[Freesurfer] MP2RAGE recon-all

[Renew Andrade]

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Dear Freesurfer experts:

I am having trouble processing with recon-all the file I obtain with presurfer 
from an MP2RAGE. I don’t know if you have any experience with this. The data I 
obtained from this 
https://secure-web.cisco.com/1DoAeFvUHnYto_t5xoLbWcFtbuOwQtmlS1ENoWBmeeHffDpNErW4_gUBNrL5wbRsqdn8Lvt8o-hftAn4O3mHZlavh98oBX5sjSMs6gyoyT47B4jGytWCy0opSP505tXZd0usKIHMHIWlSmIqHKG6eDzK-1hhavHJFtmcsFeyidS8mPmaHdP-KpuCotmuwqgIPCppobf5sCRfNWndHYDvrfUWS7cnm05Gepyhhd9wWDL3SOx7eMSw78OvBAoGp4jAtzA51dgT22RZWjsiDkVkZhxVB65cvL3d0EEIQEb3b-Pvc_aXfazlGDtAv_BN8ebkALkCERCl8XVgThOSIi-yo1DOledDb39I-AMQQIyh_XeQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsmData
 


Then I use subject “fsm08un”. 

I run presurfer as in 
https://secure-web.cisco.com/1avsRdF8F2mgWmm0OUulJTd3eZF6z9U3j9ezKhlvZi12HC0IpY4Nah1yM9zPdaEgn4XgbjeONuQbMGr9DrUl1ib_zBmc-EE50cnExQ7r-SquKETECpYIH8FI2PNE_wseQcG9IdIgbmgUS28z8SgosW5HOBtqPlBxbH_624ZNh7HPzc7i6nPoue8uM5ePZ_Ro_AHX9ld3OtrW6lwse45wPv2u3LUCxXJvzjGyuTogJ0vKoxfw65J2DT-hcJs3sC5VIZfVWiyxjgoy6-5P7oV--mxBJYd5c4h4nKHW3xfcLKzdKMl2UZTYYHtCxqY-E4Hgw7yh-06jF6j9eVH3-h8Qkv97Kmur_vXvB1bBLBTy21Jo/https%3A%2F%2Fgithub.com%2Fsrikash%2Fpresurfer

Then I run 

recon-all -all -i MPRAGEised_stripped.nii.gz -s fsm08un_MPRAGEised -openmp 8




.
.
.

TEMPLATE DEFORMATION

  second estimation of the COG coord: x=130,y=125, z=130, r=124102 
iterations
 couldn't find WM with original limits - expanding ^^

   GLOBAL  CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1447023003
  RIGHT_CERCSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1862269955
  LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -230683617
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1409286624
 LEFT_BRAINCSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 943723776
OTHER  CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 943755195
mri_watershed Error: 
 GLOBAL region of the brain empty !
Darwin Renes-MacBook-Air.local 22.5.0 Darwin Kernel Version 22.5.0: Thu Jun  8 
22:22:19 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T8103 arm64

recon-all -s fsm08un_MPRAGEised exited with ERRORS at Tue Aug  1 15:40:57 CEST 
2023

For more details, see the log file 
/Applications/freesurfer/7.3.2/subjects/fsm08un_MPRAGEised/scripts/recon-all.log
To report a problem, see 
http://secure-web.cisco.com/1t6IHvg5_DeUlvFUHchBUPV_vqGqDEzbhHz1e6IOApGryD_Xrrkklep8jgVlZe9fJKNdDSOe6dvXPcqeE6olUXH6XkwRpSbUcCq_CYo0eJB7QJX1x8157w6wuaeu9PxMFRxj9l6U7_YsLyJ3W4BkntY5GeVn75rbX4VT9y4EqfPy4_WPODDMhEjDbZCEiiAMiUSQHDjaJvTtL1piF4w-tYrD_HViPkWHDc5wKiwkS6i1HfUcAqZBC-q2Vuz_Y1F4DL521hE0ls6V1llkejmlhXJE191JBHRwAJluOe4DF6n3DFAN7b2GGf1zrBWBiyozzxImlnLVnx11viFmCh-qC9ksePIwjrMFh0B-vMaSzS0E/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting


If you need the recon-all.log I can send it. 

Best, 
Rene Andrade. 


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Re: [Freesurfer] lh.pial lh.pialT1n same file?

[Renew Andrade]

External Email - Use CautionI am afraid the links didn’t survive the copy and can’t be undone because they were deleted from Mac when copied to the disc where they are used later on in ubuntu. Thank you all for the help. Then shall I create a copy of all those files missing as suggested by Yujing. Eg rh.fsaverage.sphere.reg And Rh.white.preaparc.K??? On 22 Dec 2022, at 19:08, Kumar, Avnish  wrote:





If you want your links to also be copied over in Linux/Mac you can use the --a argument
 with the cp command:
cp
 --a 


From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Douglas N. Greve 
Sent: Thursday, December 22, 2022 11:59 AM
To: Huang, Yujing ; Renew Andrade ; Dicamillo, Robert 
Cc: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?
 

yes, you can copy that. I'm cc'ing Rob in case he has any insights. @ Renew, you should try running the whole recon-all in a single platform. If you copied it from Mac to ubuntu, it is possible that those links weren't
 created in Mac or did not survive the copy.

On 12/22/2022 10:28 AM, Huang, Yujing wrote:





Hi Rene,
 
From your recon-all.log, I see you ran freesurfer-darwin-macOS-7.1.1-20200811-8b40551 on your MacBook:
BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551  User: root  Machine: Renes-MacBook-Air.local  Platform: Darwin  PlatformVersion: 21.6.0  CompilerName: Clang  CompilerVersion: 10.0.1
 
It looks like recon-all failed to create these links in ‘surf’ directory because of the permission issues:
rh.pial -> rh.pial.T1
lh.pial -> lh.pial.T1
rh.fsaverage.sphere.reg -> rh.sphere.reg
lh.fsaverage.sphere.reg -> lh.sphere.reg
 
I think you can copy in these files for now
cp  rh.pial.T1 rh.pial
cp  lh.pial.T1 lh.pial
cp rh.sphere.reg rh.fsaverage.sphere.reg
cp lh.sphere.reg lh.fsaverage.sphere.reg
 
Doug, can you confirm that? 
 
Also, I can’t tell from recon-all script if in 7.1.1, we create these links?
rh.white.K -> rh.white.preaparc.K
rh.white.H -> rh.white.preaparc.H
lh.white.K -> lh.white.preaparc.K
lh.white.H -> lh.white.preaparc.H
 
Best,
 
Yujing
 


From: Renew Andrade 
 
Sent: Thursday, December 22, 2022 4:27 AM
To: Huang, Yujing 

Cc: 
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?


 
External Email - Use Caution
Hi Yujing 

 


I’m using this  in ubuntu I don’t remember if I did recon-all in Mac and may be that’s why you are assuming I’m working on Mac. 


 


 


Anyways ln -sf works as I am in ubuntu.


 


The problem is as you will see there seems to be an issue with permission even with sudo. 


 


So ls -l testlink I din’t try as I couldn’t do any symbolic link. 


 


Best, 


Rene. 


