[Freesurfer] license file not working

[Saemann Philipp]

Hello users or support team,

after using FS successfully for some time, now, after
a trivial command such as 

mri_convert -it analyze T1.img -ot mgz 001.mgz

an error appears as follows:

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from T1.img...
--
ERROR: Invalid FreeSurfer license key found in license file
/net/PE1/raid1/enigma-mdd/freesurfer/.license
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.
--

I re-applied for a license file which was the EXACT one I already had at
the specified location, and it still does produce the error message.

What makes this licence "invalid" here? Is there some problem with 
C-compiler versions? (though I would not this should appear right now)

Thanks for any ideas,
Philipp Saemann

Facharzt für Nervenheilkunde
Arbeitsgruppe Neuroimaging
Max-Planck-Institut für Psychiatrie
Kraepelinstr. 2-10
80804 Munich
Mail: saem...@mpipsykl.mpg.de
Phone: 0049-89-30622-413


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Re: [Freesurfer] license file not working

[Saemann Philipp]

Hello Douglas,

the file created on Linux, no Windows involved, and was 100% identical
to the old license file that was successfully used for some time.

Do I need a new download?

Thanks,
Philipp

At 16:14 01.08.2014 -0400, you wrote:
>
>not sure what is going wrong. How did you create the file? Make sure it 
>is a simple ascii text file not created under Windows
>
>
>On 08/01/2014 04:10 PM, Saemann Philipp wrote:
>> Hello users or support team,
>>
>> after using FS successfully for some time, now, after
>> a trivial command such as
>>
>> mri_convert -it analyze T1.img -ot mgz 001.mgz
>>
>> an error appears as follows:
>>
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from T1.img...
>> --
>> ERROR: Invalid FreeSurfer license key found in license file
>> /net/PE1/raid1/enigma-mdd/freesurfer/.license
>>If you are outside the NMR-Martinos Center,
>>go to http://surfer.nmr.mgh.harvard.edu to
>>get a valid license file (it's free).
>>If you are inside the NMR-Martinos Center,
>>make sure to source the standard environment.
>> --
>>
>> I re-applied for a license file which was the EXACT one I already had at
>> the specified location, and it still does produce the error message.
>>
>> What makes this licence "invalid" here? Is there some problem with
>> C-compiler versions? (though I would not this should appear right now)
>>
>> Thanks for any ideas,
>> Philipp Saemann
>>
>> Facharzt für Nervenheilkunde
>> Arbeitsgruppe Neuroimaging
>> Max-Planck-Institut für Psychiatrie
>> Kraepelinstr. 2-10
>> 80804 Munich
>> Mail: saem...@mpipsykl.mpg.de
>> Phone: 0049-89-30622-413
>>
>>
>> ___
>> 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
>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>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.
>
>
>
Facharzt für Nervenheilkunde
Arbeitsgruppe Neuroimaging
Max-Planck-Institut für Psychiatrie
Kraepelinstr. 2-10
80804 Munich
Mail: saem...@mpipsykl.mpg.de
Phone: 0049-89-30622-413


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[Freesurfer] license file not working

[Saemann, Philipp]

External Email - Use Caution

Hi FreeSurfer specalists,


for some historical reconstruction I had to download an old FS5.3-Version,

on a Linux System, untarred etc. - it seems there was no .license = hidden 
license

file coming with the download, and no license.txt file.



I requested one (usual link) and received a license.txt file, and put that

into the FS home folder. When using the command mri_convert I get the

error message that an invalid License file is used.

Questions:


(1) Is a .license file (so, a hidden file) needed for itself or in addition?

(2) Why does a freshly delivered license.txt file not work?

(3) Any other solutions or ideas?



