Re: [Freesurfer] X graphics issues via SSH

[R Edgar]

On 12 May 2016 at 17:12, Z K  wrote:
> Eli, Thanks for this update. I am very much interested in the where this
> is headed.

Me too - sorry for missing the bit about "used to work"

Richard
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Re: [Freesurfer] X graphics issues via SSH

[Z K]

Eli, Thanks for this update. I am very much interested in the where this 
is headed.

-Zeke

On 05/12/2016 04:08 PM, Rockers, Elijah D. wrote:
> After much scouring, this appears to be a problem with XQuartz. I spoke
> to someone on the XQuartz team and they are basically on life-support.
> It looks like support for this may be going down the toilet, and
> migration to an entirely new architecture is needed. I am not the only
> person experiencing problems with GLX either, which apparently qdec and
> other freesurfer applications depends on via SSH.
>
> For now I will look into a work around, VNC/RDP or something of the sort.
>
> Just to keep you up to date, here is the discussion:
> https://bugs.freedesktop.org/show_bug.cgi?id=93953#c6
>
> Cheers,
>
> Eli
>
> On 05/11/2016 03:03 PM, Eli wrote:
>> Hello freesurfers,
>>
>> Running a Mac Pro, OS X El Capitan 10.11.4
>> With ATI Radeon Graphics card, and XQuartz v 2.7.9
>>
>> I am able to run Qdec and freeview perfectly fine on my machine. The
>> problem comes when I attempt to SSH into another machine and use these
>> programs (it used to work fine, but I am wondering if something in our
>> configuration has changed now)
>>
>> I get the following errors
>>
>> [belen@picasso:~]freeview
>> Xlib:  extension "NV-GLX" missing on display "localhost:10.0".
>> X Error: BadValue (integer parameter out of range for operation) 2
>>   Extension:150 (Uknown extension)
>>   Minor opcode: 3 (Unknown request)
>>   Resource id:  0x0
>> Abort (core dumped)
>>
>> [belen@picasso:~]qdec
>> Xlib:  extension "NV-GLX" missing on display "localhost:10.0".
>> X Error of failed request:  BadValue (integer parameter out of range
>> for operation)
>>   Major opcode of failed request:  150 (GLX)
>>   Minor opcode of failed request:  3 (X_GLXCreateContext)
>>   Value in failed request:  0x0
>>   Serial number of failed request:  1504
>>   Current serial number in output stream:  1505
>>
>> Based on my limited knowledge, It seems likely to be a problem with X
>> / SSH, and the graphics card, but I am unsure on how to proceed from
>> here. If anyone has any ideas on how to overcome this, I would be
>> incredibly grateful.
>>
>> The server machine itself also has a monitor, and can run Qdec and
>> Freeview fine locally, with no problems. the issue seems to happen
>> over SSH
>
> Houston Methodist. Leading Medicine.
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Re: [Freesurfer] Defining ROI and Finding the Cortical Thickness

[Douglas N Greve]

On 05/12/2016 05:46 AM, Mahtab Farahbakhsh wrote:
> Dear freeSurfer,
>
> I have problems with defining new labels for my brain scan or even of 
> fsaverage. I need to define a new label (ROI) to be able to find the 
> grey matter thickness for that specific region.
>
> My first problem is that when I define a new label on fsaverage, it 
> does not save it for me and it gives me the following error:
>
> mghRead(/Applications/freesurfer/experimental_data/TG/fsaverage/mri/wm.mgz, 
> -1): could not open file
> /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview: could 
> not open label file 
> /Applications/freesurfer/subjects/fsaverage/label/ROI_test.label
>
> I intend to define a new label (ROI) on fsaverage and then use the 
> mri_labe2label command to copy it on my desired structural MRI image. 
> But it does not work for me.
How are you doing this? What tool are you using? What steps with the 
tool are you executing?
>
> My second problem is that when I define a new label on my subject's 
> MRI image and I run the mri_anatomical_stats with the label of my 
> subject, it does not give me any output and this is what I get:
>
> bash-3.2$ mris_anatomical_stats -l anon/label/lh.test.label anon lh
> limiting computations to label anon/label/lh.test.label.
> reading volume 
> /Applications/freesurfer/experimental_data/TG//anon/mri/wm.mgz...
> reading input surface 
> /Applications/freesurfer/experimental_data/TG//anon/surf/lh.white...
> reading input pial surface 
> /Applications/freesurfer/experimental_data/TG//anon/surf/lh.pial...
> reading input white surface 
> /Applications/freesurfer/experimental_data/TG//anon/surf/lh.white...
>
> and the error is that it could not find the file lh.test.label, 
> however I can see it in the label folder.
Use the -b or -f flags to specify an output
>
> Please guide me with this issue.
>
> Best Regards,
> Mahtab.
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] X graphics issues via SSH

