Re: [Freesurfer] make_average_subject error

[Douglas N. Greve]

When I look at the README, this is the contents. Are you looking at 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/README ?


Download make_average_subject and the platform-specific version of 
mri_aparc2aseg

from this directory and move them to your freesurfer bin directory via:

mv make_average_subject $FREESURFER_HOME/bin
mv mri_aparc2aseg.platform $FREESURFER_HOME/bin/mri_aparc2aseg
chmod +x $FREESURFER_HOME/bin/mri_aparc2aseg 
$FREESURFER_HOME/bin/make_average_subject


We currently do not have a mac build of mri_aparc2aseg, and we recommend
downloading the freesurfer dev release to resolve this issue.


On 4/6/2021 6:29 PM, Jordan Mullins wrote:


External Email - Use Caution

The patch (see text below) only directed me to replace a file in the 
freesurfer/gcc/lib directory, which I did. Do I also need to replace 
the make_average_subject and mri_aparc2aseg files in my freesurfer bin?


/To patch the existing 6.0.0 release you may need administrator 
privileges to do the following:/

/
/
/1) Remove your existing Freeview.app application bundle by sending it 
to the trash (and then emtying the trash)./
/   You can also do this from the terminal by cd'ing to the top level 
./freesurfer subdirectory and then doing,/

/   "rm -rf Freeview.app". /
/
/
/2) Copy the new Freeview.app.zip to where your old Freeview.app was 
located aund uncompress it (so it becomes/
/   the replacement Freeview.app in your current freesrufer 
installation)./

/
/
/3) Remove ./freesurfer/lib/gcc/lib/libgomp.1.dylib from your existing 
freesurfer installation./

/
/
/4) Copy the ./freesurfer/lib/gcc/lib/libgomp.1.dylib from the patch 
archive to /freesurfer/lib/gcc/lib in your current/

/   freesurfer installtion./
/
/
/5) Try running the Freeview.app and loading a volume with it./

On Mon, Apr 5, 2021 at 6:43 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


It looks like you are still using the old make_average_subject as
the time stamp is from Jan 19, 2017 (same for mri_aparc2aseg). Can
you confirm that those are really the patches?

On 3/29/2021 12:52 PM, Jordan Mullins wrote:


External Email - Use Caution

Hi Douglas,

Just following up on this. Thanks!

On Wed, Mar 17, 2021 at 6:12 PM Jordan Mullins
mailto:jordan.mull...@email.ucr.edu>> wrote:

Yes! Results attached.

On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:


Can you run
ls -l $FREESURFER_HOME/bin/mri_aparc2aseg
$FREESURFER_HOME/bin/make_average_subject
and send the result?

Also, the result of
which mri_aparc2aseg
which make_average_subject



On 3/17/2021 8:36 PM, Jordan Mullins wrote:


External Email - Use Caution

Yes, I had seen that report and had downloaded the
patch, but still got the same error. Are there any other
steps I can take?

On Wed, Mar 17, 2021 at 2:59 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>
wrote:

This problem is documented (along with a fix) on our
release notes
*MailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes




On 3/16/2021 3:39 PM, Jordan Mullins wrote:


External Email - Use Caution

Yes, I used the make_average_subject command. I've
attached a text file below of the command line and
terminal output from my attempt to average two
subjects. I get the same error when I try this with
the full sample.

On Tue, Mar 16, 2021 at 9:12 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

What command are you using?
make_average_subject? Send the command line and
terminal output

On 3/10/2021 3:53 PM, Jordan Mullins wrote:


External Email - Use Caution

Hello,

I am trying to create an average subject from
a set of subjects, but keep getting an error
that says "mghRead(mri/norm.mgz, -1): could
not open file". I've read that several others
have solved this 

Re: [Freesurfer] make_average_subject error

[Jordan Mullins]

External Email - Use Caution

The patch (see text below) only directed me to replace a file in the
freesurfer/gcc/lib directory, which I did. Do I also need to replace the
make_average_subject and mri_aparc2aseg files in my freesurfer bin?

*To patch the existing 6.0.0 release you may need administrator privileges
to do the following:*

*1) Remove your existing Freeview.app application bundle by sending it to
the trash (and then emtying the trash).*
*   You can also do this from the terminal by cd'ing to the top level
./freesurfer subdirectory and then doing,*
*   "rm -rf Freeview.app". *

*2) Copy the new Freeview.app.zip to where your old Freeview.app was
located aund uncompress it (so it becomes*
*   the replacement Freeview.app in your current freesrufer installation).*

*3) Remove ./freesurfer/lib/gcc/lib/libgomp.1.dylib from your existing
freesurfer installation.*

*4) Copy the ./freesurfer/lib/gcc/lib/libgomp.1.dylib from the patch
archive to /freesurfer/lib/gcc/lib in your current*
*   freesurfer installtion.*

*5) Try running the Freeview.app and loading a volume with it.*

On Mon, Apr 5, 2021 at 6:43 AM Douglas N. Greve 
wrote:

> It looks like you are still using the old make_average_subject as the time
> stamp is from Jan 19, 2017 (same for mri_aparc2aseg). Can you confirm that
> those are really the patches?
>
> On 3/29/2021 12:52 PM, Jordan Mullins wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
> Just following up on this. Thanks!
>
> On Wed, Mar 17, 2021 at 6:12 PM Jordan Mullins <
> jordan.mull...@email.ucr.edu> wrote:
>
>> Yes! Results attached.
>>
>> On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve 
>> wrote:
>>
>>>
>>> Can you run
>>> ls -l $FREESURFER_HOME/bin/mri_aparc2aseg
>>> $FREESURFER_HOME/bin/make_average_subject
>>> and send the result?
>>>
>>> Also, the result of
>>> which mri_aparc2aseg
>>> which make_average_subject
>>>
>>>
>>>
>>> On 3/17/2021 8:36 PM, Jordan Mullins wrote:
>>>
>>> External Email - Use Caution
>>> Yes, I had seen that report and had downloaded the patch, but still got
>>> the same error. Are there any other steps I can take?
>>>
>>> On Wed, Mar 17, 2021 at 2:59 PM Douglas N. Greve 
>>> wrote:
>>>
 This problem is documented (along with a fix) on our release notes
 *MailScanner has detected a possible fraud attempt from
 "secure-web.cisco.com" claiming to be*
 https://secure-web.cisco.com/1YfLt6Uo2POilcp5VVpawd5Rf6iYNbRNnN5p7YWIrXFkgOYzSbUKXWvIkN4VpVQw_G7PRfTa5KGJR2BDD2zO3u9QtkFi3pMaNwBr8iStogzC4Y530jtsRbSvCu04x1CZqLvhJ6DP3nik5TffvKZwcn8dLKc9LptaVEOJ5CVS_qKCcovJHhhWY61DzjwbkYtpxDisIl7eR_04s3JDuj9d8xXPiqn5ffEV1q00I6rgImD3Y4goobWay4h91YA_L4oW8sGXLsfnUKq0X5WtCiWH_gQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
 


 On 3/16/2021 3:39 PM, Jordan Mullins wrote:

 External Email - Use Caution
 Yes, I used the make_average_subject command. I've attached a text file
 below of the command line and terminal output from my attempt to average
 two subjects. I get the same error when I try this with the full sample.

 On Tue, Mar 16, 2021 at 9:12 AM Douglas N. Greve <
 dgr...@mgh.harvard.edu> wrote:

> What command are you using? make_average_subject? Send the command
> line and terminal output
>
> On 3/10/2021 3:53 PM, Jordan Mullins wrote:
>
> External Email - Use Caution
> Hello,
>
> I am trying to create an average subject from a set of subjects, but
> keep getting an error that says "mghRead(mri/norm.mgz, -1): could not open
> file". I've read that several others have solved this issue by installing
> the patch available at *MailScanner has detected a possible fraud
> attempt from "secure-web.cisco.com" claiming to be*
> http://secure-web.cisco.com/1hZOnX5ZyoNBvuPdU7nwHA01_Q0xGjVvb4LN7phnE7_ESZ8rlXaERJDxY96UzmyuwC-RaiRyN5fUK56kcL4mnUlm5wRSpqUjYxJvn4e8mWUu-Cblpy06eO_7VgzY8yojF9sBrwaMsU5cnF5xojFZ3eMoKwywaYIwHhY_Inj5DsyRaUeR_Qc8Sbl0eMicp9bG2jt2Puz052S8D1yk3a_W51SNv0Q3rQ6VMjIgJrtuRldI1ELgyBFJRMM8RUUcNNxzPKhmC6n_vtnnpg2htaQi3Lg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F6.0.0-patch%2F
> .
> 

Re: [Freesurfer] make_average_subject error

[Douglas N. Greve]

It looks like you are still using the old make_average_subject as the 
time stamp is from Jan 19, 2017 (same for mri_aparc2aseg). Can you 
confirm that those are really the patches?


On 3/29/2021 12:52 PM, Jordan Mullins wrote:


External Email - Use Caution

Hi Douglas,

Just following up on this. Thanks!

On Wed, Mar 17, 2021 at 6:12 PM Jordan Mullins 
mailto:jordan.mull...@email.ucr.edu>> 
wrote:


Yes! Results attached.

On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:


Can you run
ls -l $FREESURFER_HOME/bin/mri_aparc2aseg
$FREESURFER_HOME/bin/make_average_subject
and send the result?

Also, the result of
which mri_aparc2aseg
which make_average_subject



On 3/17/2021 8:36 PM, Jordan Mullins wrote:


External Email - Use Caution

Yes, I had seen that report and had downloaded the patch, but
still got the same error. Are there any other steps I can take?

On Wed, Mar 17, 2021 at 2:59 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

This problem is documented (along with a fix) on our
release notes
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes




On 3/16/2021 3:39 PM, Jordan Mullins wrote:


External Email - Use Caution

Yes, I used the make_average_subject command. I've
attached a text file below of the command line and
terminal output from my attempt to average two subjects.
I get the same error when I try this with the full sample.

On Tue, Mar 16, 2021 at 9:12 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>>
wrote:

What command are you using? make_average_subject?
Send the command line and terminal output

On 3/10/2021 3:53 PM, Jordan Mullins wrote:


External Email - Use Caution

Hello,

I am trying to create an average subject from a set
of subjects, but keep getting an error that says
"mghRead(mri/norm.mgz, -1): could not open file".
I've read that several others have solved this
issue by installing the patch available at
*MailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be*

http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/

.
I did this, but continue to get the same error. I'm
working with Freesurver Version 6.0.0 and MacOS Big
Sur Version 11.2.3. I've attached the recon-all.log
below, but please let me know if you need
additional information.

Any insight on this would be appreciated! Thank you!

Jordan

-- 
*Jordan L. Mullins, B.A.*

Doctoral Student, Department of Psychology
University of California, Riverside
*MailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be*
http://ucrkindlab.com




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu  

*MailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 

Re: [Freesurfer] make_average_subject error

[Jordan Mullins]

External Email - Use Caution

Hi Douglas,

Just following up on this. Thanks!

On Wed, Mar 17, 2021 at 6:12 PM Jordan Mullins 
wrote:

> Yes! Results attached.
>
> On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve 
> wrote:
>
>>
>> Can you run
>> ls -l $FREESURFER_HOME/bin/mri_aparc2aseg
>> $FREESURFER_HOME/bin/make_average_subject
>> and send the result?
>>
>> Also, the result of
>> which mri_aparc2aseg
>> which make_average_subject
>>
>>
>>
>> On 3/17/2021 8:36 PM, Jordan Mullins wrote:
>>
>> External Email - Use Caution
>> Yes, I had seen that report and had downloaded the patch, but still got
>> the same error. Are there any other steps I can take?
>>
>> On Wed, Mar 17, 2021 at 2:59 PM Douglas N. Greve 
>> wrote:
>>
>>> This problem is documented (along with a fix) on our release notes
>>> *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1u1Z-uFR5fxuGqNlR5v1xrK8erCTHmH3u-GMZLm7k-SucWfLQ_ZGnDhkfR3eHFG2BYz4n4fFD_IphMenUgkeHN6_KDGkBXZKw2dD2lXqcIkrJNrRKqNsjFTAiDMC7-z4k6WGP8lSmOzdCyk7vG0ZpBli-I2mTyzQSi7j1Gj3tyHImeatyu_KS1BG54P2UK8RpEowofIba-HUt-sH0P0hjgD0r-L6Z3OxeZBCpegAPyCz8bmz_iKyyhZb4JD8npYtXZzE7pQmEt-icPsvs9i6fvQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
>>> 
>>>
>>>
>>> On 3/16/2021 3:39 PM, Jordan Mullins wrote:
>>>
>>> External Email - Use Caution
>>> Yes, I used the make_average_subject command. I've attached a text file
>>> below of the command line and terminal output from my attempt to average
>>> two subjects. I get the same error when I try this with the full sample.
>>>
>>> On Tue, Mar 16, 2021 at 9:12 AM Douglas N. Greve 
>>> wrote:
>>>
 What command are you using? make_average_subject? Send the command line
 and terminal output

 On 3/10/2021 3:53 PM, Jordan Mullins wrote:

 External Email - Use Caution
 Hello,

 I am trying to create an average subject from a set of subjects, but
 keep getting an error that says "mghRead(mri/norm.mgz, -1): could not open
 file". I've read that several others have solved this issue by installing
 the patch available at *MailScanner has detected a possible fraud
 attempt from "secure-web.cisco.com" claiming to be*
 http://secure-web.cisco.com/1PFeDAVc139N82htFQiJN3EfkbyA7F5UAzXWNALk8zD7J-ELJBX3mhFTTg1bjNL3feCaiBf4Qu3pMFMD4F8yiNEV4pVgA-MhL1o8NrZMbXzXcNCoBvyDEtQdE1FRVuC2FCurEQF9-QkjKoG52S5y2_sjizkwZRGzs78OOoWeWWXHHdqBPJb7yYYPnvtuylms-MFEz64YdzkufSjRrvgDt-DHvi_6E4nhZiR_8ckN1Eq0YjzIrTrmUmD9v_r_w47fQGF-2q1SEfF9cozdxI0nZAg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F6.0.0-patch%2F
 .
 I did this, but continue to get the same error. I'm working with Freesurver
 Version 6.0.0 and MacOS Big Sur Version 11.2.3. I've attached the
 recon-all.log below, but please let me know if you need additional
 information.

 Any insight on this would be appreciated! Thank you!

 Jordan

 --
 *Jordan L. Mullins, B.A.*
 Doctoral Student, Department of Psychology
 University of California, Riverside
 *MailScanner has detected a possible fraud attempt from
 "secure-web.cisco.com" claiming to be* 
 http://secure-web.cisco.com/1fpwAcAdfpPcgXwG26yDXqSP95kASeRHLMrJFeIUyDibUdqUVH2p0VRezzhwnATWC6T9xIybL_yMoJMsNYkzaaVhiVJdvQu1-4tRXyaLHYAOvnAYvGKVrX8cOnPzcAg5idnKgh43DE29cfOdy3c4LUI1r_TID4tgkTklyuy2ABBPRZ2zSpiirU0OI5NjaFLgnMDI_7ogEQ9p2DJ4NhEZz8pjoQRTmM3jYxd9v5Zi-6dvsU6pgZDmP-fTnealh-Gpw3Ga8ejexqF6eJ9hhYpEf2w/http%3A%2F%2Fucrkindlab.com
 


 ___
 Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
 detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
 be* 
 

Re: [Freesurfer] make_average_subject error

[Jordan Mullins]

External Email - Use Caution

Yes! Results attached.