Bw,

Philipp
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Re: [Freesurfer] license file not working

[Saemann, Philipp]

External Email - Use Caution

Hi Andrew,


it works on the "frontend" of  our cluster:


NAME="Scientific Linux"
VERSION="7.9 (Nitrogen)"
ID="scientific"
ID_LIKE="rhel centos fedora"
VERSION_ID="7.9"
PRETTY_NAME="Scientific Linux 7.9 (Nitrogen)"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:scientificlinux:scientificlinux:7.9:GA"
HOME_URL="http://secure-web.cisco.com/1klnZRW4M4WW9ZVKaWotlbPIVMzmb4T29Qe_78f_eVmTDoUgcEiBiiw5Tlc63lzUMN--Y21kFEP_CCOGZhFevGautv0mNoXcqYUdmw3SsWi-iG94jmMauGXSIQGPNdxEmgsVTYPprF-6etRYZMIoyu4rYCK3FLWA4GhEUQmNBBN-0KsNddnKocuKicc7ztuKAIYGAmtAoJZGTnfDahGeSvq-KCO5jqKx9FB8U2W_v3jXsVuHbrLhAnRo42wMsXIMVFA0tUBOpYs919bxPfACPtQ/http%3A%2F%2Fwww.scientificlinux.org%2F%2F";
BUG_REPORT_URL="mailto:scientific-linux-de...@listserv.fnal.gov";
REDHAT_BUGZILLA_PRODUCT="Scientific Linux 7"
REDHAT_BUGZILLA_PRODUCT_VERSION=7.9
REDHAT_SUPPORT_PRODUCT="Scientific Linux"
REDHAT_SUPPORT_PRODUCT_VERSION="7.9"



But not any more on the nodes:

NAME="CentOS Linux"

VERSION="8"
ID="centos"
ID_LIKE="rhel fedora"
VERSION_ID="8"
PLATFORM_ID="platform:el8"
PRETTY_NAME="CentOS Linux 8"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:centos:centos:8"
HOME_URL="https://secure-web.cisco.com/155QFGor0BvTWlPUXIVYeBXT-03HZvvbL_y_LFA__5voZlqIklvV3A9iWM50dUr0CmmbnHh3aOye4TpK7jd3sjvBQO7C8SDg5EnqUHFugRNSwIICKvk5EPRFPrTuTxxXBIbG-dpy3h71VyDY3nLMJrdBQ57Lsb_FualDCAbM1J-w2_EfxHFLPPap6E3qDsFmwmprCUus6fZ9h6Wn5xHrRWK2F0oge7qjB9vnZuKx3JpCBSdVoyfWNwfcXVU5HdwsLB0T96aElwgy2MDb06sul3w/https%3A%2F%2Fcentos.org%2F";
BUG_REPORT_URL="https://secure-web.cisco.com/1-z9ny04ggwstoxf8wX8eOhQDvv5yOR_STzc_48_IynJfMZzrYIuUG60St8GdD3yjJCNTGWoYzmJ0DgbM21EDQe_ag0huuDf9MHiQqeQyuXKxI7ggayfubotvDh12nkF1GfeOwxEqKO0RblPhtT7xxRBq7BoAOAZ_gZ7g63-R3m2AeIIt3Dk-ZZGkVt_pZauvPldw2QSqZdtmdu5Js43pZumaajfNbrgXf4ufZ6WfLxZUS7f0vP4cD-eTrXo6jw80aDJDm1R24eDQyGdbicBKjA/https%3A%2F%2Fbugs.centos.org%2F";
CENTOS_MANTISBT_PROJECT="CentOS-8"
CENTOS_MANTISBT_PROJECT_VERSION="8"



Thanks in advance,

best,

Philipp




Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Hoopes, Andrew 

Gesendet: Montag, 15. März 2021 20:29
An: Freesurfer support list
Betreff: Re: [Freesurfer] license file not working


Hi Philipp,



Can you let us know the OS and version you’re running on? The license format 
was updated for v6. It should be backwards compatible, but it’s possible it’s 
not anymore on newer systems.



thanks

Andrew



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Saemann, Philipp 

Date: Monday, March 15, 2021 at 2:36 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] license file not working

External Email - Use Caution

Hi FreeSurfer specalists,



for some historical reconstruction I had to download an old FS5.3-Version,

on a Linux System, untarred etc. - it seems there was no .license = hidden 
license

file coming with the download, and no license.txt file.