[Rockers, Elijah D.]

After much scouring, this appears to be a problem with XQuartz. I spoke to 
someone on the XQuartz team and they are basically on life-support. It looks 
like support for this may be going down the toilet, and migration to an 
entirely new architecture is needed. I am not the only person experiencing 
problems with GLX either, which apparently qdec and other freesurfer 
applications depends on via SSH.

For now I will look into a work around, VNC/RDP or something of the sort.

Just to keep you up to date, here is the discussion:
https://bugs.freedesktop.org/show_bug.cgi?id=93953#c6

Cheers,

Eli

On 05/11/2016 03:03 PM, Eli wrote:
Hello freesurfers,

Running a Mac Pro, OS X El Capitan 10.11.4
With ATI Radeon Graphics card, and XQuartz v 2.7.9

I am able to run Qdec and freeview perfectly fine on my machine. The problem 
comes when I attempt to SSH into another machine and use these programs (it 
used to work fine, but I am wondering if something in our configuration has 
changed now)

I get the following errors

[belen@picasso:~] freeview
Xlib:  extension "NV-GLX" missing on display "localhost:10.0".
X Error: BadValue (integer parameter out of range for operation) 2
  Extension:150 (Uknown extension)
  Minor opcode: 3 (Unknown request)
  Resource id:  0x0
Abort (core dumped)

[belen@picasso:~] qdec
Xlib:  extension "NV-GLX" missing on display "localhost:10.0".
X Error of failed request:  BadValue (integer parameter out of range for 
operation)
  Major opcode of failed request:  150 (GLX)
  Minor opcode of failed request:  3 (X_GLXCreateContext)
  Value in failed request:  0x0
  Serial number of failed request:  1504
  Current serial number in output stream:  1505

Based on my limited knowledge, It seems likely to be a problem with X / SSH, 
and the graphics card, but I am unsure on how to proceed from here. If anyone 
has any ideas on how to overcome this, I would be incredibly grateful.

The server machine itself also has a monitor, and can run Qdec and Freeview 
fine locally, with no problems. the issue seems to happen over SSH


Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S.News & 
World Report as one of America's "Best Hospitals" in 11 specialties and 
designated as a Magnet hospital for excellence in nursing.  Houston Methodist 
has also been named to FORTUNE®  Magazine's "100 Best Companies to Work For®" 
list for 10 years in a row. Visit us at  houstonmethodist.org. Follow us at  
twitter.com/MethodistHosp and facebook.com/HoustonMethodist.  
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Re: [Freesurfer] Volumetric Data Discrepancies

[Z K]

The 5th ventricle is a very small structure, so larger deltas are to be 
expected (due to a few missagned voxels). Otherwise I would categorize 
those differences as normal.

However, I must specify, if you are doing cross subject comparisons, 
please stick with the same version of freesurfer (i.e same platform).