 



surfer/controls/s25633_T1MPRAGE_1mm_reconall/surf$ sudo ln -sf lh.pial.T1 testlink

ln: failed to create symbolic link 'testlink': Operation not permitted

 


 


(base) andraderenew@andraderenew:/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25633_T1MPRAGE_1mm_reconall/surf$
 ls -lt ?h.pial* ?h.white* ?h*.sphere.reg

-rwxr-xr-x 1 andraderenew andraderenew 4551861 ago 23 03:05 lh.pial.T1


-rwxr-xr-x 1 andraderenew andraderenew 4553578 ago 23 03:05 lh.sphere.reg


-rwxr-xr-x 1 andraderenew andraderenew  505671 ago 23 03:05 lh.white.preaparc.H


-rwxr-xr-x 1 andraderenew andraderenew  502915 ago 23 03:05 rh.white.preaparc.H


-rwxr-xr-x 1 andraderenew andraderenew 4527057 ago 23 03:05 rh.pial.T1


-rwxr-xr-x 1 andraderenew andraderenew 4551861 ago 23 03:05 lh.white.preaparc


-rwxr-xr-x 1 andraderenew andraderenew 4551861 ago 23 03:05 lh.white


-rwxr-xr-x 1 andraderenew andraderenew 4528774 ago 23 03:05 rh.sphere.reg


-rwxr-xr-x 1 andraderenew andraderenew 4527057 ago 23 03:05 rh.white


-rwxr-xr-x 1 andraderenew andraderenew  505671 ago 23 03:05 lh.white.preaparc.K


-rwxr-xr-x 1 andraderenew andraderenew  502915 ago 23 03:05 rh.white.preaparc.K


-rwxr-xr-x 1 andraderenew andraderenew 4527057 ago 23 03:05 rh.white.preaparc








On 21 Dec 2022, at 20:17, Huang, Yujing <yhuan...@mgh.harvard.edu> wrote:

 


Hi Rene,


 


I don’t see any errors in your recon-all log.


 


I’m wondering if ‘ln -sf’ works on Mac.


 


Can you try the following:


1. cd to ‘surf’ directory


2. ln -sf lh.pial.T1 testlink


3. ls -l testlink


4. ls -lt ?h.pial* ?h.white* ?h*.sphere.reg


 


Can you send the output from those commands?


 


Yujing


 


 




From: Renew Andrade <andradere...@yahoo.com> 
Sent: Tuesday, December 20, 2022 11:04 AM
To: Huang, Yujing <yhuan...@mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?




 


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andraderenew@andraderenew:/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25633_T1MPRAGE_1mm_reconall/surf$



      ls -l lh.pial*




-rwxr-xr-x 1 andraderenew an

Re: [Freesurfer] lh.pial lh.pialT1n same file?

[Renew Andrade]

External Email - Use Caution

Hi Yujing 

I’m using this  in ubuntu I don’t remember if I did recon-all in Mac and may be 
that’s why you are assuming I’m working on Mac. 


Anyways ln -sf works as I am in ubuntu.

The problem is as you will see there seems to be an issue with permission even 
with sudo. 

So ls -l testlink I din’t try as I couldn’t do any symbolic link. 

Best, 
Rene. 

surfer/controls/s25633_T1MPRAGE_1mm_reconall/surf$ sudo ln -sf lh.pial.T1 
testlink
ln: failed to create symbolic link 'testlink': Operation not permitted


(base) 
andraderenew@andraderenew:/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25633_T1MPRAGE_1mm_reconall/surf$
 ls -lt ?h.pial* ?h.white* ?h*.sphere.reg
-rwxr-xr-x 1 andraderenew andraderenew 4551861 ago 23 03:05 lh.pial.T1
-rwxr-xr-x 1 andraderenew andraderenew 4553578 ago 23 03:05 lh.sphere.reg
-rwxr-xr-x 1 andraderenew andraderenew  505671 ago 23 03:05 lh.white.preaparc.H
-rwxr-xr-x 1 andraderenew andraderenew  502915 ago 23 03:05 rh.white.preaparc.H
-rwxr-xr-x 1 andraderenew andraderenew 4527057 ago 23 03:05 rh.pial.T1
-rwxr-xr-x 1 andraderenew andraderenew 4551861 ago 23 03:05 lh.white.preaparc
-rwxr-xr-x 1 andraderenew andraderenew 4551861 ago 23 03:05 lh.white
-rwxr-xr-x 1 andraderenew andraderenew 4528774 ago 23 03:05 rh.sphere.reg
-rwxr-xr-x 1 andraderenew andraderenew 4527057 ago 23 03:05 rh.white
-rwxr-xr-x 1 andraderenew andraderenew  505671 ago 23 03:05 lh.white.preaparc.K
-rwxr-xr-x 1 andraderenew andraderenew  502915 ago 23 03:05 rh.white.preaparc.K
-rwxr-xr-x 1 andraderenew andraderenew 4527057 ago 23 03:05 rh.white.preaparc

> On 21 Dec 2022, at 20:17, Huang, Yujing  wrote:
> 
> Hi Rene,
>  
> I don’t see any errors in your recon-all log.
>  
> I’m wondering if ‘ln -sf’ works on Mac.
>  
> Can you try the following:
> 1. cd to ‘surf’ directory
> 2. ln -sf lh.pial.T1 testlink
> 3. ls -l testlink
> 4. ls -lt ?h.pial* ?h.white* ?h*.sphere.reg
>  
> Can you send the output from those commands?
>  
> Yujing
>  
>  
> From: Renew Andrade mailto:andradere...@yahoo.com>> 
> Sent: Tuesday, December 20, 2022 11:04 AM
> To: Huang, Yujing mailto:yhuan...@mgh.harvard.edu>>
> Cc: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?
>  
> External Email - Use Caution
> 
> andraderenew@andraderenew:/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25633_T1MPRAGE_1mm_reconall/surf$
>   ls -l lh.pial*
> -rwxr-xr-x 1 andraderenew andraderenew 4551861 ago 23 03:05 lh.pial.T1
>  
>  
>  
> This is all I have. Thanks for the help in advance. 
> 
> 
> On 20 Dec 2022, at 15:12, Huang, Yujing  <mailto:yhuan...@mgh.harvard.edu>> wrote:
>  
> Hi Rene,
>  
> Can you send your recon-all.log? It is in the ‘scripts’ directory. 
>  
> ‘lh.pial’ should be created as a link to ‘lh.pial.T1’ if you are not 
> processing T2/FLAIR.  If you go ‘surf’ directory, do ‘ls -l lh.pial*’, what 
> does it shows?
>  
> Best,
>  
> Yujing
>  
> From: Renew Andrade mailto:andradere...@yahoo.com>> 
> Sent: Tuesday, December 20, 2022 1:23 AM
> To: Huang, Yujing  <mailto:yhuan...@mgh.harvard.edu>>; freesurfer@nmr.mgh.harvard.edu 
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?
>  
> External Email - Use Caution
> 
> Dear Yujing:
> I wasn’t aware that there was an answer to my email that’s the reason it took 
> me a while to write back. But I answer here. 
> Yes I mean lh.pial.T1. I don’t have any other lh.pial. The recon-all command 
> is properly correct like recon-all -all -i -s -openmp 8. Yes the freesurfer 
> version is 7.1.1. 
>  
> Best, 
> Rene Andrade. 
>  
>  
>  
>  
>  
>  
> Hi Rene,
>  
> Do you mean lh.pial.T1? Do you have any other lh.pial* files in the directory?
> What is your recon-all command line? And can you also provide the Freesurfer 
> version you are running?
>  
> Best,
>  
> Yujing
>  
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Renew Andrade
> Sent: Tuesday, December 13, 2022 7:24 AM
> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] lh.pial lh.pialT1n same file?
>  
> External Email - Use Caution
>  
> Dear experts:
>  
> I am wondering if lh.pial and lh.pialT1 are the same f

Re: [Freesurfer] lh.pial lh.pialT1n same file?

