[Freesurfer] License issue

[Danny Deng]

Dear FDs,

According to the instructions, I have cut the 4 lines between the “CUT HERE”, 
copy and past the 4 lines into my license.txt file in the home directory to 
freesurfer folder as follow:

---
PART C. MISCELLANEOUS

This Agreement shall be governed by and construed in accordance with
the laws of The Commonwealth of Massachusetts without regard to
principles of conflicts of law. This Agreement shall supercede and
replace any license terms that you may have agreed to previously with
respect to FreeSurfer.

dannytang...@gmail.com
33367
*CL6BxmQcdv6k
FScW2..sWlD9c

However,when I tried to test my installation using the sample-001, it shows the 
error message as follow:

Xues-MacBook-Air:~ DannyDeng$ cp $FREESURFER_HOME/subjects/sample-001.mgz
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file
   cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... 
target_directory
Xues-MacBook-Air:~ DannyDeng$ mri_Convert sample-001.mgz sample-001.nii.gz
mri_convert.bin sample-001.mgz sample-001.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from sample-001.mgz...
--
ERROR: Invalid FreeSurfer license key found in license file 
/Applications/freesurfer/license.txt
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu/registration.html to 
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.
--
Xues-MacBook-Air:~ DannyDeng$ 


Please help. thanks


However
Best Regards,
Danny Deng

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Re: [Freesurfer] Helping with convert tool

[Bruce Fischl]

Hi Rosalia

you give a *single* one of your 192 .ima files to recon-all with the -i 
switch. It will figure out all the other files in your volume and process 
them. You could also give it a .nii.gz file as well, but in general we 
like to start with the dicoms if possible


cheers
Bruce
On Sun, 5 Nov 2017, Rosalia 
Dacosta Aguayo wrote:



Dear FreeSurfer list,

My name is Rosalia and this is the first time I post an email on your list. 

I have never run FreeSurfer before and I have a doubt regarding the converting 
process.

For every T1 folder, I have 192.ima files. I do not know how to pass from this 
point to .mgz. It seems that in
the tutorial you are speaking about converting one .dcm file to .mgz file. In 
my case, I have 192 .ima files and
I do not know how to pass them to one .dcm file and then to .mgz file. Even, I 
am not sure if I could work with
.nii.gz files instead of .mgz because I know that my .nii.gz files are well 
oriented but I do not know if my .mgz
files will have any orienting problem.

I would be more than grateful if you could kindly help me with this question.

Kind regards,
Rosalia

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Re: [Freesurfer] Question about Xhemi

[lanbo Wang]

Dear Douglas,

The comman line and terminal output show is this:
[mtobia@localhost subjects_results_symptom]$ mris_apply_reg --src
lh.map.mgh --trg lh.map.lh.fsaverage_sym.mgh \
> --streg $SUBJECTS_DIR/s02_base/surf/lh.fsaverage_sym.sphere.reg
$FREESURFER_HOME/subjects/fsaverage_sym/surf/lh.sphere.reg
ERROR: lh.map.mgh does not exist or is not readable by you

And also I have other 2 questions:
1) When I run left-right hemisphere paired t-test, can I add age as
covariate? If use fsgd to add covariate, to this paired t-test analysis,
how to make the fsgd table?
2) I want to reorganize the hemisphere from left-right to symptom-nosymptom
according to body symptom side record and compare different between symptom
hemisphere and nosymptom hemisphere. Can I use freesurfer to do it?

Thanks for your patient and help.

All best,
Lanbo Wang


On Sun, Nov 5, 2017 at 1:27 PM, Douglas Greve 
wrote:

> Can you send the command line you are using and the full terminal output?
>
> On 11/2/17 3:09 PM, lanbo Wang wrote:
>
> Dear Freesurfer experts,
>
> When I try run mris_apply_reg according to Xhemi:
> "the error is lh.map.mgh does not exist or is not readable by you"
> lh.map.mgh is made by which step?
>
> Thank you in advance.
>
> best,
> Lanbo
>
>
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>
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> 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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> properly
> dispose of the e-mail.
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Re: [Freesurfer] mris_apply_reg

[lanbo Wang]

Dear Mohamad,

You're right, after I use version 6.0, it works. Thanks for your help.