-Zele



On 05/12/2016 03:02 PM, Tamara Tavares wrote:
> Hi Zeke,
>
> Thank you for your quick reply.
>
> I am specifically interested in examining the ventricles and calculated
> the percent differences for these segmented areas:
>
> Left lateral ventricle = 2.08%
>
> Left inferior lateral ventricle = 6.81%
>
> 3^rd ventricle= 6.31%
>
> 4^th ventricle =2.68%
>
> Right lateral ventricle = 0.40%
>
> 5^th ventricle =200%
>
>   I am a bit concerned of the 5^th ventricle as it is well greater than
> the expected 5% difference you suggested. However, I assume the other
> percent differences are within normal range? This is the first time I am
> using Freesurfer so I just want to confirm that my results are correct.
>
>   Thank you in advance for your help. It is very much appreciated!
>
> Tamara
>
>
> On Thu, May 12, 2016 at 1:36 PM, Z K  > wrote:
>
> Hello Tamara,
>
> It IS expected to see differences in volumetric data calculated when
> using versions if freesurfer compiled for different platforms. That
> is why we make the claim of "When processing a group of subjects for
> your study, it is essential to process all your subjects with the
> same version of freesurfer, on the same OS platform".
>
> You dont specify the % differences in your email below, but we have
> found that the differences observed in Mac vs. Linux will typically
> have deltas of less than 5%. Sometimes larger percent differences
> are observed in smaller structures, only because the delta of a
> single voxel can carry a larger percentage weight for smaller
> structures.
>
> -Zeke
>
>
>
> On 05/12/2016 10:20 AM, Tamara Tavares wrote:
>
> Hello All,
>
> I was hoping someone would be able to shed some light on an
> issue I have
> been having concerning the volumetric data calculated by FreeSurfer
> (version 5.3) using the asegstats output file. For information
> purposes,
> I am currently using the following command line: recon-all –I
> [path] –s
> –sd [Path] –segmentation –all.
>
>
> I have noticed some differences in the volumetric outputs from a
> scan I
> ran on a Linux computer (ubuntu kernal version 3.13.0-85) and
> the same
> scan ran on a Mac OS version 10.10.5. These differences in
> volume range
> from 5.2-639.4. I have been having difficulty in finding the
> source of
> this discrepancy. Are discrepancies commonly found? Could the
> different
> computers and operating systems be the reason for these
> discrepancies?
>
>
> I really appreciate your time and assistant with this issue.
>
> Thank you in advance for your help!
>
>
> Tamara
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Longitudinal analysis: creat cluster ROI and extract baseline and followup values

[Douglas N Greve]

If you used mri_glmfit, then you can use mri_glmfit-sim to create 
significant clusters. It will create an annotation of the significant 
clusters, and you can pass that to mri_segstats along with the stack of 
thickness images to extract the mean thickness in each cluster.

On 05/12/2016 04:23 AM, Liu Y wrote:
> Hi Freesurfers,
>
> I am using the degree of cortical atrophy between two groups. The 
> atrophy rate had no significant difference between two groups, but the 
> average thickness of the baseline and followup showed significant 
> clusters in two regions between the two groups. My question is how to 
> create the ROIs covering the clusters, and then extract the 
> thicknesses on baseline and followup MRIs?
>
> Thanks,
> Yawu
>
>
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Volumetric Data Discrepancies

[Bruce Fischl]

and just to chime in, before anyone flames us on this topic (as has 
happened in the past), we would *love* to have the resources to track down 
and eliminate this kind of thing, but it is very, very difficult to get NIH 
funding to do so.


cheers
Bruce


On Thu, 12 May 2016, Z K wrote:


Hello Tamara,

It IS expected to see differences in volumetric data calculated when
using versions if freesurfer compiled for different platforms. That is
why we make the claim of "When processing a group of subjects for your
study, it is essential to process all your subjects with the same
version of freesurfer, on the same OS platform".

You dont specify the % differences in your email below, but we have
found that the differences observed in Mac vs. Linux will typically have
deltas of less than 5%. Sometimes larger percent differences are
observed in smaller structures, only because the delta of a single voxel
can carry a larger percentage weight for smaller structures.

-Zeke


On 05/12/2016 10:20 AM, Tamara Tavares wrote:

Hello All,

I was hoping someone would be able to shed some light on an issue I have
been having concerning the volumetric data calculated by FreeSurfer
(version 5.3) using the asegstats output file. For information purposes,
I am currently using the following command line: recon-all –I [path] –s
–sd [Path] –segmentation –all.


