date:20181120

External Email - Use Caution

Yes, I set the FreeSurfer home environment and added the license file to that 
folder. It is Word readable.

Sarah

> On Nov 20, 2018, at 12:03 PM, Greve, Douglas N.,Ph.D. 
>  wrote:
> 
> did you put it in $FREESURFER_HOME/.license ? Is it world-readable?
> 
> On 11/20/18 2:38 PM, Sarah Haigh wrote:
>> External Email - Use Caution
>> 
>> Hello Freesurfers,
>> 
>> Can anyone help with a licensing issue I have? I downloaded Freesurfer the 
>> other day with a brand new license and got the following message: “ERROR: 
>> Invalid FreeSurfer license key was found in license file”. I tried getting a 
>> new license and even borrowed someone else’s license and they all came up 
>> with the same error. Any ideas?
>> 
>> Thanks for your help.
>> 
>> Sarah
>> 
>> _
>> 
>> Assistant Professor,
>> University of Nevada, Reno,
>> Department of Psychology and Center for Integrative Neuroscience,
>> 1664 N. Virginia Street
>> Reno, NV 89557-0296
>> 
>> Carnegie Mellon University,
>> Department of Psychology and Center for the Neural Basis of Cognition,
>> 5000 Forbes Avenue,
>> Pittsburgh, PA 15213.
>> 
>> 
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[Freesurfer] CerebralWhiteMatterVol

2018-11-20 Thread Song, Da-Yea

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Hello,

Does the CerebralWhiteMatterVol (from the aseg.stats) include the cerebellum?

Thank you so much in advance for your help!

Best,
Da-yea

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Re: [Freesurfer] aseg.stats calculations



On 11/20/18 1:37 PM, Song, Da-Yea wrote:

External Email - Use Caution
Hello,

I had a question regarding the aseg.stats and was hoping to get some help.


1.   How is the TotalGray calculated? On the wiki page it mentioned that it 
is the sum of lhCortex + rhCortex + SubCortGray + CerebellumGM. I tried 
calculating this based on the formula but got different results.

a.   TotalGray (from the aseg.stats) = 751765.612392

b.  298534.487540 (lhCortex) + 287682.124852 (rhCortex) +  58860.00 
(SubCortGray) + 49.3682 (L_cerebellum-cortex) + 50.1232 (R_cerebellum-cortex) = 
645176.103792

Check your value for cerebellum cortex. It should be more like 60,000 mm3. You 
probably are looking at the mean intensity.



2.   We have subjects that were processed in v4.0.4 and v6.0.0. Since the 
TotalGray measure did not exist in the v.4.0.4, what could we use to calculate 
the volume?

How about the above formula?

Thank you so much in advance for your help!

Best,
Da-Yea

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[Freesurfer] License issue

External Email - Use Caution

Hello Freesurfers,

Can anyone help with a licensing issue I have? I downloaded Freesurfer the 
other day with a brand new license and got the following message: “ERROR: 
Invalid FreeSurfer license key was found in license file”. I tried getting a 
new license and even borrowed someone else’s license and they all came up with 
the same error. Any ideas?

Thanks for your help.

Sarah

_

Assistant Professor,
University of Nevada, Reno,
Department of Psychology and Center for Integrative Neuroscience,
1664 N. Virginia Street 
Reno, NV 89557-0296

Carnegie Mellon University,
Department of Psychology and Center for the Neural Basis of Cognition,
5000 Forbes Avenue,
Pittsburgh, PA 15213.


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Re: [Freesurfer] License issue

2018-11-20 Thread fsbuild

External Email - Use Caution

Hello Sarah,



If you can bring up a terminal with your freesurfer environment set, then 
please try the following commands, i.e.,



$ cd $FREESURFER_HOME

$ cat $FS_LICENSE


output deleted

Without posting the contents of your license, I think the first line is 
an email address, followed by a line with several numbers, followed by 2 
lines of text.
$ ls -l $FS_LICENSE-rw-r--r--@ 1 userid staff 57 Jan 9 
2018 /Users/userid/license.txt
the rw-r-r privileges (644) mean its writeable only by you (which is fine).
- R.




- R.






Sarah HaighNovember 20, 2018 at 16:42
  External Email - Use Caution

Yes, I set the FreeSurfer home environment and added the license file to that 
folder. It is Word readable.

Sarah



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Greve, Douglas N.,Ph.D.November 20, 2018 at 15:03
  did you put it in $FREESURFER_HOME/.license ? Is it world-readable?


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Sarah HaighNovember 20, 2018 at 14:38
  External Email - Use Caution

Hello Freesurfers,

Can
 anyone help with a licensing issue I have? I downloaded Freesurfer the 
other day with a brand new license and got the following message: 
“ERROR: Invalid FreeSurfer license key was found in license file”. I 
tried getting a new license and even borrowed someone else’s license and
 they all came up with the same error. Any ideas?

Thanks for your help.

Sarah

_

Assistant Professor,
University of Nevada, Reno,
Department of Psychology and Center for Integrative Neuroscience,
1664 N. Virginia Street 
Reno, NV 89557-0296

Carnegie Mellon University,
Department of Psychology and Center for the Neural Basis of Cognition,
5000 Forbes Avenue,
Pittsburgh, PA 15213.


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Re: [Freesurfer] aseg.stats calculations {Disarmed}

2018-11-20 Thread Song, Da-Yea

External Email - Use Caution

Thank you for pointing that out! I took another look and was able to get the 
following;

TotalGray (from the aseg.stats) = 751765.612392

298534.487540 (lhCortex) + 287682.124852 (rhCortex) +  58860.00 
(SubCortGray) + 52358.1 (L_cerebellum-cortex) + 52661.8 (R_cerebellum-cortex) = 
750096.512392

There is still a difference of 1669.1. What could account for the difference?

Best,
Da-Yea

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas 
N.,Ph.D.
Sent: Tuesday, November 20, 2018 1:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aseg.stats calculations


On 11/20/18 1:37 PM, Song, Da-Yea wrote:

External Email - Use Caution
Hello,

I had a question regarding the aseg.stats and was hoping to get some help.


1.   How is the TotalGray calculated? On the wiki page it mentioned that it 
is the sum of lhCortex + rhCortex + SubCortGray + CerebellumGM. I tried 
calculating this based on the formula but got different results.

a.   TotalGray (from the aseg.stats) = 751765.612392

b.  298534.487540 (lhCortex) + 287682.124852 (rhCortex) +  58860.00 
(SubCortGray) + 49.3682 (L_cerebellum-cortex) + 50.1232 (R_cerebellum-cortex) = 
645176.103792
Check your value for cerebellum cortex. It should be more like 60,000 mm3. You 
probably are looking at the mean intensity.




2.   We have subjects that were processed in v4.0.4 and v6.0.0. Since the 
TotalGray measure did not exist in the v.4.0.4, what could we use to calculate 
the volume?
How about the above formula?