On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve 
wrote:

>
> Can you run
> ls -l $FREESURFER_HOME/bin/mri_aparc2aseg
> $FREESURFER_HOME/bin/make_average_subject
> and send the result?
>
> Also, the result of
> which mri_aparc2aseg
> which make_average_subject
>
>
>
> On 3/17/2021 8:36 PM, Jordan Mullins wrote:
>
> External Email - Use Caution
> Yes, I had seen that report and had downloaded the patch, but still got
> the same error. Are there any other steps I can take?
>
> On Wed, Mar 17, 2021 at 2:59 PM Douglas N. Greve 
> wrote:
>
>> This problem is documented (along with a fix) on our release notes
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1edBCITcgawUIS-zRnC8VM1AIPGos4K5RQ9rL3tFPx3df0zWA9LCBvL1H4_DJHaFSciy7WmfebtvWLrHGcbubUnd0eIk0-MdxTwgHCWX0AO2eB9J4cHW6QQdHra1Mvp04M2Fx7sxpKkR8oUz8zACU2Kl9T8V_8FO5z_sEtSrkVBAPBuDF71EX-W93lChEOuYSWK41lRyAcD6gB5pqAkn-ZjWIEACCCjohHQ7_CgJLj0vu9EET6uyAb4sBTSYIxvvEkA3jmSfTATDHsXbMvlSMWQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
>> 
>>
>>
>> On 3/16/2021 3:39 PM, Jordan Mullins wrote:
>>
>> External Email - Use Caution
>> Yes, I used the make_average_subject command. I've attached a text file
>> below of the command line and terminal output from my attempt to average
>> two subjects. I get the same error when I try this with the full sample.
>>
>> On Tue, Mar 16, 2021 at 9:12 AM Douglas N. Greve 
>> wrote:
>>
>>> What command are you using? make_average_subject? Send the command line
>>> and terminal output
>>>
>>> On 3/10/2021 3:53 PM, Jordan Mullins wrote:
>>>
>>> External Email - Use Caution
>>> Hello,
>>>
>>> I am trying to create an average subject from a set of subjects, but
>>> keep getting an error that says "mghRead(mri/norm.mgz, -1): could not open
>>> file". I've read that several others have solved this issue by installing
>>> the patch available at *MailScanner has detected a possible fraud
>>> attempt from "secure-web.cisco.com" claiming to be*
>>> http://secure-web.cisco.com/1t8K97RYlziVlBgu38RYQs4VfxkUfG2F0ku1em0TQ5_1RFDkKaO70Tf-bbv-9bicog71dMMsOeEqFZOdRoXLLKGOKDFCEDkoYVV2b7HXEHVxBHFSRTeyAW2-8iCX0793SDVlup5S8DPrv_JIbUxMynp9-v7rnpZB-dEevY3NhJ3APFQTJ5DdOzd_RbNP5Ue0q2VKTL68vb7kDa2ZGDbiWHV7XrPQ24Z6Nh-4ImyhuKZ1O8yu1igETuDAdD62iBN5sllJ6dMRloPhWdy4xjz-f3w/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F6.0.0-patch%2F
>>> .
>>> I did this, but continue to get the same error. I'm working with Freesurver
>>> Version 6.0.0 and MacOS Big Sur Version 11.2.3. I've attached the
>>> recon-all.log below, but please let me know if you need additional
>>> information.
>>>
>>> Any insight on this would be appreciated! Thank you!
>>>
>>> Jordan
>>>
>>> --
>>> *Jordan L. Mullins, B.A.*
>>> Doctoral Student, Department of Psychology
>>> University of California, Riverside
>>> *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be* 
>>> http://secure-web.cisco.com/1dJju8r2CqbsF9UOo8NNjxFOt8vdI4bOA8cevVR_prTQIqLNel7W-Sh8dkakNDG7biWWkDbTV7bPsTwbUkKGnUzmqq6lVYZswG0Ga05gwqYA1LgTlixzJIYwDmOVdmRRl-P0nRFwnYRHIhX0tqQNfIDkuxyOriroB9kld2tQ41EwMxa1veWcRGrctIjIbpgmZ46GPNZzARpbc4T0nb6JGtIqp6X_NHTFSRFmski9mX6qfJriratIEOJzRQgaATRNhnpJy_-8-8llizmtmj2w0sA/http%3A%2F%2Fucrkindlab.com
>>> 
>>>
>>>
>>> ___
>>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>>> be* 
>>> 

Re: [Freesurfer] make_average_subject error

[Douglas N. Greve]

Can you run
ls -l $FREESURFER_HOME/bin/mri_aparc2aseg 
$FREESURFER_HOME/bin/make_average_subject

and send the result?

Also, the result of
which mri_aparc2aseg
which make_average_subject



On 3/17/2021 8:36 PM, Jordan Mullins wrote:


External Email - Use Caution

Yes, I had seen that report and had downloaded the patch, but still 
got the same error. Are there any other steps I can take?


On Wed, Mar 17, 2021 at 2:59 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


This problem is documented (along with a fix) on our release notes
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes




On 3/16/2021 3:39 PM, Jordan Mullins wrote:


External Email - Use Caution

Yes, I used the make_average_subject command. I've attached a
text file below of the command line and terminal output from my
attempt to average two subjects. I get the same error when I try
this with the full sample.

On Tue, Mar 16, 2021 at 9:12 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

What command are you using? make_average_subject? Send the
command line and terminal output

On 3/10/2021 3:53 PM, Jordan Mullins wrote:


External Email - Use Caution

Hello,

I am trying to create an average subject from a set of
subjects, but keep getting an error that says
"mghRead(mri/norm.mgz, -1): could not open file". I've read
that several others have solved this issue by installing the
patch available at *MailScanner has detected a possible
fraud attempt from "secure-web.cisco.com" claiming to be*
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/

.
I did this, but continue to get the same error. I'm working
with Freesurver Version 6.0.0 and MacOS Big Sur Version
11.2.3. I've attached the recon-all.log below, but please
let me know if you need additional information.

Any insight on this would be appreciated! Thank you!

Jordan

-- 
*Jordan L. Mullins, B.A.*

Doctoral Student, Department of Psychology
University of California, Riverside
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be* http://ucrkindlab.com




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu  
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  



___
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*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] make_average_subject error

[Jordan Mullins]

External Email - Use Caution

Yes, I had seen that report and had downloaded the patch, but still got the
same error. Are there any other steps I can take?

On Wed, Mar 17, 2021 at 2:59 PM Douglas N. Greve 
wrote:

> This problem is documented (along with a fix) on our release notes
> https://secure-web.cisco.com/1-guBCff1jWC1GKEt4a1kTf7-FWdC1pS-TRdvmtUoD4S5H1J9YevmGvFyfqiToxhlWyLk9yd2FL9ynWWyw9qrc4GMYipR_nQh2TsGzvrJem91qDSlnoJGUp3ytyyvEyT2e5q0-T2Fe_vnxBPOY0VICsRivaAxfyjEStvnGMVSnIqi0A2H-XZ1L8c6qkEpahiB8VCJNBXV1NivRiX6xTWyRasWhu0yxn3-RD6-RLySEjmUaCVHSjs3m1Zl3XCSNcbhISIuIENnF2bSSgZiJSOpGg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
>
>
> On 3/16/2021 3:39 PM, Jordan Mullins wrote:
>
> External Email - Use Caution
> Yes, I used the make_average_subject command. I've attached a text file
> below of the command line and terminal output from my attempt to average
> two subjects. I get the same error when I try this with the full sample.
>
> On Tue, Mar 16, 2021 at 9:12 AM Douglas N. Greve 
> wrote:
>
>> What command are you using? make_average_subject? Send the command line
>> and terminal output
>>
>> On 3/10/2021 3:53 PM, Jordan Mullins wrote:
>>
>> External Email - Use Caution
>> Hello,
>>
>> I am trying to create an average subject from a set of subjects, but keep
>> getting an error that says "mghRead(mri/norm.mgz, -1): could not open
>> file". I've read that several others have solved this issue by installing
>> the patch available at *MailScanner has detected a possible fraud
>> attempt from "secure-web.cisco.com" claiming to be*
>> http://secure-web.cisco.com/1NjUZjui5nJgDGrr9dhkxnEPaAXJL7_V_mzY5ft38QMMXIUNrwbt0hDfXpnNdIVw6YDNWKsYG29_xZzkXkG_IAio0_6ZDpw8VtjuSS4KBLsHH0buidZityVgEdSth1zZNSjiXLMGTwe1NPXXG7Yrywxpxml_iCMmexbT7IU-Aepmk4V_vww2HFW73PeIb29w0NOeTiyfdU446btUXEH52ORxpTWXrx-B71cYqlhr9RbJmHc5ADwB-cgONz2D6_waMLg8fnTJIPORQf5ktWFciLg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F6.0.0-patch%2F
>> .
>> I did this, but continue to get the same error. I'm working with Freesurver
>> Version 6.0.0 and MacOS Big Sur Version 11.2.3. I've attached the
>> recon-all.log below, but please let me know if you need additional
>> information.
>>
>> Any insight on this would be appreciated! Thank you!
>>
>> Jordan
>>
>> --
>> *Jordan L. Mullins, B.A.*
>> Doctoral Student, Department of Psychology
>> University of California, Riverside
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be* 
>> http://secure-web.cisco.com/1Hb5eBrObpHBXZQD2S7ILWEKBRwR7OK46HlRQPn5nJhb1RK-RjdWkJcRfRQ7GXWEg-inGg35_0zu6O99dGJj3Y8PD_juHovVy61Q0FdPx7DqeUdDfAzy_bx4T2i8AtjXYITBt1FTsolPdZrS1JpBSWgnGw-BigkMI1kVhbHJ6nXXolmhIlo9OSpWZpwiDnGkpJgvXuWSpE8G08RHw6izT-f7A09E9Xdfooja5o0AyNaUZ6JfixfKFSdx_Xtr5JP3Ge38Kd3xiqliWRnmLLhvInw/http%3A%2F%2Fucrkindlab.com
>> 
>>
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
>> https://secure-web.cisco.com/18ekJrFGSKJvrjW_N8XnUIHQ7WEdFV8flsrhGU5xVLbtdoDWAxlJAfeCO39Y_Y7SuZrm5gjV7YKn7QP-BYeoOGCzRp6i_wBOLTjPnCFpLjvlem7x58eSM_tr29537KEjV1db8pZthAkbaxjwjstfRnheTmWQrxmQoQ9qOUjSov2NeAQCi6YVEN-5f-s7Pj1BhccSCJe7ctnccQNr1n8HC30M1vQ04bsqqh9e6hznkkRFHmXsKHdCfsHaSr64SLAXTThxzbc5Hy3jCXnNbuTjE7Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>  
>> 
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> 

Re: [Freesurfer] make_average_subject error

[Douglas N. Greve]

This problem is documented (along with a fix) on our release notes
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes


On 3/16/2021 3:39 PM, Jordan Mullins wrote:


External Email - Use Caution

Yes, I used the make_average_subject command. I've attached a text 
file below of the command line and terminal output from my attempt to 
average two subjects. I get the same error when I try this with the 
full sample.


On Tue, Mar 16, 2021 at 9:12 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


What command are you using? make_average_subject? Send the command
line and terminal output

On 3/10/2021 3:53 PM, Jordan Mullins wrote:


External Email - Use Caution

Hello,

I am trying to create an average subject from a set of subjects,
but keep getting an error that says "mghRead(mri/norm.mgz, -1):
could not open file". I've read that several others have solved
this issue by installing the patch available at *MailScanner has
detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be*
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/

.
I did this, but continue to get the same error. I'm working with
Freesurver Version 6.0.0 and MacOS Big Sur Version 11.2.3. I've
attached the recon-all.log below, but please let me know if you
need additional information.

Any insight on this would be appreciated! Thank you!

Jordan

-- 
*Jordan L. Mullins, B.A.*

Doctoral Student, Department of Psychology
University of California, Riverside
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be* http://ucrkindlab.com




___
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*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  



___
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Freesurfer@nmr.mgh.harvard.edu 
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer





--
*Jordan L. Mullins, B.A.*
Doctoral Student, Department of Psychology
University of California, Riverside
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* http://ucrkindlab.com 




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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] make_average_subject error

[Douglas N. Greve]

What command are you using? make_average_subject? Send the command line 
and terminal output


On 3/10/2021 3:53 PM, Jordan Mullins wrote:


External Email - Use Caution

Hello,

I am trying to create an average subject from a set of subjects, but 
keep getting an error that says "mghRead(mri/norm.mgz, -1): could not 
open file". I've read that several others have solved this issue by 
installing the patch available at *MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to be* 
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ 
. 
I did this, but continue to get the same error. I'm working with 
Freesurver Version 6.0.0 and MacOS Big Sur Version 11.2.3. I've 
attached the recon-all.log below, but please let me know if you need 
additional information.


Any insight on this would be appreciated! Thank you!

Jordan

--
*Jordan L. Mullins, B.A.*
Doctoral Student, Department of Psychology
University of California, Riverside
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* http://ucrkindlab.com 




___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] make_average_subject error

[Jordan Mullins]

External Email - Use Caution

Hello,

I am trying to create an average subject from a set of subjects, but keep
getting an error that says "mghRead(mri/norm.mgz, -1): could not open
file". I've read that several others have solved this issue by installing
the patch available at
http://secure-web.cisco.com/1holHARxUGo27ZLvlj5vX0sbezsRgmRaNdE1T-Z728EASqGjdSamQfU6_udvX8lNDAGu6fMmZJqlcAAuJtuijJsAYfi7M55moSpWy1McHpeqmMGAqqWT-7M-IStYk9Qs2pOnTfoJznpdLsEgVASogVifdHzPfK1t3pQowp_WCXSDaaHhTDzz7qCl-DUbTHTPKKgBhR1NruBOW9_7sIsS86UbWXqE7CaL5hUOQNwrRGh4iX37y5CgC4I9HuJDYQNG_3fPAfLJmyVuWMB5QC4E_jw/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F6.0.0-patch%2F.
 I did
this, but continue to get the same error. I'm working with Freesurver
Version 6.0.0 and MacOS Big Sur Version 11.2.3. I've attached the
recon-all.log below, but please let me know if you need additional
information.

Any insight on this would be appreciated! Thank you!

Jordan

-- 
*Jordan L. Mullins, B.A.*
Doctoral Student, Department of Psychology
University of California, Riverside
http://secure-web.cisco.com/1mshZJHsrG2WjtWWNRNV7vunyA6LicMMo4DqXl-CgSaJWwHVpzdDUXsf8sRfvrwwkKf_KCQA4CYMRZs_am6IcPJO32Jd2eKl8shUDgQlOekTOscmE92Qtz70DWtJSOKxC8By5T4JuwEig2QC0e1ectPTPZjOGXa_t8ycn5bPjuoIWCqI8uXn86bmPqLVHkPzX-YRnSkCSbiIVsQ8zLNZ4ZNr58YvZl22BNeoGzuyye1eQfd_y4ENFJHQxgCNS7c9JXTBAX_N76Z_PQM9TFwvJPA/http%3A%2F%2Fucrkindlab.com


recon-all.log
Description: Binary data
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Re: [Freesurfer] make_average_subject error

[Maxime Perron]

External Email - Use Caution
Hi Andrew,


I am very sorry for the delay of my answer. 


Everything works with the patch. 


Thank you so much!


Cheers,
Maxime


On Oct 10, 2019, at 11:39 AM, Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote:




Hi Maxine,

 

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ contains
 executables and a README file that details how you can patch your freesurfer install to fix this issue.

 

best

Andrew

 

 


From: <freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Maxime Perron <maxime.perro...@ulaval.ca>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, September 6, 2019 at 5:08 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] make_average_subject error



 

External Email - Use Caution
​Hi Douglas, 
 
I'm sorry for the misunderstanding! Thanks for the command.
 
I attached the mas.log. 
 
Cheers,
Maxime 



​

 







De : freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
 de la part de Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu>
Envoyé : 6 septembre 2019 10:30
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] make_average_subject error


 




That is the recon-all.log file. What I want is the terminal output from make_average_subject
You can capture it with 
make_average_subject [your arguments] |& tee mas.log





On 9/4/2019 9:16 PM, Maxime Perron wrote:


    External Email - Use Caution    
 
Good evening Greve,
 
Thanks for your quick answer.
 
I attached the file containing the output.
 
Best,
Maxime 




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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 


On Sep 4, 2019, at 6:10 PM, Greve, Douglas N.,Ph.D.  wrote: 


Can you send the full text of the terminal output?
 