I have noticed some differences in the volumetric outputs from a scan I
ran on a Linux computer (ubuntu kernal version 3.13.0-85) and the same
scan ran on a Mac OS version 10.10.5. These differences in volume range
from 5.2-639.4. I have been having difficulty in finding the source of
this discrepancy. Are discrepancies commonly found? Could the different
computers and operating systems be the reason for these discrepancies?


I really appreciate your time and assistant with this issue.

Thank you in advance for your help!


Tamara



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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Volumetric Data Discrepancies

[Z K]

Hello Tamara,

It IS expected to see differences in volumetric data calculated when 
using versions if freesurfer compiled for different platforms. That is 
why we make the claim of "When processing a group of subjects for your 
study, it is essential to process all your subjects with the same 
version of freesurfer, on the same OS platform".

You dont specify the % differences in your email below, but we have 
found that the differences observed in Mac vs. Linux will typically have 
deltas of less than 5%. Sometimes larger percent differences are 
observed in smaller structures, only because the delta of a single voxel 
can carry a larger percentage weight for smaller structures.

-Zeke


On 05/12/2016 10:20 AM, Tamara Tavares wrote:
> Hello All,
>
> I was hoping someone would be able to shed some light on an issue I have
> been having concerning the volumetric data calculated by FreeSurfer
> (version 5.3) using the asegstats output file. For information purposes,
> I am currently using the following command line: recon-all –I [path] –s
> –sd [Path] –segmentation –all.
>
>
> I have noticed some differences in the volumetric outputs from a scan I
> ran on a Linux computer (ubuntu kernal version 3.13.0-85) and the same
> scan ran on a Mac OS version 10.10.5. These differences in volume range
> from 5.2-639.4. I have been having difficulty in finding the source of
> this discrepancy. Are discrepancies commonly found? Could the different
> computers and operating systems be the reason for these discrepancies?
>
>
> I really appreciate your time and assistant with this issue.
>
> Thank you in advance for your help!
>
>
> Tamara
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] WmParc

[Douglas N Greve]

What version of FS are you using? You may need a newer version of 
mri_aparc2aseg. Try this one

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_aparc2aseg

On 05/12/2016 06:53 AM, Caroline Beelen wrote:
>
> If we changed the command –-ribbon to –- no ribbon, the script ran, 
> but when we looked at the stats-file, only cortical grey matte
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] group roi to individual native functional

[Patrick Beukema]

Thanks very much. That did it.
PB

On Wed, May 11, 2016 at 10:27 AM, Douglas Greve 
wrote:

> Register your average subject to each individual with mri_coreg (see
> below) using --s subject --dof 12, then use mri_label2vol with --seg
> ROI.nii.gz  to map the ROI into the individual space. If the ROI is
> surface-based, then you could recon-all your average, map the ROI to the
> surface with mri_vol2surf, then to the individual subject with mri_surf2surf
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
>
>
> On 5/11/16 9:40 AM, Patrick Beukema wrote:
>
> The average subject is the average of my own subjects (18). I registered
> each individual subject's functional data to the average subject with
> spm_register.
>
>
> On Tue, May 10, 2016 at 5:43 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> What is the average subject? How did you compute the registration
>> between the average subject volume and the individual?
>>
>> On 05/10/2016 01:37 PM, Patrick Beukema wrote:
>> > Hi,
>> > I am trying to register a volumetric roi from an average subject that
>> > I created to each individual subject's functional space. I have the
>> > transformation matrices that I applied to the functional data to bring
>> > them into the average space. When I apply the inverse of those
>> > transforms to the roi, the results are way off so I think I must be
>> > missing something.
>> >
>> > 1. I created a volume from a label with mri_label2vol.
>> > 2. I map the volume in the average space to the native functional
>> > space with mri_vol2vol.
>> >
>> > I take it this is not correct and would appreciate any guidance.
>> > Thank you,
>> > pb
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] Manual correction for brainstem module

[Eugenio Iglesias]

Yes! But take all the medulla volumes from the script. In other words: do not 
use the script to compute the medulla volumes of the cases you edited, and take 
the medulla volumes from the text file for all other cases. If you do that, 
you'd be introducing a fairly ugly bias in the study. 
Cheers, 
/E 


Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Jacky Lee"  
To: "Eugenio Iglesias"  
Cc: "Freesurfer support list"  
Sent: Thursday, May 12, 2016 4:11:20 PM 
Subject: Re: [Freesurfer] Manual correction for brainstem module 

Hi Eugenio, 

Thanks, the script worked. 