Thank you so much in advance for your help!

Best,
Da-Yea

Disclaimer:


The materials in this e-mail are private and may contain Protected Information. 
Please note that e-mail communication is not encrypted by default. You have the 
right to request further emails be encrypted by notifying the sender. Your 
continued use of e-mail constitutes your acknowledgment of these 
confidentiality and security limitations. If you are not the intended 
recipient, be advised that any unauthorized use, disclosure, copying, 
distribution, or the taking of any action in reliance on the contents of this 
information is strictly prohibited. If you have received this e-mail in error, 
please immediately notify the sender via telephone or return e-mail.




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Re: [Freesurfer] License issue

did you put it in $FREESURFER_HOME/.license ? Is it world-readable?

On 11/20/18 2:38 PM, Sarah Haigh wrote:
>  External Email - Use Caution
>
> Hello Freesurfers,
>
> Can anyone help with a licensing issue I have? I downloaded Freesurfer the 
> other day with a brand new license and got the following message: “ERROR: 
> Invalid FreeSurfer license key was found in license file”. I tried getting a 
> new license and even borrowed someone else’s license and they all came up 
> with the same error. Any ideas?
>
> Thanks for your help.
>
> Sarah
>
> _
>
> Assistant Professor,
> University of Nevada, Reno,
> Department of Psychology and Center for Integrative Neuroscience,
> 1664 N. Virginia Street
> Reno, NV 89557-0296
>
> Carnegie Mellon University,
> Department of Psychology and Center for the Neural Basis of Cognition,
> 5000 Forbes Avenue,
> Pittsburgh, PA 15213.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] CerebralWhiteMatterVol

No, it does not.

On 11/20/18 3:54 PM, Song, Da-Yea wrote:

External Email - Use Caution
Hello,

Does the CerebralWhiteMatterVol (from the aseg.stats) include the cerebellum?

Thank you so much in advance for your help!

Best,
Da-yea

Disclaimer:


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Please note that e-mail communication is not encrypted by default. You have the 
right to request further emails be encrypted by notifying the sender. Your 
continued use of e-mail constitutes your acknowledgment of these 
confidentiality and security limitations. If you are not the intended 
recipient, be advised that any unauthorized use, disclosure, copying, 
distribution, or the taking of any action in reliance on the contents of this 
information is strictly prohibited. If you have received this e-mail in error, 
please immediately notify the sender via telephone or return e-mail.



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[Freesurfer] Surface based paired t test

2018-11-20 Thread john Anderson

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Dear Freesurfer experts,
I would like to run surface based paired  t test of PET data on surface. For 
every subject I have visit pre treatment and post treatment. I tried to follow 
the instructions here https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis 
but the toturial seems to be for cortical thickness data.
How can i modify the command mris_preproc to do paired test of PEt data on 
brain surface

mris_preproc --target fsaverage --hemi lh \
   --meas thickness --out lh.paired-diff.thickness.mgh \
   --fsgd pairs.fsgd --paired-diff

thanks for any suggestion
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[Freesurfer] nu_correct ERROR (FreeSurfer v6)

2018-11-20 Thread Korom, Marta

External Email - Use Caution

Dear FreeSurfer Developers,

I have the most recent version of FreeSurfer installed on a MacOS Mojave
(10.14) and as I was running recon-all, I received the following error
message:

"Assertion failed at line 742 in file templates/CachedArray.cc
nu_estimate_np_and_em: crashed while running volume_stats (termination
status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=256)
ERROR: nu_correct
Darwin Martas-MacBook-Pro.local 18.0.0 Darwin Kernel Version 18.0.0: Wed
Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64

recon-all -s plc0061 exited with ERRORS at Tue Nov 20 22:32:15 EST 2018"

I reviewed many threads on the same error message, but none of them were
solved. I have the same version of FreeSurfer on two other MacBooks (with
older versions of iOS) and both work fine. I ran fixup_mni_paths as it was
suggested on multiple threads and nu_correct, as well and I got the
following message:

"nu_correct
nu_correct, version 1.12.0
Usage: nu_correct [-help] [options] in.mnc out.mnc"

Any thoughts on what the problem might be and how it could be fixed? Could
this be an iOS compatibility issue?

Gratefully,
Marta
-- 
*Marta Korom  |  *PhD Candidate
University of Delaware, Clinical Science
e-mail: mko...@udel.edu
phone: 646 861 8461
http://www.abcintervention.org/
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Re: [Freesurfer] License issue

2018-11-20 Thread fsbuild

External Email - Use Caution

Hi Sarah,
I would just move that file aside (rename it to something that is not 
license.txt) and follow the instructions on the wiki to generate another 
license.txt file. Then you could check it again with the previous 
commands.
 https://surfer.nmr.mgh.harvard.edu/fswiki/License
- R.

On Nov 20, 2018, at 18:30, Sarah Haigh sha...@unr.edu 
wrote:External Email - Use 
CautionHi,I ran the code and 
the license appeared, but no email address or numbers. These were the first few 
lines:FreeSurfer Software License Agreement ("Agreement")   
   Version 1.0 (February 2011)Is 
this wrong? The rwx settings look correct.ThanksSarahOn Nov 20, 2018, at 
2:52 PM, fsbuild fsbu...@contbay.com 
wrote:External Email - Use 
CautionHello Sarah,If you can 
bring up a terminal with your freesurfer environment set, then please try the 
following commands, i.e.,$ cd $FREESURFER_HOME$ cat $FS_LICENSEoutput 
deletedWithout posting the contents of your license, I think the first line 
is an email address, followed by a line with several numbers, followed by 2 
lines of text.$ ls -l $FS_LICENSE-rw-r--r--@ 1 userid staff 57 
Jan 9 2018 /Users/userid/license.txtthe rw-r-r privileges (644) 
mean its writeable only by you (which is fine).- R.- R.Sarah 
HaighNovember 20, 2018 at 16:42External Email - Use CautionYes, I 
set the FreeSurfer home environment and added the license file to that folder. 
It is Word 
readable.Sarah___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferGreve,
 Douglas N.,Ph.D.November 20, 2018 at 15:03did you put it in 
$FREESURFER_HOME/.license ? Is it 
world-readable?___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferSarah
 HaighNovember 20, 2018 at 14:38External Email - Use CautionHello 
Freesurfers,Can anyone help with a licensing issue I have? I downloaded 
Freesurfer the other day with a brand new license and got the following 
message: “ERROR: Invalid FreeSurfer license key was found in license file”. I 
tried getting a new license and even borrowed someone else’s license and they 
all came up with the same error. Any ideas?Thanks for your 
help.Sarah_Assistant Professor,University of Nevada, Reno,Department of 
Psychology and Center for Integrative Neuroscience,1664 N. Virginia 
StreetReno, NV 89557-0296Carnegie Mellon University,Department of 
Psychology and Center for the Neural Basis of Cognition,5000 Forbes 
Avenue,Pittsburgh, PA 
15213.___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurferamp;data=01%7C01%7Cshaigh%40unr..edu%7C16c5246a561d4631f7bc08d64f3ae949%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1amp;sdata=W1G8vsv2ubqApboTTM9kTHllGoV%2Bc4aX9gC6sW2fTqI%3Damp;reserved=0___Freesurfer
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[Freesurfer] differences between 'lh_G_front_middle_thickness' and 'lh_S_front_middle_thickness'

2018-11-20 Thread charujing123

External Email - Use Caution

Hi FS experts and users
I found two middle frontal cortex in thickness, with different prefix. So what 
is the difference?
Another question: Can I get the thickness of hippocampus and amygdala?
Thanks.
Rujing

2018-11-21


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Re: [Freesurfer] License issue

External Email - Use Caution

Hi,

I ran the code and the license appeared, but no email address or numbers. These
were the first few lines:
FreeSurfer Software License Agreement ("Agreement")
Version 1.0 (February 2011)

Is this wrong? The rwx settings look correct.

