Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum

[UQAM]

Hi Zeke,

We tried the new version of mri_cc and we still do not get 12 segments of
the corpus callosum when we open the aseg.12segmentsCC.mgz in a viewer.

Could you send us the script you launch after the recon_all to get aseg.mgz
files with 12 segments? basically the mri_cc

Could you also please explain how to edit the ColorLut.txt file

Finally, what is the precise script of the mri_segstats to generate stats
tables.

Thanks again,

Cheers,
Genevieve

On Tue, Nov 24, 2015 at 11:20 PM, Z K  wrote:

> Hello Genevieve,
>
> Below is a link to the newest version of mri_cc. Please copy it to your
> FREESURFER_HOME directory and backup the original.
>
>   ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc
>
> Hope this help.
>
> -Zeke
>
>
> On 11/24/2015 05:56 AM, UQAM wrote:
>
>> Hi Bruce,
>>
>> DELL R910
>> Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores)
>> 32 Go RAM
>> CentOS release 5.10 (Final)
>> kernel 2.6.18-371.3.1.el5
>>
>> On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl
>> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>>
>> Hi Genevieve
>>
>> I just tracked this down and it is a bug in mri_cc. If you tell Zeke
>> your hardware/software environment he can get you a new version that
>> should work
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 23 Nov 2015, UQAM wrote:
>>
>> Hi Bruce,
>> Please find the two files attached.
>>
>> Genevieve
>>
>>
>>
>> On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl
>> mailto:fis...@nmr.mgh.harvard.edu>>
>>
>> wrote:
>>Hi Geneviève
>>
>>if you send us the $SUBJECTS_DIR/CColorLUT.txt and
>> $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a
>>look
>>
>>cheers
>>Bruce
>>On Mon, 23 Nov 2015, UQAM wrote:
>>
>>  Hi,
>>  This a a "re-posting" of a question I've raised
>> last week ; )
>>
>>  I would like to segment the corpus callosum
>> into twelve even lenght segments
>>  instead of the five segments that freesurfer
>> includes by default.
>>
>>  - First I ran a mri_cc on subject e0070:
>>
>>  mri_cc -aseg aseg.auto_noCCseg.mgz -o
>> aseg.12segmentsCC.mgz -d 12 e0070
>>
>>  - Then I edited the ColorLUT.txt file and renamed
>> it CColorLUT.txt (see
>>  attachment, segments 251 to 262).
>>
>>  - Finally I ran a mri_segstats to compute the
>> statistics on segmented
>>  volumes.
>>
>>  mri_segstats seg
>> $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab
>>  $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid
>> 0 sum
>>  --e0070_CC12.aseg.stats
>>
>>  The e0070_CC12.aseg.stats file still displays only
>> five segments of the
>>  corpus callosum.
>>
>>  Any tips or clues on how I could do things
>> differently to get 12 segments?
>>
>>  Thanks in advance,
>>
>>  Geneviève
>>
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>> to whom it is
>> addressed. If you believe this e-mail was sent to you in error
>> and the e-mail
>> contains patient information, please contact the Partners
>> Compliance HelpLine at
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>> sender and properly
>> dispose of the e-mail.
>>
>>
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>>
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>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
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>> you in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
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>>
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>> https://mail.nmr

[Freesurfer] Quality Check of Subcortical Segmentation

[Jurij Wiede]

   Hi,

 

I'm sitting on a bunch of data that requires quality control (QC). While there are several guidelines for skullstrip or gray/white matter segmentation QC, I couldn't find anything on subcortical QC. As far as I know freesurfer classifies the different structures probabilistically using a preexisting atlas. This makes it rather impossible to QC the segmentation purely based on intensity differences. 

So I was asking myself if there might be any additional possibility than to merely rate the quality of the subcortical segmentation by more or less subjectively comparing their forms with a hypothetical ideal form?


 

Thanks,

 

Jurij


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[Freesurfer] mris_pmake bilateral

[Silvia Desiree Thielemann]

Dear freesurfer experts,

I want to calculate the distance between two vertices which are  
located on different hemispheres. I was wondering how I could do this  
with mris_pmake because a hemisphere is required within the analysis.  
Is there any possibility to obtain the distance between a vertices on  
the right hemisphere and a vertices on the left hemisphere? I already  
streamed out the maximum activated voxels which are my start and end  
vertices.