[Renew Andrade]

External Email - Use Caution

Dear Yujing:
I wasn’t aware that there was an answer to my email that’s the reason it took 
me a while to write back. But I answer here. 
Yes I mean lh.pial.T1. I don’t have any other lh.pial. The recon-all command is 
properly correct like recon-all -all -i -s -openmp 8. Yes the freesurfer 
version is 7.1.1. 

Best, 
Rene Andrade. 






Hi Rene,

Do you mean lh.pial.T1? Do you have any other lh.pial* files in the directory?
What is your recon-all command line? And can you also provide the Freesurfer 
version you are running?

Best,

Yujing

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Renew Andrade
Sent: Tuesday, December 13, 2022 7:24 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] lh.pial lh.pialT1n same file?

External Email - Use Caution

Dear experts:

I am wondering if lh.pial and lh.pialT1 are the same files. I don’t have 
lh.pial is that an error from recon-all? Should I rerun recon-all. Or just 
autorecon-pial? Would that change anything?

Best, 
Rene Andrade. 

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[Freesurfer] lh.pial lh.pialT1n same file?

[Renew Andrade]

External Email - Use Caution

Dear experts:

I am wondering if lh.pial and lh.pialT1 are the same files. I don’t have 
lh.pial is that an error from recon-all? Should I rerun recon-all. Or just 
autorecon-pial? Would that change anything?

Best, 
Rene Andrade. 

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[Freesurfer] Medial wall mask for FSL tractography

[Renew Andrade]

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Dear experts:

I have a doubt about finding the medial wall mask of a subject. 


Would this be ok?
 
mri_label2label --srclabel lh.cortex.label --trglabel lh.cortex.label --outmask 
lh.cortex.mask.nii.gz --regmethod surface --hemi lh --srcsubject 25633 
--trgsubject 25633
 
fscalc lh.cortex.mask.mgz not -o lh.medialwall.mask.mgz 
 
mri_convert lh.medialwall.mask.mgz lh.medialwall.mask.gii


If I use mris_decimate to downsample the surface does it change anything of 
previous and how should I proceed in that case to change it?

Best, 
Rene Andrade.___
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Re: [Freesurfer] format bvalues bvectors tracula

[Renew Andrade]

External Email - Use Caution

Dear Yendiki Anastasia:

I am replying for second time. I haven’t received an answer about this issue. I 
don’t know if it is silly but I don’t know how to fix it. It is not / slashes 
in this case. 



dmrirc.IXI
Description: Binary data


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[Freesurfer] tracula error too many ('s

[Renew Andrade]

External Email - Use Caution

Dear FreeSurfer experts:

I mentioned an error that I still cannot fix. I don’t think is the “\” because 
as you can see in the file attached everything seems correct. I cannot fix the 
issue with TRACULA I attach the configuration file so you can check in effect 
is correct. 



dmrirc.IXI
Description: Binary data


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[Freesurfer] Functional connectivity analysis ERROR: cannot find.../dof

[Renew Andrade]

External Email - Use Caution

Dear FreeSurfer experts:
I cannot fix the problem that I mention in the subject. I put the output of the 
terminal below. I was doing functional connectivity analysis walkthrough 
tutorial and I followed until group analysis when applying "isxconcat-sess”. I 
cannot proceed because the “.dof” files are in "/sessx/rest/*” where x is a 
number from 0 to 9 and * indicates location. So I don’t know why this files are 
here and not in the analysis subdirectory i.e. “fc.lpccseed.lh”. 

What is the problem? How should I fix it?

Thank you for all the help!!

Sincerely,
Andrade. 

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[Freesurfer] study design flair T1

[Renew Andrade]

External Email - Use Caution

Dear FreeSurfer experts: 

I am dealing with a crossectional retrospective case control  study where I 
don't have all subjects with the same inaging protocols. I do have T1 for all 
of them although some have T2 others FLAIR others T2+FLAIR (besides T1 for all 
of them). My question is regarding VBM can I do inference on images with 
different characteristics? Or should them all have T1 + T2 or T1 + FLAIR. I 
guess this is the case that is all subjects should be processed with the same 
protocols.  This is in Multiple Sclerosis by the way just in case it matters. 

Sincerely,
Andrade. 

Sent from my iPhone


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[Freesurfer] format bvalues bvectors tracula

[Renew Andrade]

External Email - Use Caution

Dear FreeSurfer experts:I have tried to run tracula -prep but I cannot get to 
no where for the moment. I keep receiving this error. I assumed numbers had to 
be aligned in rows and columns. But none either that or one space in between 
seems to work. I don't know what format means with respect to bvalues o 
bvectors. It is not clear enough to me in the tutorial how do I have to fix the 
issue. 

Sincerely, 
Andrade. 


root@andraderenew:/home/andraderenew# trac-all -prep -c 
'/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/dmrirc.IXI'
 
Too many ('s.
INFO: SUBJECTS_DIR is 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed
INFO: Diffusion root is 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed
Actual FREESURFER_HOME /usr/local/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: current FREESURFER_HOME does not match that of previous processing.
    Current: /usr/local/freesurfer
    Previous: /Applications/freesurfer
trac-preproc -c 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/dmrirc.local
 -log 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.log
 -cmd 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.cmd
#-
/usr/local/freesurfer/bin/trac-preproc 
#-
#@# Image corrections mié ene 29 17:42:22 CET 2020
mri_convert --bvec-voxel 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz
 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz
 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz
 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998725, -0.0503472, 0.00377193)
j_ras = (-0.0504772, 0.994141, -0.0955763)
k_ras = (-0.00106217, 0.0956448, 0.995415)
writing to 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz...
cp 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/bvec/gradients.txt
 
/media/andraderenew/backup/image_databases/processed_data/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.bvecs
ERROR: Must specify input table of b-values
Linux andraderenew 5.0.0-37-generic #40~18.04.1-Ubuntu SMP Thu Nov 14 12:06:39 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at mié ene 29 17:42:22 CET 2020









dmrirc.IXI
Description: Binary data
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[Freesurfer] tracula error gradient vectors too many ('s

[Renew Andrade]

External Email - Use Caution

Dear FreeSurfer experts:
I am trying to run tracula in 4 subjects of a public dataset. I have 
encountered one error. I leave the output of terminal below. I also attach the 
configuration file. I hope you can follow from there. 
Sincerely, 
Andrade. 