Thanks

Sarah

On Nov 20, 2018, at 2:52 PM, fsbuild
mailto:fsbu...@contbay.com>> wrote:

External Email - Use Caution

Hello Sarah,

If you can bring up a terminal with your freesurfer environment set, then
please try the following commands, i.e.,

$ cd $FREESURFER_HOME
$ cat $FS_LICENSE

Without posting the contents of your license, I think the first line is an
email address, followed by a line with several numbers, followed by 2 lines of
text.

$ ls -l $FS_LICENSE
-rw-r--r--@ 1 userid staff 57 Jan 9 2018 /Users/userid/license.txt

the rw-r-r privileges (644) mean its writeable only by you (which is fine).

- R.

Sarah Haigh
November 20, 2018 at 16:42
External Email - Use Caution

Yes, I set the FreeSurfer home environment and added the license file to that
folder. It is Word readable.

Sarah

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Greve, Douglas N.,Ph.D.
November 20, 2018 at 15:03
did you put it in $FREESURFER_HOME/.license ? Is it world-readable?

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Sarah Haigh
November 20, 2018 at 14:38
External Email - Use Caution

Hello Freesurfers,

Can anyone help with a licensing issue I have? I downloaded Freesurfer the
other day with a brand new license and got the following message: “ERROR:
Invalid FreeSurfer license key was found in license file”. I tried getting a
new license and even borrowed someone else’s license and they all came up with
the same error. Any ideas?

Thanks for your help.

Sarah

Assistant Professor,
University of Nevada, Reno,
Department of Psychology and Center for Integrative Neuroscience,
1664 N. Virginia Street
Reno, NV 89557-0296

Carnegie Mellon University,
Department of Psychology and Center for the Neural Basis of Cognition,
5000 Forbes Avenue,
Pittsburgh, PA 15213.

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Re: [Freesurfer] License issue {Disarmed}

External Email - Use Caution

Thank you! This seemed to work. I got my email address and the numbers this
time in the license. Not sure what happened there. Good check.

Sarah

On Nov 20, 2018, at 3:46 PM, fsbuild
mailto:fsbu...@contbay.com>> wrote:

External Email - Use Caution

Hi Sarah,

I would just move that file aside (rename it to something that is not
license.txt) and follow the instructions on the wiki to generate another
license.txt file. Then you could check it again with the previous commands.

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

- R.

On Nov 20, 2018, at 18:30, Sarah Haigh mailto:sha...@unr.edu>>
wrote:

External Email - Use Caution

Hi,

I ran the code and the license appeared, but no email address or numbers. These
were the first few lines:
FreeSurfer Software License Agreement ("Agreement")
Version 1.0 (February 2011)

Is this wrong? The rwx settings look correct.

Thanks

Sarah

On Nov 20, 2018, at 2:52 PM, fsbuild
mailto:fsbu...@contbay.com>> wrote:

External Email - Use Caution

Hello Sarah,

If you can bring up a terminal with your freesurfer environment set, then
please try the following commands, i.e.,

$ cd $FREESURFER_HOME
$ cat $FS_LICENSE

Without posting the contents of your license, I think the first line is an
email address, followed by a line with several numbers, followed by 2 lines of
text.

$ ls -l $FS_LICENSE
-rw-r--r--@ 1 userid staff 57 Jan 9 2018 /Users/userid/license.txt

the rw-r-r privileges (644) mean its writeable only by you (which is fine).

- R.

Sarah Haigh

November 20, 2018 at 16:42
External Email - Use Caution

Yes, I set the FreeSurfer home environment and added the license file to that
folder. It is Word readable.

Sarah

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Greve, Douglas N.,Ph.D.

November 20, 2018 at 15:03
did you put it in $FREESURFER_HOME/.license ? Is it world-readable?

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Sarah Haigh

November 20, 2018 at 14:38
External Email - Use Caution

Hello Freesurfers,

Thanks for your help.

Sarah

Assistant Professor,
University of Nevada, Reno,
Department of Psychology and Center for Integrative Neuroscience,
1664 N. Virginia Street
Reno, NV 89557-0296

Carnegie Mellon University,
Department of Psychology and Center for the Neural Basis of Cognition,
5000 Forbes Avenue,
Pittsburgh, PA 15213.

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Re: [Freesurfer] Bonferroni correction of 2spaces or 3spaces

2018-11-20 Thread YAN Chao-Gan

External Email - Use Caution

Thanks, Douglas!

I found subcort.mask.mgz there, that should work (subcortical mask in MNI
space)!