Thanks in advance,
Desiree

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Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum

[Bruce Fischl]

Hi Genevieve

are you sure you are using the correct mri_cc? I used your command line 
and got 12 segments. How many segents do you get? It should generate 
segments numbered 230-241 I think. You'll need to make your own entries in 
the ColorLUT.txt file if you want to see them in prespecified colors and 
names and such


cheers
Bruce
On Fri, 27 Nov 2015, UQAM 
wrote:



Hi Zeke,
We tried the new version of mri_cc and we still do not get 12 segments of the 
corpus callosum when we open
the aseg.12segmentsCC.mgz in a viewer.

Could you send us the script you launch after the recon_all to get aseg.mgz 
files with 12 segments?
basically the mri_cc

Could you also please explain how to edit the ColorLut.txt file

Finally, what is the precise script of the mri_segstats to generate stats 
tables. 

Thanks again,

Cheers,
Genevieve

On Tue, Nov 24, 2015 at 11:20 PM, Z K  wrote:
  Hello Genevieve,

  Below is a link to the newest version of mri_cc. Please copy it to your 
FREESURFER_HOME
  directory and backup the original.

    ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc

  Hope this help.

  -Zeke


  On 11/24/2015 05:56 AM, UQAM wrote:
Hi Bruce,

DELL R910
Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores)
32 Go RAM
CentOS release 5.10 (Final)
kernel 2.6.18-371.3.1.el5

On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl
mailto:fis...@nmr.mgh.harvard.edu>> 
wrote:

    Hi Genevieve

    I just tracked this down and it is a bug in mri_cc. If you tell 
Zeke
    your hardware/software environment he can get you a new version 
that
    should work

    cheers
    Bruce


    On Mon, 23 Nov 2015, UQAM wrote:

        Hi Bruce,
        Please find the two files attached.

        Genevieve



        On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl
        mailto:fis...@nmr.mgh.harvard.edu>>
        wrote:
               Hi Geneviève

               if you send us the $SUBJECTS_DIR/CColorLUT.txt and
        $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will 
take a
               look

               cheers
               Bruce
               On Mon, 23 Nov 2015, UQAM wrote:

                     Hi,
                     This a a "re-posting" of a question I've raised
        last week ; )

                     I would like to segment the corpus callosum
        into twelve even lenght segments
                     instead of the five segments that freesurfer
        includes by default.

                     - First I ran a mri_cc on subject e0070:

                     mri_cc -aseg aseg.auto_noCCseg.mgz -o
        aseg.12segmentsCC.mgz -d 12 e0070

                     - Then I edited the ColorLUT.txt file and 
renamed
        it CColorLUT.txt (see
                     attachment, segments 251 to 262).

                     - Finally I ran a mri_segstats to compute the
        statistics on segmented
                     volumes.

                     mri_segstats seg
        $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab
                     $SUBJECTS_DIR/CColorLUT.txt --nonempty 
--excludeid
        0 sum
                     --e0070_CC12.aseg.stats

                     The e0070_CC12.aseg.stats file still displays 
only
        five segments of the
                     corpus callosum.

                     Any tips or clues on how I could do things
        differently to get 12 segments?

                     Thanks in advance,

                     Geneviève


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Re: [Freesurfer] Quality Check of Subcortical Segmentation

[Bruce Fischl]

Hi Jurij

no sorry, that sounds like a research project!

cheers
Bruce
On Fri, 27 Nov 2015, Jurij 
Wiede wrote:



   Hi,  
I'm sitting on a bunch of data that requires quality control (QC). While there 
are several guidelines for
skullstrip or gray/white matter segmentation QC, I couldn't find anything on 
subcortical QC. As far as I
know freesurfer classifies the different structures probabilistically using a 
preexisting atlas. This
makes it rather impossible to QC the segmentation purely based on intensity 
differences. 
So I was asking myself if there might be any additional possibility than to 
merely rate the quality of the
subcortical segmentation by more or less subjectively comparing their forms 
with a hypothetical ideal
form?
 
Thanks,
 
Jurij

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Re: [Freesurfer] report a bug

[Niels Bergsland]

Hi - sounds like it's running out of memory and getting killed. How much
RAM do you have?