best,
Lanbo


On Fri, Nov 3, 2017 at 3:12 PM, Alshikho, Mohamad J. <
malshi...@mgh.harvard.edu> wrote:

> Hi Lanbo,
>
> You need Freesurfer 6 to run this command. The flag --src-label is not
> part of FS5.3
>
>
>
> Best,
>
> M_
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@
> nmr.mgh.harvard.edu] *On Behalf Of *lanbo Wang
> *Sent:* Friday, November 3, 2017 11:49 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] mris_apply_reg
>
>
>
> Dear Freesurfer experts,
>
> I try run this code according to Xhemi：
> mris_apply_reg --src-label label/rh.V1_exvivo.thresh.label --trg 
> rh-on-lh.V1_exvivo.thresh.label \
>
> --streg xhemi/surf/lh.fsaverage_sym.sphere.reg 
> surf/lh.fsaverage_sym.sphere.reg
>
> However, error shows: Option --src-label unknown. And also mris_apply_reg 
> --help didn't show how to correctly use -label.
>
> What's the correctly code.
>
> Thanks for your advices.
>
> Best,
>
> Lanbo
>
>
>
>
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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
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] Helping with convert tool

[Rosalia Dacosta Aguayo]

Dear FreeSurfer list,

My name is Rosalia and this is the first time I post an email on your list.

I have never run FreeSurfer before and I have a doubt regarding the
converting process.

For every T1 folder, I have 192.ima files. I do not know how to pass from
this point to .mgz. It seems that in the tutorial you are speaking about
converting one .dcm file to .mgz file. In my case, I have 192 .ima files
and I do not know how to pass them to one .dcm file and then to .mgz file.
Even, I am not sure if I could work with .nii.gz files instead of .mgz
because I know that my .nii.gz files are well oriented but I do not know if
my .mgz files will have any orienting problem.

I would be more than grateful if you could kindly help me with this
question.

Kind regards,
Rosalia
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Re: [Freesurfer] mask volume calculation

[Douglas Greve]

Look in the recon-all.log file for the command that generates the 
aseg.stats file. Use that command but change aseg.mgz to whatever your 
mask is (and change the output). Don't include the LUT on the command line.



On 11/1/17 10:24 PM, Ehsan Tadayon wrote:

Hello FS experts,

I'm trying to get the volume of a binary mask on orig.mgz. I know that 
FS uses a more sophisitcated approach than simply counting the number 
of voxels within the mask and I'd like to apply the same approach. Is 
there any way to get the volume for a defined mask with the same 
approach that FS computes the volumes for aseg.mgz?


thanks.
Ehsan



‌


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Re: [Freesurfer] Question about Xhemi

[Douglas Greve]

Can you send the command line you are using and the full terminal output?


On 11/2/17 3:09 PM, lanbo Wang wrote:

Dear Freesurfer experts,

When I try run mris_apply_reg according to Xhemi:
"the error is lh.map.mgh does not exist or is not readable by you"
lh.map.mgh is made by which step?

Thank you in advance.

best,
Lanbo


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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] bug report 2

[Douglas Greve]

try looking here to submit a bug report with information that we can use 
to help you


https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


On 11/5/17 8:17 AM, Danny Deng wrote:

Dear Freesurfer developers,

when I tried to perform example 3: perform a full recon-all on a 
preexisting subject folder


The error occurs as follow:

syntax error near unexpected token `newline’

I don’t know how to proceed further.

please help.

Thanks.

Best Regards,
Danny Deng


Begin forwarded message:

*From: *Danny Deng >

*Subject: **Fwd: bug report*
*Date: *November 5, 2017 at 9:08:54 PM GMT+8
*To: *freesurfer@nmr.mgh.harvard.edu 




Dear Freesurfer developers,

I encountered a problem when I tried to open the sample-001. with 
information as follow:


ERROR: Invalid FreeSurfer license key found in license file 
/Applications/freesurfer/license.txt

  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu/registration.html to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.

In fact I have already saved the license and directed from the 
desktop into my home directory.


Please help. thanks so much!


Best Regards,
Danny Deng


Best Regards,
Danny Deng


Begin forwarded message:

*From: *Danny Deng >

*Subject: **bug report*
*Date: *November 5, 2017 at 9:04:43 PM GMT+8
*To: *freesurfer@nmr.mgh.harvard.edu 



Dear Freesurfer developers,

I encountered a problem when I tried to open the sample-001. with 
information as follow:


ERROR: Invalid FreeSurfer license key found in license file 
/Applications/freesurfer/license.txt

  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu/registration.html to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.