Actually I only edited the medulla segmentation in 3 out of the 49 subjects 
that I have. I suppose the original volumetric estimates for midbrain and pons 
are still valid and I can just calculate and compare the new medulla volumes 
for all subjects. Is that correct? 

Jacky 

2016-05-12 12:05 GMT+02:00 Eugenio Iglesias < e.igles...@bcbl.eu > : 



My email client is replacing the combination colon + right parenthesis by a 
smiley! If the same thing happened to you, please replace the smiley by a colon 
and a right parenthesis... 
Next time I'll just attach the code. 
Sorry for the inconvenience 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Eugenio Iglesias" < e.igles...@bcbl.eu > 
To: "Jacky Lee" < cyle...@gmail.com > 
Cc: "Freesurfer support list" < Freesurfer@nmr.mgh.harvard.edu > 
Sent: Thursday, May 12, 2016 5:59:33 AM 

Subject: Re: [Freesurfer] Manual correction for brainstem module 

Of course! I haven't tested the code below, but I think it should work right 
away. 

Let's assume that FreeSurfer is installed in /usr/local/freesurfer/ (if not, 
replace the location in the code below). Also, you'd need to replace the name 
of your subject directory. 
Finally, I have assumed that brainstemSsLabels.v10.mgz was modified and saved 
as brainstemSsLabels.v10.edited.mgz (again, replace as needed). 


subjectdir='/mysubjectdir/'; 
editedFileName='brainstemSsLabels.v10.edited.mgz'; 

addpath /usr/local/freesurfer/matlab 

d=dir(subjectdir); 

for i=1:length(d) 

tentativeSegFile=[subjectdir '/' d(i).name '/mri/' editedFileName]; 
if d(i).isdir && exist(tentativeSegFile,'file') 

A=MRIread(tentativeSegFile); 
MidbrainVol=8*sum(A.vol(:)==173); % the eight is because each voxel of the 
segmentation has a volume equal to 0.125 cubic mm 
PonsVol=8*sum(A.vol(:)==174); 
MedullaVol=8*sum(A.vol(:)==175); 
SCPvol=8*sum(A.vol(:)==178); 

disp(['Subject ' d(i).name ', midbrain = ' num2str(MidbrainVol) ', pons = ' 
num2str(PonsVol) ', medulla = ' num2str(MedullaVol) ', SCP = ' 
num2str(SCPvol)]); 

end 

end 

One more thing: if you haven't edited anything around the SCP, I would use the 
original estimate for this structure. The reason is that, because the SCP is 
very thing, the voxel count is a much poorer approximation for the volume as 
computed by the code (i.e., using soft segmentations). 

Cheers, 

Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Jacky Lee" < cyle...@gmail.com > 
To: "Freesurfer support list" < Freesurfer@nmr.mgh.harvard.edu > 
Cc: "Eugenio Iglesias" < e.igles...@bcbl.eu > 
Sent: Thursday, May 12, 2016 10:32:24 AM 
Subject: Re: [Freesurfer] Manual correction for brainstem module 

Hi Eugenio, 

Yes please give me some advice on the matlab commands for this since I am not 
very familiar with matlab... 