Best,

Chao-Gan

On Wed, Nov 21, 2018 at 12:45 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> The masking is not done as part of the correction for mult comp but when
> you run mri_glmfit. When you run it on a volume, you have to specify the
> mask, so the mask depends upon your application. For fsfast, the mask in
> $FREESURFER_HOME/subjects/fsaverage/mri.2mm is used.
>
> On 11/20/18 4:57 AM, YAN Chao-Gan wrote:
>
> External Email - Use Caution
> Dear Douglas,
>
> When doing --3spaces, is there a default subcortical mask in MNI space
> provided by freesurfer? Where is it stored?
>
> Thanks,
>
> Chao-Gan
>
> On Tue, Nov 20, 2018 at 10:12 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>>
>>
>> On 11/16/18 7:34 PM, YAN Chao-Gan wrote:
>>
>> External Email - Use Caution
>> Dear freesurfer experts,
>>
>> I have a pretty naive question but would like to confirm.
>>
>> When we use --3spaces option in multiple comparison correction, does that
>> mean we set the Cluster-wise threshold (cwp, not Cluster Defining Threshold
>> or Cluster Forming Threshold) to 0.5/3=0.0167 for lh. Similar cwp at 0.0167
>> for rh and subcortical?
>>
>> Correct.
>>
>>
>> In addition, if we use "--cortex" to restrict the calculation on cortex
>> only, where can we find the corresponding mask or label file for cortex?
>>
>> Load the ?h.cortex.label in fsaverage
>>
>>
>> Thanks,
>>
>> Chao-Gan
>>
>> --
>> Chao-Gan YAN, Ph.D.
>> Professor, Principal Investigator
>> Deputy Director, Magnetic Resonance Imaging Research Center
>> Institute of Psychology, Chinese Academy of Sciences
>> 16 Lincui Road, Chaoyang District, Beijing 100101, China
>> -
>> Initiator
>> DPABI 
>> , DPARSF
>> , PRN  and The R-fMRI
>> Network  (RFMRI.ORG )
>> http://rfmri.org/yan
>> http://scholar.google.com/citations?user=lJQ9B58J
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://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
>
>
>
> --
> Chao-Gan YAN, Ph.D.
> Professor, Principal Investigator
> Deputy Director, Magnetic Resonance Imaging Research Center
> Institute of Psychology, Chinese Academy of Sciences
> 16 Lincui Road, Chaoyang District, Beijing 100101, China
> -
> Initiator
> DPABI 
> , DPARSF
> , PRN  and The R-fMRI
> Network  (RFMRI.ORG )
> http://rfmri.org/yan
> http://scholar.google.com/citations?user=lJQ9B58J
>
>
> ___
> Freesurfer mailing 
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>
>
> ___
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-- 
Chao-Gan YAN, Ph.D.
Professor, Principal Investigator
Deputy Director, Magnetic Resonance Imaging Research Center
Institute of Psychology, Chinese Academy of Sciences
16 Lincui Road, Chaoyang District, Beijing 100101, China
-
Initiator
DPABI 
, DPARSF
, PRN  and The R-fMRI Network
 (RFMRI.ORG )
http://rfmri.org/yan
http://scholar.google.com/citations?user=lJQ9B58J
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Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

2018-11-20 Thread C.P.E. Rollins

External Email - Use Caution

Hi Douglas,
Thanks for the response. Yes, I confirm that the file 
/home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can 
view it in freeview. Any other possible errors?
Also, would you mind elaborating how to use permutation to correct for 
MC for LGI? (as in what
to enter for command line?). I don't quite understand from the 
documentation.
Thanks again,
Colleen

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Re: [Freesurfer] How to automate recon-all command for multiple subjects

2018-11-20 Thread Vivek Sharma

External Email - Use Caution

Hi
The following code worked.
for asubject in /home/vivek/Downloads/freesurfer/subjects/*.nii; do
recon-all -s ${asubject%.nii} -i $asubject -all -qcache; done

Thank you.

On Tue, Nov 20, 2018 at 12:19 PM Vivek Sharma 
wrote:

> I have a folder, lets name xyz which contains .nii file. Now I want to run
> recon-all for all the files in that folder. Please let me know how I can do
> that.
>
> On Tue, Nov 20, 2018 at 11:40 AM Vivek Sharma 
> wrote:
>
>> I'm trying to run this code but it's not working. What should be $i in
>> the code?
>> On Mon, Nov 19, 2018 at 9:15 PM Bruce Fischl 
>> wrote:
>>
>>> or you could do that all on a single line:
>>>
>>> recon-all -i $SUBJECTS_DIR/$i/ -s $i -all
>>>
>>> cheers
>>> Bruce
>>>
>>> On Mon, 19 Nov 2018,
>>> Alex Hanganu
>>> wrote:
>>>
>>> >
>>> > External Email - Use Caution
>>> >
>>> > HI Vivek,
>>> > you probably need 2 steps, first registration, second recon-all.
>>> Something
>>> > like:
>>> >
>>> > ...
>>> > do
>>> >recon-all -i $SUBJECTS_DIR/$i/ -s $i
>>> >recon-all -all -subjid $i
>>> >
>>> >
>>> > I didn't check if the scrips runs. That's the general structure.
>>> >
>>> > Best,
>>> > Alex
>>> >
>>> > Le lun. 19 nov. 2018, à 06 h 26, Vivek Sharma <
>>> vivek.sharma1...@gmail.com> a
>>> > écrit :
>>> >
>>> >   External Email - Use Caution
>>> >
>>> >   Hi,
>>> > I'm using freesurfer to generate head surfaces using MRI file.
>>> > I want to execute recon-all command for number of subjects, but unable
>>> > to run it.
>>> > The script I'm using is:
>>> >
>>> > for i in `cat *subs.txt*`
>>> > do
>>> > recon-all -s $i -all -qcache
>>> > done
>>> >
>>> > subs.txt contains the name of folder that contains .nii file.
>>> > The scripts ends with the following error:
>>> >
>>> > ERROR: no run data found in
>>> > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make sure to
>>> > have a volume called 001.mgz in
>>> > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig.
>>> > If you have a second run of data call it 002.mgz, etc.
>>> > See also:
>>> > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
>>> > Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26
>>> > 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>>> >
>>> > Please let me know how I can run recon-all for multiple subjects.
>>> > Thank you.
>>> >
>>> > --
>>> > Vivek Sharma
>>> > Mobile: +919953582034
>>> > Skype: vivek.sharma1015
>>> > ___
>>> > 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
>>
>>
>>
>> --
>> Vivek Sharma
>> Mobile: +919953582034
>> Skype: vivek.sharma1015
>>
>
>
> --
> Vivek Sharma
> Mobile: +919953582034
> Skype: vivek.sharma1015
>


-- 
Vivek Sharma
Mobile: +919953582034
Skype: vivek.sharma1015
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[Freesurfer] 'lh_G_Ins_lg_cent_ins_volume' and 'lh_G_insular_short_volume'

2018-11-20 Thread charujing123

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Hi, what is difference between 'lh_G_Ins_lg_cent_ins_volume' and 
'lh_G_insular_short_volume'. Are these both insula?
Thanks.
Rujing

2018-11-21


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Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

2018-11-20 Thread C.P.E. Rollins

   External Email - Use Caution

Thanks Douglas, I've attached here the output from mri_glmfit-sim 
--glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces 
--debug


Could you clarify how to use permutation to correct for MC for LGI? (as 
in what to enter for command line?). I don't quite understand from the 
documentation.


