge chunk of 
the occipital cortex in several of my subjects. I have searched the 
archive and have not found any report of similar issues. Could you 
please help me figure out how to solve this issue. I have attached a 
screenshot showing the missing occipital cortex segmentation and a 
copy of the recon-all.log.


I performed the analysis using:
- Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20150828
- Platform: Linux 3.10.0-1127.el7.x86_64

Thank you and hope you will be able to help me resolve the issue.

Isaac


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Re: [Freesurfer] Problem_mri_watershed

[Douglas N. Greve]

You can try -more or -less when running mri_watershed

You can correct is manually to get a better inner skull. See 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview

After fixing you can run mri_binarize with the --surf option

Not sure about the outerskull if you are doing manual labeling

For the skin, you can run mkheadsurf





On 5/27/2020 7:35 AM, Edoardo Pinzuti wrote:


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Dear Freesurfer community,

using the mri_watershed and -surf to crate inner_skull, outer_skin and 
outer_skull I get a incorrect inner_skull segmentation, probably due 
to an erroneous skullstrip. I tried to modify the parameters available 
but it does not help.  Is there a way to correct this, 
manually correct or with a mask ?

 Any other suggestions will be really appreciated

Thanks
Edoardo

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Re: [Freesurfer] FS6: Mapping data to fsaverage6

[Douglas N. Greve]

It is probably easier if you don't use mris_preproc and run the 
resampling yourself, eg,


mris_apply_reg --src lh.thickness --streg lh.sphere.reg 
$SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg --streg 
$SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg 
$SUBJECTS_DIR/fsaverage6/surf/lh.sphere.reg --trg lh.thickness.fsa6.mgz




On 5/27/2020 7:06 AM, Tim Schäfer wrote:

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Dear FreeSurfer experts,

I'm trying to resample cortical thickness data onto the fsaverage6 template 
subject in FreeSurfer v6. I have copied fsaverage6 into my $SUBJECTS_DIR.

I tried the following 2 commands:
* mris_preproc --s subject1 --target fsaverage6 --hemi lh --meas thickness 
--fwhm 5 --out lh.thickness.fwhm5.fsaverage6.mgh

and alternatively:

* recon-all -s subject1 -qcache -measure thickness -target fsaverage6

Both fail because the file subject1/surf/lh.fsaverage6.sphere.reg is missing 
(see attached recon-all.log file).

How can I generate the ?h.fsaverage6.sphere.reg file?

I tried:
mris_register subject1/surf/lh.sphere fsaverage6/surf/lh.sphere 
subject1/surf/lh.fsaverage6.sphere.reg

However, that fails as well, see attached file mris_reg_output.txt for the 
error message.


All the best,

Tim

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

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Re: [Freesurfer] PETsurfer: --usf in gtmseg

[Douglas N. Greve]

yes, that controls how finely the surface-based segmentations are 
resampled into the volume. The surface is semi-continuous so you can 
sample them into the volume as finely as you like. 0.5mm seems to work fine.


On 5/26/2020 4:33 PM, Julie Ottoy wrote:


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Hi,

In PETsurfer gtmseg, there is the --usf (upsampling factor) which is 
by default 2, corresponding to 0.5 mm voxelsize. I was wondering if 
the usf is recommended to be chosen depending on your mri 
voxelsize (eg, usf 1 for 1mm voxelsize of the mri), or will it just 
depend on how "accurate" you want your segmentation to be? Can you 
safely use --usf 2 for an mri with 1mm voxelsize?


Thank you!
best regards
Julie

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Re: [Freesurfer] Feat to fsfast

[Douglas N. Greve]

Yes. You can try this tutorial, though it has not been run in a while 
and everything might not work

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer


On 5/26/2020 10:27 AM, Alshelh, Zeynab wrote:

Hi all,

Is it possible to do the first level unsmoothed using feat and the 
second level surface based group analysis using fsfast?