On 9/4/19 10:44 AM, Maxime Perron wrote:

    External Email - Use Caution
 
Hi Greve,
 
The exact script is the following :

 
setenv SUBJECTS_DIR /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data
 
make_average_subject --subjects "Freesurfer_S002" "Freesurfer_S003" "Freesurfer_S004" "Freesurfer_S014" "Freesurfer_S018_2" "Freesurfer_S020" "Freesurfer_S021" "Freesurfer_S023"  "Freesurfer_S024" "Freesurfer_S027" "Freesurfer_S029" "Freesurfer_S035" "Freesurfer_S037" "Freesurfer_S039" "Freesurfer_S040" "Freesurfer_S043" "Freesurfer_S044" "Freesurfer_S046" "Freesurfer_S048" "Freesurfer_S053" "Freesurfer_S060" "Freesurfer_S061" "Freesurfer_S064" "Freesurfer_S066" "Freesurfer_S068" "Freesurfer_S070" "Freesurfer_S071" "Freesurfer_S078" "Freesurfer_S083" "Freesurfer_S084" "Freesurfer_S088" "Freesurfer_S090" "Freesurfer_S093" "Freesurfer_S095" "Freesurfer_S103" "Freesurfer_S105" "Freesurfer_S106" "Freesurfer_S108" "Freesurfer_S110" "Freesurfer_S111" "Freesurfer_S113" "Freesurfer_S114" "Freesurfer_S115" "Freesurfer_S117" "Freesurfer_S118" "Freesurfer_S119" "Freesurfer_S120" "Freesurfer_S122" "Freesurfer_S123" "Freesurfer_S125" "Freesurfer_S126" "Freesurfer_S129" "Freesurfer_S130" "Freesurfer_S133" "Freesurfer_S134" "Freesurfer_S139" "Freesurfer_S141" "Freesurfer_S142" "Freesurfer_S144" "Freesurfer_S145" "Freesurfer_S146" "Freesurfer_S147" "Freesurfer_S148" "Freesurfer_S150" "Freesurfer_S151" "Freesurfer_S152" "Freesurfer_S153" "Freesurfer_S154" "Freesurfer_S155" "Freesurfer_S156" "Freesurfer_S158" "Freesurfer_S164"  --out BrainaverageN72
 
cd /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
mkdir ori
 
cd /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
@SUMA_Make_Spec_FS -NIFTI -sid BrainaverageN72
 
_
 
BrainaverageN72 is the output name.
 
Thanks,
Maxime Perron

De : freesurfer-boun...@nmr.mgh.harvard.edu  de la part de Greve, Douglas N.,Ph.D. 
Envoyé : 4 septembre 2019 10:37
À : f

Re: [Freesurfer] make_average_subject error

[Hoopes, Andrew]

Hi Maxine,

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ contains 
executables and a README file that details how you can patch your freesurfer 
install to fix this issue.

best
Andrew


From:  on behalf of Maxime Perron 

Reply-To: FS Help 
Date: Friday, September 6, 2019 at 5:08 PM
To: FS Help 
Subject: Re: [Freesurfer] make_average_subject error


External Email - Use Caution

​Hi Douglas,



I'm sorry for the misunderstanding! Thanks for the command.



I attached the mas.log.



Cheers,

Maxime

​




De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Greve, Douglas N.,Ph.D. 

Envoyé : 6 septembre 2019 10:30
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] make_average_subject error

That is the recon-all.log file. What I want is the terminal output from 
make_average_subject
You can capture it with
make_average_subject [your arguments] |& tee mas.log


On 9/4/2019 9:16 PM, Maxime Perron wrote:

External Email - Use Caution



Good evening Greve,



Thanks for your quick answer.



I attached the file containing the output.



Best,

Maxime



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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


On Sep 4, 2019, at 6:10 PM, Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu> wrote:

Can you send the full text of the terminal output?



On 9/4/19 10:44 AM, Maxime Perron wrote:

External Email - Use Caution



Hi Greve,



The exact script is the following :





setenv SUBJECTS_DIR 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data



make_average_subject --subjects "Freesurfer_S002" "Freesurfer_S003" 
"Freesurfer_S004" "Freesurfer_S014" "Freesurfer_S018_2" "Freesurfer_S020" 
"Freesurfer_S021" "Freesurfer_S023"  "Freesurfer_S024" "Freesurfer_S027" 
"Freesurfer_S029" "Freesurfer_S035" "Freesurfer_S037" "Freesurfer_S039" 
"Freesurfer_S040" "Freesurfer_S043" "Freesurfer_S044" "Freesurfer_S046" 
"Freesurfer_S048" "Freesurfer_S053" "Freesurfer_S060" "Freesurfer_S061" 
"Freesurfer_S064" "Freesurfer_S066" "Freesurfer_S068" "Freesurfer_S070" 
"Freesurfer_S071" "Freesurfer_S078" "Freesurfer_S083" "Freesurfer_S084" 
"Freesurfer_S088" "Freesurfer_S090" "Freesurfer_S093" "Freesurfer_S095" 
"Freesurfer_S103" "Freesurfer_S105" "Freesurfer_S106" "Freesurfer_S108" 
"Freesurfer_S110" "Freesurfer_S111" "Freesurfer_S113" "Freesurfer_S114" 
"Freesurfer_S115" "Freesurfer_S117" "Freesurfer_S118" "Freesurfer_S119" 
"Freesurfer_S120" "Freesurfer_S122" "Freesurfer_S123" "Freesurfer_S125" 
"Freesurfer_S126" "Freesurfer_S129" "Freesurfer_S130" "Freesurfer_S133" 
"Freesurfer_S134" "Freesurfer_S139" "Freesurfer_S141" "Freesurfer_S142" 
"Freesurfer_S144" "Freesurfer_S145" "Freesurfer_S146" "Freesurfer_S147" 
"Freesurfer_S148" "Freesurfer_S150" "Freesurfer_S151" "Freesurfer_S152" 
"Freesurfer_S153" "Freesurfer_S154" "Freesurfer_S155" "Freesurfer_S156" 
"Freesurfer_S158" "Freesurfer_S164"  --out BrainaverageN72



cd 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72

mkdir ori



cd 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72

@SUMA_Make_Spec_FS -NIFTI -sid BrainaverageN72



_



BrainaverageN72 is the output name.



Thanks,

Maxime Perron



De : 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 de la part de Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>

Envoyé : 4 septembre 2019 10:37

À : freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>

Objet : Re: [Freesurfer] make_average_subject error



Is BrainaverageN72 in the subjects list?



On 9/3/19 12:39 PM, Maxime Perron wrote:

External Email - Use Caution



​Dear Freesurfer Experts,





I have the following issue when running the make_average_subject command (



make_average_subject --subjects (Subjid) 

Re: [Freesurfer] make_average_subject error

[Greve, Douglas N.,Ph.D.]

That is the recon-all.log file. What I want is the terminal output from 
make_average_subject
You can capture it with
make_average_subject [your arguments] |& tee mas.log



On 9/4/2019 9:16 PM, Maxime Perron wrote:

External Email - Use Caution

Good evening Greve,

Thanks for your quick answer.

I attached the file containing the output.

Best,
Maxime




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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



On Sep 4, 2019, at 6:10 PM, Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu> wrote:


Can you send the full text of the terminal output?

On 9/4/19 10:44 AM, Maxime Perron wrote:


External Email - Use Caution

Hi Greve,

The exact script is the following :


setenv SUBJECTS_DIR 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data

make_average_subject --subjects "Freesurfer_S002" "Freesurfer_S003" 
"Freesurfer_S004" "Freesurfer_S014" "Freesurfer_S018_2" "Freesurfer_S020" 
"Freesurfer_S021" "Freesurfer_S023"  "Freesurfer_S024" "Freesurfer_S027" 
"Freesurfer_S029" "Freesurfer_S035" "Freesurfer_S037" "Freesurfer_S039" 
"Freesurfer_S040" "Freesurfer_S043" "Freesurfer_S044" "Freesurfer_S046" 
"Freesurfer_S048" "Freesurfer_S053" "Freesurfer_S060" "Freesurfer_S061" 
"Freesurfer_S064" "Freesurfer_S066" "Freesurfer_S068" "Freesurfer_S070" 
"Freesurfer_S071" "Freesurfer_S078" "Freesurfer_S083" "Freesurfer_S084" 
"Freesurfer_S088" "Freesurfer_S090" "Freesurfer_S093" "Freesurfer_S095" 
"Freesurfer_S103" "Freesurfer_S105" "Freesurfer_S106" "Freesurfer_S108" 
"Freesurfer_S110" "Freesurfer_S111" "Freesurfer_S113" "Freesurfer_S114" 
"Freesurfer_S115" "Freesurfer_S117" "Freesurfer_S118" "Freesurfer_S119" 
"Freesurfer_S120" "Freesurfer_S122" "Freesurfer_S123" "Freesurfer_S125" 
"Freesurfer_S126" "Freesurfer_S129" "Freesurfer_S130" "Freesurfer_S133" 
"Freesurfer_S134" "Freesurfer_S139" "Freesurfer_S141" "Freesurfer_S142" 
"Freesurfer_S144" "Freesurfer_S145" "Freesurfer_S146" "Freesurfer_S147" 
"Freesurfer_S148" "Freesurfer_S150" "Freesurfer_S151" "Freesurfer_S152" 
"Freesurfer_S153" "Freesurfer_S154" "Freesurfer_S155" "Freesurfer_S156" 
"Freesurfer_S158" "Freesurfer_S164"  --out BrainaverageN72

cd 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
mkdir ori

cd 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
@SUMA_Make_Spec_FS -NIFTI -sid BrainaverageN72

_

BrainaverageN72 is the output name.

Thanks,
Maxime Perron

De : 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 de la part de Greve, Douglas N.,Ph.D. 
<mailto:dgr...@mgh.harvard.edu>
Envoyé : 4 septembre 2019 10:37
À : freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Objet : Re: [Freesurfer] make_average_subject error

Is BrainaverageN72 in the subjects list?

On 9/3/19 12:39 PM, Maxime Perron wrote:


External Email - Use Caution

​Dear Freesurfer Experts,


I have the following issue when running the make_average_subject command (

make_average_subject --subjects (Subjid) --out BrainaverageN72) :


Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
Segmentation fault
Darwin tulipe.crulrg.local 17.7.0 Darwin Kernel Version 17.7.0: Sun
Jun  2 20:31:42 PDT 2019; root:xnu-4570.71.46~1/RELEASE_X86_64 

Re: [Freesurfer] make_average_subject error

[Maxime Perron]

External Email - Use Caution

Good evening Greve,

Thanks for your quick answer.

I attached the file containing the output.

Best,
Maxime 


recon-all.log
Description: recon-all.log


> On Sep 4, 2019, at 6:10 PM, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> Can you send the full text of the terminal output?
> 
> On 9/4/19 10:44 AM, Maxime Perron wrote:
>> External Email - Use Caution
>> 
>> Hi Greve,
>> 
>> The exact script is the following :
>> 
>> 
>> setenv SUBJECTS_DIR 
>> /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data
>> 
>> make_average_subject --subjects "Freesurfer_S002" "Freesurfer_S003" 
>> "Freesurfer_S004" "Freesurfer_S014" "Freesurfer_S018_2" "Freesurfer_S020" 
>> "Freesurfer_S021" "Freesurfer_S023"  "Freesurfer_S024" "Freesurfer_S027" 
>> "Freesurfer_S029" "Freesurfer_S035" "Freesurfer_S037" "Freesurfer_S039" 
>> "Freesurfer_S040" "Freesurfer_S043" "Freesurfer_S044" "Freesurfer_S046" 
>> "Freesurfer_S048" "Freesurfer_S053" "Freesurfer_S060" "Freesurfer_S061" 
>> "Freesurfer_S064" "Freesurfer_S066" "Freesurfer_S068" "Freesurfer_S070" 
>> "Freesurfer_S071" "Freesurfer_S078" "Freesurfer_S083" "Freesurfer_S084" 
>> "Freesurfer_S088" "Freesurfer_S090" "Freesurfer_S093" "Freesurfer_S095" 
>> "Freesurfer_S103" "Freesurfer_S105" "Freesurfer_S106" "Freesurfer_S108" 
>> "Freesurfer_S110" "Freesurfer_S111" "Freesurfer_S113" "Freesurfer_S114" 
>> "Freesurfer_S115" "Freesurfer_S117" "Freesurfer_S118" "Freesurfer_S119" 
>> "Freesurfer_S120" "Freesurfer_S122" "Freesurfer_S123" "Freesurfer_S125" 
>> "Freesurfer_S126" "Freesurfer_S129" "Freesurfer_S130" "Freesurfer_S133" 
>> "Freesurfer_S134" "Freesurfer_S139" "Freesurfer_S141" "Freesurfer_S142" 
>> "Freesurfer_S144" "Freesurfer_S145" "Freesurfer_S146" "Freesurfer_S147" 
>> "Freesurfer_S148" "Freesurfer_S150" "Freesurfer_S151" "Freesurfer_S152" 
>> "Freesurfer_S153" "Freesurfer_S154" "Freesurfer_S155" "Freesurfer_S156" 
>> "Freesurfer_S158" "Freesurfer_S164"  --out BrainaverageN72
>> 
>> cd 
>> /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
>> mkdir ori
>> 
>> cd 
>> /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
>> @SUMA_Make_Spec_FS -NIFTI -sid BrainaverageN72
>> 
>> _
>> 
>> BrainaverageN72 is the output name.
>> 
>> Thanks,
>> Maxime Perron
>> 
>> De : freesurfer-boun...@nmr.mgh.harvard.edu 
>>  de la part de Greve, Douglas 
>> N.,Ph.D. 
>> Envoyé : 4 septembre 2019 10:37
>> À : freesurfer@nmr.mgh.harvard.edu
>> Objet : Re: [Freesurfer] make_average_subject error
>> 
>> Is BrainaverageN72 in the subjects list?
>> 
>> On 9/3/19 12:39 PM, Maxime Perron wrote:
>>> External Email - Use Caution
>>> 
>>> ​Dear Freesurfer Experts,
>>> 
>>> 
>>> I have the following issue when running the make_average_subject command (
>>> 
>>> make_average_subject --subjects (Subjid) --out BrainaverageN72) :
>>> 
>>> 
>>> Building hash of lh white
>>> 
>>> Building hash of lh pial
>>> 
>>> Building hash of rh white
>>> 
>>> Building hash of rh pial
>>> 
>>> Loading aseg from
>>> /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72/mri/aseg.presurf.hypos.mgz
>>> ASeg Vox2RAS: ---
>>> -1.0   0.0   0.0   128.0;
>>>  0.0   0.0   1.0  -128.0;
>>>  0.0  -1.0   0.0   128.0;
>>>  0.0   0.0   0.0   1.0;
>>> mghRead(mri/norm.mgz, -1): could not open file
>>> -
&

Re: [Freesurfer] make_average_subject error

[Greve, Douglas N.,Ph.D.]

Can you send the full text of the terminal output?