I requested one (usual link) and received a license.txt file, and put that

into the FS home folder. When using the command mri_convert I get the

error message that an invalid License file is used.

Questions:



(1) Is a .license file (so, a hidden file) needed for itself or in addition?

(2) Why does a freshly delivered license.txt file not work?

(3) Any other solutions or ideas?



Bw,

Philipp
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Re: [Freesurfer] 2mm thick image for hippocampal segmentation.

[Saemann, Philipp]

External Email - Use Caution

Hi,


I try to answer but Eugenio may also add comments. Several points that are 
important:

- 1.5 Tesla and 1x1x1 mm3 are at the limit of what the algorithm can manage.

- Post-aquisition reslicing to a higher resolution does not really increase the 
information content. Internally the algorithm works at a much higher 
resolution, anyway.

- If possible, switch to 3 Tesla.

- If possible and this is a prospective study, add a coronal T2 image and use 
the bi-channel option. See papers of Iglesias et al. on this.

- What you could also do on a 1.5 T is acquire the T1WI double and average it 
after coregistration, this increases the SNR.

- Generally, isometric resolutions are good due to the symmetry, of course.

- Also on 1.5 T, you may go bit below 1 mm with good head immobilization, and a 
longer scanning time. BRAVO in general is a good T1 option.


Best,

Philipp



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Ramesh Babu 

Gesendet: Freitag, 2. April 2021 09:29
An: Freesurfer support list; Umesh Rurdrapatna
Betreff: Re: [Freesurfer] 2mm thick image for hippocampal segmentation.


External Email - Use Caution

Dear experts,
Sorry for reposting. I am expecting some response from experts, so that I can 
proceed with confidence.
For our project work, we are looking for hippocampal  and its subfield volumes. 
Using GE 1.5T scanner, we tried a 3D BRAVO sequence with 1x1x1 resolution, 
256x256x160 dimension with 8* flip angle which produced images with a lot of 
noise. Then we tried the same sequence with 1x1x2 resolution, and 256x256x80 
FOV, which produced a clean image without noise. When we reformatted the 
images, it produces 0.5x0.5x1 resolution with 512x512x172 dimension.

Is this sequence good for hippocampal volume estimation and subfield 
segmentation (also for whole-brain VBM analysis)?
Could you please suggest to me a correct sequence, if need to be changed?

Regards
Ramesh
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[Freesurfer] perl version needed for FS5.3

[Saemann, Philipp]

External Email - Use Caution

Hi all,


we have problems in launching the recon-all command of FS5.3 (needed for a 
reconstruction of old results):

during the nu_correct command various perl commands are called with a fix


#!/usr/bin/perl -w


The primary error is some "Can't used 'define(@Array)'.


A bit of search showed that this seems perl version issue. Up to versio 5.18 
this only seems to produce a warning,

but no fatal error.


On the respective node of our cluster we have installed another perl and call 
this module before,

so the "which perl" correctly points to that perl main function.


Still, errors appear, e. g. cannot locate MNI/Startup.pm, so obviously some 
packages are not correctly linked.


What is the Installation recommendation on a Linux 64 Bit System to maFS5.3 
compatible with the local perl?


Best,

Philipp

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[Freesurfer] addon question perl version needed for FS5.3

[Saemann, Philipp]

External Email - Use Caution

Hi all,


sorry for a short additional question on the same perl topic:


I found that the critical syntax of an "if(defined(@...)" has been omitted in 
FS6.0.


Where there other changes to the perl scripts in the subfolder "mni" or could 
they be exchanged by the mni folder of FS6.0 in order to avoid the break of the 
perl script due to a version problem?