On Thu, Nov 26, 2015 at 1:21 PM, salvatoreandrea...@libero.it <
salvatoreandrea...@libero.it> wrote:

> Hi!
> - I am using Ubuntu 14.4 (trusty).
>
> -  This is my subject directory: /home/salvatore/freesurfer/subjects
>
> - This is the output of *which recon-all *(that is the tool I am trying
> to use): /home/salvatore/freesurfer/bin/recon-all
>
> - The command line that I run is
>
> *recon-all -s /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis
> -i /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis/T1.nii.gz
> -all*Following the error that I got after 12 hours of processing:
>
>
> sysname  Linux
> hostname salvatore-HP-630-Notebook-PC
> machine  x86_64
>
> setenv SUBJECTS_DIR /home/salvatore/freesurfer/subjects
> cd /home/salvatore/freesurfer/subjects/FreeSurfer_analysis/mri
> mri_ca_label -align norm.mgz transforms/talairach.m3z
> /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca
> aseg.auto_noCCseg.mgz
>
> renormalizing sequences with structure alignment, equivalent to:
> -renormalize
> -renormalize_mean 0.500
> -regularize 0.500
> reading 1 input volumes...
> reading classifier array from
> /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca...
> reading input volume from norm.mgz...
> Killed
> Linux salvatore-HP-630-Notebook-PC 3.19.0-33-generic #38~14.04.1-Ubuntu
> SMP Fri Nov 6 18:17:28 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s FreeSurfer_analysis exited with ERRORS at gio 26 nov 2015,
> 12.42.40, CET
>
>
> Could you please help me to fix this problem? I tried to ran it again in
> an other terminal, without succeding...Thank you
>
>
> Best,
>
> Salvatore
>
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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>
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Re: [Freesurfer] ERROR: Invalid FreeSurfer license key

[Neda Mohammadi]

Hi Bruce,

I'm sure about it, but I get the error.

*Best Regards,*
*Neda*
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[Freesurfer] FSGD File Formatting Error

[Shady El Damaty]

Hi Freesurfers,

I'm having some issues running mri_glmfit using a simple custom GLM file.
I've double checked to make sure the subject session file passed to
isxconcat-sess is the same as the fsgd file and also checked the formatting
corresponds with what is posted online however I keep getting the same
error:

ERROR: gdfReadV1: Input line 1, subjid = A02217-w2

   Found 43 variables, expected. 1

FSGDF Format Error: file =
/Users/seldamat/Dropbox/Projects/ADS/data/ads.emostroop.marketing/new.exposure.fsgd,
tag=Input

ERROR: cannot find glm-exposure


​My fsgd file is attached.  Please any help would be greatly appreciated on
this time sensitive matter.

Thank you,
Shady​

On Thu, Nov 26, 2015 at 12:00 PM, 
wrote:

> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
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> or, via email, send a message with subject or body 'help' to
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>
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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. voxel value scaling (Rockers, Elijah D.)
>2. Re: voxel value scaling (Douglas Greve)
>3. Re: voxel value scaling (Rockers, Elijah D.)
>4. Re: Error - extracting percent signal (Douglas Greve)
>5. Re: bring volumes to fsaverage space (Andrew Bock)
>6. FS v.6.0 (Th?c Trinh)
>7. recon-all with more than 10 inputs (???)
>8. Re: Multiple comparisons to confirm atrophy (Anderson M. Winkler)
>9. report a bug (salvatoreandrea...@libero.it)
>
>
> --
>
> Message: 1
> Date: Wed, 25 Nov 2015 17:08:28 +
> From: "Rockers, Elijah D." 
> Subject: [Freesurfer] voxel value scaling
> To: Freesurfer support list 
> Message-ID: <5655eb0c.1000...@houstonmethodist.org>
> Content-Type: text/plain; charset="utf-8"
>
> I am interested in finding a way to apply a slope scaling factor to the
> voxel values in a NIfTI image.
>
> I have done this in MATLAB and PMOD so far, but for some reason both
> methods change the origin or otherwise distort the dimensions of the
> image and render it impossible for me to process further.
>
> Something that simply scales the values without touching the header (or
> at least as little as possible) would be great. Is anything like this
> out there?
>
> Thanks,
>
> Eli
>
> Houston Methodist. Leading Medicine.
>
> Ranked by U.S.News & World Report as one of America's "Best Hospitals" in
> 11 specialties. Named to FORTUNE? Magazine's "100 Best Companies to Work
> For?" list 10 years in a row. Designated as a Magnet hospital for
> excellence in nursing. Visit us at houstonmethodist.org. Follow us at
> twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.
>
> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston
> Methodist Hospital and/or its relevant affiliates and may contain
> restricted and privileged material for the sole use of the intended
> recipient(s). Any review, use, distribution or disclosure by others is
> strictly prohibited. If you are not the intended recipient (or authorized
> to receive for the recipient), please contact the sender and delete all
> copies of the message. Thank you.
>
>
>
> --
>
> Message: 2
> Date: Wed, 25 Nov 2015 12:54:23 -0500
> From: Douglas Greve 
> Subject: Re: [Freesurfer] voxel value scaling
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <5655f5cf.8050...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> You can use  fscalc, something like
> fscalc input.nii mul 10 -o output.nii
> I think you can use fslmaths as well
>
> On 11/25/15 12:08 PM, Rockers, Elijah D. wrote:
> > I am interested in finding a way to apply a slope scaling factor to the
> > voxel values in a NIfTI image.
> >
> > I have done this in MATLAB and PMOD so far, but for some reason both
> > methods change the origin or otherwise distort the dimensions of the
> > image and render it impossible for me to process further.
> >
> > Something that simply scales the values without touching the header (or
> > at least as little as possible) would be great. Is anything like this
> > out there?
> >
> > Thanks,
> >
> > Eli
> >
> > Houston Methodist. Leading Medicine.
> >
> > Ranked by U.S.News & World Report as one of America's "Best Hospitals"
> in 11 specialties. Named to FORTUNE? Magazine's "100 Best Companies to Work
> For?" list 10 years in a row. Designated as a Magnet hospital for
> excellence in nursing. Visit us at houstonmethodist.org. Follow us at
> twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist.
> >
> > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston
> Methodist Hospital and/or its rel