On 9/4/19 10:44 AM, Maxime Perron wrote:
>  External Email - Use Caution
>
> Hi Greve,
>
> The exact script is the following :
> 
>
> setenv SUBJECTS_DIR 
> /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data
>
> make_average_subject --subjects "Freesurfer_S002" "Freesurfer_S003" 
> "Freesurfer_S004" "Freesurfer_S014" "Freesurfer_S018_2" "Freesurfer_S020" 
> "Freesurfer_S021" "Freesurfer_S023"  "Freesurfer_S024" "Freesurfer_S027" 
> "Freesurfer_S029" "Freesurfer_S035" "Freesurfer_S037" "Freesurfer_S039" 
> "Freesurfer_S040" "Freesurfer_S043" "Freesurfer_S044" "Freesurfer_S046" 
> "Freesurfer_S048" "Freesurfer_S053" "Freesurfer_S060" "Freesurfer_S061" 
> "Freesurfer_S064" "Freesurfer_S066" "Freesurfer_S068" "Freesurfer_S070" 
> "Freesurfer_S071" "Freesurfer_S078" "Freesurfer_S083" "Freesurfer_S084" 
> "Freesurfer_S088" "Freesurfer_S090" "Freesurfer_S093" "Freesurfer_S095" 
> "Freesurfer_S103" "Freesurfer_S105" "Freesurfer_S106" "Freesurfer_S108" 
> "Freesurfer_S110" "Freesurfer_S111" "Freesurfer_S113" "Freesurfer_S114" 
> "Freesurfer_S115" "Freesurfer_S117" "Freesurfer_S118" "Freesurfer_S119" 
> "Freesurfer_S120" "Freesurfer_S122" "Freesurfer_S123" "Freesurfer_S125" 
> "Freesurfer_S126" "Freesurfer_S129" "Freesurfer_S130" "Freesurfer_S133" 
> "Freesurfer_S134" "Freesurfer_S139" "Freesurfer_S141" "Freesurfer_S142" 
> "Freesurfer_S144" "Freesurfer_S145" "Freesurfer_S146" "Freesurfer_S147" 
> "Freesurfer_S148" "Freesurfer_S150" "Freesurfer_S151" "Freesurfer_S152" 
> "Freesurfer_S153" "Freesurfer_S154" "Freesurfer_S155" "Freesurfer_S156" 
> "Freesurfer_S158" "Freesurfer_S164"  --out BrainaverageN72
>
> cd 
> /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
> mkdir ori
>
> cd 
> /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
> @SUMA_Make_Spec_FS -NIFTI -sid BrainaverageN72
>
> _
>
> BrainaverageN72 is the output name.
>
> Thanks,
> Maxime Perron
> 
> De : freesurfer-boun...@nmr.mgh.harvard.edu 
>  de la part de Greve, Douglas 
> N.,Ph.D. 
> Envoyé : 4 septembre 2019 10:37
> À : freesurfer@nmr.mgh.harvard.edu
> Objet : Re: [Freesurfer] make_average_subject error
>
> Is BrainaverageN72 in the subjects list?
>
> On 9/3/19 12:39 PM, Maxime Perron wrote:
>>  External Email - Use Caution
>>
>> ​Dear Freesurfer Experts,
>>
>>
>> I have the following issue when running the make_average_subject command (
>>
>> make_average_subject --subjects (Subjid) --out BrainaverageN72) :
>>
>>
>> Building hash of lh white
>>
>> Building hash of lh pial
>>
>> Building hash of rh white
>>
>> Building hash of rh pial
>>
>> Loading aseg from
>> /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72/mri/aseg.presurf.hypos.mgz
>> ASeg Vox2RAS: ---
>> -1.0   0.0   0.0   128.0;
>>   0.0   0.0   1.0  -128.0;
>>   0.0  -1.0   0.0   128.0;
>>   0.0   0.0   0.0   1.0;
>> mghRead(mri/norm.mgz, -1): could not open file
>> -
>>
>> Labeling Slice
>> relabeling unlikely voxels in interior of white matter
>> Segmentation fault
>> Darwin tulipe.crulrg.local 17.7.0 Darwin Kernel Version 17.7.0: Sun
>> Jun  2 20:31:42 PDT 2019; root:xnu-4570.71.46~1/RELEASE_X86_64 x86_64
>>
>> recon-all -s BrainaverageN72 exited with ERRORS at Tue Sep  3 11:33:02
>> EDT 2019
>>
>>
>> I appreciate any help.
>>
>> ​Regards,
>> Maxime
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ​
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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Re: [Freesurfer] make_average_subject error

[Maxime Perron]

External Email - Use Caution

Hi Greve, 

The exact script is the following : 


setenv SUBJECTS_DIR 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data

make_average_subject --subjects "Freesurfer_S002" "Freesurfer_S003" 
"Freesurfer_S004" "Freesurfer_S014" "Freesurfer_S018_2" "Freesurfer_S020" 
"Freesurfer_S021" "Freesurfer_S023"  "Freesurfer_S024" "Freesurfer_S027" 
"Freesurfer_S029" "Freesurfer_S035" "Freesurfer_S037" "Freesurfer_S039" 
"Freesurfer_S040" "Freesurfer_S043" "Freesurfer_S044" "Freesurfer_S046" 
"Freesurfer_S048" "Freesurfer_S053" "Freesurfer_S060" "Freesurfer_S061" 
"Freesurfer_S064" "Freesurfer_S066" "Freesurfer_S068" "Freesurfer_S070" 
"Freesurfer_S071" "Freesurfer_S078" "Freesurfer_S083" "Freesurfer_S084" 
"Freesurfer_S088" "Freesurfer_S090" "Freesurfer_S093" "Freesurfer_S095" 
"Freesurfer_S103" "Freesurfer_S105" "Freesurfer_S106" "Freesurfer_S108" 
"Freesurfer_S110" "Freesurfer_S111" "Freesurfer_S113" "Freesurfer_S114" 
"Freesurfer_S115" "Freesurfer_S117" "Freesurfer_S118" "Freesurfer_S119" 
"Freesurfer_S120" "Freesurfer_S122" "Freesurfer_S123" "Freesurfer_S125" 
"Freesurfer_S126" "Freesurfer_S129" "Freesurfer_S130" "Freesurfer_S133" 
"Freesurfer_S134" "Freesurfer_S139" "Freesurfer_S141" "Freesurfer_S142" 
"Freesurfer_S144" "Freesurfer_S145" "Freesurfer_S146" "Freesurfer_S147" 
"Freesurfer_S148" "Freesurfer_S150" "Freesurfer_S151" "Freesurfer_S152" 
"Freesurfer_S153" "Freesurfer_S154" "Freesurfer_S155" "Freesurfer_S156" 
"Freesurfer_S158" "Freesurfer_S164"  --out BrainaverageN72

cd 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
mkdir ori

cd 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
@SUMA_Make_Spec_FS -NIFTI -sid BrainaverageN72

_

BrainaverageN72 is the output name.

Thanks,
Maxime Perron

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Greve, Douglas N.,Ph.D. 

Envoyé : 4 septembre 2019 10:37
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] make_average_subject error

Is BrainaverageN72 in the subjects list?

On 9/3/19 12:39 PM, Maxime Perron wrote:
>
> External Email - Use Caution
>
> ​Dear Freesurfer Experts,
>
>
> I have the following issue when running the make_average_subject command (
>
> make_average_subject --subjects (Subjid) --out BrainaverageN72) :
>
>
> Building hash of lh white
>
> Building hash of lh pial
>
> Building hash of rh white
>
> Building hash of rh pial
>
> Loading aseg from
> /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72/mri/aseg.presurf.hypos.mgz
> ASeg Vox2RAS: ---
> -1.0   0.0   0.0   128.0;
>  0.0   0.0   1.0  -128.0;
>  0.0  -1.0   0.0   128.0;
>  0.0   0.0   0.0   1.0;
> mghRead(mri/norm.mgz, -1): could not open file
> -
>
> Labeling Slice
> relabeling unlikely voxels in interior of white matter
> Segmentation fault
> Darwin tulipe.crulrg.local 17.7.0 Darwin Kernel Version 17.7.0: Sun
> Jun  2 20:31:42 PDT 2019; root:xnu-4570.71.46~1/RELEASE_X86_64 x86_64
>
> recon-all -s BrainaverageN72 exited with ERRORS at Tue Sep  3 11:33:02
> EDT 2019
>
>
> I appreciate any help.
>
> ​Regards,
> Maxime
>
>
>
>
>
>
>
>
>
> ​
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] make_average_subject error

[Greve, Douglas N.,Ph.D.]

Is BrainaverageN72 in the subjects list?

On 9/3/19 12:39 PM, Maxime Perron wrote:
>
> External Email - Use Caution
>
> ​Dear Freesurfer Experts,
>
>
> I have the following issue when running the make_average_subject command (
>
> make_average_subject --subjects (Subjid) --out BrainaverageN72) :
>
>
> Building hash of lh white
>
> Building hash of lh pial
>
> Building hash of rh white
>
> Building hash of rh pial
>
> Loading aseg from 
> /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72/mri/aseg.presurf.hypos.mgz
> ASeg Vox2RAS: ---
> -1.0   0.0   0.0   128.0;
>  0.0   0.0   1.0  -128.0;
>  0.0  -1.0   0.0   128.0;
>  0.0   0.0   0.0   1.0;
> mghRead(mri/norm.mgz, -1): could not open file
> -
>
> Labeling Slice
> relabeling unlikely voxels in interior of white matter
> Segmentation fault
> Darwin tulipe.crulrg.local 17.7.0 Darwin Kernel Version 17.7.0: Sun 
> Jun  2 20:31:42 PDT 2019; root:xnu-4570.71.46~1/RELEASE_X86_64 x86_64
>
> recon-all -s BrainaverageN72 exited with ERRORS at Tue Sep  3 11:33:02 
> EDT 2019
>
>
> I appreciate any help.
>
> ​Regards,
> Maxime
>
>
>
>
>
>
>
>
>
> ​
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
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[Freesurfer] make_average_subject error

[Maxime Perron]

External Email - Use Caution
​Dear Freesurfer Experts,



I have the following issue when running the make_average_subject command (

make_average_subject --subjects (Subjid) --out BrainaverageN72) : 







Building hash of lh white


Building hash of lh pial


Building hash of rh white


Building hash of rh pial


Loading aseg from /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-


Labeling Slice
relabeling unlikely voxels in interior of white matter
Segmentation fault
Darwin tulipe.crulrg.local 17.7.0 Darwin Kernel Version 17.7.0: Sun Jun  2 20:31:42 PDT 2019; root:xnu-4570.71.46~1/RELEASE_X86_64 x86_64


recon-all -s BrainaverageN72 exited with ERRORS at Tue Sep  3 11:33:02 EDT 2019



I appreciate any help.


​Regards, 


Maxime 


















​






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[Freesurfer] make_average_subject error

[Niels Janssen .]

External Email - Use Caution

Dear all,

I have seen this error mentioned several times on the list but I have never
seen a solution posted. It is claimed that there is a patch and a README
that explains the patch at:

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/

In this folder there are a bunch of files but there is no README so I am
not sure what exactly I need to do. I tried replacing the files in my
/usr/local/freesurfer/bin with those in this patch folder but the error
remains. This error appears with all my data sets that I have tried. So it
doesnt seem to be something specific to my data.

Loading aseg from
/media/fMRI_21/studyname/freesurfer/avgsub3/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
Segmentation fault (core dumped)
Linux nielsj-XXXYYY 4.18.0-25-generic #26~18.04.1-Ubuntu SMP Thu Jun 27
07:28:31 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s avgsub3 exited with ERRORS at mié jul 31 12:05:20 WEST 2019


-- 
Niels Janssen
Brain Imaging Laboratory
Institute of Biomedical Technologies
Institute of Neurosciences
University of La Laguna
Tenerife, Spain
https://sites.google.com/view/nielsjanssen/
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Re: [Freesurfer] make_average_subject error: could not load norm volume from (null)

[Greve, Douglas N.,Ph.D.]

I think it is crashing outside of make_average_surface and make_average_volume, 
so the log files are not telling me what is going on. Can you capture the full 
terminal output? Also, you can try it with two subjects so that it runs faster  
(but it might not crash).

On 7/10/2019 5:39 AM, Mads Jensen wrote:

External Email - Use Caution

Thank you very much for spending time on this!

I have attached the make_average_volume.log and make_average_surface.log files.

Den man. 8. jul. 2019 kl. 16.44 skrev Greve, Douglas N.,Ph.D.
:



Can you send the full terminal output of make_average_subject? There should 
also be some log files (make_average_volume.log and make_average_surface.log) 
in the average subject that would be helpful

On 7/4/2019 4:36 AM, Mads Jensen wrote:

External Email - Use Caution

HI FreeSurfer Developers,

I'm attempting to create an average subject make_average_subject but I
get the error message the following error when I run the
make_average_command:

Loading aseg from REMOVED-PATH/avg_elder/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from (null)

Linux 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:53:28 UTC 2018
x86_64 x86_64 x86_64 GNU/Linux

I cannot find anything similar on the mailing list. I hope anyone have
any thoughts on how to trouble-shoot this one? Also, Ive attached the
recon-all.log in case it's of any use.

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu 16.04.4 LTS
3) uname -a: Linux hyades02 4.4.0-130-generic #156-Ubuntu SMP Thu Jun
14 08:53:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached


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Re: [Freesurfer] make_average_subject error: could not load norm volume from (null)

[Greve, Douglas N.,Ph.D.]

Can you send the full terminal output of make_average_subject? There should 
also be some log files (make_average_volume.log and make_average_surface.log) 
in the average subject that would be helpful

On 7/4/2019 4:36 AM, Mads Jensen wrote:

External Email - Use Caution

HI FreeSurfer Developers,

I'm attempting to create an average subject make_average_subject but I
get the error message the following error when I run the
make_average_command:

Loading aseg from REMOVED-PATH/avg_elder/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from (null)

Linux 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:53:28 UTC 2018
x86_64 x86_64 x86_64 GNU/Linux

I cannot find anything similar on the mailing list. I hope anyone have
any thoughts on how to trouble-shoot this one? Also, Ive attached the
recon-all.log in case it's of any use.

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu 16.04.4 LTS
3) uname -a: Linux hyades02 4.4.0-130-generic #156-Ubuntu SMP Thu Jun
14 08:53:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached




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[Freesurfer] make_average_subject error: could not load norm volume from (null)

[Mads Jensen]

External Email - Use Caution

HI FreeSurfer Developers,

I'm attempting to create an average subject make_average_subject but I
get the error message the following error when I run the
make_average_command:

Loading aseg from REMOVED-PATH/avg_elder/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from (null)

Linux 4.4.0-130-generic #156-Ubuntu SMP Thu Jun 14 08:53:28 UTC 2018
x86_64 x86_64 x86_64 GNU/Linux

I cannot find anything similar on the mailing list. I hope anyone have
any thoughts on how to trouble-shoot this one? Also, Ive attached the
recon-all.log in case it's of any use.

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu 16.04.4 LTS
3) uname -a: Linux hyades02 4.4.0-130-generic #156-Ubuntu SMP Thu Jun
14 08:53:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached


recon-all.log
Description: Binary data
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Re: [Freesurfer] make_average_subject error

[C.P.E. Rollins]

   External Email - Use Caution


Hi Douglas,
Yes - attached here is the make_average_subject.log file. The command 
used was:

make_average_subject --out average_v2 --subjects $(cat subjects.txt)

subjects.txt also attached.
Thanks again for your help
Colleen
setenv SUBJECTS_DIR /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
/applications/freesurfer/freesurfer_6.0.0/bin/make_average_subject --subjects 
Sub_001 Sub_002 Sub_003 Sub_004 Sub_005 Sub_006 Sub_008 Sub_009 Sub_010 Sub_011 
Sub_013 Sub_014 Sub_015 Sub_016 Sub_017 Sub_018 Sub_020 Sub_021 Sub_023 Sub_024 
Sub_025 Sub_026 Sub_027 Sub_028 Sub_029 Sub_031 Sub_032 Sub_033 Sub_034 Sub_035 
Sub_036 Sub_037 Sub_038 Sub_039 Sub_040 Sub_041 Sub_042 Sub_043 Sub_044 Sub_045 
Sub_046 Sub_047 Sub_048 Sub_049 Sub_050 Sub_051 Sub_052 Sub_053 Sub_054 Sub_055 
Sub_056 Sub_058 Sub_059 Sub_060 Sub_061 Sub_062 Sub_063 Sub_064 Sub_065 --out 
average_v2

$Id: make_average_subject,v 1.23.2.1 2016/08/02 21:20:04 greve Exp $
Fri Sep 21 07:58:48 BST 2018
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
output ddir is /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
uid=15714(cper2) gid=15714(cper2) 
groups=15714(cper2),827(biomed),1100(hphi),31075(wbic-p00305),31106(wbic-p00355),31180(wbic-q10005)
Sub_001
Sub_002
Sub_003
Sub_004
Sub_005
Sub_006
Sub_008
Sub_009
Sub_010
Sub_011
Sub_013
Sub_014
Sub_015
Sub_016
Sub_017
Sub_018
Sub_020
Sub_021
Sub_023
Sub_024
Sub_025
Sub_026
Sub_027
Sub_028
Sub_029
Sub_031
Sub_032
Sub_033
Sub_034
Sub_035
Sub_036
Sub_037
Sub_038
Sub_039
Sub_040
Sub_041
Sub_042
Sub_043
Sub_044
Sub_045
Sub_046
Sub_047
Sub_048
Sub_049
Sub_050
Sub_051
Sub_052
Sub_053
Sub_054
Sub_055
Sub_056
Sub_058
Sub_059
Sub_060
Sub_061
Sub_062
Sub_063
Sub_064
Sub_065
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Re: [Freesurfer] make_average_subject error

[Greve, Douglas N.,Ph.D.]