Thanks for any hints,

Philipp



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Saemann, Philipp 

Gesendet: Montag, 12. April 2021 22:06
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] perl version needed for FS5.3


External Email - Use Caution

Hi all,


we have problems in launching the recon-all command of FS5.3 (needed for a 
reconstruction of old results):

during the nu_correct command various perl commands are called with a fix


#!/usr/bin/perl -w


The primary error is some "Can't used 'define(@Array)'.


A bit of search showed that this seems perl version issue. Up to versio 5.18 
this only seems to produce a warning,

but no fatal error.


On the respective node of our cluster we have installed another perl and call 
this module before,

so the "which perl" correctly points to that perl main function.


Still, errors appear, e. g. cannot locate MNI/Startup.pm, so obviously some 
packages are not correctly linked.


What is the Installation recommendation on a Linux 64 Bit System to maFS5.3 
compatible with the local perl?


Best,

Philipp

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Re: [Freesurfer] Use Hippocampal segmentation sub-nuclei on other brain softwares

[Saemann, Philipp]

External Email - Use Caution

Hi Gregorio,


you need to transform the *mgz output images accordingy to NIFTIs images. Here 
is some exemplary shell code for the left hemisphere - operating in a subject's 
mri folder, using the FS6.0 type of aggregation (if you used FS7.1, you might 
to adapt the v-snippet in the filename):



cd 

mkdir test

cp lh.hippoAmygLabels-T1.v21.FS60.mgz test/left_discreteLabels.mgz

cp nu.mgz test

cp aparc+aseg.mgz test

cd test

mri_convert --resample_type nearest --out_orientation RSA 
left_discreteLabels.mgz left_discreteLabels.nii.gz
mri_convert --resample_type nearest --out_orientation RSA aparc+aseg.mgz 
aparc+aseg.nii.gz
mri_convert --resample_type nearest --out_orientation RSA --reslice_like 
left_discreteLabels.mgz nu.mgz nu_left.nii.gz
mri_convert --resample_type nearest --out_orientation RSA --reslice_like 
left_discreteLabels.mgz aparc+aseg.mgz aparc+aseg_highres_L.nii.gz

Then try to overlay the nu_left.nii.gz with the left_discreteLabels.nii.gz in 
some viewer (e. g. MRICron, or freeview).
By extracting only the voxels with a specific regional code you could create 
masks for your analyses, letting aside
the problem of the usually very coarse fMRI resolution.

Best,
Philipp




Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Borghi, G. (Gregorio) 

Gesendet: Montag, 12. April 2021 19:23
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Use Hippocampal segmentation sub-nuclei on other brain 
softwares


External Email - Use Caution

Dear All,


I have been stuck on this issue for quite some time. What I am trying to do is 
running a segmentation on both amygdala and hippocampus, and then to look at 
the different activation of the segmented sub-fields of both structures during 
a social-emotional task. However, despite my efforts I have not been able to 
find a way for translating either the segmented output files  to bring them in 
a format that can be used by R, FSL, or SPM. Is there anyone who might have an 
answer on how to do that? Or is there a function in freesurfer that provides 
the list of voxel coordinates per volume for each hippocampal and amygdala 
subfields?


Kind regards,
Gregorio Borghi

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Re: [Freesurfer] Hippocampal Subfields

[Saemann, Philipp]

External Email - Use Caution

Hi Saurabh,


you have to run (and QC) recon-all before,


Best,

Philipp



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Jindal, Saurabh 

Gesendet: Donnerstag, 22. April 2021 20:55
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Hippocampal Subfields


External Email - Use Caution

Hi experts,

I am focusing on hippocampus for my work using subfield analysis on freesurfer 
7.1. Is there is way to run the container only for subfields or do we have to 
run recon_all on the subject first always? Thanks.

Saurabh
Postdoc Research Fellow


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Re: [Freesurfer] Hippocampal Subfields/ASEG

[Saemann, Philipp]

External Email - Use Caution

Hello Yiota,


the whole hippocampus value is a sum of all subregions except for the 
hippocampal fissure - best try to reproduce this in an example.