Cheers, 

Jacky 

Hi Jacky, 
this is a good question, and unfortunately there isn't a great answer to it. 
The volume is computed upong a probabilitic segmentation of the voxels that is 
not written to disk (this is very similar to what happens with aseg.mgz and 
aseg.stats). In order to properly update the volume estimates, you would have 
to know the probability that the inpainted voxels belong to the brainstem as 
estimated by the algorithm, which we don't currently write to disk. 
Another option would be to toss the volumes given by the algorithm, and compute 
new volumes for all cases and brainstem structures using the hard 
segmentations. You would simply have to count the number of voxels labeled as 
midbrain, pons, SCP and medulla for each subject. You can easily do this e.g. 
with Matlab (let me know if you need help with this). 
Cheers, 
Eugenio 
Juan Eugenio Iglesias 
Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal 
disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jacky 
Lee" < cyle...@gmail.com > 
To: "Freesurfer support list" < Freesurfer@nmr.mgh.harvard.edu > 
Sent: Monday, May 9, 2016 2:01:53 AM 
Subject: [Freesurfer] Manual correction for 

[Freesurfer] Volumetric Data Discrepancies

[Tamara Tavares]

Hello All,

I was hoping someone would be able to shed some light on an issue I have
been having concerning the volumetric data calculated by FreeSurfer
(version 5.3) using the asegstats output file. For information purposes, I am
currently using the following command line: recon-all –I [path] –s –sd
[Path] –segmentation –all.


I have noticed some differences in the volumetric outputs from a scan I ran
on a Linux computer (ubuntu kernal version 3.13.0-85) and the same scan ran
on a Mac OS version 10.10.5. These differences in volume range from
5.2-639.4. I have been having difficulty in finding the source of this
discrepancy. Are discrepancies commonly found? Could the different
computers and operating systems be the reason for these discrepancies?


I really appreciate your time and assistant with this issue.

Thank you in advance for your help!


Tamara
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[Freesurfer] WmParc

[Caroline Beelen]

Dear FS team,

We want to create a ROI based on the wm parcellation in the 2009s atlas. We ran 
the following command:
mri_aparc2aseg --s  --labelwm --hypo-as-wm --rip-unknown --ribbon --o 
mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz ( was replaced by 
our subject)

We get the following error: option --ribbon unknown.

The ribbon.mgz folders exist and are located in the right directory. We also 
tried to re-create them and this worked fine, but again after running the 
command above we got the same error.
If we changed the command --ribbon to -- no ribbon, the script ran, but when we 
looked at the stats-file, only cortical grey matter labels were segmented (no 
wm).
The same applies to other subjects we tried.

Could you please help us out?

Many thanks.
Jolijn & Caroline

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Re: [Freesurfer] Manual correction for brainstem module

[Eugenio Iglesias]

My email client is replacing the combination colon + right parenthesis by a 
smiley! If the same thing happened to you, please replace the smiley by a colon 
and a right parenthesis... 
Next time I'll just attach the code. 
Sorry for the inconvenience 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Eugenio Iglesias"  
To: "Jacky Lee"  
Cc: "Freesurfer support list"  
Sent: Thursday, May 12, 2016 5:59:33 AM 
Subject: Re: [Freesurfer] Manual correction for brainstem module 

Of course! I haven't tested the code below, but I think it should work right 
away. 

Let's assume that FreeSurfer is installed in /usr/local/freesurfer/ (if not, 
replace the location in the code below). Also, you'd need to replace the name 
of your subject directory. 
Finally, I have assumed that brainstemSsLabels.v10.mgz was modified and saved 
as brainstemSsLabels.v10.edited.mgz (again, replace as needed). 


subjectdir='/mysubjectdir/'; 
editedFileName='brainstemSsLabels.v10.edited.mgz'; 

addpath /usr/local/freesurfer/matlab 

d=dir(subjectdir); 

for i=1:length(d) 

tentativeSegFile=[subjectdir '/' d(i).name '/mri/' editedFileName]; 
if d(i).isdir && exist(tentativeSegFile,'file') 

A=MRIread(tentativeSegFile); 
MidbrainVol=8*sum(A.vol(:)==173); % the eight is because each voxel of the 
segmentation has a volume equal to 0.125 cubic mm 
PonsVol=8*sum(A.vol(:)==174); 
MedullaVol=8*sum(A.vol(:)==175); 
SCPvol=8*sum(A.vol(:)==178); 

disp(['Subject ' d(i).name ', midbrain = ' num2str(MidbrainVol) ', pons = ' 
num2str(PonsVol) ', medulla = ' num2str(MedullaVol) ', SCP = ' 
num2str(SCPvol)]); 

end 

end 

One more thing: if you haven't edited anything around the SCP, I would use the 
original estimate for this structure. The reason is that, because the SCP is 
very thing, the voxel count is a much poorer approximation for the volume as 
computed by the code (i.e., using soft segmentations). 