Thanks,



*Zeynab Alshelh, PhD*| Postdoctoral Research Fellow

Pain and Neuroinflammation Imaging Laboratory


Harvard Medical School | A. A. Martinos Center for Biomedical Imaging

Massachusetts General Hospital | 149 Thirteenth Street, Room 1101

Charlestown, MA 02129

+1 (617) 794 6838

zalsh...@mgh.harvard.edu | www.nmr.mgh.harvard.edu



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Re: [Freesurfer] Are my slice-time corrected files being used in selxavg3-sess?

[Douglas N. Greve]

What is your mkanalysis-sess command line? You have to specify the STC 
there; if not, it will run without STC




On 5/22/2020 1:35 PM, Mcnorgan, Christopher wrote:


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Hi all,
There was some ambiguity in communication from a previous MR 
technician regarding the slice ordering in our BOLD data.

preproc-sess was applied to our data:
preproc-sess -sf SUBJECTS -surface fsaverage lhrh -per-run -fsd bold 
-sliceorder up -fwhm 4
I then ran selxavg3-sess on the data, followed by mri_glmfit to 
produce contrast maps


As an experiment, I deleted the fmcpr.up.* data, and re-ran 
preproc-sess, this time specifying sliceorder down:
preproc-sess -sf SUBJECTS -surface fsaverage lhrh -per-run -fsd bold 
-sliceorder down -fwhm 4
After re-running selxavg3-sess and mri_glmfit on the 
reverse-stc-corrected data, the contrast maps were identical, which 
seemed peculiar, given that the slice time corrections for a 2-second 
TR were in the opposite direction.


I note that when I run selxavg3-sess, it generates a set of fmcpr.sm4 
files, and I suspect that the GLM is run on those novel non-stc files. 
Is there a switch I am missing in the call to selxavg3-sess or 
mkanalysis-sess that will ensure that will allow me to ensure that the 
GLM is run on fmcpr.[STC].sm4.fsaverage.[rl]h.nii.gz?


Thanks
/**
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo,
* The State University of New York
* http://ccnlab.buffalo.edu/
* Office: 716.645.0236
* Lab: 716.645.0222
**/


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Re: [Freesurfer] Recon-all error in CA Normalize (FreeSurfer V 7.1)

[Douglas N. Greve]

Are all your subjects skull stripped or just this one?

On 5/24/2020 9:08 AM, Schranzer René wrote:


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Hi Douglas,

First of all, thank you for your help.

I forgot to mention that I am already using skull-stripped data for 
the recon-all processing stream. Therefore, I stopped after 
-autorecon1 and copied the T1.mgz to brainmask.mgz and 
brainmask.auto.mgz and continued processing with -autorecon2 and 
-autorecon3. In some subjects (at some timepoints), the recon-all 
-autorecon2 -autorecon3 excited with errors, as mentioned below. Now I 
have used the following command "recon-all -hires -skullstrip 
-no-wsgcaatlas -s ${sbjID} -i ${sbj} -all" with the skull-stripped 
data and it worked fine without errors. I also compared the T1.mgz 
from both approaches and they looked identical.


My question, can I use this approach with the "-no-wsgcaatlas" for all 
subjects or is there something to consider here?


Best, René


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Re: [Freesurfer] Command cannot recognise session from sessid file

[Douglas N. Greve]

Are you in the funcionals  folder when you run your command? If not, you 
have to specify the session folder with -d /path/to/functionals


What is a command line that fails? Try running the command substituting 
the command name with gestsesspath and adding -debug as the first option


On 5/23/2020 4:28 AM, Marco Ninghetto wrote:


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  Dear experts,
I looked through your mailing list, but I cannot find any question 
like mine.
When I run whatever command in my analysis for retinotopy, I have to 
specify subject after subject using:


-s subj001 -s subj002 -s subj00x

and so on. To avoid that, inside my project directory, I have the 
"sessid" (actually two sessid files) file in which are listed all the 
names of the subjects.

