Re: [Freesurfer] mri_glmfit dependent variable

[miracle ozzoude]

External Email - Use Caution

Thanks Doug. I appreciate it. I have more questions.

1) Aren't both models answering the same question regardless of which side
of the equation cortical thickness or syndromes is placed?

2) Also, I noticed in the mri_glmfit --help, it said that forward model 2
is inverted to solve for the regressor of interest. Correct if I'm wrong,
does it mean if my matrix is 0 0 0 1 where 1 represents neuropsych
syndrome, it will solve for it?

The forward model is given by:


y = W*X*B + n


where X is the Ns-by-Nb design matrix, y is the Ns-by-Nv input data

set, B is the Nb-by-Nv regression parameters, and n is noise. Ns is

the number of inputs, Nb is the number of regressors, and Nv is the

number of voxels/vertices (all cols/rows/slices). y may be surface

or volume data and may or may not have been spatially smoothed. W

is a diagonal weighing matrix.


During the estimation stage, the forward model is inverted to

solve for B:


B = inv(X'W'*W*X)*X'W'y


3) Lastly, how do I extract the beta-values after running mri_glmfit-sim
without matlab?

Many thanks,
Paul

On Tue, Feb 23, 2021 at 12:37 AM miracle ozzoude 
wrote:

> Hello Experts,
>
> I've a question about mri_glmfit. I want to investigate the association
> between thickness and neuropsychiatric syndromes, controlling for age and
> cognition. Which model below is mri_glmfit performing?
>
> Model 1
> neuropsych syndromes ~ age + cognition + cortical thickness
> or
> Model 2
> cortical thickness ~ age + cognition + neuropsych syndrome
>
> Many thanks,
> Paul
>
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Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

[Horsng Junn]

External Email - Use Caution

And you seem to be running FreeSurfer as root.
Since that could complicate matters, could you run it as a normal user?

Best,
Horsng

> On Feb 24, 2021, at 9:36 AM, Horsng Junn  wrote:
> 
> Hi Ishi,
> 
> I'm actually not a FreeSurfer developer and this question seems beyond me, 
> but my googling leads to this page:
> https://secure-web.cisco.com/1J96FRdW9b30grp2ZKVoOToURCtWoMNvRVujwywyg_8-dnzChY7mF4O26rtAy5IRwnW_AUTLc3NyneJNA50jjEVOXpbI4dZC473KwMJggVytdgBIRr71ekxd8YXDmrZITYqzNG0A84Oz0a0_j-f9chQHRFjVJfTuTpTAPNL4Wo-w6SWdOnsVA8JRnCaR8qo75dzxZNr7BeOYrzjdQM06h8MZJkqd1LV0hvaj__eT2EaJcoJ-8aqyXpOk3lldYcJCf/https%3A%2F%2Fwww.mathworks.com%2Fmatlabcentral%2Fanswers%2F459827-why-do-i-receive-a-glibcxx-not-found-error-on-my-redhat-or-centos-linux-machine
>  
> 
> 
> which seems to suggest that you add the following to your .bashrc, .profile 
> or similar places and retry.
> 
> export 
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/freesurfer/MCRv84/sys/os/glnxa64
> 
> Please try this and report your result.
> If this doesn't work, hopefully a FreeSurfer developer would chime in.
> 
> Best,
> Horsng
> 
> 
>> On Feb 23, 2021, at 8:19 PM, Ishi Tandon AIB, Jaipur 
>> mailto:ishi.tan...@student.amity.edu>> wrote:
>> 
>> External Email - Use Caution
>> 
>> 
>> 
>> Hello, 
>> 
>> I am sorry for posting up another thread. Had an issue with subscription so 
>> had to post again (will keep it in mind now). 
>> 
>> I tried that out. And that worked well. 
>> 
>> But there's another error that pops up after I run (attached in the image): -
>> recon-all -all -s bert
>> 
>> I tried the following commands in order to update libstd. 
>> apt-get update
>> apt-get install libstdc++6
>> But that didn't work. 
>> 
>> I am not able to trace the exact error. 
>> 
>> Thanks for the help.
>> 
>> 
>> On Tue, Feb 23, 2021 at 11:56 AM Horsng Junn > > wrote:
>> External Email - Use Caution
>> 
>> 
>> Hi Ishi,
>> 
>> You apparently omitted an "n": it must be libncurses5-dev (please note the n 
>> after lib).
>> 
>> And please try to keep previous correspondences intact,
>> as otherwise the devs must hunt the mail archive for the detail.
>> 
>> Best,
>> Horsng
>> 
>> 
>>> On Feb 23, 2021, at 3:10 PM, Ishi Tandon AIB, Jaipur 
>>> mailto:ishi.tan...@student.amity.edu>> 
>>> wrote:
>>> 
>>> External Email - Use Caution
>>> 
>>> 
>>> Hello experts,
>>> 
>>> In response to the previous email about matlab installation error while 
>>> attempting to use hippocampal subfields. 
>>> 
>>> I tried the following command as suggested by you :- 
>>> 
>>> sudo apt-get install libcurses5-dev
>>>  
>>> But I get the following error :- 
>>> 
>>> Reading package lists... Done 
>>> Building dependency tree Reading state information... Done 
>>> E: Unable to locate package libcurses5-dev 
>>> 
>>> Also, I am using fs version 7.1.1. 
>>> I installed freesurfer-linux-centos7_x86_64-7.1.1.tar.gz file. 
>>> 
>>> 
>>> Regards,
>>> Ishi Tandon
>>> B.Tech + M.Tech - Cognitive Neuroscience
>>> Amity University, Rajasthan
>>> Contact- +918239259846
>>> Email - ishi.tando...@gmail.com 
>>> 
>>> ___
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>>>  
>>> 
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Re: [Freesurfer] Sulcal probability maps

[Fischl, Bruce]

Did you try mris_spherical_average? I have definitely used it for this (among 
other things). I assume you saved the sulcal labels to a .label file?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Kristi Drudik
Sent: Tuesday, February 23, 2021 2:30 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Sulcal probability maps


External Email - Use Caution
Hi Doug,

That's exactly what I mean. We are drawing them directly on FreeView by 
creating a closed path on the white surface and filling it (see attachment for 
reference).