Re: [Freesurfer] FSGD File Formatting Error

[Douglas Greve]

looks like you created the fsgd file under windows? There are a bunch of 
carriage returns (look like ^M in the file). Try using a simple text 
editor under linux.



On 11/27/15 2:32 PM, Shady El Damaty wrote:

Hi Freesurfers,

I'm having some issues running mri_glmfit using a simple custom GLM 
file.  I've double checked to make sure the subject session file 
passed to isxconcat-sess is the same as the fsgd file and also checked 
the formatting corresponds with what is posted online however I keep 
getting the same error:


ERROR: gdfReadV1: Input line 1, subjid = A02217-w2

Found 43 variables, expected. 1

FSGDF Format Error: file = 
/Users/seldamat/Dropbox/Projects/ADS/data/ads.emostroop.marketing/new.exposure.fsgd, 
tag=Input


ERROR: cannot find glm-exposure



​My fsgd file is attached.  Please any help would be greatly 
appreciated on this time sensitive matter.


Thank you,
Shady​

On Thu, Nov 26, 2015 at 12:00 PM, 
> wrote:


Send Freesurfer mailing list submissions to
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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. voxel value scaling (Rockers, Elijah D.)
   2. Re: voxel value scaling (Douglas Greve)
   3. Re: voxel value scaling (Rockers, Elijah D.)
   4. Re: Error - extracting percent signal (Douglas Greve)
   5. Re: bring volumes to fsaverage space (Andrew Bock)
   6. FS v.6.0 (Th?c Trinh)
   7. recon-all with more than 10 inputs (???)
   8. Re: Multiple comparisons to confirm atrophy (Anderson M.
Winkler)
   9. report a bug (salvatoreandrea...@libero.it
)


--

Message: 1
Date: Wed, 25 Nov 2015 17:08:28 +
From: "Rockers, Elijah D." mailto:edrock...@houstonmethodist.org>>
Subject: [Freesurfer] voxel value scaling
To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: <5655eb0c.1000...@houstonmethodist.org
>
Content-Type: text/plain; charset="utf-8"

I am interested in finding a way to apply a slope scaling factor
to the
voxel values in a NIfTI image.

I have done this in MATLAB and PMOD so far, but for some reason both
methods change the origin or otherwise distort the dimensions of the
image and render it impossible for me to process further.

Something that simply scales the values without touching the
header (or
at least as little as possible) would be great. Is anything like this
out there?

Thanks,

Eli

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Message: 2
Date: Wed, 25 Nov 2015 12:54:23 -0500
From: Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] voxel value scaling
To: freesurfer@nmr.mgh.harvard.edu

Message-ID: <5655f5cf.8050...@nmr.mgh.harvard.edu
>
Content-Type: text/plain; charset=utf-8; format=flowed

You can use  fscalc, something like
fscalc input.nii mul 10 -o output.nii
I think you can use fslmaths as well

On 11/25/15 12:08 PM, Rockers, Elijah D. wrote:
> I am interested in finding a way to apply a slope scaling factor
to the
> voxel values in a NIfTI image.