I don't know why, when I try to run:

-sf sessid1

I get the error, like (random command from my pipeline):

brain@neurodebian:/media/main/fs_pRFs_functionals$ isxconcat-sess -sf 
sessid1 -a rtopy.fsaverage.lh/ -call -o retgroup_ng

ERROR: finding sessions
       ERROR: cound not find session SUBJ02NG

I tried to write differently inside the sessid file, I tried to use 
the name of the structural folders instead of the functional ones, but 
nothing seems to work.

My sessid file is something like this:

SUBJ02NG
SUBJ06NG
SUBJ07NG
SUBJ08NG

and so on.Each subject's session folder name:

SUBJ02NG
SUBJ06NG
SUBJ07NG
SUBJ08NG

The names listed are the same for the name of the session folder for 
each subject, but still, FS tells me that it cannot find the session.


tree.png
Inside each subject folder, there is the  "bold" folder and inside 
that, together with the runs folders, there is the analysis folder.


Any idea on what I'm doing wrong?
Thank you so much,
Marco
--
---
Marco Ninghetto, PhD candidate
Laboratory of Neuroplasticity
Nencki Institute of Experimental Biology
Polish Academy of Sciences
3 Pasteur Street, 02-093 Warsaw, Poland

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[Freesurfer] fs_install_mcr error

[AmirHussein Abdolalizadeh]

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Hi all,

I have installed FS7 (centOS8 version) on ubuntu 18.04. I try to install
MATLAB runtime but it gives an error when I type "fs_install_mcr R2014b":

Archive:  installer.zip
End-of-central-directory signature not found.  Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive.  In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of installer.zip or
installer.zip.zip, and cannot find installer.zip.ZIP, period.


Since I suspected it might be an access issue, I have used chmod -R
777 on my FreeSurfer installation category. Also, using "sudo" before
"fs_install_mcr" causes the bash not to recognise fs_install_mcr
command. Any suggestions?


Bests,

Amir
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Re: [Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

[Bruce Fischl]

Hi Marina

have you looked at the inputs to mri_fill? Does the aseg.auto_noCCseg.mgz 
and the wm.mgz look ok?

Bruce


On Wed, 27 May 2020, Marina 
Fernández wrote:




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Dear Freesurfer experts,

When I run "recon-all -autorecon2-wm -subjid post_006" I get the following
error:

...

#
#@# Fill Tue May 26 16:13:33 CEST 2020
/usr/local/freesurfer/subjects/post_006/mri

 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta
-segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
 1.03994   0.01456   0.07738  -16.87541;
-0.02607   1.18971   0.24142  -16.40842;
-0.06544  -0.23822   1.03825   18.09422;
 0.0   0.0   0.0   1.0;
reading colortable from MGH file...
colortable with 14176 entries read (originally
/usr/local/freesurfer/FreeSurferColorLUT.txt)
voxel to talairach voxel transform
 1.03994   0.01456   0.07738  -16.87541;
-0.02607   1.18971   0.24142  -16.40842;
-0.06544  -0.23822   1.03825   18.09422;
 0.0   0.0   0.0   1.0;
reading segmented volume aseg.auto_noCCseg.mgz...
mri_fill: could not find any points where lh and rh wm  are nbrs
No such file or directory
Linux sleep2014 4.13.0-45-generic #50~16.04.1-Ubuntu SMP Wed May 30 11:18:27
UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s post_006 exited with ERRORS at Tue May 26 16:13:41 CEST 2020

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




I have seen in other questions that this error may be due to the CC and the
aseg files, and it is interesting because when I load aseg.auto.mgz or
aseg.auto_noCCseg.mgz files in Freeview, the following message in Freeview
terminal is shown in red:
"colortable with 14176 entries read (originally
/usr/local/freesurfer/FreesurferColorLUT.txt)", when I think they should be
1475 entries.