Can you send the make_average-subject command and log file?

On 9/21/18 7:03 AM, C.P.E. Rollins wrote:
   External Email - Use Caution
Hello Freesurfer Developpers,

I'm attempting to make a study specific template using all of my subjects as 
input using the make_average_subject command, but am receiving the following 
error:
Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
Segmentation fault (core dumped)
Linux wbic-cs-5 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64 
GNU/Linux

recon-all -s average_v2 exited with ERRORS at Fri Sep 21 11:11:25 BST 2018

I've attached here the full log file.

I read in this forum: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57030.html to 
try installing the following patch: 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
and had asked our computing support team to install it before the current run 
of make_average_subject, so the error seems to be happening despite the patch. 
I would greatly appreciate your suggestions for resolving the error.

Thanks very much,

Colleen



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[Freesurfer] make_average_subject error

[C.P.E. Rollins]

   External Email - Use Caution


Hello Freesurfer Developpers,

I'm attempting to make a study specific template using all of my 
subjects as input using the make_average_subject command, but am 
receiving the following error:

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from 
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2/mri/aseg.presurf.hypos.mgz

ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
Segmentation fault (core dumped)
Linux wbic-cs-5 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) 
x86_64 GNU/Linux


recon-all -s average_v2 exited with ERRORS at Fri Sep 21 11:11:25 BST 
2018


I've attached here the full log file.

I read in this forum: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57030.html 
to try installing the following patch: 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
and had asked our computing support team to install it before the 
current run of make_average_subject, so the error seems to be happening 
despite the patch. I would greatly appreciate your suggestions for 
resolving the error.


Thanks very much,

ColleenFri Sep 21 11:06:50 BST 2018
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/average_v2
/applications/freesurfer/freesurfer_6.0.0/bin/recon-all
-s average_v2 -cortribbon -aparc2aseg
subjid average_v2
setenv SUBJECTS_DIR /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0
Actual FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux wbic-cs-5 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksizeunlimited
coredumpsize unlimited
memoryuse37748736 kbytes
vmemoryuse   unlimited
descriptors  65536 
memorylocked unlimited
maxproc  193538 
maxlocks unlimited
maxsignal193538 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:  49564564   10631376   38933188  64716 1772526734152
-/+ buffers/cache:3719972   45844592
Swap: 16200696 133356   16067340


program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/09/21-10:06:50-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: cper2  Machine: wbic-cs-5  Platform: Linux  PlatformVersion: 3.16.0-6-amd64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/09/21-10:06:50-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: cper2  Machine: wbic-cs-5  Platform: Linux  PlatformVersion: 3.16.0-6-amd64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/09/21-10:06:50-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: cper2  Machine: wbic-cs-5  Platform: Linux  PlatformVersion: 3.16.0-6-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/09/21-10:06:50-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: cper2  Machine: wbic-cs-5  Platform: Linux  PlatformVersion: 3.16.0-6-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/09/21-10:06:50-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: cper2  Machine: wbic-cs-5  Platform: Linux  PlatformVersion: 3.16.0-6-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  

Re: [Freesurfer] make_average_subject error

[Bruce Fischl]

Hi Xiaoyu

how are you trying to create an average subject? It looks like you are 
running recon-all on something. Typically we use the script 
make_average_subject for this


cheers
Bruce


On Wed, 11 Jul 2018, Wang, Xiaoyu wrote:



External Email - Use Caution

 

Hello FreeSurfer Developers,

 

I am attempting to perform group analysis on a group of subjects. However, When 
I am trying to
create an average subject I get the following error.

 

mghRead(mri/norm.mgz, -1) could not open file

 

I went into the average folder but I could not find norm.mgz anywhere.

Looking further up on the log, it would seem that norm.mgz is supposed to be 
relabled from
aseg.presurf.hypos

 

However, said file is still there.

 

I have looked in the wiki and found a few others who have had similar issues to 
me however, I can’t
see the solution or a reply. Does anyone have any Idea what I’m doing wrong?

 

I have attached the recon-all.error as well as the recon-all log if it will be 
of any help

 

Sincerely

 

Xiaoyu Wang


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[Freesurfer] make_average_subject error

[Wang, Xiaoyu]

External Email - Use Caution

Hello FreeSurfer Developers,

I am attempting to perform group analysis on a group of subjects. However, When 
I am trying to create an average subject I get the following error.

mghRead(mri/norm.mgz, -1) could not open file

I went into the average folder but I could not find norm.mgz anywhere.
Looking further up on the log, it would seem that norm.mgz is supposed to be 
relabled from aseg.presurf.hypos

However, said file is still there.

I have looked in the wiki and found a few others who have had similar issues to 
me however, I can't see the solution or a reply. Does anyone have any Idea what 
I'm doing wrong?

I have attached the recon-all.error as well as the recon-all log if it will be 
of any help

Sincerely

Xiaoyu Wang


recon-all.error
Description: recon-all.error


recon-all.log
Description: recon-all.log
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Re: [Freesurfer] make_average_subject error

[Duran, Tugce]

Please see the attached log file. 

Thanks,
Tugce

On 11/16/17, 11:35 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Douglas N Greve"  wrote:

can you send the entire log file?


On 11/16/2017 11:32 AM, Duran, Tugce wrote:
>
> Dear FreeSurfer Experts,
>
> I’m recently getting an error in make_average_subject and can’t find 
> the reason.
>
> Please see the following for the error log from recon-all.log:
>
> *Loading aseg from 
> 
/gpfs/projects/RadImagSci/CFN/test-SDA-import/VTRAK4/xserveraids/vtrak4/mci/IMAGENE/NIFTI_CENTRAL/IMAGENE_BL_DENOISED_DEOBLIQUE_FREESURFER60_DEFAULT_KARST_10092017_RES/fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop/mri/aseg.presurf.hypos.mgz*
>
> *ASeg Vox2RAS: ---*
>
> *-1.0 0.0   0.0   128.0;*
>
> *0.0 0.0   1.0  -128.0;*
>
> *0.0 -1.0   0.0   128.0;*
>
> *0.0 0.0   0.0   1.0;*
>
> *mghRead(mri/norm.mgz, -1): could not open file*
>
> *-*
>
> **
>
> *Labeling Slice*
>
> *relabeling unlikely voxels in interior of white matter*
>
> *mri/norm.mgz: could not load norm volume from (null)*
>
> **
>
> *Linux i1.karst.uits.iu.edu 2.6.32-696.13.2.el6.x86_64 #1 SMP Fri Sep 
> 22 12:32:14 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux*
>
> **
>
> *recon-all -s 
> fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop 
> exited with ERRORS at Wed Nov 15 19:14:17 EST 2017*
>
> **
>
> **
>
> It appears that during the process it doesn’t create the norm.mgz file 
> to read or open it in the later processes (I think?). What can I do to 
> fix this error?
>
> Thanks,
>
> Tugce**
>
>
>
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-- 
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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e-mail
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recon-all.log
Description: recon-all.log
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Re: [Freesurfer] make_average_subject error

[Douglas N Greve]

can you send the entire log file?


On 11/16/2017 11:32 AM, Duran, Tugce wrote:
>
> Dear FreeSurfer Experts,
>
> I’m recently getting an error in make_average_subject and can’t find 
> the reason.
>
> Please see the following for the error log from recon-all.log:
>
> *Loading aseg from 
> /gpfs/projects/RadImagSci/CFN/test-SDA-import/VTRAK4/xserveraids/vtrak4/mci/IMAGENE/NIFTI_CENTRAL/IMAGENE_BL_DENOISED_DEOBLIQUE_FREESURFER60_DEFAULT_KARST_10092017_RES/fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop/mri/aseg.presurf.hypos.mgz*
>
> *ASeg Vox2RAS: ---*
>
> *-1.0 0.0   0.0   128.0;*
>
> *0.0 0.0   1.0  -128.0;*
>
> *0.0 -1.0   0.0   128.0;*
>
> *0.0 0.0   0.0   1.0;*
>
> *mghRead(mri/norm.mgz, -1): could not open file*
>
> *-*
>
> **
>
> *Labeling Slice*
>
> *relabeling unlikely voxels in interior of white matter*
>
> *mri/norm.mgz: could not load norm volume from (null)*
>
> **
>
> *Linux i1.karst.uits.iu.edu 2.6.32-696.13.2.el6.x86_64 #1 SMP Fri Sep 
> 22 12:32:14 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux*
>
> **
>
> *recon-all -s 
> fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop 
> exited with ERRORS at Wed Nov 15 19:14:17 EST 2017*
>
> **
>
> **
>
> It appears that during the process it doesn’t create the norm.mgz file 
> to read or open it in the later processes (I think?). What can I do to 
> fix this error?
>
> Thanks,
>
> Tugce**
>
>
>
> ___
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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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[Freesurfer] make_average_subject error

[Duran, Tugce]

Dear FreeSurfer Experts,

I’m recently getting an error in make_average_subject and can’t find the reason.
Please see the following for the error log from recon-all.log:

Loading aseg from 
/gpfs/projects/RadImagSci/CFN/test-SDA-import/VTRAK4/xserveraids/vtrak4/mci/IMAGENE/NIFTI_CENTRAL/IMAGENE_BL_DENOISED_DEOBLIQUE_FREESURFER60_DEFAULT_KARST_10092017_RES/fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
0.0   0.0   1.0  -128.0;
0.0  -1.0   0.0   128.0;
0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from (null)

Linux i1.karst.uits.iu.edu 2.6.32-696.13.2.el6.x86_64 #1 SMP Fri Sep 22 
12:32:14 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 
fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop exited 
with ERRORS at Wed Nov 15 19:14:17 EST 2017


It appears that during the process it doesn’t create the norm.mgz file to read 
or open it in the later processes (I think?). What can I do to fix this error?

Thanks,
Tugce
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[Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

[Xiaowei Song]

Hi all,

Did you encounter the error message talairach.m3z does not start as 'MNI
Transform File' when making average of subjects?

I checked all the recon-all.log file and did not find error, but when
running make_average_subject after recon-all, then this error shoot.

To repeat the error message, I tried the following command which is called
by make_average_subject and found all my subjects shoot this error.

mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
/usr/local/freesurfer/average/mni305.cor.mgz --xfm
 1173622/mri/transforms/talairach.m3z --o
/tmp/make_average_vol-tmp-164320_seg-1173622.mgh --interp nearest

I found another same question asked before, but no answer.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024064.html

Any hint or help will be appreciated. Thank you.

-- 
Xiaowei Song
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Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

[Xiaowei Song]

This error may come from regio_read_mincxfm function in registerio.c.
Does this mean something wrong in recon-all?

I forgot to mention that FreeSurfer version is
 freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0


On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song dawnwei.s...@gmail.com wrote:

 Hi all,

 Did you encounter the error message talairach.m3z does not start as 'MNI
 Transform File' when making average of subjects?

 I checked all the recon-all.log file and did not find error, but when
 running make_average_subject after recon-all, then this error shoot.

 To repeat the error message, I tried the following command which is called
 by make_average_subject and found all my subjects shoot this error.

 mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
 /usr/local/freesurfer/average/mni305.cor.mgz --xfm
  1173622/mri/transforms/talairach.m3z --o
 /tmp/make_average_vol-tmp-164320_seg-1173622.mgh --interp nearest

 I found another same question asked before, but no answer.
 https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024064.html

 Any hint or help will be appreciated. Thank you.

 --
 Xiaowei Song




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

Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

[Bruce Fischl]

sorry, I don't understand. What was the error? I don't see one in this 
email. Can you send us the actual screen output?


cheers
Bruce
On Thu, 7 Mar 2013, Xiaowei Song wrote:


This error may come from regio_read_mincxfm function in registerio.c.Does
this mean something wrong in recon-all?

I forgot to mention that FreeSurfer version is
 freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0


On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song dawnwei.s...@gmail.com wrote:
  Hi all,

Did you encounter the error message talairach.m3z does not start as
'MNI Transform File' when making average of subjects?

I checked all the recon-all.log file and did not find error, but when
running make_average_subject after recon-all, then this error shoot.

To repeat the error message, I tried the following command which is
called by make_average_subject and found all my subjects shoot this
error.

mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
/usr/local/freesurfer/average/mni305.cor.mgz --xfm
 1173622/mri/transforms/talairach.m3z --o
/tmp/make_average_vol-tmp-164320_seg-1173622.mgh --interp nearest

I found another same question asked before, but noanswer. 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024
064.html

Any hint or help will be appreciated. Thank you.

--
Xiaowei Song 




--
Xiaowei Song 

___
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Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

[Xiaowei Song]

Sorry, I did not make it clear.

In make_average_volume.log, the error message is:

1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013
mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ
/usr/local/freesurfer/average/mni305.cor.mgz --xfm
/data/lis9/fs/x/1173622/mri/transforms/talairach.m3z --o
/data/lis9/fs/x/avgGrp139/tmp/make_average_vol-tmp-55832/seg-1173622.mgh
--interp nearest
ERROR: /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z does not start
as 'MNI Transform File'/spin1/users/lis9/fs/dcm.mprage.mgz
ERROR: mri_vol2vol failed.


On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 sorry, I don't understand. What was the error? I don't see one in this
 email. Can you send us the actual screen output?

 cheers
 Bruce

 On Thu, 7 Mar 2013, Xiaowei Song wrote:

  This error may come from regio_read_mincxfm function in registerio.c.Does
 this mean something wrong in recon-all?

 I forgot to mention that FreeSurfer version is
  freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0


 On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song dawnwei.s...@gmail.com
 wrote:
   Hi all,

 Did you encounter the error message talairach.m3z does not start as
 'MNI Transform File' when making average of subjects?

 I checked all the recon-all.log file and did not find error, but when
 running make_average_subject after recon-all, then this error shoot.

 To repeat the error message, I tried the following command which is
 called by make_average_subject and found all my subjects shoot this
 error.

 mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
 /usr/local/freesurfer/average/**mni305.cor.mgz --xfm
  1173622/mri/transforms/**talairach.m3z --o
 /tmp/make_average_vol-tmp-**164320_seg-1173622.mgh --interp nearest

 I found another same question asked before, but noanswer.
 https://mail.nmr.**mgh.harvard.edu/pipermail//**freesurfer/2012-May/024https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024
 064.html

 Any hint or help will be appreciated. Thank you.

 --
 Xiaowei Song




 --
 Xiaowei Song




 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/**compliancelinehttp://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.




-- 
Xiaowei Song
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

[Bruce Fischl]

what was your command line?
On Thu, 7 Mar 2013, Xiaowei Song wrote:


Sorry, I did not make it clear.
In make_average_volume.log, the error message is:

1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013
mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ
/usr/local/freesurfer/average/mni305.cor.mgz --xfm
/data/lis9/fs/x/1173622/mri/transforms/talairach.m3z --o
/data/lis9/fs/x/avgGrp139/tmp/make_average_vol-tmp-55832/seg-1173622.mgh
--interp nearest
ERROR: /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z does not start
as 'MNI Transform File'/spin1/users/lis9/fs/dcm.mprage.mgz
ERROR: mri_vol2vol failed.


On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
  sorry, I don't understand. What was the error? I don't see one
  in this email. Can you send us the actual screen output?

  cheers
  Bruce
  On Thu, 7 Mar 2013, Xiaowei Song wrote:

This error may come from regio_read_mincxfm function
in registerio.c.Does
this mean something wrong in recon-all?