Thanks very much,
Colleenset echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )

goto parse_args_return ;
goto parse_args_return

goto check_params ;
goto check_params
if ( $#glmdir == 0 ) then
if ( 1 == 0 ) then
if ( $DoSim ) then
if ( 0 ) then
set residual = ( )
set residual = ( )
if ( $nulltype == perm && $PermResid ) then
if ( == perm && 1 ) then
if ( $DiagCluster && $DoBackground ) then
if ( 0 && 0 ) then
if ( $DiagCluster && $DoPBSubmit ) then
if ( 0 && 0 ) then
if ( $DiagCluster && $DoSim == 0 ) then
if ( 0 && 0 == 0 ) then

goto check_params_return ;
goto check_params_return

if ( ! -e $glmdir ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir ) then

set glmfitlog = $glmdir/mri_glmfit.log
set glmfitlog = lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
if ( ! -e $glmfitlog ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir/mri_glmfit.log ) then

if ( $nulltype != perm ) then
if ( != perm ) then
set fwhmfile = $glmdir/fwhm.dat
set fwhmfile = lh.5.lgi_MAN_new.glmdir/fwhm.dat
if ( ! -e $fwhmfile ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir/fwhm.dat ) then

set fwhm = `cat $fwhmfile` ;
set fwhm = `cat $fwhmfile`
cat lh.5.lgi_MAN_new.glmdir/fwhm.dat
else
else

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
awk {if($1 == "cwd") print $2}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
if ( 0 && ! -e $glmfitcwd ) then
if ( 0 && ! -e /home/cper2/BeneMin/Freesurfer ) then
set glmfitcwd = `pwd` ;
set glmfitcwd = `pwd`
pwd

set anattype = volume ;
set anattype = volume
set subject = ( ) ;
set subject = ( )
set hemi = ( ) ;
set hemi = ( )
set surf = "white" ;
set surf = white
set wls = ( ) ;
set wls = ( )

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
awk {if($1 == "cwd") print $2}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log


set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`
set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`
awk {if($1 == "cmdline") print $0}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
set glmfitcmd = ( $glmfitcmd0 ) ;
set glmfitcmd = ( cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd 
FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C 
contrast_dods.txt )
echo $glmfitcmd
echo cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt 
dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods 
--glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
set gd2mtx = dods
set gd2mtx = dods
set UseTable = 0 ;
set UseTable = 0
set label = ( ) ;
set label = ( )
while ( $#glmfitcmd )
while ( 14 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = cmdline
shift glmfitcmd

switch ( $flag )
switch ( cmdline )
case "mri_glmfit"
case mri_glmfit
case "--prune"
case --prune
case "--no-prune"
case --no-prune
case "--pca"
case --pca
case "--synth"
case --synth
case "--allowsubjrep"
case --allowsubjrep
case "--illcond"
case --illcond
case "--debug"
case --debug
case "--synth"
case --synth
case "--cortex"
case --cortex
case "--kurtosis"
case --kurtosis
case "--nii"
case --nii
case "--nii.gz"
case --nii.gz
case "--rescale-x"
case --rescale-x
case "--no-rescale-x"
case --no-rescale-x
case "--fisher"
case --fisher
case "--no-pcc"
case --no-pcc
case "dods"
case dods
case "mri_glmfit.bin"
case mri_glmfit.bin
case "--save-eres"
case --save-eres
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 13 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = mri_glmfit.bin
shift glmfitcmd

switch ( $flag )
switch ( mri_glmfit.bin )
case "--save-eres"
case --save-eres
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 12 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --y
shift glmfitcmd

switch ( $flag )
switch ( --y )
if ( $#y == 0 ) set y = $glmfitcmd[1] ;
if ( 0 == 0 ) set y = lh.5.lgi_MAN_new.mgh
set y = lh.5.lgi_MAN_new.mgh
shift glmfitcmd ;
shift glmfitcmd
if ( $DoClusterMean ) then
if ( 1 ) then
if ( ! -e $y ) then
if ( ! -e lh.5.lgi_MAN_new.mgh ) then
endif
endif
if ( "$flag" == "--table" ) set UseTable = 1 ;
if ( --y == --table ) set UseTable = 1
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 10 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --fsgd
shift glmfitcmd

switch ( $flag )
switch ( --fsgd )
shift glmfitcmd ;
shift glmfitcmd
if ( $#glmfitcmd > 0 ) then
if ( 8 > 0 ) then
if ( $glmfitcmd[1] == doss ) set gd2mtx = doss
if ( dods == doss ) set gd2mtx = doss

[Freesurfer] Combining voxel-wise and vertex-wise data

2018-11-20 Thread Carola Mayer

External Email - Use Caution

Hello Freesurfer Developers,

I have a general question about how to analyse a certain combination of data. I 
have an independent variable that contains voxel-wise data and I have a 
dependent variable that contains vertex-wise cortical thickness values.

I would like to do a between-subjects analysis correlating the voxel-wise and 
vertex-wise data. What is a valid approach to do this? Should I first register 
the voxel-wise data onto the vertex-wise data and then register them into an 
average space to do group analysis? Or is a different method more valid?

Thanks in advance for your time and help,

Carola

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Re: [Freesurfer] Bonferroni correction of 2spaces or 3spaces

2018-11-20 Thread YAN Chao-Gan

External Email - Use Caution

Dear Douglas,

When doing --3spaces, is there a default subcortical mask in MNI space
provided by freesurfer? Where is it stored?

Thanks,

Chao-Gan

On Tue, Nov 20, 2018 at 10:12 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

>
>
> On 11/16/18 7:34 PM, YAN Chao-Gan wrote:
>
> External Email - Use Caution
> Dear freesurfer experts,
>
> I have a pretty naive question but would like to confirm.
>
> When we use --3spaces option in multiple comparison correction, does that
> mean we set the Cluster-wise threshold (cwp, not Cluster Defining Threshold
> or Cluster Forming Threshold) to 0.5/3=0.0167 for lh. Similar cwp at 0.0167
> for rh and subcortical?
>
> Correct.
>
>
> In addition, if we use "--cortex" to restrict the calculation on cortex
> only, where can we find the corresponding mask or label file for cortex?
>
> Load the ?h.cortex.label in fsaverage
>
>
> Thanks,
>
> Chao-Gan
>
> --
> Chao-Gan YAN, Ph.D.
> Professor, Principal Investigator
> Deputy Director, Magnetic Resonance Imaging Research Center
> Institute of Psychology, Chinese Academy of Sciences
> 16 Lincui Road, Chaoyang District, Beijing 100101, China
> -
> Initiator
> DPABI 
> , DPARSF
> , PRN  and The R-fMRI
> Network  (RFMRI.ORG )
> http://rfmri.org/yan
> http://scholar.google.com/citations?user=lJQ9B58J
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://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



-- 
Chao-Gan YAN, Ph.D.
Professor, Principal Investigator
Deputy Director, Magnetic Resonance Imaging Research Center
Institute of Psychology, Chinese Academy of Sciences
16 Lincui Road, Chaoyang District, Beijing 100101, China
-
Initiator
DPABI 
, DPARSF
, PRN  and The R-fMRI Network
 (RFMRI.ORG )
http://rfmri.org/yan
http://scholar.google.com/citations?user=lJQ9B58J
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Re: [Freesurfer] How to automate recon-all command for multiple subjects



in csh it would be something like

setenv SUBJECTS_DIR 
foreach fname ($dir/*.nii)
set fonly=${f:t}
set fnoext=${f:r}
	recon-all -i $fname -s $fnoext -all 
end



On Tue, 20 Nov 2018, Vivek Sharma wrote:



External Email - Use Caution

I have a folder, lets name xyz which contains .nii file. Now I want to run 
recon-all for all the
files in that folder. Please let me know how I can do that.