[Freesurfer] Still unsure how to create my 3g4v matrix

[nellie]

Hi expert,
Thank you for your reply. I had read the example tables, but I'm still not sure 
how to alter them into my analysis.Can you help me to check the matrix I 
designed and point out my mistakes? Thanks in advence.
3 classes ( A / B / C group) and 4 variables (gender, age, education, and Moca 
test score). 
group.diff.mtx 1 -1 0  0 0 0   0 0 0   0 0 0   0 0 0 
group-x-gender.mtx 0 0 0   1 -1 0  0 0 0   0 0 0   0 0 0
group-x-age.mtx0 0 0   0 0 0   1 -1 0  0 0 0   0 0 0
group-x-education.mtx  0 0 0   0 0 0   0 0 0   1 -1 0  0 0 0
group-x-moca.mtx   0 0 0   0 0 0   0 0 0   0 0 0   1 -1 0
group-x-gender-x-age-x-education.mtx 
   0 0 0  1 -1 0  0 0 00 0 0   0 0 0 
   0 0 0  0 0 0   1 -1 0   0 0 0   0 0 0 
   0 0 0  0 0 0   0 0 01 -1 0  0 0 0 
group-x-gender-x-age-x-education-x-moca.mtx
   0 0 0  1 -1 0  0 0 00 0 0   0 0 0 
   0 0 0  0 0 0   1 -1 0   0 0 0   0 0 0
   0 0 0  0 0 0   0 0 01 -1 0  0 0 0
   0 0 0  0 0 0   0 0 00 0 0  1 -1 0
group.diff.mtx also can write as:   1 0 0  0 0 0   0 0 0   0 0 0   0 0 0  
  0 1 0  0 0 0   0 0 0   0 
0 0   0 0 0  
  0 0 1  0 0 0   0 0 0   0 
0 0   0 0 0  
group-x-age.mtx aslo can write as:  0 0 0  1 0 0  0 0 0   0 0 0   0 0 0   
 0 0 0  0 1 0  0 0 0   
0 0 0   0 0 0   
 0 0 0  0 0 1  0 0 0   
0 0 0   0 0 0   

.
Wishes,
Li


>
>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of Freesurfer digest..."
>
>
>Today's Topics:
>
>   1. Re: How to create a 3g4v matrix (Lee Tirrell)
>
>
>--
>
>Message: 1
>Date: Mon, 23 Nov 2015 10:27:42 -0500 (EST)
>From: Lee Tirrell 
>Subject: Re: [Freesurfer] How to create a 3g4v matrix
>To: Freesurfer support list 
>Message-ID:
>   
>Content-Type: text/plain; charset="iso-8859-7"
>
>Hi Li,
>
>You can find some example FSGD tables here, which you can alter to fit your 
>analyses.
>
>https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
>
>Best,
>Lee
>
>On Sun, 22 Nov 2015, nellie wrote:
>
>> 
>> Hi Freesurfer Experts,
>> 
>> I?m a new user of Freesurfer, and I learn how to use this software mainly 
>> through Wiki. When I came to the step of using GLM to compare group 
>> differences, I was confused on the design of 3g4v matrix. In my study, there 
>> were 3 classes (
>> A / B / C group) and 4 concomitant?variables (gender, age, education, and 
>> Moca test score). It?s supposed to be 15 regressors in this design, but I 
>> don?t know how to use the numbers (like 1, -1, 0, 0.5, -0.5, etc.) to create 
>> a correct 
>> matrix. I wonder if you could provide a 3g4v matrix in detail for me. I?ll 
>> be grateful if you can help. I hope I?m not bothering you too much, and I?m 
>> looking for your reply.
>> 
>> Best wishes,
>> 
>> Li?
>> 
>> 
>> 
>> ?
>> 
>> 
>>
>
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[Freesurfer] Sign option of Monte Carlo simulation in QDEC

[Karl Liu]

Dear experts:

 

In examining QDEC results of a contrast of interest, I
noticed the results are mainly in cold color (blue), with only two small
clusters in warm color (red). When I proceeded with Monte Carlo simulation, if
I chose the abs as the sign option in simulation, then no clusters survived. In
contrast, some clusters would remain, if I chose the neg sign. Because the
uncorrected results were mainly in cold color, it seems reasonable to me to use
negative only in the simulation. But I am wondering how the option of 
abs/neg/pos
leads to the disparities and will you please elaborate how the simulation works
based on abs/neg/pos. 

 

Thank you in advance.

 

Karl

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Re: [Freesurfer] ERROR: Invalid FreeSurfer license key

[zkaufman]

Hello Neda,

Hello Neda,

Can you please send me an email with a copy of your .license file as an
attachment? *Please send it to my direct email address* and not to the
Freesurfer support list. I will take a look and send you a valid license
file if necessary.

-Zeke



> Hi Bruce,
>
> I'm sure about it, but I get the error.
>
> *Best Regards,*
> *Neda*
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