I forgot to mention that FreeSurfer version is
 freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0


On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song
dawnwei.s...@gmail.com wrote:
      Hi all,

Did you encounter the error message talairach.m3z
does not start as
'MNI Transform File' when making average of
subjects?

I checked all the recon-all.log file and did not
find error, but when
running make_average_subject after recon-all, then
this error shoot.

To repeat the error message, I tried the following
command which is
called by make_average_subject and found all my
subjects shoot this
error.

mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
/usr/local/freesurfer/average/mni305.cor.mgz --xfm
 1173622/mri/transforms/talairach.m3z --o
/tmp/make_average_vol-tmp-164320_seg-1173622.mgh
--interp nearest

I found another same question asked before, butnoanswer. 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/0
24
064.html

Any hint or help will be appreciated. Thank you.

--
Xiaowei Song 




--
Xiaowei Song 




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.




--
Xiaowei Song 

___
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

[Xiaowei Song]

Thanks for your help.

My command line is
make_average_subject --out avgGrp139  --subjects `cat
script/subjects.id`  --xform
talairach.m3z


On Thu, Mar 7, 2013 at 6:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 what was your command line?

 On Thu, 7 Mar 2013, Xiaowei Song wrote:

  Sorry, I did not make it clear.
 In make_average_volume.log, the error message is:

 1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013
 mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/**aseg.mgz --targ
 /usr/local/freesurfer/average/**mni305.cor.mgz --xfm
 /data/lis9/fs/x/1173622/mri/**transforms/talairach.m3z --o
 /data/lis9/fs/x/avgGrp139/tmp/**make_average_vol-tmp-55832/**
 seg-1173622.mgh
 --interp nearest
 ERROR: /data/lis9/fs/x/1173622/mri/**transforms/talairach.m3z does not
 start
 as 'MNI Transform File'/spin1/users/lis9/fs/dcm.**mprage.mgz
 ERROR: mri_vol2vol failed.


 On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
   sorry, I don't understand. What was the error? I don't see one
   in this email. Can you send us the actual screen output?

   cheers
   Bruce
   On Thu, 7 Mar 2013, Xiaowei Song wrote:

 This error may come from regio_read_mincxfm function
 in registerio.c.Does
 this mean something wrong in recon-all?

 I forgot to mention that FreeSurfer version is
  freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0


 On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song
 dawnwei.s...@gmail.com wrote:
   Hi all,

 Did you encounter the error message talairach.m3z
 does not start as
 'MNI Transform File' when making average of
 subjects?

 I checked all the recon-all.log file and did not
 find error, but when
 running make_average_subject after recon-all, then
 this error shoot.

 To repeat the error message, I tried the following
 command which is
 called by make_average_subject and found all my
 subjects shoot this
 error.

 mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
 /usr/local/freesurfer/average/**mni305.cor.mgz --xfm
  1173622/mri/transforms/**talairach.m3z --o
 /tmp/make_average_vol-tmp-**164320_seg-1173622.mgh
 --interp nearest

 I found another same question asked before, butnoanswer.
 https://mail.nmr.**mgh.harvard.edu/pipermail//**freesurfer/2012-May/0https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/0
 24
 064.html

 Any hint or help will be appreciated. Thank you.

 --
 Xiaowei Song




 --
 Xiaowei Song




 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/**compliancelinehttp://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.




 --
 Xiaowei Song




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

Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

[Douglas N Greve]

The xform has to be linear in the xfm format. The m3z cannot be used.
doug

On 03/07/2013 06:44 PM, Xiaowei Song wrote:
 Thanks for your help.

 My command line is
 make_average_subject --out avgGrp139 --subjects `cat 
 script/subjects.id http://subjects.id` --xform talairach.m3z


 On Thu, Mar 7, 2013 at 6:15 PM, Bruce Fischl 
 fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote:

 what was your command line?

 On Thu, 7 Mar 2013, Xiaowei Song wrote:

 Sorry, I did not make it clear.
 In make_average_volume.log, the error message is:

 1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013
 mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ
 /usr/local/freesurfer/average/mni305.cor.mgz --xfm
 /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z --o
 
 /data/lis9/fs/x/avgGrp139/tmp/make_average_vol-tmp-55832/seg-1173622.mgh
 --interp nearest
 ERROR: /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z
 does not start
 as 'MNI Transform File'/spin1/users/lis9/fs/dcm.mprage.mgz
 ERROR: mri_vol2vol failed.


 On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl
 fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu
 wrote:
   sorry, I don't understand. What was the error? I don't
 see one
   in this email. Can you send us the actual screen output?

   cheers
   Bruce
   On Thu, 7 Mar 2013, Xiaowei Song wrote:

 This error may come from regio_read_mincxfm function
 in registerio.c.Does
 this mean something wrong in recon-all?

 I forgot to mention that FreeSurfer version is
  freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0


 On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song
 dawnwei.s...@gmail.com
 mailto:dawnwei.s...@gmail.com wrote:
   Hi all,

 Did you encounter the error message talairach.m3z
 does not start as
 'MNI Transform File' when making average of
 subjects?

 I checked all the recon-all.log file and did not
 find error, but when
 running make_average_subject after recon-all, then
 this error shoot.

 To repeat the error message, I tried the following
 command which is
 called by make_average_subject and found all my
 subjects shoot this
 error.

 mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
 /usr/local/freesurfer/average/mni305.cor.mgz --xfm
  1173622/mri/transforms/talairach.m3z --o
 /tmp/make_average_vol-tmp-164320_seg-1173622.mgh
 --interp nearest

 I found another same question asked before,
 butnoanswer.
 https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/0
 24
 064.html

 Any hint or help will be appreciated. Thank you.

 --
 Xiaowei Song




 --
 Xiaowei Song




 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
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 dispose of the e-mail.




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 Xiaowei Song




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Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

[Xiaowei Song]

Thank you, doug, I will try xfm!


On Thu, Mar 7, 2013 at 7:03 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 The xform has to be linear in the xfm format. The m3z cannot be used.
 doug

 On 03/07/2013 06:44 PM, Xiaowei Song wrote:
  Thanks for your help.
 
  My command line is
  make_average_subject --out avgGrp139 --subjects `cat
  script/subjects.id http://subjects.id` --xform talairach.m3z
 
 
  On Thu, Mar 7, 2013 at 6:15 PM, Bruce Fischl
  fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote:
 
  what was your command line?
 
  On Thu, 7 Mar 2013, Xiaowei Song wrote:
 
  Sorry, I did not make it clear.
  In make_average_volume.log, the error message is:
 
  1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013
  mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ
  /usr/local/freesurfer/average/mni305.cor.mgz --xfm
  /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z --o
 
 /data/lis9/fs/x/avgGrp139/tmp/make_average_vol-tmp-55832/seg-1173622.mgh
  --interp nearest
  ERROR: /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z
  does not start
  as 'MNI Transform File'/spin1/users/lis9/fs/dcm.mprage.mgz
  ERROR: mri_vol2vol failed.
 
 
  On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl
  fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu
  wrote:
sorry, I don't understand. What was the error? I don't
  see one
in this email. Can you send us the actual screen output?
 
cheers
Bruce
On Thu, 7 Mar 2013, Xiaowei Song wrote:
 
  This error may come from regio_read_mincxfm function
  in registerio.c.Does
  this mean something wrong in recon-all?
 
  I forgot to mention that FreeSurfer version is
   freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
 
 
  On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song
  dawnwei.s...@gmail.com
  mailto:dawnwei.s...@gmail.com wrote:
Hi all,
 
  Did you encounter the error message talairach.m3z
  does not start as
  'MNI Transform File' when making average of
  subjects?
 
  I checked all the recon-all.log file and did not
  find error, but when
  running make_average_subject after recon-all, then
  this error shoot.
 
  To repeat the error message, I tried the following
  command which is
  called by make_average_subject and found all my
  subjects shoot this
  error.
 
  mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
  /usr/local/freesurfer/average/mni305.cor.mgz --xfm
   1173622/mri/transforms/talairach.m3z --o
  /tmp/make_average_vol-tmp-164320_seg-1173622.mgh
  --interp nearest
 
  I found another same question asked before,
  butnoanswer.
 
 https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/0
  24
  064.html
 
  Any hint or help will be appreciated. Thank you.
 
  --
  Xiaowei Song
 
 
 
 
  --
  Xiaowei Song
 
 
 
 
  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.
 
 
 
 
  --
  Xiaowei Song
 
 
 
 
  --
  Xiaowei Song
 
 
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 --
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 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Xiaowei Song

[Freesurfer] make_average_subject error

[leonardo kay]

Hi all

Could anyone help me with this error:

MRISreadAnnotationIntoArray: vertex index out of range: 1499028058
i=5A595959, in_array_size=133467
annot file:
/home/virtualuser/apps/freesurfer/subjects/s1/surf/../label/lh.aparc.annot


This appeared after trying to average my subject data. It says ' vertex
index out of range '. All acquisitions were made
using the same parameters so I don't know what this may mean.


Thanks in advance

-- 
Leo Kay.
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Re: [Freesurfer] make_average_subject error

[Douglas N Greve]

Hi Leo, check to see if that subject's analysis is up-to-date. This 
usually happens when it was only partially re-run.
doug

leonardo kay wrote:
 Hi all

 Could anyone help me with this error:

 MRISreadAnnotationIntoArray: vertex index out of range: 1499028058 
 i=5A595959, in_array_size=133467
 annot file: 
 /home/virtualuser/apps/freesurfer/subjects/s1/surf/../label/lh.aparc.annot


 This appeared after trying to average my subject data. It says ' 
 vertex index out of range '. All acquisitions were made
 using the same parameters so I don't know what this may mean.


 Thanks in advance
  
 -- 
 Leo Kay.

 

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Re: [Freesurfer] make_average_subject error in T1.mgz and t1.mgz

[Douglas N Greve]

that's weird. I'm not sure what to do. The log says that it is creating 
T1.mgz and not t1.mgz. Can you try this:

cd  $SUBJECTS_DIR/subject/mri
 mri_normalize -g 1 nu.mgz T1.mgz

this should create T1.mgz and not t1.mgz

doug


tulu wrote:
 Dear FS experts and Prof. Douglas N Greve,
 Here is log file. I work on other machine under CentOS 5 and FS 4.5 version
 but I copy the result from this machine to other machine and find it only
 have t1.mgz rather than T1.mgz.
 I guess is the language system problem ?
 Finally I use a short matlab script to change t1.mgz name as T1.mgz.

 Thanks in advance
 Best
 JLH

 -Original Message-
 From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] 
 Sent: Monday, June 13, 2011 11:01 PM
 To: t...@ms36.hinet.net
 Cc: freesurfer
 Subject: Re: [Freesurfer] make_average_subject error in T1.mgz and t1.mgz

 Do you mean your individual subject after running through FS has a file
 called t1.mgz and not T1.mgz? Something is definitely wrong there. Can
 you send the log file?
 doug

 t...@ms36.hinet.net wrote:
   
 Dear FS experts,
 I use FS5.1 and previous data run on other machine. When I try to
 make_average_subjects program, I get error message that it can not get
 T1.mgz data from subject folder. When I check my dataset, actually it
 has t1.mgz rather than T1.mgz. how could I change the setting from
 T1.mgz to t1.mgz
 thanks help
 JLH

 

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] make_average_subject error in T1.mgz and t1.mgz

[Douglas N Greve]

Do you mean your individual subject after running through FS has a file
called t1.mgz and not T1.mgz? Something is definitely wrong there. Can
you send the log file?
doug

t...@ms36.hinet.net wrote:

 Dear FS experts,
 I use FS5.1 and previous data run on other machine. When I try to
 make_average_subjects program, I get error message that it can not get
 T1.mgz data from subject folder. When I check my dataset, actually it
 has t1.mgz rather than T1.mgz. how could I change the setting from
 T1.mgz to t1.mgz
 thanks help
 JLH

 

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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] make_average_subject error in T1.mgz and t1.mgz

[tulu]

lt;pgt;Dear FS experts,lt;br /gt;I use FS5.1 and previous data run on other 
machine. When I try to make_average_subjects program, I get error message that 
it can not get T1.mgz data from subject folder. When I check my dataset, 
actually it has t1.mgz rather than T1.mgz. how could I change the setting from 
T1.mgz to t1.mgzlt;br /gt;thanks helplt;br /gt;JLHlt;/pgt;___
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Re: [Freesurfer] make_average_subject error about limit

[Feng-Xian]

Hi,
  Thank you for your response! I solve this problem of mris_preproc. 
  The next step is to do mri_glmfit. 
  
And, when I type the following command:
mri_glmfit --y lh.noise_0.5-1-5.thickness.10.mgh --fsgd noise_0.5-1-5.fsgd 
dods --C noise_0.5-1.mtx --surf fsaverage lh --cortex --glmdir lh.noise_0.5-
1.glmdir


The terminal shows:
ERROR: Option --cortex unknown

Would you tell me what’s wrong? And how do I do to solve this error?

Thank you in advance!

Feng-Xian



On Tue, 07 Jul 2009 11:49:32 -0400, Douglas N Greve wrote
 Is there a space between -- and hemi?
 
 caching is just a way to speed some analyses by pre-smoothing and 
 sampling to the standard space.
 
 doug
 
 Feng-Xian wrote:
  Hi,
 
 I copied the default average subject from $FREESURFER_HOME/subjects 
dir 
  to my analysis dir. 
 
  Then, I make a FSGD file and some contrast matrices and put them into my 
  analysis dir.
 
  After that, I start to run group analysis. 
 
  But, when I type the following commands: 
 
  mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh --
meas 
  thickness --out lh.noise_0.5-1-5.thickness.00.mgh
 
  The terminal shows:
 
  ERROR: flag -- not recognized
 
 
  Now, I have two problems want to ask.
 
  1) What's wrong about the commands that I type? And, how to solve the 
 problem? 
 
  2) I found this commands from the FreeSurfer web. And, I'm confused 
about 
 that two ways to do analysis.
One is cached (qcached) data, and the other is uncached data. 
What's 
 way is suitable to my subjects? (My subjects is one factor and three 
 levels, had run QDEC before, but QDEC is not good job to analysis, 
and, I 
 want to change the analysis method from QDEC to DODS) 
So, which way do I choose to analysis my subjects?? Idon't 
understand 
 the differences from them.
 
 
  Thank you in advance!
 
  Feng-Xian
 
 
 
  On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote

  in general, it is not necessary to run make_average_subject prior to
  performing an analysis.  using the default average subject that
  freesurfer provides, named 'fsaverage', is sufficient for most cases,
  because it doesnt affect the analysis, its only used as a target upon
  which to project results.  the 'fsaverage' subject is in the
  $FREESURFER_HOME/subjects dir, and you should copy it to your own
  SUBJECTS_DIR prior to performing any group analysis.
 
  Nick
 
  On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote:
  
  Hi,

 I know I wont to do QDEC now, so I want to change the method of 
group 
  analysis from QDEC to the web you tell me. But, I did QDEC before.
 
  Before I do DODS, should I do make_average_subject to view the result 
of 

  my 

  subjects? Or, I have another method to view the results??
 
  Thank you in advance!
 
  Feng-Xian
 
 
 
 
  On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote

  Feng-xian,
 
  I should also mention that i dont think creating your own average
  subject will solve the problem you describe, where you need to work 
  
  with

  three levels in your group.  for that, you wont be able to use qdec, 
  but will need to run things manually.  these pages give examples:
 
  http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
 
  and note one of them is 1 Factor, 3 Levels.
 
  Nick
 
  On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote:
  
  Feng-Xian,
 
  It appears that you do not have permission on your system to change 

  the

  limits.  So you will have to edit the scripts make_average_volume,
  make_average_surface and make_average_subject to comment out 

  the 'limit'

  line, so that it looks like this:
 
  #limit descriptors unlimited 
 
 
  Nick
 
  On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote:

  Hi,
 
 I have a problem with make_average_subject.
 
  After running all commands (including ln -s 
  $FREESURFER_HOME/subjects/fsaverage 
  and recon-all -s subjid -qcache for all my subjects) about 
  
  running 

  QDEC, I 

  found that QDEC could not analysis my group.
 