On Tue, Nov 20, 2018 at 11:40 AM Vivek Sharma  
wrote:
  I'm trying to run this code but it's not working. What should be $i in 
the code?
  On Mon, Nov 19, 2018 at 9:15 PM Bruce Fischl  
wrote:
  or you could do that all on a single line:

  recon-all -i $SUBJECTS_DIR/$i/ -s $i -all

  cheers
  Bruce

  On Mon, 19 Nov 2018,
  Alex Hanganu
  wrote:

  >
  > External Email - Use Caution
  >
  > HI Vivek,
  > you probably need 2 steps, first registration, second recon-all. 
Something
  > like:
  >
  > ...
  > do
  >    recon-all -i $SUBJECTS_DIR/$i/ -s $i
  >    recon-all -all -subjid $i
  >
  >
  > I didn't check if the scrips runs. That's the general structure.
  >
  > Best,
  > Alex
  >
  > Le lun. 19 nov. 2018, à 06 h 26, Vivek Sharma 
 a
  > écrit :
  >
  >       External Email - Use Caution
  >
  >       Hi,
  > I'm using freesurfer to generate head surfaces using MRI file.
  > I want to execute recon-all command for number of subjects, but unable
  > to run it.
  > The script I'm using is:
  >
  > for i in `cat *subs.txt*`
  > do
  >     recon-all -s $i -all -qcache
  > done
  >
  > subs.txt contains the name of folder that contains .nii file.
  > The scripts ends with the following error:
  >
  > ERROR: no run data found in
  > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make sure to
  > have a volume called 001.mgz in 
  > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig.
  > If you have a second run of data call it 002.mgz, etc.
  > See also:
  > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
  > Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26
  > 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
  >
  > Please let me know how I can run recon-all for multiple subjects.
  > Thank you.
  >
  > --
  > Vivek Sharma
  > Mobile: +919953582034
  > Skype: vivek.sharma1015
  > ___
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Mobile: +919953582034
Skype: vivek.sharma1015



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Skype: vivek.sharma1015

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Re: [Freesurfer] How to automate recon-all command for multiple subjects

oh, that was from your example. -i  should be the full path to 
the input volume *or* one file in the correct dicom series. -s  
is something you choose to uniquely identify that subject's recon-all 
outputs


cheers
Bruce


On Tue, 20 Nov 2018, Vivek Sharma wrote:



External Email - Use Caution

I'm trying to run this code but it's not working. What should be $i in the code?
On Mon, Nov 19, 2018 at 9:15 PM Bruce Fischl  wrote:
  or you could do that all on a single line:

  recon-all -i $SUBJECTS_DIR/$i/ -s $i -all

  cheers
  Bruce

  On Mon, 19 Nov 2018,
  Alex Hanganu
  wrote:

  >
  > External Email - Use Caution
  >
  > HI Vivek,
  > you probably need 2 steps, first registration, second recon-all. 
Something
  > like:
  >
  > ...
  > do
  >    recon-all -i $SUBJECTS_DIR/$i/ -s $i
  >    recon-all -all -subjid $i
  >
  >
  > I didn't check if the scrips runs. That's the general structure.
  >
  > Best,
  > Alex
  >
  > Le lun. 19 nov. 2018, à 06 h 26, Vivek Sharma 
 a
  > écrit :
  >
  >       External Email - Use Caution
  >
  >       Hi,
  > I'm using freesurfer to generate head surfaces using MRI file.
  > I want to execute recon-all command for number of subjects, but unable
  > to run it.
  > The script I'm using is:
  >
  > for i in `cat *subs.txt*`
  > do
  >     recon-all -s $i -all -qcache
  > done
  >
  > subs.txt contains the name of folder that contains .nii file.
  > The scripts ends with the following error:
  >
  > ERROR: no run data found in
  > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make sure to
  > have a volume called 001.mgz in 
  > /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig.
  > If you have a second run of data call it 002.mgz, etc.
  > See also:
  > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
  > Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26
  > 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
  >
  > Please let me know how I can run recon-all for multiple subjects.
  > Thank you.
  >
  > --
  > Vivek Sharma
  > Mobile: +919953582034
  > Skype: vivek.sharma1015
  > ___
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  >
  >
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Vivek Sharma
Mobile: +919953582034
Skype: vivek.sharma1015

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Re: [Freesurfer] Bonferroni correction of 2spaces or 3spaces

The masking is not done as part of the correction for mult comp but when you 
run mri_glmfit. When you run it on a volume, you have to specify the mask, so 
the mask depends upon your application. For fsfast, the mask in 
$FREESURFER_HOME/subjects/fsaverage/mri.2mm is used.

On 11/20/18 4:57 AM, YAN Chao-Gan wrote:

External Email - Use Caution

Dear Douglas,

When doing --3spaces, is there a default subcortical mask in MNI space provided 
by freesurfer? Where is it stored?

Thanks,

Chao-Gan

On Tue, Nov 20, 2018 at 10:12 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:


On 11/16/18 7:34 PM, YAN Chao-Gan wrote:

External Email - Use Caution

Dear freesurfer experts,

I have a pretty naive question but would like to confirm.

When we use --3spaces option in multiple comparison correction, does that mean 
we set the Cluster-wise threshold (cwp, not Cluster Defining Threshold or 
Cluster Forming Threshold) to 0.5/3=0.0167 for lh. Similar cwp at 0.0167 for rh 
and subcortical?
Correct.

In addition, if we use "--cortex" to restrict the calculation on cortex only, 
where can we find the corresponding mask or label file for cortex?
Load the ?h.cortex.label in fsaverage

Thanks,

Chao-Gan

--
Chao-Gan YAN, Ph.D.
Professor, Principal Investigator
Deputy Director, Magnetic Resonance Imaging Research Center
Institute of Psychology, Chinese Academy of Sciences
16 Lincui Road, Chaoyang District, Beijing 100101, China
-
Initiator
DPABI,
  DPARSF, PRN 
and The R-fMRI Network (RFMRI.ORG)
http://rfmri.org/yan
http://scholar.google.com/citations?user=lJQ9B58J



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Chao-Gan YAN, Ph.D.
Professor, Principal Investigator
Deputy Director, Magnetic Resonance Imaging Research Center
Institute of Psychology, Chinese Academy of Sciences
16 Lincui Road, Chaoyang District, Beijing 100101, China
-
Initiator
DPABI,
  DPARSF, PRN 
and The R-fMRI Network (RFMRI.ORG)
http://rfmri.org/yan
http://scholar.google.com/citations?user=lJQ9B58J



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Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

wow, I have no idea. Can you send us the .nii file and we will try? What 
machine is it failing on and does it print any error messages during 
conversion? Can you send us the full command line and terminal output of 
the mri_convert command that fails?


cheers
Bruce
On Tue, 20 Nov 2018, Batuhan Erkat 
wrote:




External Email - Use Caution

Dear Bruce,

On Sun, Nov 18, 2018 at 6:20 PM Bruce Fischl  wrote:
  Hi Batuhan

  what is the size of the rawavg.mgz file? Can you run mri_info on it?