root@andraderenew:/usr/local/freesurfer/subjects# trac-all -prep -c 
/usr/local/freesurfer/subjects/dmrirc.IXI
Too many ('s.
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
INFO: Diffusion root is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
trac-preproc -c 
/usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/dmrirc.local -log 
/usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/trac-all.log -cmd 
/usr/local/freesurfer/subjects/IXI_25_Guys_T1/scripts/trac-all.cmd
#-
/usr/local/freesurfer/bin/trac-preproc 
#-
#@# Image corrections sáb dic 21 15:06:13 CET 2019
mri_convert --bvec-voxel 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz
 /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz
 /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998725, -0.0503472, 0.00377193)
j_ras = (-0.0504772, 0.994141, -0.0955763)
k_ras = (-0.00106217, 0.0956448, 0.995415)
writing to /usr/local/freesurfer/subjects/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz...
ERROR: Must specify input table of gradient vectors
Linux andraderenew 5.0.0-37-generic #40~18.04.1-Ubuntu SMP Thu Nov 14 12:06:39 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at sáb dic 21 15:06:13 CET 2019


dmrirc.IXI
Description: Binary data
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[Freesurfer] fsfast no run directories

[Renew Andrade]

External Email - Use Caution

Dear FreeSurfer experts:I have some issues with "preproc-sess" because I cannot 
seem to get the setup of the directory structure or files to connect different 
things(the T1 subjects with functional bold or rest files). I have this output. 
 


root@andraderenew:/home/andraderenew/Downloads/barrios/project# preproc-sess -s 
sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
--
preproc-sess logfile is log/preproc-sess.sess1.log
--
$Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $
root
setenv FREESURFER_HOME /usr/local/freesurfer
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
Linux andraderenew 5.0.0-36-generic #39~18.04.1-Ubuntu SMP Tue Nov 12 11:09:50 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
/home/andraderenew/Downloads/barrios/project
/usr/local/freesurfer/fsfast/bin/preproc-sess
-s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
vie nov 29 07:33:28 CET 2019
instem   f 
mc   1 f fmcpr 
stc  1    fmcpr fmcpr.up
sm   0   
mask 1   brain
sess1 Template -
mktemplate-sess -s sess1 -d /home/andraderenew/Downloads/barrios/project -fsd 
bold -update
 
Session: /home/andraderenew/Downloads/barrios/project/sess1 
vie nov 29 07:33:28 CET 2019
ERROR: no run directories found



my working directory is 

root@andraderenew:/home/andraderenew/Downloads/barrios/project# pwd
/home/andraderenew/Downloads/barrios/project

and 

root@andraderenew:/home/andraderenew/Downloads/barrios/project# ls
copy.sh  sess1   sess2  sess4  sess6  sess8  sessidlist
log  sess10  sess3  sess5  sess7  sess9  sessidlist~


root@andraderenew:/home/andraderenew/Downloads/barrios/project# cd sess1
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1# ls
bold  rest  subjectname


root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1#  cd bold
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# ls
1
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# cd 1
root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold/1# ls
sub-0030689_task-resthypnotic_bold.nii.gz



And that is all. If I try with tutorial data there is no problem. One of the 
obvious differences is SUBJECTS_DIR is pointing not to subjects in freesurfer 
but to another folder where also is fsaverage. I don't know if this is required 
or I am missing another linking file. 

There you can see the files I have searched with terminal. 

Sincerely, 
Andrade. 


sessidlist
Description: Binary data


subjectname
Description: Binary data
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[Freesurfer] ERROR: Must specify input table of gradient vectors

[Renew Andrade]

External Email - Use CautionDear Anastasia Yendiki:I have tried to run TRACULA on 3 subjects as specified in configuration file attached. But the terminal output is: sh-3.2# trac-all -prep -c dmrirc.IXIdomainname: Command not found.Too many ('s.INFO: SUBJECTS_DIR is /Volumes/FREESURFER/freesurfer_preprocessedINFO: Diffusion root is /Volumes/FREESURFER/freesurfer_preprocessedActual FREESURFER_HOME /Applications/freesurfertrac-preproc -c /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/dmrirc.local -log /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.log -cmd /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/scripts/trac-all.cmd#-/Applications/freesurfer/bin/trac-preproc #-#@# Image corrections Sat Oct 26 23:06:34 CEST 2019mri_convert --bvec-voxel /Volumes/FREESURFER/old_databases/copy_IXI/IXI025-Guys-0852-T1.nii.gz /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gzmri_convert.bin --bvec-voxel /Volumes/FREESURFER/old_databases/copy_IXI/IXI025-Guys-0852-T1.nii.gz /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $reading from /Volumes/FREESURFER/old_databases/copy_IXI/IXI025-Guys-0852-T1.nii.gz...TR=0.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (0.0506412, -0.996042, 0.0730476)j_ras = (0.00618997, 0.073453, 0.997279)k_ras = (0.998698, 0.0500512, -0.00988522)writing to /Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/dmri/dwi_orig.nii.gz...ERROR: Must specify input table of gradient vectorsDarwin Renes-Air.home 19.0.0 Darwin Kernel Version 19.0.0: Wed Sep 25 20:18:50 PDT 2019; root:xnu-6153.11.26~2/RELEASE_X86_64 x86_64trac-preproc exited with ERRORS at Sat Oct 26 23:06:39 CEST 2019

dmrirc.IXI
Description: Binary data
I don’t understand why? Because I think I have specified everything correctly. May be there is an issue with “bvecs” and “bvals” files because I added .txt format manually for it to be equal to what is specified in the tutorial of TRACULA configuration file. Sincerely, Andrade. ___
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Re: [Freesurfer] Error in glmfit-sim cache

[Renew Andrade]

External Email - Use Caution

I don’t know what do you mean by not knowing what it means. I said that I have 
tried all the values the error pinpoints to. That is I have tried 
mri_glmfit-sim --glmdir lh.IXI.glmdir  --cache 4 abs —cap 0.05 --2spaces
with "1.3", "2.0", "3.0", “4.0”. And it doesn’t work. I know it doesn’t seem to 
be a software issue but I cannot run this functionality of the software only 
for the moment everything else works fine. I have two laptops one Mac and one 
BMAX I have done recon-all in one and I have done glmfit in the MAC. But this I 
hope is only temporary because makes no sense that a software works partially. 

Sincerely, 
Andrade. 