Best,
Kristi

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Douglas N. Greve
Sent: February 23, 2021 9:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Sulcal probability maps

what do you mean by painted? Do you mean you drew them on there using FreeView?
On 2/19/2021 11:37 AM, Kristi Drudik wrote:

External Email - Use Caution
Hi Doug,

The sulci are .label format because they were painted directly on the surface 
using FreeSurfer 7.1.

Best,
Kristi

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

 On Behalf Of Douglas N. Greve
Sent: February 19, 2021 10:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Sulcal probability maps

What format is your sulcus in?
On 2/16/2021 2:38 PM, Kristi Drudik wrote:

External Email - Use Caution
Good afternoon,

I hope this email finds you well.
I am in the process of "painting" MRI surfaces from the Human connectome 
project in FreeSurfer, meaning creating labels on the surfaces to analyze 
sulcal morphology. We are interested in the spatial variability of the sulcus 
and thus, want to create surface spatial probability maps using FreeSurfer 
(please see attachment for an example of such surface probability maps). These 
maps would represent the likelihood of each vertex on the FreeSurfer fsaverage 
surface belonging to the sulcus of interest (from 0% to 100%).
To obtain these probability maps, I:

  1.  Painted the sulcus of interest on the surface by creating a .label file.
  2.  Registered this .label file to fsaverage (mri_label2label)
  3.  Converted the .label file to vol (mri_label2vol)
  4.  Converted it to a surface file (mri_vol2surf)
  5.  Concatenated the data to create an average (mri_concat --mean)
  6.  Blurred the data and loaded the blurred average as an overlay onto the 
fsaverage pial (mris_fwhm)
Because this seems very convoluted, my question becomes: Is there a more direct 
way to generate these maps from the labels themselves, rather than going from 
label to vol, then back to surf?
Finally, I would like these maps to represent a 0-100% range of each vertex in 
fsaverage belonging to the sulcus of interest. However, this method creates a 
0-1 range (please see colour bar in attachment). Is there a way to change this 
to a percentage?
Thank you very much for your time and help. Please let me know if you have any 
questions.
Best,
Kristi


Kristi Drudik
Ph.D. Student, Clinical Psychology

Montreal Neurological Institute
McGill University
Montreal, Canada




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Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

[Horsng Junn]

External Email - Use Caution

Hi Ishi,

I'm actually not a FreeSurfer developer and this question seems beyond me, but 
my googling leads to this page:
https://secure-web.cisco.com/1tvdf5d8d-n_4_yvtpnDy1tW-h4qQnq2_ZkoCU5wZomtFsWZ-CDUCe9hdZND8pvg-6Zs954WFqOc9uonDsuGXWWb2s4TMIIXYq9XILmA0EKEyhdg0rluptPvl05L7EZXjriIRbGlhy0xPvNs1xn9oAvb_6jmllT-roLqOg29ZkB1Pxbt2zXGXXpo6vUxNCoUQnZHLa2q7cLAkebQkl9KScw9KdrzqfEVyt_osc_vbdzkHttdQFLzLgnSBbiPxHVn3wkpDi_HugY_LCdY90Ca0jg/https%3A%2F%2Fwww.mathworks.com%2Fmatlabcentral%2Fanswers%2F459827-why-do-i-receive-a-glibcxx-not-found-error-on-my-redhat-or-centos-linux-machine
 


which seems to suggest that you add the following to your .bashrc, .profile or 
similar places and retry.

export 
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/freesurfer/MCRv84/sys/os/glnxa64

Please try this and report your result.
If this doesn't work, hopefully a FreeSurfer developer would chime in.

Best,
Horsng


> On Feb 23, 2021, at 8:19 PM, Ishi Tandon AIB, Jaipur 
> mailto:ishi.tan...@student.amity.edu>> wrote:
> 
> External Email - Use Caution
> 
> 
> 
> Hello, 
> 
> I am sorry for posting up another thread. Had an issue with subscription so 
> had to post again (will keep it in mind now). 
> 
> I tried that out. And that worked well. 
> 
> But there's another error that pops up after I run (attached in the image): -
> recon-all -all -s bert
> 
> I tried the following commands in order to update libstd. 
> apt-get update
> apt-get install libstdc++6
> But that didn't work. 
> 
> I am not able to trace the exact error. 
> 
> Thanks for the help.
> 
> 
> On Tue, Feb 23, 2021 at 11:56 AM Horsng Junn  > wrote:
> External Email - Use Caution
> 
> 
> Hi Ishi,
> 
> You apparently omitted an "n": it must be libncurses5-dev (please note the n 
> after lib).
> 
> And please try to keep previous correspondences intact,
> as otherwise the devs must hunt the mail archive for the detail.
> 
> Best,
> Horsng
> 
> 
>> On Feb 23, 2021, at 3:10 PM, Ishi Tandon AIB, Jaipur 
>> mailto:ishi.tan...@student.amity.edu>> wrote:
>> 
>> External Email - Use Caution
>> 
>> 
>> Hello experts,
>> 
>> In response to the previous email about matlab installation error while 
>> attempting to use hippocampal subfields. 
>> 
>> I tried the following command as suggested by you :- 
>> 
>> sudo apt-get install libcurses5-dev
>>  
>> But I get the following error :- 
>> 
>> Reading package lists... Done 
>> Building dependency tree Reading state information... Done 
>> E: Unable to locate package libcurses5-dev 
>> 
>> Also, I am using fs version 7.1.1. 
>> I installed freesurfer-linux-centos7_x86_64-7.1.1.tar.gz file. 
>> 
>> 
>> Regards,
>> Ishi Tandon
>> B.Tech + M.Tech - Cognitive Neuroscience
>> Amity University, Rajasthan
>> Contact- +918239259846
>> Email - ishi.tando...@gmail.com 
>> 
>> ___
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>>  
>> 
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Re: [Freesurfer] WM volume

[Barletta, Valeria]

Thanks a lot. One more thing, is the total brain volume "BrainSegVolNotVent, 
Brain Segmentation Volume Without Ventricles" ?