This is the output I get with mri info on rawavg.mgz:
batuhan@chimere:/auto/data/batuhan/output/BE2/mri$ mri_info rawavg.mgz
Volume information for rawavg.mgz
  type: MGH
    dimensions: 224 x 256 x 176
   voxel sizes: 1., 1., 1.
  type: FLOAT (3)
   fov: 256.000
   dof: 0
    xstart: -112.0, xend: 112.0
    ystart: -128.0, yend: 128.0
    zstart: -88.0, zend: 88.0
    TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
ras xform present
    xform info: x_r =   0., y_r =   0., z_r =   1., c_r = 4.1261
  : x_a =  -1., y_a =   0., z_a =   0., c_a =    22.5211
  : x_s =   0., y_s =   1., z_s =   0., c_s =   -11.1121

talairach xfm :
Orientation   : PSR
Primary Slice Direction: sagittal

voxel to ras transform:
    0.   0.   1.   -83.8739
   -1.   0.   0.   134.5211
    0.   1.   0.  -139.1121
    0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -0.  -1.  -0.   134.5211
   -0.  -0.   1.   139.1121
    1.   0.   0.    83.8739
    0.   0.   0. 1.
 
  How
  did you create the 001.mgz? Rerunning recon-all won't help if the 001.mgz
  is already corrupted - you will need to regenerate it. That fact that we
  can't even read slice 0 suggests there is something badly wrong with it.
  Can you look at it in freeview?


This is how 001.mgz is generated, right after the recon-all command and perl 
warning:

perl: warning: Falling back to the standard locale ("C").
/auto/data/batuhan/output/BE2

mri_convert /auto/data/batuhan/output/BE2_T1.nii 
/auto/data/batuhan/output/BE2/mri/orig/001.mgz

mri_convert /auto/data/batuhan/output/BE2_T1.nii 
/auto/data/batuhan/output/BE2/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /auto/data/batuhan/output/BE2_T1.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0, -1, 0)
j_ras = (0, 0, 1)
k_ras = (1, 0, 0)
writing to /auto/data/batuhan/output/BE2/mri/orig/001.mgz...
#
#@# MotionCor Tue Nov 20 17:09:07 +03 2018
Found 1 runs
/auto/data/batuhan/output/BE2/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /auto/data/batuhan/output/BE2/mri/orig/001.mgz 
/auto/data/batuhan/output/BE2/mri/rawavg.mgz

It cannot load 001.mgz in freeview, but BE2_T1.nii seems fine:

gorkem@friston:~/Desktop$ freeview -v 001.mgz
mghRead(/home/gorkem/Desktop/001.mgz): could not read 229376 bytes at slice 0
MRIread failed: Unable to read from /home/gorkem/Desktop/001.mgz
mghRead(/home/gorkem/Desktop/001.mgz): could not read 229376 bytes at slice 0

[kjFFtSUZ3QnAGUDICTTA_6E7ANwzLBnTF64p_SYi2w0LbngPwmKeldP7AYR8g9kRc-EyfkmKGOfWu83JV6wgu1a-nTU9hIJ_6E
m2o1VJ5WeytUIQM71rTiZBLVk6wxmc3Tf86E9iM1g] Screenshot from 2018-11-20 
17-27-03.png
I manually converted anatomical image to 001.mgz on this server, it gave the 
same error. When I
tried it on my desktop, it worked fine. So forth, mri_convert function on the 
server somehow
corrupts nii files. What do you think the reason could be?

Best,
Batuhan
  cheers
  Bruce


  On Sat, 17 Nov 2018, Batuhan Erkat wrote:

  >
  > External Email - Use Caution
  >
  > Yes, unfortunately same error reoccurs in three different machines. I 
talked with some
  people at the
  > research center, they claimed that it could be due to high load. 
However, I tried
  again while the
  > average load was at 5% (via top command), the issue persists. Do you 
have any clue
  what might be the
  > underlying problem? A necessary bug fix we could have missed etc.?
  >
  > Batuhan
  >
  > On Sat, Nov 17, 2018 at 12:11 AM Greve, Douglas N.,Ph.D. 

  wrote:
  >       Probably it was interrupted and the file as not completely 
written, or you ran
  out of
  >       space on the disk. If you start over, does it continue to happen?
  >
  >       On 11/16/18 4:15 PM, Batuhan Erkat wrote:
  >
  >

[Freesurfer] Conversion of surface files to nibabel-readable files

2018-11-20 Thread Borges Pereira Ines Isabel

External Email - Use Caution

Dear FreeSurfer developers,

I am trying to segment the cortex of my subjects into multiple layers and am 
trying several approaches.
I have tried the command "mris_expand -thickness lh.white 0.5 lh.graymid" and 
it works perfectly.
I am also interested in trying other approaches from other software packages 
and have started to experiment with nighres.

Is it possible to convert the FreeSurfer surface files (pial and white) to a 
nibabel SpatialImage format or another format that can be read by the 
nibabel/nighres python library?
I have searched the FreeSurfer documentation but couldn’t find a direct answer. 
I also see that nibabel has a freesurfer module and hence I am able to load the 
images to a python script. However, when I attempt to use perform volumetric 
layering with nighres, it returns a value error, given that the “input volume 
must be either a path to a file that Nibabel can load or a nibabel 
SpatialImage."

I will also contact the nighres developers but was wondering if Freesurfer 
already takes into account the possible interaction between different software 
packages.

Many thanks!

Best regards,

Inês Pereira
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Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

can you verify that /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white 
exists and that you have read permission to it? Eg, can you load it with
freeview -f /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white




On 11/20/18 8:25 AM, C.P.E. Rollins wrote:
   External Email - Use Caution
Thanks Douglas, I've attached here the output from mri_glmfit-sim --glmdir 
lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces --debug

Could you clarify how to use permutation to correct for MC for LGI? (as in what 
to enter for command line?). I don't quite understand from the documentation.