Cheers, 

Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Jacky Lee"  
To: "Freesurfer support list"  
Cc: "Eugenio Iglesias"  
Sent: Thursday, May 12, 2016 10:32:24 AM 
Subject: Re: [Freesurfer] Manual correction for brainstem module 

Hi Eugenio, 

Yes please give me some advice on the matlab commands for this since I am not 
very familiar with matlab... 

Cheers, 

Jacky 

Hi Jacky, 
this is a good question, and unfortunately there isn't a great answer to it. 
The volume is computed upong a probabilitic segmentation of the voxels that is 
not written to disk (this is very similar to what happens with aseg.mgz and 
aseg.stats). In order to properly update the volume estimates, you would have 
to know the probability that the inpainted voxels belong to the brainstem as 
estimated by the algorithm, which we don't currently write to disk. 
Another option would be to toss the volumes given by the algorithm, and compute 
new volumes for all cases and brainstem structures using the hard 
segmentations. You would simply have to count the number of voxels labeled as 
midbrain, pons, SCP and medulla for each subject. You can easily do this e.g. 
with Matlab (let me know if you need help with this). 
Cheers, 
Eugenio 
Juan Eugenio Iglesias 
Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal 
disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jacky 
Lee" < cyle...@gmail.com > 
To: "Freesurfer support list" < Freesurfer@nmr.mgh.harvard.edu > 
Sent: Monday, May 9, 2016 2:01:53 AM 
Subject: [Freesurfer] Manual correction for brainstem module 

Hi freesurfer experts, 

I have successfully run the brainstem module for some subjects. On visual 
checking, I can see there are voxels with T1 hypointense lesions mislabelled as 
non-brainstem tissue. I manually corrected them on the 
brainstemSsLabels.v10.mgz on Freeview. Then how do I obtain this new corrected 
volume of the brainstem substructures? 

Thanks. 

Regards, 

Jacky 


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contains patient information, please contact the Partners Compliance HelpLine 
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but does not contain patient information, please contact the sender and 
properly 
dispose of the e-mail. 
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Re: [Freesurfer] Manual correction for brainstem module

[Eugenio Iglesias]

Of course! I haven't tested the code below, but I think it should work right 
away. 

Let's assume that FreeSurfer is installed in /usr/local/freesurfer/ (if not, 
replace the location in the code below). Also, you'd need to replace the name 
of your subject directory. 
Finally, I have assumed that brainstemSsLabels.v10.mgz was modified and saved 
as brainstemSsLabels.v10.edited.mgz (again, replace as needed). 


subjectdir='/mysubjectdir/'; 
editedFileName='brainstemSsLabels.v10.edited.mgz'; 

addpath /usr/local/freesurfer/matlab 

d=dir(subjectdir); 

for i=1:length(d) 

tentativeSegFile=[subjectdir '/' d(i).name '/mri/' editedFileName]; 
if d(i).isdir && exist(tentativeSegFile,'file') 

A=MRIread(tentativeSegFile); 
MidbrainVol=8*sum(A.vol(:)==173); % the eight is because each voxel of the 
segmentation has a volume equal to 0.125 cubic mm 
PonsVol=8*sum(A.vol(:)==174); 
MedullaVol=8*sum(A.vol(:)==175); 
SCPvol=8*sum(A.vol(:)==178); 

disp(['Subject ' d(i).name ', midbrain = ' num2str(MidbrainVol) ', pons = ' 
num2str(PonsVol) ', medulla = ' num2str(MedullaVol) ', SCP = ' 
num2str(SCPvol)]); 

end 

end 

One more thing: if you haven't edited anything around the SCP, I would use the 
original estimate for this structure. The reason is that, because the SCP is 
very thing, the voxel count is a much poorer approximation for the volume as 
computed by the code (i.e., using soft segmentations). 