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Tuesday, February 23, 2021 9:10 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] WM volume

Yes, that is the right value. We changed the name of it in more recent versions 
to CerebralWhiteMatter

On 2/22/2021 4:12 PM, Barletta, Valeria wrote:
Dear Freesurfers,
In what file inside the patient_name/stats folder do I find the total white 
matter volume?
In the file "aseg.stats" there is something called lh/rh "cortical white matter 
volume", is that the right value to look at?

Thank you,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823



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Re: [Freesurfer] Creating a .gcs custom atlas from nifti file for cortical parcellation

[THIBEAU SUTRE Elina]

External Email - Use Caution

Thank you for your answer!

I actually found a .gcs version of the atlas here 
https://secure-web.cisco.com/1DEIqPvOjJClzmnD0pPJe4KUO0ZGfQXNibFw42NNAFdce7z3wfEYEHkLr6hUVsVtT49h6keiOEtxdoM54OmnAKuttOm_uXHUzlLXqsnBvAgInmXl1-XvcPJ28TR2wnfF8ZQjNRniz_OW04Uf_LYdUS7_wKdXxqdbZXiKtYejiwKOhqtGkCxXD2aY0K8duznwGNsMMLGj1IzpCUoSQxy_Km-8CtuxPK4WRfXyhIEJ_3QnSfFNJc3ElrSxZ-I1JCmVKr6YpQxqzIabA4i_rJ50-Mg/https%3A%2F%2Ffigshare.com%2Farticles%2Fdataset%2FmultiAtlasTT_data%2F5998583.
I now try to reproduce the steps done in freesurfer recon-all with this atlas.

I now have another problem: when I try to reproduce the steps based on 
https://secure-web.cisco.com/1ryL0fLjnek4Tnqkk8ASdgyohf1OqhYaYARM-aoRqIgHHa4KMvcpBqGYD1SkRwj59xoxgBZGZu8HbsRTqDUPo3wdzMY3Zl4GBq4zQiiTlcGE2qkr553kCi0Nx2TQG5p5VrWJFITVb1II2aF344_5DGTQGtCCXkdaLpuuwg-vS-7XmKpTg_EoqLOmYdN_sn1Kapk9KLNy6gT0EqgCqrSBUI-CqZkqtpAktc98SlWC3c_NV3HGeO-QD1Z7ZL025sNnH_Zzg9Xz8HeI9QVlqkjxTVA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllTableStableV6.0
 with an atlas used by the pipeline (for example 
?h.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs) I do not obtain 
the same result than with recon-all.

My freesurfer version is 6.0.0 and I tried to do the two steps leading to the 
creation of statistics for one particular subject:

mris_ca_label
 -l ../label/?h.cortex.label -aseg aseg.presurf.mgz  ?h ?h.sphere.reg 
$FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs
 ?h.aparc.annot

mris_anatomical_stats
 -th3 -mgz -cortex ../label/?h.cortex.label -f stats/?h.aparc.stats -b -a 
label/?h.aparc.annot -c label/aparc.annot.ctab  ?h

Can you confirm that these are the correct steps to perform ? And that the root 
directory here is $SUBJECTS_DIR/ /mri?

Le 23 févr. 2021 à 15:07, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> a écrit :

depends on the nature of AICHA. Are these labels on a group of subjects? If so, 
you can build your own gcs file with train-gcs-atlas.
If it is just a label set, then you should run recon-all on the template 
subject, sample the labels onto the surface (mri_vol2surf), then convert the 
resulting surface segmentation to an annotation (mris_seg2annot), then map the 
annot to other subjects with mris_apply_reg

On 2/22/2021 8:59 AM, THIBEAU SUTRE Elina wrote:

External Email - Use Caution

Hello freesurfer experts,

I would like to use freesurfer recon-all to obtain the regional cortical 
thicknesses of subjects of ADNI dataset. I launched freesurfer recon-all and 
obtained the parcellations according to Destrieux and Desikan-Killiany atlases. 
I would like to know how to obtain the same parcellations with another atlas, 
AICHA (MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 

Re: [Freesurfer] segmentation is shifted with respect to NIFTI T1W

[Roman Fleysher]

External Email - Use Caution

Dear Douglas,
Dear All,

Trying to investigate the shift, I used the same pair of commands to convert 
several mgz files back to NIFTI and overlay on the original input T1W image. 
Some sort of mismatch begins with the orig.mgz file.  I see small local 
compressions and stretches. Since this is the image that will be subsequently 
segmented, segmentation will not match input T1W image. Subsequent files: 
nu.mgz, T1.mgz and brainmask.mgz carry over distorted (compared to input) 
orig.mgz but appropriately modify intensity and masking as expected.

However, I do not see overall 1 pixel shift in y-axis compared to the input 
image. This leads me to believe MGZ to NIFTI conversion is not the cause of the 
shift per se because I assume orientation information inside aseg.mgz is the 
same as in the other files. This of course could be wrong as I do not know 
details.

Thank you,

Roman


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Roman Fleysher 

Sent: Tuesday, February 23, 2021 10:54 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] segmentation is shifted with respect to NIFTI T1W

CAUTION: This email comes from an external source; the attachments and/or links 
may compromise our secure environment. Do not open or click on suspicious 
emails. Please click on the “Phish Alert” button on the top right of the 
Outlook dashboard to report any suspicious emails.

External Email - Use Caution

Thank you, Douglas. Then, fsroi as a work around is also right solution? I do 
not know what causes the issue: initial conversion of T1W from NIFTI to mgz, 
segmentation itself or transfer back to NIFTI. I do not know if other files 
(say brain mask) have the same issue. Looking into these.

Roman

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Tuesday, February 23, 2021 10:04 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] segmentation is shifted with respect to NIFTI T1W

Those commands look right

On 2/23/2021 9:27 AM, Roman Fleysher wrote:

External Email - Use Caution

Dear FreeSurfers,

I am working with version 6, starting point is T1W image in NIFTI format. I 
typically transform segmentations back to native space in NIFTI format to be 
able to use other software (FSL and such). I noticed that segmentation is 
shifted by 1 pixel in one axis (y-axis). Mapping of segmentation is a two step 
process based on description in:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
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Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

[Koch, Erin M.]