In fact I have already saved the license and directed from the 
desktop into my home directory.


Please help. thanks so much!


Best Regards,
Danny Deng







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[Freesurfer] Local gyrification index - vertex-wise analysis values

[Buse Merve Ürgen]

Dear Freesurfer developers,

I would like to run Local Gyrification Index analysis for a group of
healthy controls and a single patient. After running  recon-all -s 
-localGI  command, we get lh.pial_lgi and rh.pial_lgi surf files. In the
last stage of this analysis, local gyrification index values are calculated
at each pial vertices.

In the wiki, it is said that the next process should be done in qdec, but
since I have only one patient, GLM analysis would not be suitable. Thus, I
would like to get the LGI values of each subject as e.g. text files (like
stats files for curvature, thickness, gm volume), and use them for my own
analysis (not in qdec). I know that we can get parcel-wise anaysis values
using this command:
mri_segstats --annot CASE lh aparc \

  --i $SUBJECTS_DIR/CASE/surf/lh.pial_lgi \

  --sum lh.aparc.pial_lgi.stats

But I would like to use vertex-wise analysis values for my won analysis. Is
it possible? Can I learn the command I need to use to get these values for
each subject?

Thank you,
Buse

-- 

Buse
​ Urgen
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[Freesurfer] Extracting lGI Values

[Nguyen, Tin]

Hello,

I am attempting to extract lGI values (i.e., similarly to *.stats in 
#SUBJ/stats) with the following (generic) command:

$mris_anatomical_stats –a aparc.annot –t pial_lgi –f 
#SUBJ/stats/lh.aparc_lgi.stats #SUBJ lh

However, this newly generated lh.aparc_lgi.stats is the exact same as the 
lh.aparc.stats, which is originally and readily in the /stats folder, and does 
not contain values for lGI. Thus, I cannot proceed with aparcstats2table to 
write and export the values.

I have read through this thread 
[https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-November/016339.html],
 but it did not seem to help since the demonstrated results were to out 
thickness.

Thank you for your assistance!

-Tin
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Re: [Freesurfer] Fwd: bug report

[Douglas Greve]

Do you have read permission to that file?


On 11/5/17 8:08 AM, Danny Deng wrote:

Dear Freesurfer developers,

I encountered a problem when I tried to open the sample-001. with 
information as follow:


ERROR: Invalid FreeSurfer license key found in license file 
/Applications/freesurfer/license.txt

If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu/registration.html to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.

In fact I have already saved the license and directed from the 
desktop into my home directory.


Please help. thanks so much!


Best Regards,
Danny Deng


Best Regards,
Danny Deng


Begin forwarded message:

*From: *Danny Deng >

*Subject: **bug report*
*Date: *November 5, 2017 at 9:04:43 PM GMT+8
*To: *freesurfer@nmr.mgh.harvard.edu 



Dear Freesurfer developers,

I encountered a problem when I tried to open the sample-001. with 
information as follow:


ERROR: Invalid FreeSurfer license key found in license file 
/Applications/freesurfer/license.txt

  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu/registration.html to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.

In fact I have already saved the license and directed from the 
desktop into my home directory.


Please help. thanks so much!


Best Regards,
Danny Deng





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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Trans. : VBM question

[Douglas Greve]

Do you just want to do an ROI analysis? Or do you want to do a 
voxel-based analysis? If ROI-based, then follow the steps on the ROI 
tutorial (ie, aparcstats2table and mri_glmfit with --table input).



On 11/3/17 4:08 PM, Bruce Fischl wrote:

Hi Mohamed

Doug is away this week and can give you a more details answer next 
week. Certainly you could use mris_anatomical_stats -l name> to compute the volume/thickness/area for each subject then do 
whatever GLM analysis you want outside of FS.


cheers
Bruce


 On Fri, 3 Nov 2017, m.ba...@uliege.be wrote:


Dear All,
Does anyone have an answer to the following VBM question?