I'm using freesurfer v6.0.

Could you help me to solve this problem?
Thank you in advance!

Marina.

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[Freesurfer] ERROR: mri_fill: could not find any points where lh and rh wm are nbrs

[Marina Fernández]

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Dear Freesurfer experts,

When I run "recon-all -autorecon2-wm -subjid post_006" I get the following
error:

...

#
#@# Fill Tue May 26 16:13:33 CEST 2020
/usr/local/freesurfer/subjects/post_006/mri

 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta
-segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
 1.03994   0.01456   0.07738  -16.87541;
-0.02607   1.18971   0.24142  -16.40842;
-0.06544  -0.23822   1.03825   18.09422;
 0.0   0.0   0.0   1.0;
reading colortable from MGH file...
colortable with 14176 entries read (originally
/usr/local/freesurfer/FreeSurferColorLUT.txt)
voxel to talairach voxel transform
 1.03994   0.01456   0.07738  -16.87541;
-0.02607   1.18971   0.24142  -16.40842;
-0.06544  -0.23822   1.03825   18.09422;
 0.0   0.0   0.0   1.0;
reading segmented volume aseg.auto_noCCseg.mgz...
mri_fill: could not find any points where lh and rh wm  are nbrs
No such file or directory
Linux sleep2014 4.13.0-45-generic #50~16.04.1-Ubuntu SMP Wed May 30
11:18:27 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s post_006 exited with ERRORS at Tue May 26 16:13:41 CEST 2020

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




I have seen in other questions that this error may be due to the CC and the
aseg files, and it is interesting because when I load aseg.auto.mgz or
aseg.auto_noCCseg.mgz files in Freeview, the following message in Freeview
terminal is shown in red:
"colortable with 14176 entries read (originally
/usr/local/freesurfer/FreesurferColorLUT.txt)", when I think they should be
1475 entries.

I'm using freesurfer v6.0.

Could you help me to solve this problem?
Thank you in advance!

Marina.
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[Freesurfer] Problem_mri_watershed

[Edoardo Pinzuti]

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Dear Freesurfer community,

using the mri_watershed and -surf to crate inner_skull, outer_skin and
outer_skull I get a incorrect inner_skull segmentation, probably due to an
erroneous skullstrip. I tried to modify the parameters available but it
does not help.  Is there a way to correct this, manually correct or with a
mask ?
 Any other suggestions will be really appreciated

Thanks
Edoardo
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[Freesurfer] FS6: Mapping data to fsaverage6

[Tim Schäfer]

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Dear FreeSurfer experts,

I'm trying to resample cortical thickness data onto the fsaverage6 template 
subject in FreeSurfer v6. I have copied fsaverage6 into my $SUBJECTS_DIR.

I tried the following 2 commands:
* mris_preproc --s subject1 --target fsaverage6 --hemi lh --meas thickness 
--fwhm 5 --out lh.thickness.fwhm5.fsaverage6.mgh

and alternatively:

* recon-all -s subject1 -qcache -measure thickness -target fsaverage6

Both fail because the file subject1/surf/lh.fsaverage6.sphere.reg is missing 
(see attached recon-all.log file).

How can I generate the ?h.fsaverage6.sphere.reg file?

I tried:
mris_register subject1/surf/lh.sphere fsaverage6/surf/lh.sphere 
subject1/surf/lh.fsaverage6.sphere.reg

However, that fails as well, see attached file mris_reg_output.txt for the 
error message.