External Email - Use Caution

Is there anyway to get the lh.white and rh.white with noaseg?  Or is there a 
file in the attachment of the previous email that is a stand in for those 
missing files?

Thanks for your help.
Erin

From: Koch, Erin M. 
Sent: Wednesday, February 17, 2021 11:14 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

I am attaching a screen shot of the files in my subjects surf subfolder.  Note 
in the image you only see the lh.*** surfaces.  All correspoinding rh.*** files 
are there as well.

Thanks!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Friday, February 12, 2021 6:54 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

What surfaces are there?

On 2/11/2021 4:35 PM, Koch, Erin M. wrote:

External Email - Use Caution

Hi Douglas,

I am sorry I have to bug you once more.  While the inflation step completed 
with the suggested flag, as did the flattening step (for creating a flat map), 
when I went to register a functional scan to the inflated and flat map  the 
command:

mri_vol2surf —src 'PVal_resliced' —srcreg reg.dat —projfrac 0.5 —interp nearest 
—hemi lh —out 'PVal_lh')
mri_vol2surf —src 'PVal_resliced' —srcreg reg.dat —projfrac 0.5 —interp nearest 
—hemi rh —out 'PVal_rh')

failed because the recon-all did not create a few files including: lh.white, 
and rh.white

Is this due to the flags and expert options that were needed to complete the 
inflation?
Can I run a separate command to create these files?

thanks,

Erin

From: Koch, Erin M. 
Sent: Wednesday, January 27, 2021 10:04 PM
To: Freesurfer support list 

Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

It completed!  Thank you the help.

Get Outlook for 
iOS

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

 on behalf of Douglas N. Greve 

Sent: Wednesday, January 27, 2021 10:00:54 AM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

It should not need it for the inflation. You can try adding -no-cortex-label 
and see how far you get

On 1/27/2021 12:39 PM, Koch, Erin M. wrote:

External Email - Use Caution

Thanks for the info.  Is it possible to put in a "fake"  aseg.presurf.mgz file? 
 Do you think this is a possible work around, or is the inflation for flat map 
generation somehow reliant on this file now?

Erin

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

 on behalf of Douglas N. Greve 

Sent: Wednesday, January 27, 2021 7:40 AM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

It needs to be there. Sorry, I rewrote parts of the stream for v7 and did not 
consider the impact on NHP streams (since they are not part of our package). 
You might have to use older versions of FS to make this work.

On 1/26/2021 11:10 PM, Koch, Erin M. wrote:

External Email - Use Caution

Or, are you saying that I do not need to turn it off for NHP?

Get Outlook for 
iOS

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

 on behalf of Koch, Erin M. 
Sent: Monday, January 25, 2021 10:47:34 PM
To: Freesurfer support list 

Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation


External Email - Use Caution

Yes.  I turned off aseg because 

Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Iglesias Gonzalez, Juan E.]

Sure! The more slices the better __
Maybe it would be possible to share norm.mgz (which is skull stripped and thus 
deidentified) and the segmentation? Or maybe even crop norm.mgz around the 
thalami with Freeview?
Cheers,
/E

 
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com 
 
 

On 2/23/21, 11:00, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Gronow, Franziska"  wrote:

External Email - Use Caution

Dear Eugenio,

thank you for your response. Unfortunately it is not possible to share the 
whole subject. Would it be helpful to send you more screenshots of all three 
views (coronal, sagittal, axial) with different mask opacities?

Kind regards,
Franziska

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von 
freesurfer-requ...@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 17. Februar 2021 14:56
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Freesurfer Digest, Vol 204, Issue 33

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freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit

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When replying, please edit your Subject line so it is more specific than 
"Re: Contents of Freesurfer digest..."


Today's Topics:

   1. Re: overlap/intersection of labels? (Trisanna Sprung-Much)
   2. Re: FreeSurfer 7 vs FreeSurfer 6 surface differences
  (Mike Schmidt)
   3. VB password (?)
   4. Thalamic nuclei segmentation - PuM nucleusmis-segmentation?
  (Gronow, Franziska)
   5. Queries in qdec (Koustav Chatterjee)
   6. Re: Thalamic nuclei segmentation - PuM nucleus
  mis-segmentation? (Iglesias Gonzalez, Juan E.)
   7. Re: Thalamic nuclei segmentation - PuM nucleus
  mis-segmentation? (Iglesias Gonzalez, Juan E.)


--

Message: 1
Date: Tue, 16 Feb 2021 21:58:34 +
From: Trisanna Sprung-Much 
Subject: Re: [Freesurfer] overlap/intersection of labels?
To: Freesurfer support list 
Message-ID: 
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Hi Cornelius

I found something that computes the overlap of labels across the same 
vertex when doing some research about this, not sure if this is what you mean:


https://secure-web.cisco.com/116MIwNJShgHoW9J9evPl5bCi0xgcx82bMJ48_l7VTkyo4rsX6beTdCfGCkpiAyjUuMFA31V5ClU95ErPkQPZP8TKRthymZKTmx9z4NZ-1Q_VMNlPzPJ7PZG4H-wntegGfigUm5R6ocjIe4fS6bL4_82SxATBarpW8b6rv_vC1VPBn1ZM4Hj4ld7D7l3hMWkgB8zNZaHVjFrDQM4so73Mk3cuFXo4uZfnmiBKYK9XTJlzfFP24H6-tsGIkT4ka-7BQxMKOmF6bzTYzRo0tE8HTg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_label2annot

See specifically:
--nhits

This option creates a diagnostic file showing whether the cumulative effect 
of all the label files happens to assign more than one label to each vertex. 
The output file is a 
FreeSurfer
 'overlay' format file, in which each vertex has an associated value, in this 
case the count of labels assigned to that vertex. This can be displayed in 
tksurfer as a color. Setting fthresh to 1.5 will distinguish good vertices 
(count<=1) from bad (count>=2).

I know there is also a command merge_labels that may help?

Best,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of "Dr. Cornelius 
Kronlage" 
Reply-To: Freesurfer support list 
Date: Tuesday, February 16, 2021 at 11:19 AM
To: "'freesurfer@nmr.mgh.harvard.edu'" 
Subject: [Freesurfer] overlap/intersection of labels?