  Because the group have 1 factor and three levels, QDEC can't run.
 
  So, I want to change the method of analysis from QDEC to DODS.
 
 
  I had a fsaverage file when I running QDEC, but the fsaverage did 
  
  not 

  use my 

  subjects to make. 
 
  So, can I use the fsaverage file to run DODS? 
 
  If not, I should make a new fsaverage with my subjects. 
 
  But, I encounter the problem about make_average_subject.
 
 
  When I type:
 
  make_average_subject --subects subjid1 subjid2 ...
 
  the terminal show that:
 
  limit: descriptors: Can't remove limit 
 
 
  What's wrong about the command I type? And, how to solve the 
  
  problem?

 
 
  Thank you in advance!
 
  Feng-Xian
 
 
  -
  Chang Gung University Mail Server 

Re: [Freesurfer] make_average_subject error about limit

[Douglas N Greve]

You probably have an older version that does not recoginze --cortex. Try 
--label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label instead


Feng-Xian wrote:

Hi,
  Thank you for your response! I solve this problem of mris_preproc. 
  The next step is to do mri_glmfit. 
  
And, when I type the following command:
mri_glmfit --y lh.noise_0.5-1-5.thickness.10.mgh --fsgd noise_0.5-1-5.fsgd 
dods --C noise_0.5-1.mtx --surf fsaverage lh --cortex --glmdir lh.noise_0.5-

1.glmdir


The terminal shows:
ERROR: Option --cortex unknown

Would you tell me what’s wrong? And how do I do to solve this error?

Thank you in advance!

Feng-Xian



On Tue, 07 Jul 2009 11:49:32 -0400, Douglas N Greve wrote
  

Is there a space between -- and hemi?

caching is just a way to speed some analyses by pre-smoothing and 
sampling to the standard space.


doug

Feng-Xian wrote:


Hi,

   I copied the default average subject from $FREESURFER_HOME/subjects 
  
dir 
  
to my analysis dir. 

Then, I make a FSGD file and some contrast matrices and put them into my 
analysis dir.


After that, I start to run group analysis. 

But, when I type the following commands: 


mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh --
  
meas 
  

thickness --out lh.noise_0.5-1-5.thickness.00.mgh

The terminal shows:

ERROR: flag -- not recognized


Now, I have two problems want to ask.

1) What's wrong about the commands that I type? And, how to solve the 
   problem? 

2) I found this commands from the FreeSurfer web. And, I'm confused 
  
about 
  

   that two ways to do analysis.
  One is cached (qcached) data, and the other is uncached data. 
  
What's 
  
   way is suitable to my subjects? (My subjects is one factor and three 
   levels, had run QDEC before, but QDEC is not good job to analysis, 
  
and, I 
  
   want to change the analysis method from QDEC to DODS) 
  So, which way do I choose to analysis my subjects?? Idon't 
  
understand 
  

   the differences from them.


Thank you in advance!

Feng-Xian



On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote
  
  

in general, it is not necessary to run make_average_subject prior to
performing an analysis.  using the default average subject that
freesurfer provides, named 'fsaverage', is sufficient for most cases,
because it doesnt affect the analysis, its only used as a target upon
which to project results.  the 'fsaverage' subject is in the
$FREESURFER_HOME/subjects dir, and you should copy it to your own
SUBJECTS_DIR prior to performing any group analysis.

Nick

On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote:



Hi,
  
   I know I wont to do QDEC now, so I want to change the method of 
  
group 
  

analysis from QDEC to the web you tell me. But, I did QDEC before.

Before I do DODS, should I do make_average_subject to view the result 
  
of 
  
  
  
my 
  
  

subjects? Or, I have another method to view the results??

Thank you in advance!

Feng-Xian




On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote
  
  

Feng-xian,

I should also mention that i dont think creating your own average
subject will solve the problem you describe, where you need to work 



with
  
  
three levels in your group.  for that, you wont be able to use qdec, 
but will need to run things manually.  these pages give examples:


http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples

and note one of them is 1 Factor, 3 Levels.

Nick

On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote:



Feng-Xian,

It appears that you do not have permission on your system to change 
  
  

the
  
  

limits.  So you will have to edit the scripts make_average_volume,
make_average_surface and make_average_subject to comment out 
  
  

the 'limit'
  
  

line, so that it looks like this:

#limit descriptors unlimited 



Nick

On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote:
  
  

Hi,

   I have a problem with make_average_subject.

After running all commands (including ln -s 
$FREESURFER_HOME/subjects/fsaverage 
and recon-all -s subjid -qcache for all my subjects) about 


running 
  
  
QDEC, I 
  
  

found that QDEC could not analysis my group.

Because the group have 1 factor and three levels, QDEC can't run.

So, I want to change the method of analysis from QDEC to DODS.


I had a fsaverage file when I running QDEC, but the fsaverage did 


not 
  
  
use my 
  
  
subjects to make. 

So, can I use the fsaverage file to run DODS? 

If not, I should make a new fsaverage with my subjects. 


But, I encounter the problem about make_average_subject.


When I type:

make_average_subject --subects subjid1 subjid2 ...

the terminal show that:

limit: descriptors: Can't remove limit 



What's wrong 

Re: [Freesurfer] make_average_subject error about limit

[Feng-Xian]

Hi,

   I copied the default average subject from $FREESURFER_HOME/subjects dir 
to my analysis dir. 

Then, I make a FSGD file and some contrast matrices and put them into my 
analysis dir.

After that, I start to run group analysis. 

But, when I type the following commands: 

mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh --meas 
thickness --out lh.noise_0.5-1-5.thickness.00.mgh

The terminal shows:

ERROR: flag -- not recognized


Now, I have two problems want to ask.

1) What's wrong about the commands that I type? And, how to solve the 
   problem? 

2) I found this commands from the FreeSurfer web. And, I'm confused about 
   that two ways to do analysis.
  One is cached (qcached) data, and the other is uncached data. What's 
   way is suitable to my subjects? (My subjects is one factor and three 
   levels, had run QDEC before, but QDEC is not good job to analysis, and, I 
   want to change the analysis method from QDEC to DODS) 
  So, which way do I choose to analysis my subjects?? Idon't understand 
   the differences from them.


Thank you in advance!

Feng-Xian



On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote
 in general, it is not necessary to run make_average_subject prior to
 performing an analysis.  using the default average subject that
 freesurfer provides, named 'fsaverage', is sufficient for most cases,
 because it doesnt affect the analysis, its only used as a target upon
 which to project results.  the 'fsaverage' subject is in the
 $FREESURFER_HOME/subjects dir, and you should copy it to your own
 SUBJECTS_DIR prior to performing any group analysis.
 
 Nick
 
 On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote:
  Hi,

 I know I wont to do QDEC now, so I want to change the method of group 
  analysis from QDEC to the web you tell me. But, I did QDEC before.
  
  Before I do DODS, should I do make_average_subject to view the result of 
my 
  subjects? Or, I have another method to view the results??
  
  Thank you in advance!
  
  Feng-Xian
  
  
  
  
  On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote
   Feng-xian,
   
   I should also mention that i dont think creating your own average
   subject will solve the problem you describe, where you need to work 
with
   three levels in your group.  for that, you wont be able to use qdec, 
   but will need to run things manually.  these pages give examples:
   
   http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
   
   and note one of them is 1 Factor, 3 Levels.
   
   Nick
   
   On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote:
Feng-Xian,

It appears that you do not have permission on your system to change 
the
limits.  So you will have to edit the scripts make_average_volume,
make_average_surface and make_average_subject to comment out 
the 'limit'
line, so that it looks like this:

#limit descriptors unlimited 


Nick

On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote:
 Hi,
 
I have a problem with make_average_subject.
 
 After running all commands (including ln -s 
 $FREESURFER_HOME/subjects/fsaverage 
 and recon-all -s subjid -qcache for all my subjects) about 
running 
  QDEC, I 
 found that QDEC could not analysis my group.
 
 Because the group have 1 factor and three levels, QDEC can't run.
 
 So, I want to change the method of analysis from QDEC to DODS.
 
 
 I had a fsaverage file when I running QDEC, but the fsaverage did 
not 
  use my 
 subjects to make. 
 
 So, can I use the fsaverage file to run DODS? 
 
 If not, I should make a new fsaverage with my subjects. 
 
 But, I encounter the problem about make_average_subject.
 
 
 When I type:
 
 make_average_subject --subects subjid1 subjid2 ...
 
 the terminal show that:
 
 limit: descriptors: Can't remove limit 
 
 
 What's wrong about the command I type? And, how to solve the 
problem?
 
 
 
 
 Thank you in advance!
 
 Feng-Xian
 
 
 -
 Chang Gung University Mail Server Web Mail system
 By Chang-Gung University Information Center
 (http://www.cgu.edu.tw/ic/)
 
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Re: [Freesurfer] make_average_subject error about limit

[Douglas N Greve]

Is there a space between -- and hemi?

caching is just a way to speed some analyses by pre-smoothing and 
sampling to the standard space.


doug

Feng-Xian wrote:

Hi,

   I copied the default average subject from $FREESURFER_HOME/subjects dir 
to my analysis dir. 

Then, I make a FSGD file and some contrast matrices and put them into my 
analysis dir.


After that, I start to run group analysis. 

But, when I type the following commands: 

mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh --meas 
thickness --out lh.noise_0.5-1-5.thickness.00.mgh


The terminal shows:

ERROR: flag -- not recognized


Now, I have two problems want to ask.

1) What's wrong about the commands that I type? And, how to solve the 
   problem? 

2) I found this commands from the FreeSurfer web. And, I'm confused about 
   that two ways to do analysis.
  One is cached (qcached) data, and the other is uncached data. What's 
   way is suitable to my subjects? (My subjects is one factor and three 
   levels, had run QDEC before, but QDEC is not good job to analysis, and, I 
   want to change the analysis method from QDEC to DODS) 
  So, which way do I choose to analysis my subjects?? Idon't understand 
   the differences from them.



Thank you in advance!

Feng-Xian



On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote
  

in general, it is not necessary to run make_average_subject prior to
performing an analysis.  using the default average subject that
freesurfer provides, named 'fsaverage', is sufficient for most cases,
because it doesnt affect the analysis, its only used as a target upon
which to project results.  the 'fsaverage' subject is in the
$FREESURFER_HOME/subjects dir, and you should copy it to your own
SUBJECTS_DIR prior to performing any group analysis.

Nick

On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote:


Hi,
  
   I know I wont to do QDEC now, so I want to change the method of group 
analysis from QDEC to the web you tell me. But, I did QDEC before.


Before I do DODS, should I do make_average_subject to view the result of 
  
my 
  

subjects? Or, I have another method to view the results??

Thank you in advance!

Feng-Xian




On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote
  

Feng-xian,

I should also mention that i dont think creating your own average
subject will solve the problem you describe, where you need to work 


with
  
three levels in your group.  for that, you wont be able to use qdec, 
but will need to run things manually.  these pages give examples:


http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples

and note one of them is 1 Factor, 3 Levels.

Nick

On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote:


Feng-Xian,

It appears that you do not have permission on your system to change 
  

the
  

limits.  So you will have to edit the scripts make_average_volume,
make_average_surface and make_average_subject to comment out 
  

the 'limit'
  

line, so that it looks like this:

#limit descriptors unlimited 



Nick

On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote:
  

Hi,

   I have a problem with make_average_subject.

After running all commands (including ln -s 
$FREESURFER_HOME/subjects/fsaverage 
and recon-all -s subjid -qcache for all my subjects) about 

running 
  
QDEC, I 
  

found that QDEC could not analysis my group.

Because the group have 1 factor and three levels, QDEC can't run.

So, I want to change the method of analysis from QDEC to DODS.


I had a fsaverage file when I running QDEC, but the fsaverage did 

not 
  
use my 
  
subjects to make. 

So, can I use the fsaverage file to run DODS? 

If not, I should make a new fsaverage with my subjects. 


But, I encounter the problem about make_average_subject.


When I type:

make_average_subject --subects subjid1 subjid2 ...

the terminal show that:

limit: descriptors: Can't remove limit 



What's wrong about the command I type? And, how to solve the 


problem?
  



Thank you in advance!

Feng-Xian


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By Chang-Gung University Information Center
(http://www.cgu.edu.tw/ic/)

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--
Douglas 

[Freesurfer] make_average_subject error about limit

[Feng-Xian]

Hi,

   I have a problem with make_average_subject.

After running all commands (including ln -s 
$FREESURFER_HOME/subjects/fsaverage 
and recon-all -s subjid -qcache for all my subjects) about running QDEC, I 
found that QDEC could not analysis my group.

Because the group have 1 factor and three levels, QDEC can't run.

So, I want to change the method of analysis from QDEC to DODS.


I had a fsaverage file when I running QDEC, but the fsaverage did not use my 
subjects to make. 

So, can I use the fsaverage file to run DODS? 

If not, I should make a new fsaverage with my subjects. 

But, I encounter the problem about make_average_subject.


When I type:

make_average_subject --subects subjid1 subjid2 ...

the terminal show that:

limit: descriptors: Can't remove limit 


What's wrong about the command I type? And, how to solve the problem?




Thank you in advance!

Feng-Xian


-
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(http://www.cgu.edu.tw/ic/)

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Re: [Freesurfer] make_average_subject error about limit

[Nick Schmansky]

Feng-Xian,

It appears that you do not have permission on your system to change the
limits.  So you will have to edit the scripts make_average_volume,
make_average_surface and make_average_subject to comment out the 'limit'
line, so that it looks like this:

#limit descriptors unlimited 


Nick

On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote:
 Hi,
 
I have a problem with make_average_subject.
 
 After running all commands (including ln -s 
 $FREESURFER_HOME/subjects/fsaverage 
 and recon-all -s subjid -qcache for all my subjects) about running QDEC, I 
 found that QDEC could not analysis my group.
 
 Because the group have 1 factor and three levels, QDEC can't run.
 
 So, I want to change the method of analysis from QDEC to DODS.
 
 
 I had a fsaverage file when I running QDEC, but the fsaverage did not use my 
 subjects to make. 
 
 So, can I use the fsaverage file to run DODS? 
 
 If not, I should make a new fsaverage with my subjects. 
 
 But, I encounter the problem about make_average_subject.
 
 
 When I type:
 
 make_average_subject --subects subjid1 subjid2 ...
 
 the terminal show that:
 
 limit: descriptors: Can't remove limit 
 
 
 What's wrong about the command I type? And, how to solve the problem?
 
 
 
 
 Thank you in advance!
 
 Feng-Xian
 
 
 -
 Chang Gung University Mail Server Web Mail system
 By Chang-Gung University Information Center
 (http://www.cgu.edu.tw/ic/)
 
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Re: [Freesurfer] make_average_subject error about limit

[Nick Schmansky]

Feng-xian,

I should also mention that i dont think creating your own average
subject will solve the problem you describe, where you need to work with
three levels in your group.  for that, you wont be able to use qdec, but
will need to run things manually.  these pages give examples:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples

and note one of them is 1 Factor, 3 Levels.

Nick


On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote:
 Feng-Xian,
 
 It appears that you do not have permission on your system to change the
 limits.  So you will have to edit the scripts make_average_volume,
 make_average_surface and make_average_subject to comment out the 'limit'
 line, so that it looks like this:
 
 #limit descriptors unlimited 
 
 
 Nick
 
 On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote:
  Hi,
  
 I have a problem with make_average_subject.
  
  After running all commands (including ln -s 
  $FREESURFER_HOME/subjects/fsaverage 
  and recon-all -s subjid -qcache for all my subjects) about running QDEC, 
  I 
  found that QDEC could not analysis my group.
  
  Because the group have 1 factor and three levels, QDEC can't run.
  
  So, I want to change the method of analysis from QDEC to DODS.
  
  
  I had a fsaverage file when I running QDEC, but the fsaverage did not use 
  my 
  subjects to make. 
  
  So, can I use the fsaverage file to run DODS? 
  
  If not, I should make a new fsaverage with my subjects. 
  
  But, I encounter the problem about make_average_subject.
  