The recon-all pipeline also delivers a total hippocampal volume, but it is an 
entity/result of its own and produced independently of

the subfield segmentation. It indirectly also contains areas that in the 
subfield segmentation would go to the fissure.


There is several papers out that compared the two, generally the subfield based 
sum value is considered more reliable.


Best,

Philipp



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Panayiota Ventura 

Gesendet: Montag, 21. Juni 2021 21:27
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Hippocampal Subfields/ASEG


External Email - Use Caution

Hello,

I have a couple of questions concerning the hippocampal subfield extractions as 
well as the hippocampus extraction included in ASEG. I have looked around and 
tried to find as much information as possible about the two but I can't seem to 
find a clear answer. I'm hoping someone can help me out with this.

1. In the hippocampal subfields extraction, one of the labels is called "whole 
hippocampus". I would like to know what exactly is meant by that? In other 
words, what hippocampal regions are included in this "whole hippocampus" label?

2. The ASEG atlas also includes a hippocampus extraction. However this value is 
different from that of the hippocampal subfield extraction. What hippocampal 
regions are being included in this hippocampal extraction.

3. Which of the two would be a better estimate of hippocampal volume?

Thank you for your time and help!

Kind regards,

Yiota Ventura

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Re: [Freesurfer] Is ICV needed as a covariate if matched between groups

[Saemann, Philipp]

External Email - Use Caution

Hi Carly,


plus, if I may answer in addition, make sure that the ICV differences are 
checked with sex as covariate,

so that statement of yours is only valid, if analyzed also per sex separately, 
or with sex as covariate.


Next, you should also (once) test for ICV-by-Dgx effects, as you cannot know in 
advance, if the relationship

between ICV and local measures is the same.


Best,

Philipp Sämann



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Iglesias Gonzalez, Juan 
E. 
Gesendet: Montag, 8. Juli 2024 19:39
An: Freesurfer support list
Betreff: Re: [Freesurfer] Is ICV needed as a covariate if matched between groups


It’s always a good idea to divide the volumes by ICV (or add ICV as a 
regressor). This is very unlikely, but what if your controls happened to have 
smaller heads than your patients? For peace of mind, I’d correct by ICV.

Cheers,

/Eugenio



--

Juan Eugenio Iglesias

http://www.jeiglesias.com



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Carly McIntyre-Wood 

Date: Monday, July 8, 2024 at 12:06 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Is ICV needed as a covariate if matched between groups

External Email - Use Caution

Hi there,



I am investigating differences in hipp/amyg volume between a patient and HC 
sample and am wondering if there is any reason I would still need to include 
ICV as a covariate if the groups do not differ on ICV (p=.793).



Thanks so much,

Carly
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contains patient information, please contact the Mass General Brigham 
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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[Freesurfer] Question on mri_nu_correct for 3 Tesla data

[Saemann, Philipp]

External Email - Use Caution

Hi FreeSurfer specialists,


we have problems with a strong non-intensity in 3 Tesla data of GE (mainly 
temporal poles and occipital area).

We managed to rescue the occipital errors by a pre-Bias-field correction using 
SPM, but would of course try

to optimize this in recon-all itself.


When I open the recon-all scrip tin FS v7.1.1 I can find no difference in the 
parameters depending on if the

the flag "-3T" is set or not.


In both cases the parameters forwarded are:


--n 1 --proto-iters 1000 --distance 50


(in line 1536 and line 1540 of /bin/recon-all.)


 Could someone explain this?


What could be done (manual corrections etc. are obsolete due to the large 
sample size...) to improve the WM detection

in the temporolateral/polar area (subsequently cortex detection)? The brainmask 
looks okay; the ribbon.mgz shows the

cut off lateral parts of the cortex.


Thanks in advance for any hints,

Philipp

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