External Email - Use Caution

Dear freesurfers,



is there an elegant way of computing the intersection or overlap of 
different labels or - which would be even more useful for my application - 
annotations?



I only managed to find 

Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Gronow, Franziska]

External Email - Use Caution

Dear Eugenio,

thank you for your response. Unfortunately it is not possible to share the 
whole subject. Would it be helpful to send you more screenshots of all three 
views (coronal, sagittal, axial) with different mask opacities?

Kind regards,
Franziska

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von 
freesurfer-requ...@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 17. Februar 2021 14:56
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Freesurfer Digest, Vol 204, Issue 33

Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit

https://secure-web.cisco.com/1ak9QaJ1_1rhd69MSCjVvSgBkkgvkfHMc4AJu1OKXYs9k4pS-cXKoec4wiYPdDwg42lFLhj-haNv_GCV3Snd16puLCeHA5stbmdlVVtWyi0yA8m5ZoPUlysAuaBeKGDKuHTOzx0kRataF20Nbjkb4OwRlP7Qzj_VWuz3_mulTKpUfgmhnKsMhd2C0a6-7JDU27JTE70NvqsdJbZHa8OJpTUnN4Dc91ezjJKunzolpTFv9X-OQ174u6iZ_1Q8Sxk1efKBLe99Oyk2osGRyl25Zsw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu

You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific than "Re: 
Contents of Freesurfer digest..."


Today's Topics:

   1. Re: overlap/intersection of labels? (Trisanna Sprung-Much)
   2. Re: FreeSurfer 7 vs FreeSurfer 6 surface differences
  (Mike Schmidt)
   3. VB password (?)
   4. Thalamic nuclei segmentation - PuM nucleusmis-segmentation?
  (Gronow, Franziska)
   5. Queries in qdec (Koustav Chatterjee)
   6. Re: Thalamic nuclei segmentation - PuM nucleus
  mis-segmentation? (Iglesias Gonzalez, Juan E.)
   7. Re: Thalamic nuclei segmentation - PuM nucleus
  mis-segmentation? (Iglesias Gonzalez, Juan E.)


--

Message: 1
Date: Tue, 16 Feb 2021 21:58:34 +
From: Trisanna Sprung-Much 
Subject: Re: [Freesurfer] overlap/intersection of labels?
To: Freesurfer support list 
Message-ID: 
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Hi Cornelius

I found something that computes the overlap of labels across the same vertex 
when doing some research about this, not sure if this is what you mean:

https://secure-web.cisco.com/116MIwNJShgHoW9J9evPl5bCi0xgcx82bMJ48_l7VTkyo4rsX6beTdCfGCkpiAyjUuMFA31V5ClU95ErPkQPZP8TKRthymZKTmx9z4NZ-1Q_VMNlPzPJ7PZG4H-wntegGfigUm5R6ocjIe4fS6bL4_82SxATBarpW8b6rv_vC1VPBn1ZM4Hj4ld7D7l3hMWkgB8zNZaHVjFrDQM4so73Mk3cuFXo4uZfnmiBKYK9XTJlzfFP24H6-tsGIkT4ka-7BQxMKOmF6bzTYzRo0tE8HTg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_label2annot

See specifically:
--nhits

This option creates a diagnostic file showing whether the cumulative effect of 
all the label files happens to assign more than one label to each vertex. The 
output file is a 
FreeSurfer
 'overlay' format file, in which each vertex has an associated value, in this 
case the count of labels assigned to that vertex. This can be displayed in 
tksurfer as a color. Setting fthresh to 1.5 will distinguish good vertices 
(count<=1) from bad (count>=2).

I know there is also a command merge_labels that may help?

Best,

Trisanna Sprung-Much
Research Associate
McGill University
MD Anderson Cancer Centre
--


From:  on behalf of "Dr. Cornelius 
Kronlage" 
Reply-To: Freesurfer support list 
Date: Tuesday, February 16, 2021 at 11:19 AM
To: "'freesurfer@nmr.mgh.harvard.edu'" 
Subject: [Freesurfer] overlap/intersection of labels?


External Email - Use Caution

Dear freesurfers,



is there an elegant way of computing the intersection or overlap of different 
labels or - which would be even more useful for my application - annotations?



I only managed to find labels_intersect (which appears to be from MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 

Re: [Freesurfer] segmentation is shifted with respect to NIFTI T1W

[Roman Fleysher]

External Email - Use Caution

Thank you, Douglas. Then, fsroi as a work around is also right solution? I do 
not know what causes the issue: initial conversion of T1W from NIFTI to mgz, 
segmentation itself or transfer back to NIFTI. I do not know if other files 
(say brain mask) have the same issue. Looking into these.

Roman

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Tuesday, February 23, 2021 10:04 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] segmentation is shifted with respect to NIFTI T1W

Those commands look right

On 2/23/2021 9:27 AM, Roman Fleysher wrote:

External Email - Use Caution

Dear FreeSurfers,

I am working with version 6, starting point is T1W image in NIFTI format. I 
typically transform segmentations back to native space in NIFTI format to be 
able to use other software (FSL and such). I noticed that segmentation is 
shifted by 1 pixel in one axis (y-axis). Mapping of segmentation is a two step 
process based on description in:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://secure-web.cisco.com/1J1L3AyP2jHsP00pdcGHI5jDmBBow-gpkVjETS3XayfErJQhkWNxxPVtHY-0BDSxvCOEd8GHg4BRvJk7eOyqcgJpz9XwQhdQE8PkJLeX0K1rTO3mUyn8Sk8rman983yF-VqTKQE8AJAPURBDGpF_Qb1QDvcwHlj4eoGOJwF9u-XlATqjvcxeeYoC-T4fsNVFzCfOubJMR5jFdvWzCAIqoc0TBtfJ_abd4YjFUHOlkVlC9Py6szBX7yhUGWHSng9M1DCW7ra7PKAQhhEXYVQL1Rg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat


Specific commands are (schematically) :

# realign to original MGZ

mri_label2vol --seg inputSegmentationInMGZ --temp mri/orig/001.mgz --o 
outputSegmentationInOrigMGZ --regheader inputSegmentationInMGZ


# convert to NIFTI (*.nii.gz)

mri_convert --in_type mgz --out_type nii outputSegmentationInOrigMGZ 
outputSegmentationInOrigNIFTI.nii.gz

Are these steps correct? I can shift NIFTI by one pixel using fslroi, but I 
want to be sure nothing else is happening and that this shift is the correct 
work around.