Cheers, 

Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Jacky Lee"  
To: "Freesurfer support list"  
Cc: "Eugenio Iglesias"  
Sent: Thursday, May 12, 2016 10:32:24 AM 
Subject: Re: [Freesurfer] Manual correction for brainstem module 

Hi Eugenio, 

Yes please give me some advice on the matlab commands for this since I am not 
very familiar with matlab... 

Cheers, 

Jacky 

Hi Jacky, 
this is a good question, and unfortunately there isn't a great answer to it. 
The volume is computed upong a probabilitic segmentation of the voxels that is 
not written to disk (this is very similar to what happens with aseg.mgz and 
aseg.stats). In order to properly update the volume estimates, you would have 
to know the probability that the inpainted voxels belong to the brainstem as 
estimated by the algorithm, which we don't currently write to disk. 
Another option would be to toss the volumes given by the algorithm, and compute 
new volumes for all cases and brainstem structures using the hard 
segmentations. You would simply have to count the number of voxels labeled as 
midbrain, pons, SCP and medulla for each subject. You can easily do this e.g. 
with Matlab (let me know if you need help with this). 
Cheers, 
Eugenio 
Juan Eugenio Iglesias 
Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal 
disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Jacky 
Lee" < cyle...@gmail.com > 
To: "Freesurfer support list" < Freesurfer@nmr.mgh.harvard.edu > 
Sent: Monday, May 9, 2016 2:01:53 AM 
Subject: [Freesurfer] Manual correction for brainstem module 

Hi freesurfer experts, 

I have successfully run the brainstem module for some subjects. On visual 
checking, I can see there are voxels with T1 hypointense lesions mislabelled as 
non-brainstem tissue. I manually corrected them on the 
brainstemSsLabels.v10.mgz on Freeview. Then how do I obtain this new corrected 
volume of the brainstem substructures? 

Thanks. 

Regards, 

Jacky 

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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Defining ROI and Finding the Cortical Thickness

[Mahtab Farahbakhsh]

Dear freeSurfer,

I have problems with defining new labels for my brain scan or even of
fsaverage. I need to define a new label (ROI) to be able to find the grey
matter thickness for that specific region.

My first problem is that when I define a new label on fsaverage, it does
not save it for me and it gives me the following error:

mghRead(/Applications/freesurfer/experimental_data/TG/fsaverage/mri/wm.mgz,
-1): could not open file
/Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview: could not
open label file
/Applications/freesurfer/subjects/fsaverage/label/ROI_test.label

I intend to define a new label (ROI) on fsaverage and then use the
mri_labe2label command to copy it on my desired structural MRI image. But
it does not work for me.

My second problem is that when I define a new label on my subject's MRI
image and I run the mri_anatomical_stats with the label of my subject, it
does not give me any output and this is what I get:

bash-3.2$ mris_anatomical_stats -l anon/label/lh.test.label anon lh
limiting computations to label anon/label/lh.test.label.
reading volume
/Applications/freesurfer/experimental_data/TG//anon/mri/wm.mgz...
reading input surface
/Applications/freesurfer/experimental_data/TG//anon/surf/lh.white...
reading input pial surface
/Applications/freesurfer/experimental_data/TG//anon/surf/lh.pial...
reading input white surface
/Applications/freesurfer/experimental_data/TG//anon/surf/lh.white...

and the error is that it could not find the file lh.test.label, however I
can see it in the label folder.

Please guide me with this issue.

Best Regards,
Mahtab.
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[Freesurfer] Longitudinal analysis: creat cluster ROI and extract baseline and followup values

[Liu Y]

Hi Freesurfers,

I am using the degree of cortical atrophy between two groups. The atrophy
rate had no significant difference between two groups, but the average
thickness of the baseline and followup showed significant clusters in two
regions between the two groups. My question is how to create the ROIs
covering the clusters, and then extract the thicknesses on baseline and
followup MRIs?

Thanks,
Yawu
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