All the best,

Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, GermanyWed May 27 12:54:22 CEST 2020
/Users/timschaefer/data/tim_only/subject1
/Applications/freesurfer/bin/recon-all
-s subject1 -qcache -measure thickness -target fsaverage6
subjid subject1
setenv SUBJECTS_DIR /Users/timschaefer/data/tim_only
FREESURFER_HOME /Applications/freesurfer
Actual FREESURFER_HOME /Applications/freesurfer
build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Darwin BloodyiMac4.local 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct  4 
23:08:59 PDT 2019; root:xnu-4570.71.57~1/RELEASE_X86_64 x86_64
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
descriptors  256 
memorylocked unlimited
maxproc  2837 

PhysMem: 17G used (2795M wired), 15G unused.


program versions used
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2020/05/27-10:54:22-GMT  BuildTimeStamp: Jan 19 
2017 22:24:12  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp 
$  User: timschaefer  Machine: BloodyiMac4.local  Platform: Darwin  
PlatformVersion: 17.7.0  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2020/05/27-10:54:23-GMT  BuildTimeStamp: Jan 19 
2017 22:24:12  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve 
Exp $  User: timschaefer  Machine: BloodyiMac4.local  Platform: Darwin  
PlatformVersion: 17.7.0  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by ni...@gust.nmr.mgh.harvard.edu 
(x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2020/05/27-10:54:23-GMT  BuildTimeStamp: Jan 19 
2017 22:24:12  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ 
 User: timschaefer  Machine: BloodyiMac4.local  Platform: Darwin  
PlatformVersion: 17.7.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2020/05/27-10:54:23-GMT  BuildTimeStamp: Jan 19 2017 22:24:12  
CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: 
timschaefer  Machine: BloodyiMac4.local  Platform: Darwin  PlatformVersion: 
17.7.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2020/05/27-10:54:23-GMT  BuildTimeStamp: Jan 19 2017 
22:24:12  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp 
$  User: timschaefer  Machine: BloodyiMac4.local  Platform: Darwin  
PlatformVersion: 17.7.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2020/05/27-10:54:23-GMT  BuildTimeStamp: Jan 19 2017 
22:24:12  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: 
timschaefer  Machine: BloodyiMac4.local  Platform: Darwin  PlatformVersion: 
17.7.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2020/05/27-10:54:23-GMT  BuildTimeStamp: Jan 19 2017 22:24:12  
CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: 
timschaefer  Machine: BloodyiMac4.local  Platform: Darwin  PlatformVersion: 
17.7.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  

[Freesurfer] the -label flag in mri_cnr

[Pradyumna Bharadwaj]

External Email - Use Caution

Hello!


I had a couple of questions about how mri_cnr computes the contrast to
noise ratio.

From previous posts, a command such as mri_cnr
 $FREESURFER_HOME/subjects/bert/surf
$FREESURFER_HOME/subjects/bert/mri/norm.mgz
gives the lh cnr, rh cnr, and total cnr for bert.

1) What exactly is happening when you reference the /surf directory here?
2) Are the CNR values for the norm.mgz volume being computed by using the
lh white + lh pial; and rh white + rh pial surfaces?
3) Are the subcortical gm structures somehow involved in this calculation
as well?

I'm asking question 3 because when you add a -label
$FREESURFER_HOME/subjects/bert /label/lh.cortex.label
$FREESURFER_HOME/subjects/bert/label/rh.cortex.label  the lh cnr, rh cnr,
and total cnr values that you get are now different.


The outputs for bert for each case is as follows (FreeSurfer v6 bert was
used here):
1) *With /surf alone*

  white = 96.6+-6.0, gray = 75.7+-13.5, csf = 55.3+-16.6 gray/white CNR =
1.983, gray/csf CNR = 0.907 *lh CNR = 1.445*

white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2 gray/white CNR =
1.952, gray/csf CNR = 0.943 *rh CNR = 1.448*

*total CNR = 1.446*


*2) With /surf and -label *

white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5 gray/white CNR =
1.389, gray/csf CNR = 0.644 *lh CNR = 1.016*

white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3 gray/white CNR =
1.353, gray/csf CNR = 0.652 *rh CNR = 1.002*

*total CNR = 1.009*


Any inputs or thoughts on this matter are greatly appreciated!

Thanks,
Prad
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