Thank you,

Roman





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Re: [Freesurfer] segmentation is shifted with respect to NIFTI T1W

[Douglas N. Greve]

Those commands look right

On 2/23/2021 9:27 AM, Roman Fleysher wrote:


External Email - Use Caution

Dear FreeSurfers,

I am working with version 6, starting point is T1W image in NIFTI 
format. I typically transform segmentations back to native space in 
NIFTI format to be able to use other software (FSL and such). I 
noticed that segmentation is shifted by 1 pixel in one axis (y-axis). 
Mapping of segmentation is a two step process based on description in:


*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat 




Specific commands are (schematically) :

# realign to original MGZ

mri_label2vol --seg inputSegmentationInMGZ --temp mri/orig/001.mgz --o 
outputSegmentationInOrigMGZ --regheader inputSegmentationInMGZ



# convert to NIFTI (*.nii.gz)

mri_convert --in_type mgz --out_type nii outputSegmentationInOrigMGZ 
outputSegmentationInOrigNIFTI.nii.gz


Are these steps correct? I can shift NIFTI by one pixel using fslroi, 
but I want to be sure nothing else is happening and that this shift is 
the correct work around.


Thank you,

Roman



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[Freesurfer] segmentation is shifted with respect to NIFTI T1W

[Roman Fleysher]

External Email - Use Caution

Dear FreeSurfers,

I am working with version 6, starting point is T1W image in NIFTI format. I 
typically transform segmentations back to native space in NIFTI format to be 
able to use other software (FSL and such). I noticed that segmentation is 
shifted by 1 pixel in one axis (y-axis). Mapping of segmentation is a two step 
process based on description in:

http://secure-web.cisco.com/1OQ80xn8YGeWjUO2KyO4RDGDpL87LZ0EBpX6Z7_yDHTAQnUvI_i-ZbX3oYGnWNGBEv3FGrWEfu7Q0-EGZNpUg5oWefQhW2PyflL-E_EDawtfFyF3JoxX9ejxMQcJ_IO4g-glHmBjogdC6b5ZDBj12aMiOPktjP3Q4et2CD9zxjZvyHw4RmulypFF1W7xr921ryGHf1Xcg23EWcl4SQf5PZRnflYvp9NMjHufQ237e-27rWqRrlssP2RVE8NKaUYSS1jXZXdgg9PzheIilaEj7MQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnat


Specific commands are (schematically) :

# realign to original MGZ

mri_label2vol --seg inputSegmentationInMGZ --temp mri/orig/001.mgz --o 
outputSegmentationInOrigMGZ --regheader inputSegmentationInMGZ


# convert to NIFTI (*.nii.gz)

mri_convert --in_type mgz --out_type nii outputSegmentationInOrigMGZ 
outputSegmentationInOrigNIFTI.nii.gz

Are these steps correct? I can shift NIFTI by one pixel using fslroi, but I 
want to be sure nothing else is happening and that this shift is the correct 
work around.

Thank you,

Roman


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Re: [Freesurfer] mri_glmfit dependent variable

[Douglas N. Greve]

Model 2 is the only one we have the ability to fit. Model 1 would need 
some kind of machine learning method


On 2/23/2021 12:37 AM, miracle ozzoude wrote:


External Email - Use Caution

Hello Experts,

I've a question about mri_glmfit. I want to investigate the 
association between thickness and neuropsychiatric syndromes, 
controlling for age and cognition. Which model below is mri_glmfit 
performing?


Model 1
neuropsych syndromes ~ age + cognition + cortical thickness
or
Model 2
cortical thickness ~ age + cognition + neuropsych syndrome

Many thanks,
Paul

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Re: [Freesurfer] problems about freesurfer7 with T2pial flag

[Douglas N. Greve]

That appears to be a bug in 7.1.1. As long as the surfaces are ok, you 
don't need to worry.


On 2/22/2021 11:57 PM, Yijun Chen wrote:


External Email - Use Caution

Hi freesurfer experts:

I encountered a problem about freesurfer 7 with the T2pial flag.
when I use the freesurfer 6 — recon-all -all -i -s -T2 -T2pial, the resulting 
T2.mgz is skull-stripped.
however, when I switch to the freesurfer 7, the resulting T2.mgz is with skull.
Is there anything wrong?

Thanks,

Yijun.

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Re: [Freesurfer] rerunning FS 7.1.1 after brainmask.mgz edits

[Douglas N. Greve]

Yes, that is right. Not sure whether the time stamp thing will cause a 
problem. Mostly, we don't look at time stamps, but some parts do. When 
you make a copy, you can include the -p flag when running cp and it will 
preserve time stamps (and permissions)


On 2/22/2021 4:58 PM, Alexopoulos, Dimitrios wrote:


External Email - Use Caution

Thnaks. Some of the data may have been copied from different places so 
I’m concerned the time stamps might not be accurate which is why I’d 
prefer to run from scratch using *recon-all -s -i  -hires –all*


**

Nothing else is needed, correct? Only FS output from the original run 
with the new/revised  brainmask.mgz.


Jim

**

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Douglas N. Greve

*Sent:* Friday, February 19, 2021 9:23 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] rerunning FS 7.1.1 after brainmask.mgz edits

** External Email - Caution **

That is fine. You could save a few min by not starting from scratch, 
but the brainmasking happens very close to the beginning.


On 2/17/2021 3:57 PM, Alexopoulos, Dimitrios wrote:

*External Email - Use Caution *

Hi,

We are finding that the skull-stripping  in standard  FS 7.1.1. in
a few of our 3yo subjects is  a little aggressive and  is removing
brain from the brainmask primarily in the occipital pole region.
We decided to use the “cloning to T1 method”,  using  the Recon
Edit tool in Freeview for adding brain back to the brainmask.mgz.

Once the revised brainmask.mgz is re-saved with the same file
name, what command needs to be run to regenerated the entire pipeline?