ERROR: 
> thresh = 4,0 must be 1.3, 2.0, 3.0, 4.0




I don't know what this refers to

On 10/18/19 4:45 PM, Renew Andrade wrote:
>  External Email - Use Caution
>
> I have tried all the values it pinpoints to but none seem to work.
>
> ___
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[Freesurfer] mri_cvs_register error while diffusion imaging processing

[Renew Andrade]

External Email - Use Caution

Dear FreeSurfer experts:
I am trying to run Spatial Normalization but I cannot get the morph file 
because I get this error. I don’t know what to do with these libraries. Do I 
need to copy them from where they are in freesurfer to somewhere else in the 
Mac?

sh-3.2# mri_cvs_register --mov IXI_25_Guys_T1
Using the CVS template as registration target...
The outdir:
/Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/cvs

Log file is 
/Volumes/FREESURFER/freesurfer_preprocessed/IXI_25_Guys_T1/cvs/IXI_25_Guys_T1_to_cvs_avg35.mri_cvs_register.1910241722.log

Thu Oct 24 17:22:55 CEST 2019
--mov IXI_25_Guys_T1
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
Renes-Air.home
Darwin Renes-Air.home 19.0.0 Darwin Kernel Version 19.0.0: Wed Sep 25 20:18:50 
PDT 2019; root:xnu-6153.11.26~2/RELEASE_X86_64 x86_64
asegfname aseg
Using m3z type morph files.
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

Abort 





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Re: [Freesurfer] Learning dti processing tutorial

[Renew Andrade]

External Email - Use Caution

In other words I cannot process TRACULA without the T1w images of my subjects? 
Because this Parkinson database is from NITRC and I only have the diffusion 
images not the T1. I can practice on other subjects that I have both the T1 and 
diffusion images but I was expecting on using this Parkinson tractography and 
do the analysis. In case you want to know is this 
https://www.nitrc.org/projects/parktdi/ 
<https://www.nitrc.org/projects/parktdi/>. 
Sincerely,
Andrade. 

Hi, you need to run recon-all on the T1, not on the diffusion scan. This will 
produce an anatomical segmentation of each subject based on the T1s, which 
TRACULA will then use to extract anatomical priors on white matter tracts, to 
aid tractography. When you run trac-all to do the actual tractography, then you 
run it on the diffusion scan.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Renew Andrade 

Sent: Friday, October 18, 2019 5:02:35 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Learning dti processing tutorial

External Email - Use Caution

I am using a database of NITRC repository 
https://www.nitrc.org/projects/parktdi/ 
<https://www.nitrc.org/projects/parktdi/> . This images have a nifti file for 
1000s/mm^2 and 2500s/mm^2. I don’t know if it is MPRAGE or not. Can you help me?



What is the input file that you are supplying? Often this happens when
the input it a multi-echo MPRAGE. If so, you can run
mri_concat multi-echo-mprage.mgz --rms --o mprage.mgz
then use mprage.mgz as the input to recon-all

On 10/12/2019 4:48 PM, Renew Andrade wrote:
>  External Email - Use Caution
>
> Dear freesurfer experts:
> I am trying to learn dti processing. For using Tracula it appears there is a
> need for running "recon-all -all -i -s” on every subject before starting to
> run Tracula. But there seems to be a problem. I have a Parkinson dwi images
> database and every subject gives me an error of the type “input(s) cannot
> have multiple frames!”. I am a little bit stuck on this step. Is it a problem
> of the file as input? Am I putting the wrong file? Can it be done a recon-all
> analysis to a dwi image? With trackvis I can obtain the results without any
> problem. My doubt comes from FreeSurfer only and may be my little knowledge
> about it.
> Thanks for your help!
> Sincerely,
> Andrade.
>
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> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>


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Re: [Freesurfer] Learning fsfast tutorial

[Renew Andrade]

External Email - Use Caution

Dear FreeSurfer experts:
I am trying to use my own data so I don’t have the same tutorial structure. I 
do keep the folder structure as similar as possible in order for FreeSurfer to 
run but I cannot have different sessions for example I just have resting or 
bold but not both. Is it a problem when running this analysis?


This is my directory structure


➜  ~ cd /Users/andraderenew/Downloads/2 
➜  2 git:(master) ✗ ls
rest
➜  2 git:(master) ✗ cd rest 
➜  rest git:(master) ✗ ls
dti_FA.nii.gz dti_L2.nii.gz dti_MD.nii.gz dti_S0.nii.gz dti_V2.nii.gz
dti_L1.nii.gz dti_L3.nii.gz dti_MO.nii.gz dti_V1.nii.gz dti_V3.nii.gz
➜  rest git:(master) ✗ 

Sincerely,
 Andrade.


look in sess01/bold, you should see 001 and 002. Do you?

On 10/22/2019 9:40 AM, Renew Andrade wrote:
External Email - Use Caution

Dear experts:
I am trying to run preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage 
lhrh -mni305 -fwhm 5 -per-run
But the outcome is ERROR: no run directories found.

What could be wrong?
If you need more information let me know!

Sincerely,
Andrade.



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[Freesurfer] Learning fsfast tutorial

[Renew Andrade]

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Dear experts:
I am trying to run preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage 
lhrh -mni305 -fwhm 5 -per-run
But the outcome is ERROR: no run directories found. 

What could be wrong? 
If you need more information let me know!

Sincerely,
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Re: [Freesurfer] Learning dti processing tutorial

[Renew Andrade]

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I am using a database of NITRC repository 
https://www.nitrc.org/projects/parktdi/ 
<https://www.nitrc.org/projects/parktdi/> . This images have a nifti file for 
1000s/mm^2 and 2500s/mm^2. I don’t know if it is MPRAGE or not. Can you help me?


What is the input file that you are supplying? Often this happens when 
the input it a multi-echo MPRAGE. If so, you can run
mri_concat multi-echo-mprage.mgz --rms --o mprage.mgz
then use mprage.mgz as the input to recon-all
On 10/12/2019 4:48 PM, Renew Andrade wrote:
>  External Email - Use Caution
>
> Dear freesurfer experts:
> I am trying to learn dti processing. For using Tracula it appears there is a 
> need for running "recon-all -all -i -s” on every subject before starting to 
> run Tracula. But there seems to be a problem. I have a Parkinson dwi images 
> database and every subject gives me an error of the type “input(s) cannot 
> have multiple frames!”. I am a little bit stuck on this step. Is it a problem 
> of the file as input? Am I putting the wrong file? Can it be done a recon-all 
> analysis to a dwi image? With trackvis I can obtain the results without any 
> problem. My doubt comes from FreeSurfer only and may be my little knowledge 
> about it.
> Thanks for your help!
> Sincerely,
> Andrade.
>
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Re: [Freesurfer] Error in glmfit-sim cache

[Renew Andrade]

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I have tried all the values it pinpoints to but none seem to work.

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[Freesurfer] Learning dti processing tutorial

[Renew Andrade]

External Email - Use Caution

Dear freesurfer experts:
I am trying to learn dti processing. For using Tracula it appears there is a 
need for running "recon-all -all -i -s” on every subject before starting to run 
Tracula. But there seems to be a problem. I have a Parkinson dwi images 
database and every subject gives me an error of the type “input(s) cannot have 
multiple frames!”. I am a little bit stuck on this step. Is it a problem of the 
file as input? Am I putting the wrong file? Can it be done a recon-all analysis 
to a dwi image? With trackvis I can obtain the results without any problem. My 
doubt comes from FreeSurfer only and may be my little knowledge about it. 
Thanks for your help!
Sincerely, 
Andrade. 

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[Freesurfer] Error in glmfit-sim cache

[Renew Andrade]

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Dear FreeSurfer experts:
I have an issue when running correction for multiple comparisons. I enter this 
(mri_glmfit-sim --glmdir lh.IXI.glmdir  --cache 4 abs —cap 0.05 --2spaces) in 
the terminal and I only receive messages of this sort (ERROR: thresh = 4,0 must 
be 1.3, 2.0, 3.0, 4.0)
What can I do to fix this?
Sincerely, 
Andrade. 