Many thanks in advance,
Regards

-Mail original-
De: "Mohamed Ali Bahri" 
À: "Freesurfer support list" 
Envoyé: Jeudi, Novembre 2, 2017 06:08:33 PM
Objet: [Freesurfer] VBM question

Dear Freesurfer users,

I would like to study the between groups changes of volume/cortical
thickness of one region (Perirhinal) belonging to the Brodmann areas. I
tried to do that with Qdec tool but unfortunately Qdec does not load the
Brodmann areas stat list. I am wondering if I could use the GLM
formalism with of course regressing out the ITV. Any suggestion/advice
will be very welcome.

Many thanks in advance,

Best regards,

Mohamed





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[Freesurfer] bug report 2

[Danny Deng]

Dear Freesurfer developers,

when I tried to perform example 3: perform a full recon-all on a preexisting 
subject folder

The error occurs as follow:

syntax error near unexpected token `newline’

I don’t know how to proceed further.

please help.

Thanks.

Best Regards,
Danny Deng

> Begin forwarded message:
> 
> From: Danny Deng 
> Subject: Fwd: bug report
> Date: November 5, 2017 at 9:08:54 PM GMT+8
> To: freesurfer@nmr.mgh.harvard.edu
> 
>> Dear Freesurfer developers,
>> 
>> I encountered a problem when I tried to open the sample-001. with 
>> information as follow:
>> 
>> ERROR: Invalid FreeSurfer license key found in license file 
>> /Applications/freesurfer/license.txt
>>   If you are outside the NMR-Martinos Center,
>>   go to http://surfer.nmr.mgh.harvard.edu/registration.html 
>>  to 
>>   get a valid license file (it's free).
>>   If you are inside the NMR-Martinos Center,
>>   make sure to source the standard environment.
>> 
>> In fact I have already saved the license and directed from the desktop into 
>> my home directory.
>> 
>> Please help. thanks so much!
>> 
>> 
>> Best Regards,
>> Danny Deng
> 
> Best Regards,
> Danny Deng
> 
>> Begin forwarded message:
>> 
>> From: Danny Deng >
>> Subject: bug report
>> Date: November 5, 2017 at 9:04:43 PM GMT+8
>> To: freesurfer@nmr.mgh.harvard.edu 
>> 
>> Dear Freesurfer developers,
>> 
>> I encountered a problem when I tried to open the sample-001. with 
>> information as follow:
>> 
>> ERROR: Invalid FreeSurfer license key found in license file 
>> /Applications/freesurfer/license.txt
>>   If you are outside the NMR-Martinos Center,
>>   go to http://surfer.nmr.mgh.harvard.edu/registration.html 
>>  to 
>>   get a valid license file (it's free).
>>   If you are inside the NMR-Martinos Center,
>>   make sure to source the standard environment.
>> 
>> In fact I have already saved the license and directed from the desktop into 
>> my home directory.
>> 
>> Please help. thanks so much!
>> 
>> 
>> Best Regards,
>> Danny Deng
>> 
> 

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[Freesurfer] Fwd: bug report

[Danny Deng]

> Dear Freesurfer developers,
> 
> I encountered a problem when I tried to open the sample-001. with information 
> as follow:
> 
> ERROR: Invalid FreeSurfer license key found in license file 
> /Applications/freesurfer/license.txt
>   If you are outside the NMR-Martinos Center,
>   go to http://surfer.nmr.mgh.harvard.edu/registration.html 
>  to 
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
> 
> In fact I have already saved the license and directed from the desktop into 
> my home directory.
> 
> Please help. thanks so much!
> 
> 
> Best Regards,
> Danny Deng

Best Regards,
Danny Deng

> Begin forwarded message:
> 
> From: Danny Deng 
> Subject: bug report
> Date: November 5, 2017 at 9:04:43 PM GMT+8
> To: freesurfer@nmr.mgh.harvard.edu
> 
> Dear Freesurfer developers,
> 
> I encountered a problem when I tried to open the sample-001. with information 
> as follow:
> 
> ERROR: Invalid FreeSurfer license key found in license file 
> /Applications/freesurfer/license.txt
>   If you are outside the NMR-Martinos Center,
>   go to http://surfer.nmr.mgh.harvard.edu/registration.html 
>  to 
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
> 
> In fact I have already saved the license and directed from the desktop into 
> my home directory.
> 
> Please help. thanks so much!
> 
> 
> Best Regards,
> Danny Deng
> 

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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
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.