We originally ran: *recon-all -s -i  -hires –all*

**

Do we run the same command again or should  we use: r*econ-all –s
–make –hires all***

**

Thanks.

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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Re: [Freesurfer] WM volume

[Douglas N. Greve]

Yes, that is the right value. We changed the name of it in more recent 
versions to CerebralWhiteMatter


On 2/22/2021 4:12 PM, Barletta, Valeria wrote:

Dear Freesurfers,
In what file inside the patient_name/stats folder do I find the total 
white matter volume?
In the file "aseg.stats" there is something called lh/rh "cortical 
white matter volume", is that the right value to look at?


Thank you,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823

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Re: [Freesurfer] FDR correction for statistical maps in Freeview?

[Douglas N. Greve]

There is nothing interactive. You can use mri_fdr. It will compute the 
threshold, which you can then use in freeview. It will also do the 
thresholding for you.


On 2/22/2021 9:25 AM, Hannah Eichhorn wrote:


External Email - Use Caution

Dear all,

I am using glmfit to analyse changes in cortical thickness, but I 
couldn't find a description on how to perform FDR correction with 
FreeSurfer.


Is there a way to perform FDR correction of the statistical maps in 
Freeview, analogous to how it is described for tksurfer in this 
tutorial: *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization 
?


Thank you very much for your help!

Best regards,

Hannah


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Re: [Freesurfer] Creating a .gcs custom atlas from nifti file for cortical parcellation

[Douglas N. Greve]

depends on the nature of AICHA. Are these labels on a group of subjects? 
If so, you can build your own gcs file with train-gcs-atlas.
If it is just a label set, then you should run recon-all on the template 
subject, sample the labels onto the surface (mri_vol2surf), then convert 
the resulting surface segmentation to an annotation (mris_seg2annot), 
then map the annot to other subjects with mris_apply_reg


On 2/22/2021 8:59 AM, THIBEAU SUTRE Elina wrote:


External Email - Use Caution

Hello freesurfer experts,

I would like to use freesurfer recon-all to obtain the regional 
cortical thicknesses of subjects of ADNI dataset. I launched 
freesurfer recon-all and obtained the parcellations according 
to Destrieux and Desikan-Killiany atlases. I would like to know how to 
obtain the same parcellations with another atlas, AICHA (*MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be* https://www.gin.cnrs.fr/en/tools/aicha/ 
), 
which is only available in nifti format.


I understood that I should create a .gcs file from the nifti version 
but I am not sure how. I saw that mris_ca_train could be used to 
create such a file from a a manually labelled dataset but I don’t know 
how to create these labelled subjects from the nifti atlas.


If anyone has already this kind of conversion .nii -> .gcs I would be 
really interested to know how you have done that!


Best regards,
Elina

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Re: [Freesurfer] Sulcal probability maps

[Douglas N. Greve]

what do you mean by painted? Do you mean you drew them on there using 
FreeView?


On 2/19/2021 11:37 AM, Kristi Drudik wrote:


External Email - Use Caution

Hi Doug,

The sulci are .label format because they were painted directly on the 
surface using FreeSurfer 7.1.


Best,

Kristi

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Douglas N. Greve

*Sent:* February 19, 2021 10:16 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Sulcal probability maps

What format is your sulcus in?

On 2/16/2021 2:38 PM, Kristi Drudik wrote:

*External Email - Use Caution *

Good afternoon,

I hope this email finds you well.

I am in the process of “painting” MRI surfaces from the Human
connectome project in FreeSurfer, meaning creating labels on the
surfaces to analyze sulcal morphology. We are interested in the
spatial variability of the sulcus and thus, want to create surface
spatial probability maps using FreeSurfer (*please see attachment
for an example of such surface probability maps*). These maps
would represent the likelihood of each vertex on the FreeSurfer
fsaverage surface belonging to the sulcus of interest (from 0% to
100%).

To obtain these probability maps, I:

 1. Painted the sulcus of interest on the surface by creating a
.label file.
 2. Registered this .label file to fsaverage (mri_label2label)
 3. Converted the .label file to vol (mri_label2vol)
 4. Converted it to a surface file (mri_vol2surf)
 5. Concatenated the data to create an average (mri_concat --mean)
 6. Blurred the data and loaded the blurred average as an overlay
onto the fsaverage pial (mris_fwhm)

Because this seems very convoluted, my question becomes*_: Is
there a more direct way to generate these maps from the labels
themselves, rather than going from label to vol, then back to surf? _*

Finally, I would like these maps to represent a 0-100% range of
each vertex in fsaverage belonging to the sulcus of interest.
However, this method creates a 0-1 range (please see colour bar in
attachment). *_Is there a way to change this to a percentage?_*

Thank you very much for your time and help. Please let me know if
you have any questions.

Best,
Kristi

**

*Kristi Drudik *

Ph.D. Student, Clinical Psychology

Montreal Neurological Institute

McGill University

Montreal, Canada



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Re: [Freesurfer] Question about statistical data for cerebellar segmentation ?

[Douglas N. Greve]

You will need to run mri_segstats on the output segmentation for each 
subject, like

mri_segstats --seg seg.mgz --sum sum.subject.dat --ctab colortable.dat
Then run asegstats2table passing al lthe sum.subject.dat files (run with 
--help to see how)
The only problem will be to get the proper color table for use with 
mri_segstats. You can run it without --ctab, but you won't get the names 
of the labels. The colortable needs to be formatted like 
$FREESURFER_HOME/FreeSurferColorLUT.txt


On 2/19/2021 8:58 AM, Viktor-Jan De Deken wrote:


External Email - Use Caution

Hi Freesurfer

I would like to perform statistical analesys on cerebellar 
segmentation data.
For my purposes, The atlases that come with Freesurfer don't give 
enoughparcellation of the cerebellum.
I tried looking online and found this email conversation: *MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be* 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65121.html 

I applied this and it worked visually but I want statistical data like 
in the aseg.stats or aparc.stats files.


Can you help me?