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[Freesurfer] Libraries not found Freeview ubuntu 18

[Renew Andrade]

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Dear FreeSurfer experts:
I have a problem with Freeview running I ubuntu. Some libraries missing. I read 
this thread 
“https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63255.html 
” 
and my question is regarding the installation of the libraries. Do I need to 
install manually one by one or is there any package to install most of them? 
Plus I couldn´t find any of them by the name in "sudo apt-get install *”.  Some 
of them are OpenGL, qtscript, volumerendering, vtkftgl, vtkhybrid, vtkIO, 
vtkDICOMParser, ...___
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[Freesurfer] Fwd: Error in Analyze: Couldn't open ... fwhm10.fsaverage.mgz

[Renew Andrade]

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Dear FreeSurfer experts:
I am processing in qdec 3 subjects with the GUI and I have this terminal 
output. 


Error in Analyze: Couldn't open 
/Applications/freesurfer/subjects/IXI_22_Guys_T1/surf/lh.thickness.fwhm10.fsaverage.mgz
 or .mgh file.
lh-Avg-Intercept-thickness ---
Does the average thickness differ from zero?
Nuisance factors: Right-Hippocampus
 1.000   0.000   0.000;



I have executed recon-all -s IXI_20_Guys_T1 -s IXI_22_Guys_T1 -s IXI_25_Guys_T1 
-qcache -target avgsubj20_22_25 -no-isrunning without any errors. Also 
make_average_subject make_average_subject --out avgsubj20_22_25 --subjects 
IXI_20_Guys_T1 IXI_22_Guys_T1 IXI_25_Guys_T1 without any errors. 

The problem is that I only have files like “...fwhm10.fsaverage.mgz" in one 
subject in this case IXI_25_Guys_T1 not in IXI_22_Guys_T1 or IXI_20_Guys_T1. I 
do not know if that is a mistake of processing or myself it seems by the output 
in qdec that I need files like “...fwhm10.fsaverage.mgz” in every subject 
subdirectory “surf”. 


Thanks for your help in advance!___
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[Freesurfer] Error in Analyze: Couldn't open ... fwhm10.fsaverage.mgz

[Renew Andrade]

External Email - Use Caution

Dear FreeSurfer experts:
I am processing in qdec 3 subjects with the GUI and I have this terminal 
output. 


Error in Analyze: Couldn't open 
/Applications/freesurfer/subjects/IXI_22_Guys_T1/surf/lh.thickness.fwhm10.fsaverage.mgz
 or .mgh file.
lh-Avg-Intercept-thickness ---
Does the average thickness differ from zero?
Nuisance factors: Right-Hippocampus
 1.000   0.000   0.000;



I have executed recon-all -s IXI_20_Guys_T1 -s IXI_22_Guys_T1 -s IXI_25_Guys_T1 
-qcache -target avgsubj20_22_25 -no-isrunning without any errors. Also 
make_average_subject make_average_subject --out avgsubj20_22_25 --subjects 
IXI_20_Guys_T1 IXI_22_Guys_T1 IXI_25_Guys_T1 without any errors. 

The problem is that I only have files like “...fwhm10.fsaverage.mgz" in one 
subject in this case IXI_25_Guys_T1 not in IXI_22_Guys_T1 or IXI_20_Guys_T1. I 
do not know if that is a mistake of processing or myself it seems by the output 
in qdec that I need files like “...fwhm10.fsaverage.mgz” in every subject 
subdirectory “surf”. 


Thanks for your help in advance!


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[Freesurfer] How to visualise DTI

[Renew Andrade]

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Dear community!
I would like to know how can I use Freeview or any tool of FreeSurfer to 
visualise preprocessed DTI files from a database. They are in a standard output 
like it appears in Tracula output page of FreeSurfer wiki. It shouldn’t be a 
problem to use these files in FreeSurfer. Everything (details of output and 
preprocessing stages) is explained in this website. 
https://www.nitrc.org/plugins/mwiki/index.php/neurobureau:INDIpreproc 


Thanks for your help!


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[Freesurfer] x y dimension mismatch dt_recon

[Renew Andrade]

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Dear community:
I have an issue that I have seen in the past still don´t know how to fix. Bval 
shows rows of 16 values and bvecs 17 values in one row only the rest 2 show 16 
as apparently should be.  What can I do?
Sincerely,
Andrade. 

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[Freesurfer] About FreeSurfer source code

[Renew Andrade]

External Email - Use Caution

Dear community:
I was curious about how the software is made and I decided to write an email to 
Dr. Bruce Fischl who answered all of the questions I asked, but he gave me the 
input to ask these questions also in FreeSurfer Community. I first asked the 
programming language of the software(I didn’t know that it was even open 
source). He says its mostly C but also some Matlab and C++. I am concerned with 
the long preprocessing time of raw T1 data so if anyone has some insights about 
which is the longest part and how faster it can get with nowadays hardware of 
course share with us. I think perhaps if some of the code of C were translated 
to C++ may be it could be faster. Although I don’t know how faster in fact but 
it could be a start. It should be easier if there were someone with clear head 
picture of time processing in different parts of the program in different 
hardware specifics. I know there is an entry in FreeSurfer wiki but I’m talking 
of an exchange of experiences with different machines with the same version of 
the software. May be I am going too far on my expectations. It would be nice to 
have a thread where we all shared our knowledge about how to improve 
performance. May be programming language translation is a bit of a lazy start 
and a change in some of the algorithms is the what we should  encourage. 

Sincerely, 
Andrade. 

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Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

[Renew Andrade]

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Hello again:
I have downloaded this raw data from a database that’s the reason I’m not sure 
it is T1w but I think what they call ntdi it is. So when I run recon-all from 
this ntdi.nifti file it gives me a Talairach error. 

I send you the output terminal. 

Sun Aug  5 21:16:32 -05 2018
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_ntdi
/Applications/freesurfer/bin/recon-all
-all -i 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/ntdi/NIfTI/p06316_bmatrix_2500_CSD_tracked_normalized_filt_TDI.nii.gz
 -s Parkinson_p06316_ntdi
subjid Parkinson_p06316_ntdi
setenv SUBJECTS_DIR /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir
FREESURFER_HOME /Applications/freesurfer
Actual FREESURFER_HOME /Applications/freesurfer
build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
descriptors  256 
memorylocked unlimited
maxproc  709 

PhysMem: 6923M used (1652M wired), 1269M unused.


program versions used
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 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: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 
2017 22:24:12  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp 
$  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  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: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 
2017 22:24:12  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve 
Exp $  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin 
 PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by ni...@gust.nmr.mgh.harvard.edu 
(x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 
2017 22:24:12  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ 
 User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 22:24:12  
CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: 
andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 
22:24:12  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp 
$  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 
22:24:12  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: 
andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 22:24:12  
CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: 
andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin  
PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 
22:24:12  CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman 
Exp $  User: andraderenew  Machine: Renes-MacBook-Air-2.local  Platform: Darwin 
 PlatformVersion: 17.5.0  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2018/08/06-02:16:33-GMT  BuildTimeStamp: Jan 19 2017 
22:24:12  CVS: $Id: 

[Freesurfer] ERROR: dimension mismatch between y and X.