  
  When I type:
  
  make_average_subject --subects subjid1 subjid2 ...
  
  the terminal show that:
  
  limit: descriptors: Can't remove limit 
  
  
  What's wrong about the command I type? And, how to solve the problem?
  
  
  
  
  Thank you in advance!
  
  Feng-Xian
  
  
  -
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  By Chang-Gung University Information Center
  (http://www.cgu.edu.tw/ic/)
  
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Re: [Freesurfer] make_average_subject error about limit

[Douglas N Greve]

You don't *have to* to run make_average_subject to do your analysis, 
only if you want to view the results on a map with the curvature 
patterns averaged over your subjects. As for the limit error, how old is 
your version of freesurfer? That line was removed about 1.5 years ago...


doug

Feng-Xian wrote:

Hi,

   I have a problem with make_average_subject.

After running all commands (including ln -s 
$FREESURFER_HOME/subjects/fsaverage 
and recon-all -s subjid -qcache for all my subjects) about running QDEC, I 
found that QDEC could not analysis my group.


Because the group have 1 factor and three levels, QDEC can't run.

So, I want to change the method of analysis from QDEC to DODS.


I had a fsaverage file when I running QDEC, but the fsaverage did not use my 
subjects to make. 

So, can I use the fsaverage file to run DODS? 

If not, I should make a new fsaverage with my subjects. 


But, I encounter the problem about make_average_subject.


When I type:

make_average_subject --subects subjid1 subjid2 ...

the terminal show that:

limit: descriptors: Can't remove limit 



What's wrong about the command I type? And, how to solve the problem?




Thank you in advance!

Feng-Xian


-
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By Chang-Gung University Information Center
(http://www.cgu.edu.tw/ic/)

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


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] Make_average_subject error

[Furlong, Carolyn]

Thanks Doug, 
 
I have tried your suggestion and set the command make_average_subject running 
again.  I has been going for several hours but there is no visible 
change/activity on the console, is this unusual?.   
 
Also, there are only 13 subjects, how long would you expect this process to 
take per subject?
 
Best wishes
Carolyn



From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Wed 5/9/2007 6:21 PM
To: Furlong, Carolyn
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Make_average_subject error



you may be using a version that does not have this option. Try using these

doug

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

Furlong, Carolyn wrote: 


Hi all,

I tried running it again with --no-symlink but this error came up

ERROR: Flag --no-symlink unrecognized.

any advice?

Best wishes
Carolyn 





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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] Make_average_subject error

[Doug Greve]

it should not be taking that long. It must be hanging somewhere. Try 
re-running it with --debug as the first option. It will print out a 
bunch of stuff to the screen, but you should be able to see where it 
hangs (if it does).


doug

Furlong, Carolyn wrote:


Thanks Doug,
 
I have tried your suggestion and set the command make_average_subject 
running again.  I has been going for several hours but there is no 
visible change/activity on the console, is this unusual?.   
 
Also, there are only 13 subjects, how long would you expect this 
process to take per subject?
 
Best wishes

Carolyn


From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Wed 5/9/2007 6:21 PM
To: Furlong, Carolyn
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Make_average_subject error


you may be using a version that does not have this option. Try using these

doug

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

Furlong, Carolyn wrote:



Hi all,

I tried running it again with --no-symlink but this error came up

ERROR: Flag --no-symlink unrecognized.

any advice?

Best wishes
Carolyn



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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

 




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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
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[Freesurfer] Make_average_subject error

[Furlong, Carolyn]

Hi all

I have run the script make_average_subject and the error message at the end is: 

ln: creating symbolic link `rh.sphere' to `rh.sphere.reg': Operation not 
permitted

only rh* files have been created.

Can you help?

Best wishes
Carolyn

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[Freesurfer] Make_average_subject error

[Furlong, Carolyn]

Hi all,

I tried running it again with --no-symlink but this error came up

ERROR: Flag --no-symlink unrecognized.

any advice?

Best wishes
Carolyn
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Re: [Freesurfer] Make_average_subject error

[Anthony Steven Dick]

I have been able to run it with --no-symlink (the flag has to go last), 
but I get errors like this:


mris_make_average_surface: could not read surface file 
/Volumes/data/NL-GCS/subjects/freesurfer_3.0.1/GCS_adults/--no-symlink/surf/rh.sphere.reg


Thanks.

Anthony


Furlong, Carolyn wrote:


Hi all,

I tried running it again with --no-symlink but this error came up

ERROR: Flag --no-symlink unrecognized.

any advice?

Best wishes
Carolyn



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Post-Doctoral Scholar
Human Neuroscience Laboratory
Department of Neurology
The University of Chicago
5841 S. Maryland Ave. MC-2030
Chicago, IL 60637
Phone: (773)-834-7770
Email: [EMAIL PROTECTED]
Web: http://home.uchicago.edu/~adick/

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Re: [Freesurfer] Make_average_subject error

[Doug Greve]

you may be using a version that does not have this option. Try using these

doug

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

Furlong, Carolyn wrote:



Hi all,

I tried running it again with --no-symlink but this error came up

ERROR: Flag --no-symlink unrecognized.

any advice?

Best wishes
Carolyn



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--
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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] make_average_subject error?

[Brian Schweinsburg, Ph.D.]

Title: Re: [Freesurfer] make_average_subject error?



Hi Doug,
I changed the flags to efxv as you recommend, and here is the output for make_average_subject, make_average_volume and make_average_surface. The script doesnt seem to be accepting my command line arguments. I am using the current dev version on a Fedora Core 4 system, if that helps.

Thanks,
Brian

[EMAIL PROTECTED] subjects]$ make_average_subject --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036

set VERSION = '$Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp $'
set VERSION = $Id: make_average_subject,v 1.2 2005/09/09 14:37:17 nicks Exp $

set PrintHelp = 0 ;
set PrintHelp = 0

if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif

set average_subject=average
set average_subject=average
set ddir = ${SUBJECTS_DIR}/${average_subject}
set ddir = /apps/freesurfer/subjects/average
set transform_fname=
set transform_fname=
set XFORM_FLAG=
set XFORM_FLAG=

if ( $#argv == 0 ) then
if ( 27 == 0 ) then

set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l

**
[EMAIL PROTECTED] subjects]$ make_average_volume --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036

set VERSION = '$Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp $' ;
set VERSION = $Id: make_average_volume,v 1.2 2005/08/19 21:27:19 greve Exp $

set PrintHelp = 0 ;
set PrintHelp = 0
set cleanup = 0 ;
set cleanup = 0
set transform_fname = talairach.xfm
set transform_fname = talairach.xfm

if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif

set average_subject = average
set average_subject = average

set cmdargs = ( $argv ) ;
set cmdargs = ( --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036 )
if ( $#argv == 0 ) then
if ( 27 == 0 ) then

set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l

**
[EMAIL PROTECTED] subjects]$ make_average_surface --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036
set VERSION = '$Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve Exp $' ;
set VERSION = $Id: make_average_surface,v 1.10 2005/08/19 21:36:46 greve Exp $

set PrintHelp = 0 ;
set PrintHelp = 0

if ( $?SUBJECTS ) then
if ( 0 ) then
if ( $?SUBJECTS_DIR ) then
if ( 1 ) then
set SUBJECTS_DIR= ( $SUBJECTS_DIR )
set SUBJECTS_DIR= ( /apps/freesurfer/subjects )
endif
endif

set average_subject=average
set average_subject=average
set ddir = ${SUBJECTS_DIR}/${average_subject}
set ddir = /apps/freesurfer/subjects/average
set transform_fname=
set transform_fname=
set XFORM_FLAG=
set XFORM_FLAG=

if ( $#argv == 0 ) then
if ( 27 == 0 ) then

set n = `echo $argv | grep -e --help | wc -l`
set n = `echo $argv | grep -e --help | wc -l`
echo --out average_bcs --subjects SC010 SC011 SC012 SC013 SC015 SC016 SC017 SC018 SC019 SC020 SC021 SC022 SC023 SC024 SC025 SC026 SC027 SC030 SC031 SC032 SC033 SC034 SC035 SC036
grep -e --help
wc -l





From: Doug Greve [EMAIL PROTECTED]
Date: Tue, 27 Sep 2005 15:04:59 -0400
To: Brian Schweinsburg, Ph.D. [EMAIL PROTECTED]
Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] make_average_subject error?


Try editing those scripts so that the first line is:

#!/bin/tcsh -efxv

ie, adding xv

This turns on all kinds of debugging


Brian Schweinsburg, Ph.D. wrote: 
 Re: [Freesurfer] make_average_subject error? Hi Doug,
The same thing happens when I try to run them separately. It exits to the prompt with no messages.

Brian

-- 
Brian C. Schweinsburg, Ph.D.
Assistant Adjunct Professor of Psychiatry
University of California, San Diego
Office: 858-552-8585 x6109
Cell: 858-354-3756



From: Doug Greve [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] 
Date: Tue, 27 Sep 2005 11:16:00 -0400
To: Brian Schweinsburg, Ph.D. [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] 
Cc: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer

Re: [Freesurfer] make_average_subject error?

[Doug Greve]

Can you run make_average_surface and make_average_volume separately?

Brian Schweinsburg, Ph.D. wrote:

  I ran it with make_average_subject --debug \
--subjects SC010 SC012 ...

I also tried it with --echo. It provides no output.

I checked the script and it is executable. I looked through the code and
everything seems reasonable given my system except the part that says:
"if person = brian; exit 0"

Brian

  
  
From: Doug Greve [EMAIL PROTECTED]
Date: Mon, 26 Sep 2005 16:40:48 -0400
To: "Brian Schweinsburg, Ph.D." [EMAIL PROTECTED]
Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] make_average_subject error?


try running it with --debug and send us the output

Brian Schweinsburg, Ph.D. wrote:



  Hi Folks,

I tried running the latest make_average_subject script (and the
make_average_surface/volume scripts) using the expected command line syntax
and after hitting enter it immediately exits to the csh without error, but
does not produce anything.

make_average_subject --subjects SC010 SC011 SC012 ...

I am running the latested dev release with Fedora Core 4.

Any ideas as to the problem?
Brian



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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422


  
  

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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422



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Re: [Freesurfer] make_average_subject error?

[Brian Schweinsburg, Ph.D.]

Title: Re: [Freesurfer] make_average_subject error?



Hi Doug,
The same thing happens when I try to run them separately. It exits to the prompt with no messages.

Brian

-- 
Brian C. Schweinsburg, Ph.D.
Assistant Adjunct Professor of Psychiatry
University of California, San Diego
Office: 858-552-8585 x6109
Cell: 858-354-3756


From: Doug Greve [EMAIL PROTECTED]
Date: Tue, 27 Sep 2005 11:16:00 -0400
To: Brian Schweinsburg, Ph.D. [EMAIL PROTECTED]
Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] make_average_subject error?


Can you run make_average_surface and make_average_volume separately?

Brian Schweinsburg, Ph.D. wrote: 
 
I ran it with make_average_subject --debug \
--subjects SC010 SC012 ...

I also tried it with --echo. It provides no output.

I checked the script and it is executable. I looked through the code and
everything seems reasonable given my system except the part that says:
if person = brian; exit 0

Brian



 
From: Doug Greve [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] 
Date: Mon, 26 Sep 2005 16:40:48 -0400
To: Brian Schweinsburg, Ph.D. [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] 
Cc: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] make_average_subject error?


try running it with --debug and send us the output

Brian Schweinsburg, Ph.D. wrote:



 
Hi Folks,

I tried running the latest make_average_subject script (and the
make_average_surface/volume scripts) using the expected command line syntax
and after hitting enter it immediately exits to the csh without error, but
does not produce anything.

make_average_subject --subjects SC010 SC011 SC012 ...

I am running the latested dev release with Fedora Core 4.

Any ideas as to the problem?
Brian



___
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
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422



 


___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer





-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422





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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] make_average_subject error?

[Doug Greve]

Try editing those scripts so that the first line is:

#!/bin/tcsh -efxv

ie, adding "xv"

This turns on all kinds of debugging


Brian Schweinsburg, Ph.D. wrote:

  Re: [Freesurfer] make_average_subject error?
  Hi
Doug,
The same thing happens when I try to run them separately. It exits to
the prompt with no messages.
  
Brian
  
-- 
Brian C. Schweinsburg, Ph.D.
Assistant Adjunct Professor of Psychiatry
University of California, San Diego
Office: 858-552-8585 x6109
Cell: 858-354-3756
  
  
  From: Doug Greve
[EMAIL PROTECTED]
  Date: Tue, 27 Sep 2005 11:16:00 -0400
  To: "Brian Schweinsburg, Ph.D." [EMAIL PROTECTED]
  Cc: "freesurfer@nmr.mgh.harvard.edu"
freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] make_average_subject error?
  
  
Can you run make_average_surface and make_average_volume separately?
  
Brian Schweinsburg, Ph.D. wrote: 
  
   
I ran it with make_average_subject --debug \
--subjects SC010 SC012 ...

I also tried it with --echo. It provides no output.

I checked the script and it is executable. I looked through the code and
everything seems reasonable given my system except the part that says:
"if person = brian; exit 0"

Brian




 
From: Doug Greve [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
  
Date: Mon, 26 Sep 2005 16:40:48 -0400
To: "Brian Schweinsburg, Ph.D." [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
  
Cc: "freesurfer@nmr.mgh.harvard.edu" mailto:freesurfer@nmr.mgh.harvard.edu
freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
  
Subject: Re: [Freesurfer] make_average_subject error?
  
  
try running it with --debug and send us the output
  
Brian Schweinsburg, Ph.D. wrote:
  


  
   
Hi Folks,

I tried running the latest make_average_subject script (and the
make_average_surface/volume scripts) using the expected command line
syntax
and after hitting enter it immediately exits to the csh without error,
but
does not produce anything.

make_average_subject --subjects SC010 SC011 SC012 ...

I am running the latested dev release with Fedora Core 4.

Any ideas as to the problem?
Brian



___
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
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
  


  
 


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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422
  
  
  

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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422



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[Freesurfer] make_average_subject error?

[Brian Schweinsburg, Ph.D.]

Hi Folks,

I tried running the latest make_average_subject script (and the
make_average_surface/volume scripts) using the expected command line syntax
and after hitting enter it immediately exits to the csh without error, but
does not produce anything.

make_average_subject --subjects SC010 SC011 SC012 ...

I am running the latested dev release with Fedora Core 4.

Any ideas as to the problem?
Brian



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] make_average_subject error?

[Doug Greve]

try running it with --debug and send us the output

Brian Schweinsburg, Ph.D. wrote:


Hi Folks,

I tried running the latest make_average_subject script (and the
make_average_surface/volume scripts) using the expected command line syntax
and after hitting enter it immediately exits to the csh without error, but
does not produce anything.

make_average_subject --subjects SC010 SC011 SC012 ...

I am running the latested dev release with Fedora Core 4.

Any ideas as to the problem?
Brian



___
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
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422


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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] make_average_subject error?

[Brian Schweinsburg, Ph.D.]

I ran it with make_average_subject --debug \
--subjects SC010 SC012 ...

I also tried it with --echo. It provides no output.

I checked the script and it is executable. I looked through the code and
everything seems reasonable given my system except the part that says:
if person = brian; exit 0

Brian

 From: Doug Greve [EMAIL PROTECTED]
 Date: Mon, 26 Sep 2005 16:40:48 -0400
 To: Brian Schweinsburg, Ph.D. [EMAIL PROTECTED]
 Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] make_average_subject error?
 
 
 try running it with --debug and send us the output
 
 Brian Schweinsburg, Ph.D. wrote:
 
 Hi Folks,
 
 I tried running the latest make_average_subject script (and the
 make_average_surface/volume scripts) using the expected command line syntax
 and after hitting enter it immediately exits to the csh without error, but
 does not produce anything.
 
 make_average_subject --subjects SC010 SC011 SC012 ...
 
 I am running the latested dev release with Fedora Core 4.
 
 Any ideas as to the problem?
 Brian
 
 
 
 ___
 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
 [EMAIL PROTECTED]
 Phone Number: 617-724-2358
 Fax: 617-726-7422
 


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