Kind regards
Viktor-Jan

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Re: [Freesurfer] recon-all error: No such file or directory

[Douglas N. Greve]

My guess is that the problem is the spaces in the folder name. Try 
removing those spaces and see if it works


On 2/18/2021 7:29 PM, Eduardo Bergonzoni Junqueira wrote:


External Email - Use Caution

Running the command in another directory I got another error:

(base) eduardo@eduardo-X555UB:/usr/local/freesurfer/subjects$ 
recon-all -i /home/eduardo/Área\ de\ 
Trabalho/Grant_Tractography/t1.nii.gz -s Grant_sub -all

Traceback (most recent call last):
  File "/usr/local/freesurfer/python/scripts/rca-config", line 137, in 


    file.write(arg + '\n')
UnicodeEncodeError: 'ascii' codec can't encode character '\udcc1' in 
position 14: ordinal not in range(128)

ERROR: could not configure recon-all parameters

On Thu, Feb 18, 2021 at 9:20 PM Eduardo Bergonzoni Junqueira 
mailto:dubergonz...@usp.br>> wrote:


Hello FreeSurfer Developers,

I'm attempting to preprocesss a t1.nii.gz image in freesurfer with 
recon-all. I'm following the tutorial for linux in*MailScanner has detected a 
possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall  
.

(base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ export 
FREESURFER_HOME=/usr/local/freesurfer
(base) eduardo@eduardo-X555UB:~/Área de Trabalho/Grant_Tractography$ . 
$FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
FSL_DIR           /home/eduardo/fsl

I'm getting the following error when I run the command:

(base) eduardo@eduardo-X555UB:~/Área de
Trabalho/Grant_Tractography$ recon-all -s Grant_sub -i t1.nii.gz -all

   ERROR:

/home/eduardo/\301rea de Trabalho/Grant_Tractography: No such file or 
directory.

This error is strange for me. I don't know why it is showing
"\301rea de Trabalho/" if the correct name of the directory is
"Área de Trabalho". The t1.nii.gz is in the path directory I'm using in the 
terminal.

Please, can anybody help how to fix this bug? I've looked for similar bug 
reports. Probably it is something simple, but I couln't found how to solve the 
problem.

1) FreeSurfer version:
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 2)
Platform: Ubuntu 20.04.1 3) uname -a: Linux eduardo-X555UB
5.8.0-43-generic #49~20.04.1-Ubuntu SMP Fri Feb 5 09:57:56 UTC
2021 x86_64 x86_64 x86_64 GNU/Linux

Best regards


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Re: [Freesurfer] Brain normalisation to intracranial volume

[Douglas N. Greve]

On 2/18/2021 3:25 PM, Carolina Rimkus wrote:


External Email - Use Caution

I would like to know which are the best ways to normalize the VOI's to 
intracranial volume.
It is a little controversial right now. Some will simply scale the 
volume by the eTIV, others will use eTIV as a regressor. I use the first 
method.


Also, what is the variable BrainSegVol-to-eTIV in aseg? Is it a 
scaling factor?
This is the ratio of the brain volume as measured by the segmentation to 
the eTIV. I originally meant it as a QA measure.


Does freesurfer segmentation provide a scaling factor?
The eTIV. If you are running asegstats2table, you can add --etiv and the 
output table will be the 10*vol/eTIV (ie, thousands of a percent of 
eTIV)


Best regards, Carolina

--
Carolina M Rimkus, MD, PhD
Neuroradiologist
Department of Radiology, Faculty of Medicine, University of São 
Paulo-SP, Brazil

email: carolina.rim...@usp.br 
carolina.rim...@gmail.com 

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Re: [Freesurfer] QDEC/mri_glmfit questions

[Douglas N. Greve]

It might be easiest to start with running the ROI values in mri_glmfit. 
How did you extract the ROI values for use in SPSS? You can use 
aparcstats2table to create a table, and then feed that table into
mri_glmfit --table table.dat --o glmdir

—fsgd inflammatory_markers.fsgd —C Inflammatory_group.mtx —C 
group_inflammatory.mtx

The sig output will be in glmdir/sig.table.dat (or something like that).
Oftentimes, SPSS and mri_glmfit will be using different design matrices.

On 2/18/2021 1:15 PM, Erin Moe wrote:
>  External Email - Use Caution
>
> Hi Freesurfer experts,
> I’ve been running mri_glmfit and QDEC to investigate the effect of 
> inflammatory markers on cortical thickness and don’t really get much. 
> However, when I extract the cortical thickness values (with 
> aparc/asegstats2table) and run a linear regression with those same 
> inflammatory markers in SPSS, I get several significant results. I’m assuming 
> it might be due to me setting up the QDEC/mri_glmfit analysis wrong.
>
> For QDEC I have a two column .dat file with the subject IDs in the FSID 
> column and the inflammatory markers for each participant in the other column 
> and running the QDEC thickness analysis on that and I don’t get much in terms 
> of results.
>
> For mri_glmfit I used an FSGD file set up just like the .dat file for QDEC 
> with the exception of formatting. However, we wanted to constrain the 
> analysis to an ROI (entorhinal in this case), I ran mris_preproc with the 
> following command:
> mris_preproc —fsgd inflammatory_markers.fsgd —cache-in 
> thickness.fwhm10.fsaverage —target fsaverage —hemi lh —out 
> lh.thickness.inflammatory.10.mgh
>
> Then fed that output into mri_glmfit as:
> mri_glmfit —y lh.thickness.inflammatory.10.mgh —fsgd 
> inflammatory_markers.fsgd —C Inflammatory_group.mtx —C group_inflammatory.mtx 
> —surf fsaverage —label entorhinal.label —glmdir 
> Inflammatory_entorhinal.lh.thickness.10.glmdir
> The results from this look the same as the QDEC analysis but just masked out 
> for the entorhinal ROI. So, to constrain the analysis to the ROI, I ran a 
> Monte Carlo correction with mri_surfcluster.
>
> So a few questions:
> Would running mri_surfcluster on the sig.mgh output from the mri_glmfit 
> analysis actually constrain the analysis to the ROI specified?
>
> How can I get my results to match that of what I’m seeing in SPSS?
>
> Is my analysis set up correctly for what I’m trying to do?
>
>
>
> Thank you in advance for your patience with this lengthy inquiry.
>
> Best,
> Erin
>
>
>
>
>
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