[Renew Andrade]

External Email - Use Caution

Hello Community!

I have an issue while running dt_recon because as can be seen in the output 
terminal there is some error in matrix dimensions. 


Renes-MacBook-Air-2:~ andraderenew$ dt_recon --b 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bval/bvals.txt
  
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bvec/bvecs.txt
   --i 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz
   --s /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_recon   --o 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon 
-rwxrwxrwx  1 andraderenew  staff  660396 Feb 23  2015 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz
INFO: SUBJECTS_DIR is /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir
dt_recon logfile
Mon Aug  6 15:24:20 -05 2018
VERSION $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
setenv SUBJECTS_DIR /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir
cd /Users/andraderenew
/Applications/freesurfer/bin/dt_recon --b 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bval/bvals.txt
 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bvec/bvecs.txt
 --i 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz
 --s /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_recon --o 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon
Renes-MacBook-Air-2.local
andraderenew
/usr/local/fsl/bin/eddy_correct
ECRefTP 0
#@#---
Converting input
Mon Aug  6 15:24:20 -05 2018
cd /Users/andraderenew
mri_convert 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz
 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii
mri_convert.bin 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz
 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998806, -0.048201, -0.00797414)
j_ras = (-0.0487688, 0.993409, 0.10373)
k_ras = (-0.00292168, -0.103995, 0.994574)
writing to 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii...


#@#---
Eddy/Motion Correct
Mon Aug  6 15:24:20 -05 2018
cd /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/ectmp
eddy_correct 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii 0
processing 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec_tmp


#@#---
Fitting Tensors
Mon Aug  6 15:24:39 -05 2018
gzip /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii


gzip 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii


cd /Users/andraderenew
mri_glmfit --y 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii.gz
 --glmdir /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon 
--dti 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bval/bvals.txt
 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bvec/bvecs.txt

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Users/andraderenew
cmdline mri_glmfit.bin --y 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii.gz
 --glmdir /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon 
--dti 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bval/bvals.txt
 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bvec/bvecs.txt
 
sysname  Darwin
hostname Renes-MacBook-Air-2.local
machine  x86_64
user andraderenew
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii.gz
logyflag 1
usedti  1
glmdir /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating 

[Freesurfer] ERROR: input(s) cannot have multiple frames!

[Renew Andrade]

External Email - Use Caution

Hello community!

I have an issue while running recon-all -all in a dpi file. What do you suggest 
as a solution?
Thank you!

Renes-MacBook-Air-2:~ andraderenew$ recon-all -all  -i 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz
   -s Parkinson_p06316_dwi_2500
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir
Actual FREESURFER_HOME /Applications/freesurfer
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500
\n mri_convert 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz
 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
 \n
mri_convert.bin 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz
 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0.973179, 0.23005)
k_ras = (0, -0.23005, 0.973179)
writing to 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz...
#
#@# MotionCor Sun Aug  5 21:11:50 -05 2018
Found 1 runs
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz
 has 121 frames
Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64

recon-all -s Parkinson_p06316_dwi_2500 exited with ERRORS at Sun Aug  5 
21:11:50 -05 2018

For more details, see the log file 
/Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting___
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[Freesurfer] Freeview modalSession has been exited prematurely - check for a reentrant call to endModalSession:

[Renew Andrade]

External Email - Use Caution

Hello:
I attach here the command output of an error that I have while using Freeview. 
It doesn’t allows me to read any file. 


sh-3.2# freeview -v \
> good_output/mri/T1.mgz \
> good_output/mri/wm.mgz \
> good_output/mri/brainmask.mgz \
> good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \
> -f good_output/surf/lh.white:edgecolor=blue \
> good_output/surf/lh.pial:edgecolor=red \
> good_output/surf/rh.white:edgecolor=blue \
> good_output/surf/rh.pial:edgecolor=red
mghRead(/Volumes/TOSHIBA_EXT/otros/Acad?mico/Research/image_processing/freesurfer_data_tutorial/buckner_data/tutorial_subjs/good_output/mri/T1.mgz,
 -1): could not open file
MRIread failed: Unable to read from 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/buckner_data/tutorial_subjs/good_output/mri/T1.mgz
mghRead(/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/buckner_data/tutorial_subjs/good_output/mri/T1.mgz,
 -1): could not open file
2018-07-14 20:54:25.295 Freeview[63733:8866675] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:



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[Freesurfer] ERROR: Transform file should be eddy_correct/eddy log file or .mat file

[Renew Andrade]

External Email - Use Caution

Hello:
I have a problem when running trac-all preprocessing. I have X11 and FSL 
installed. Not Matlab I don’t know if I need it I think only for fMRI. 
Sincerely,
Andrade. 

Renes-MacBook-Air-2:diffusion_tutorial andraderenew$ trac-all -prep -c 
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
INFO: SUBJECTS_DIR is 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_recons
INFO: Diffusion root is 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial
Actual FREESURFER_HOME /Applications/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20130423
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Applications/freesurfer
Previous: /usr/local/freesurfer/dev
trac-preproc -c 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/dmrirc.local
 -log 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.log
 -cmd 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.cmd
#-
/Applications/freesurfer/bin/trac-preproc 
#-
#@# Image corrections Wed Jul 11 17:53:23 CEST 2018
mri_convert --bvec-voxel 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm...
Getting Series No 
INFO: Found 75 files in 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig
INFO: Scanning for Series Number 11
Scanning Directory 
INFO: found 70 files in series
INFO: loading series header info.

RunNo = 10
WARNING: Run 1 appears to be truncated
  Files Found: 70, Files Expected (lRep+1): 120
FileName
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
NumarisVersyngo MR 2004A 4VA25A 
ScannerModel  Trio
PatientName   Trio_calib_002_run2 
Date and time
StudyDate 20050905
StudyTime 100821.656000 
SeriesTime104226.748000 
AcqTime   104209.522496 
Acquisition parameters
PulseSeq  ep_b0#0 
Protocol  DIFFUSION_HighRes 
PhEncDir  COL
EchoNo0
FlipAngle 90
EchoTime  100
InversionTime -1
RepetitionTime10100
PhEncFOV  256
ReadoutFOV256
Image information
RunNo 10
SeriesNo  11
ImageNo   1
NImageRows1024
NImageCols1024
NFrames   70
SliceArraylSize   60
IsMosaic  1
ImgPos1048.1801 1002.6923 -265.4914 
VolRes  2.   2.   2. 
VolDim128  128   60 
Vc -0.9997   0.0244   0.0005 
Vr -0.0238  -0.9764   0.2147 
Vs  0.0057   0.2147   0.9767 
VolCenter   0.   0.   0. 
TransferSyntaxUID unknown
INFO: sorting.
INFO: (128 128  60), nframes = 70, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Numaris Version: syngo MR 2004A 4VA25A  Maj = 4, Min=2, MinMin = 5 
Repetition Time = 10100, TR = 10100 ms
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix - 
 0.99970   0.02376  -0.00570  -0.49480;
-0.02443   0.97638  -0.21466  -40.55519;
 0.00047   0.21474   0.97667   12.50291;
 0.0   0.0   0.0   1.0;