Thanks very much,
Colleen



set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )

goto parse_args_return ;
goto parse_args_return

goto check_params ;
goto check_params
if ( $#glmdir == 0 ) then
if ( 1 == 0 ) then
if ( $DoSim ) then
if ( 0 ) then
set residual = ( )
set residual = ( )
if ( $nulltype == perm && $PermResid ) then
if ( == perm && 1 ) then
if ( $DiagCluster && $DoBackground ) then
if ( 0 && 0 ) then
if ( $DiagCluster && $DoPBSubmit ) then
if ( 0 && 0 ) then
if ( $DiagCluster && $DoSim == 0 ) then
if ( 0 && 0 == 0 ) then

goto check_params_return ;
goto check_params_return

if ( ! -e $glmdir ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir ) then

set glmfitlog = $glmdir/mri_glmfit.log
set glmfitlog = lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
if ( ! -e $glmfitlog ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir/mri_glmfit.log ) then

if ( $nulltype != perm ) then
if ( != perm ) then
set fwhmfile = $glmdir/fwhm.dat
set fwhmfile = lh.5.lgi_MAN_new.glmdir/fwhm.dat
if ( ! -e $fwhmfile ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir/fwhm.dat ) then

set fwhm = `cat $fwhmfile` ;
set fwhm = `cat $fwhmfile`
cat lh.5.lgi_MAN_new.glmdir/fwhm.dat
else
else

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
awk {if($1 == "cwd") print $2}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
if ( 0 && ! -e $glmfitcwd ) then
if ( 0 && ! -e /home/cper2/BeneMin/Freesurfer ) then
set glmfitcwd = `pwd` ;
set glmfitcwd = `pwd`
pwd

set anattype = volume ;
set anattype = volume
set subject = ( ) ;
set subject = ( )
set hemi = ( ) ;
set hemi = ( )
set surf = "white" ;
set surf = white
set wls = ( ) ;
set wls = ( )

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
awk {if($1 == "cwd") print $2}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log


set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`
set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`
awk {if($1 == "cmdline") print $0}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
set glmfitcmd = ( $glmfitcmd0 ) ;
set glmfitcmd = ( cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd 
FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C 
contrast_dods.txt )
echo $glmfitcmd
echo cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt 
dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods 
--glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
set gd2mtx = dods
set gd2mtx = dods
set UseTable = 0 ;
set UseTable = 0
set label = ( ) ;
set label = ( )
while ( $#glmfitcmd )
while ( 14 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = cmdline
shift glmfitcmd

switch ( $flag )
switch ( cmdline )
case "mri_glmfit"
case mri_glmfit
case "--prune"
case --prune
case "--no-prune"
case --no-prune
case "--pca"
case --pca
case "--synth"
case --synth
case "--allowsubjrep"
case --allowsubjrep
case "--illcond"
case --illcond
case "--debug"
case --debug
case "--synth"
case --synth
case "--cortex"
case --cortex
case "--kurtosis"
case --kurtosis
case "--nii"
case --nii
case "--nii.gz"
case --nii.gz
case "--rescale-x"
case --rescale-x
case "--no-rescale-x"
case --no-rescale-x
case "--fisher"
case --fisher
case "--no-pcc"
case --no-pcc
case "dods"
case dods
case "mri_glmfit.bin"
case mri_glmfit.bin
case "--save-eres"
case --save-eres
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 13 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = mri_glmfit.bin
shift glmfitcmd

switch ( $flag )
switch ( mri_glmfit.bin )
case "--save-eres"
case --save-eres
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 12 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --y
shift glmfitcmd

switch ( $flag )
switch ( --y )
if ( $#y == 0 ) set y = $glmfitcmd[1] ;
if ( 0 == 0 ) set y = lh.5.lgi_MAN_new.mgh
set y = lh.5.lgi_MAN_new.mgh
shift glmfitcmd ;
shift glmfitcmd
if ( $DoClusterMean ) then
if ( 1 ) then
if ( ! -e $y ) then
if ( ! -e lh.5.lgi_MAN_new.mgh ) then
endif
endif
if ( "$flag" == "--table" ) set UseTable = 1 ;
if ( --y == --table ) set UseTable = 1
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 10 )
set flag = $glmfitcmd[1]

Re: [Freesurfer] Conversion of surface files to nibabel-readable files


Hi Inês

nibabel should be able to read freesurfer images directly (thanks to Satra! 
I think):


http://nipy.org/nibabel/reference/nibabel.freesurfer.html

cheers
Bruce

On Tue, 20 Nov 
2018, Borges Pereira  Ines Isabel wrote:




External Email - Use Caution

Dear FreeSurfer developers,
I am trying to segment the cortex of my subjects into multiple layers and am 
trying several
approaches.
I have tried the command "mris_expand -thickness lh.white 0.5 lh.graymid" and 
it works perfectly.
I am also interested in trying other approaches from other software packages 
and have started to
experiment with nighres.

Is it possible to convert the FreeSurfer surface files (pial and white) to a 
nibabel SpatialImage
format or another format that can be read by the nibabel/nighres python library?
I have searched the FreeSurfer documentation but couldn’t find a direct answer. 
I also see that
nibabel has a freesurfer module and hence I am able to load the images to a 
python script. However,
when I attempt to use perform volumetric layering with nighres, it returns a 
value error, given that
the “input volume must be either a path to a file that Nibabel can load or a nibabel 
SpatialImage."

I will also contact the nighres developers but was wondering if Freesurfer 
already takes into
account the possible interaction between different software packages.

Many thanks!

Best regards,

Inês Pereira

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Re: [Freesurfer] Conversion of surface files to nibabel-readable files

2018-11-20 Thread ts+ml

External Email - Use Caution

As you said, you can load FreeSurfer data (both the surface files and volume 
data) with the respective nibabel functions, i.e., read_geometry and 
read_morph_data. The ?h.pial and ?h.white files are surface meshes, so 
read_geometry would apply.

I'm not familiar with nighres, but from your description of what you want to 
do, it seems that you would need volume data for that. It seems impossible to 
do volumetric layering based on just a mesh.

Tim

> On November 20, 2018 at 5:08 PM Borges Pereira  Ines Isabel 
>  wrote:
> 
> 
> External Email - Use Caution
> 
> Dear FreeSurfer developers,
> 
> I am trying to segment the cortex of my subjects into multiple layers and am 
> trying several approaches.
> I have tried the command "mris_expand -thickness lh.white 0.5 lh.graymid" and 
> it works perfectly.
> I am also interested in trying other approaches from other software packages 
> and have started to experiment with nighres.
> 
> Is it possible to convert the FreeSurfer surface files (pial and white) to a 
> nibabel SpatialImage format or another format that can be read by the 
> nibabel/nighres python library?
> I have searched the FreeSurfer documentation but couldn’t find a direct 
> answer. I also see that nibabel has a freesurfer module and hence I am able 
> to load the images to a python script. However, when I attempt to use perform 
> volumetric layering with nighres, it returns a value error, given that the 
> “input volume must be either a path to a file that Nibabel can load or a 
> nibabel SpatialImage."
> 
> I will also contact the nighres developers but was wondering if Freesurfer 
> already takes into account the possible interaction between different 
> software packages.
> 
> Many thanks!
> 
> Best regards,
> 
> Inês Pereira
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-- 
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Forschung - Klinische Bildgebung
Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und 
Jugendalters
Universitätsklinikum Frankfurt / Haus 93, Raum A 305
Deutschordenstr. 50, 60528 Frankfurt am Main
Email: tim.schae...@kgu.de| Tel.: +49 (0)69 6301 85832

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Re: [Freesurfer] Conversion of surface files to nibabel-readable files