FileName
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
NumarisVersyngo MR 2004A 4VA25A 

[Freesurfer] Eddy correct command not found

[Renew Andrade]

External Email - Use Caution

Dear community:
I have a problem with trac-all processing with the tutorial data. 

sh-3.2# trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
INFO: SUBJECTS_DIR is 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_recons
INFO: Diffusion root is 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial
Actual FREESURFER_HOME /Applications/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20130423
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
flirt: Command not found.
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Applications/freesurfer
Previous: /usr/local/freesurfer/dev
trac-preproc -c 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/dmrirc.local
 -log 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.log
 -cmd 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.cmd
#-
/Applications/freesurfer/bin/trac-preproc 
#-
#@# Image corrections Fri Jun 29 21:19:12 CEST 2018
mri_convert --bvec-voxel 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz
 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm...
Getting Series No 
INFO: Found 75 files in 
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig
INFO: Scanning for Series Number 11
Scanning Directory 
INFO: found 70 files in series
INFO: loading series header info.

RunNo = 10
WARNING: Run 1 appears to be truncated
  Files Found: 70, Files Expected (lRep+1): 120
FileName
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
NumarisVersyngo MR 2004A 4VA25A 
ScannerModel  Trio
PatientName   Trio_calib_002_run2 
Date and time
StudyDate 20050905
StudyTime 100821.656000 
SeriesTime104226.748000 
AcqTime   104209.522496 
Acquisition parameters
PulseSeq  ep_b0#0 
Protocol  DIFFUSION_HighRes 
PhEncDir  COL
EchoNo0
FlipAngle 90
EchoTime  100
InversionTime -1
RepetitionTime10100
PhEncFOV  256
ReadoutFOV256
Image information
RunNo 10
SeriesNo  11
ImageNo   1
NImageRows1024
NImageCols1024
NFrames   70
SliceArraylSize   60
IsMosaic  1
ImgPos1048.1801 1002.6923 -265.4914 
VolRes  2.   2.   2. 
VolDim128  128   60 
Vc -0.9997   0.0244   0.0005 
Vr -0.0238  -0.9764   0.2147 
Vs  0.0057   0.2147   0.9767 
VolCenter   0.   0.   0. 
TransferSyntaxUID unknown
INFO: sorting.
INFO: (128 128  60), nframes = 70, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Numaris Version: syngo MR 2004A 4VA25A  Maj = 4, Min=2, MinMin = 5 
Repetition Time = 10100, TR = 10100 ms
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix - 
 0.99970   0.02376  -0.00570  -0.49480;
-0.02443   0.97638  -0.21466  -40.55519;
 0.00047   0.21474   0.97667   12.50291;
 0.0   0.0   0.0   1.0;

FileName
/Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm
Identification
NumarisVersyngo MR 2004A 4VA25A 
ScannerModel  Trio
PatientName   Trio_calib_002_run2 
Date and time
StudyDate 20050905
 

[Freesurfer] Yendiki Anastasia config file

[Renew Andrade]

Here is the configuration file. I think is the default by tutorial. 


dmrirc.tutorial
Description: Binary data
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Re: [Freesurfer] To Yendiki, Anastasia on TRACULA (Yendiki, Anastasia)

[Renew Andrade]

What is the configuration file or where can I find it?
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[Freesurfer] To Yendiki, Anastasia on TRACULA

[Renew Andrade]

Dear Anastasia:
All the output I get is the if Expression Syntax. 
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[Freesurfer] tracula flags

[Renew Andrade]

Hello everyone!
I have this problem with TRACULA. When I go to the second part of the tutorial 
I can´t keep going. I acknowledge that during the first part I have switch from 
tcsh to bash depending on errors but I’m not sure if that is normal or a 
mistake. The error is for example:
trac-all -prep -c home/andraderenew/Downloads/freesurfer data 
tutorial/diffusion_tutorial/dmrirc.tutorial
if: Expression Syntax
Thanks!
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[Freesurfer] bert log file

[Renew Andrade]

Hello everyone!I write to you because I can't get the process done in 
freesurfer. I attach the log file. Thank you!
Mon Jan 22 01:16:35 CET 2018
/home/andraderenew/Downloads/SUBJECTS_DIR/bert
/home/andraderenew/Downloads/freesurfer/bin/recon-all
-i /home/andraderenew/Downloads/SUBJECTS_DIR/sample-001.nii.gz -s bert -all
subjid bert
setenv SUBJECTS_DIR /home/andraderenew/Downloads/SUBJECTS_DIR
FREESURFER_HOME /home/andraderenew/Downloads/freesurfer
Actual FREESURFER_HOME /home/andraderenew/Downloads/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux ubuntu 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  3712 
maxlocks unlimited
maxsignal3712 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem: 994868  653428  1072847324  234156  146784
Swap:   1046524  589148  457376


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: 2018/01/22-00:16:35-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: andraderenew  Machine: ubuntu  Platform: Linux  PlatformVersion: 4.10.0-28-generic  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: 2018/01/22-00:16:35-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: andraderenew  Machine: ubuntu  Platform: Linux  PlatformVersion: 4.10.0-28-generic  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: 2018/01/22-00:16:35-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: andraderenew  Machine: ubuntu  Platform: Linux  PlatformVersion: 4.10.0-28-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/01/22-00:16:35-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: andraderenew  Machine: ubuntu  Platform: Linux  PlatformVersion: 4.10.0-28-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/01/22-00:16:35-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: andraderenew  Machine: ubuntu  Platform: Linux  PlatformVersion: 4.10.0-28-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/01/22-00:16:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: andraderenew  Machine: ubuntu  Platform: Linux  PlatformVersion: 4.10.0-28-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/01/22-00:16:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: andraderenew  Machine: ubuntu  Platform: Linux  PlatformVersion: 4.10.0-28-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/01/22-00:16:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: andraderenew  Machine: ubuntu  Platform: Linux  PlatformVersion: 4.10.0-28-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/01/22-00:16:35-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $  User: andraderenew  Machine: ubuntu  Platform: Linux  PlatformVersion: 4.10.0-28-generic  CompilerName: GCC  

[Freesurfer] corRead(): can't open file /home/andraderenew/COR-.info

[Renew Andrade]

> Begin forwarded message:
> 
> From: Renew Andrade <andradere...@yahoo.com>
> Subject: corRead(): can't open file /home/andraderenew/COR-.info
> Date: 18 January 2018 at 12:15:49 CET
> To: freesurfer@nmr.mgh.harvard.edu
> 
> Hello:
> I run the command to open freeview -v…(the installation guide example in 
> Bert) and I get the error in I point out in the subject of this email. Thanks 
> for the help in advance!
> Sincerely,
> Rene Andrade. 
> 

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[Freesurfer] corRead(): can't open file /home/andraderenew/COR-.info

[Renew Andrade]

Hello:
I run the command to open freeview -v…(the installation guide example in Bert) 
and I get the error in I point out in the subject of this email. Thanks for the 
help in advance!
Sincerely,
Rene Andrade. 


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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.