subject:"Re\: \[Freesurfer\] TRACULA question"

Re: [Freesurfer] TRACULA question

2022-05-04 Thread Yendiki, Anastasia

Hi Gonzalo - The input to TRACULA can be any file that can be converted to 
nifti by mri_convert. See:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula#line-156

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Gonzalo Rojas Costa 

Sent: Friday, April 22, 2022 11:10 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] TRACULA question

External Email - Use Caution

Hi:

  Is it possible to use input diffusion files in MOSAIC IMA Siemens
file format directly? Or is it necessary to convert to nifti file
format first?

  Sincerely,


Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
https://secure-web.cisco.com/13PUT3U3zuLu0QBvcZiGdm18njGuoQr6dUsSQj9e5H3gOiFfFDIQfzquemma2IXSELZNdhFwGi3w3goGxGPnOUdDoh9pHJjjlEzyWgHhOvtSI1rWfiptKHRGKPqroO3HfU5LOzYece7gEBewcRdacnxbyoGkrInzayFlpCHDwMovVj2RsZXoAPA1TJD0c6qPpjpyNdRSfvWEQjlWFseO0XmY2GzERvEGLNZ2jVD7cFivFtsBZI6QKXubnoVYv7ZIhYdk8IDuEDnUGkM6aGN0fQdo0EfKqqQ5mvrA_-URQ1HAlx7fGFKcWaS-msf5JV3UYewMKh29ySoudmFsGrqP2Jg/https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DLO7LZ3oJ
https://secure-web.cisco.com/1TdZ-Zm0eaCvN4RyCzzXuq6HNPTVfbbxwGyNTIGMGFiRfybDhlZfcJej5DuQlBFxYwDJwSO1NbZisBp1yVrq7nyw2kMBF6oos5kUwQY5n5PaU_F0e5FlhFPXN8jHJ9-2ZjvCR48B8WX_Z98dUDwJgPDp6W5J9Qx86YoNJpPWxzK2nlRZBUv4m4xJZ1yZl8bc-y_rLC_yBmefTddoYvHRgxm-Sx-sI3urGbmLlgo1GW0ejAy5O87MgIVb9l10EMEi9Scz6WXE-mZCKUDK68bg0_py0KqpFw23M8fQvUlt-KsNQxJKwM0xjpEwDF8JFFDEW1fwAuuxSsUuDnVYZUTIW-g/https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGonzalo_Rojas2
https://secure-web.cisco.com/1lJu3jBI0nOfv9_IwBeCbcBNGA2K6pj5tSumDqMfk3ZItRd8BPyGam7Jzi5vwYgKSWZn_h3NHNpB-2LvnR0NG2dicPxcNLIMT9-kyIhxlIVn9KJDnI0UkMvvB_bwD35c9Wo8ZgYrmeeME-Xhopc25SP0b4uZ_ac8eyRU7siPGYplCIdV_wlbcpaf4QKngZ0GQ0OlKTSFA0kUvGppEUPh0dKLd1GGfVI7ta1xtDWAEeQDRZIJPDNENvLEMET8cajKIPIxhR0Pj9mFACW91chNeZqqgUH-RWTQD6lH1n-FqHFhQVN7buFLIgM89GsJppvGFD4sZGKjuTmnCpl4rS9rfaw/https%3A%2F%2Fcvn.fecyt.es%2F-0002-6228-2678
http://secure-web.cisco.com/1vs-E3PvUdSdie9Xm5LpQNiLpowx1KB-bnADkKZ76Vp4VANi--BPTBe90wM8SCdFK734_gIbmMr3PBFV4ZJOOJBA24RG16y2k3uomDr6zt-G7miVY8bETh1mVxRJXumLpmc3Yy3dH2PFE6uhzJNvuE5hUZqhTfQw-X7c4anBMhN_zYMez258yi_VwfB2Bz28yNTA0qClOp844_ELq3fX0tWSuBqUJmcCh8gyVYmA64LHU5lnFXwPdUjWzaoH9ZZ273niweURIdtncHPz5NN3wKifGl9r1dIbi8P9MG0Z64fjTArReR1NbSk-Z64E3_nvqJ-7Si7om181qm26Y05GJJQ/http%3A%2F%2Fwww.researcherid.com%2Frid%2FB-2036-2013
https://secure-web.cisco.com/1FM_I0dgNRRtoYqJmIXPdHgx__9woRyRSo5bnLSxgt51fCtFxOKP6SAvGDvzMdI6MlI8dr1A-GDLm7Ugbz4xQx_eBa-r6rF_KXZvcjQcG7c3HVqDBJ5Osza-xTwzP_JY8XT3vlujEpbz8lruWJRubpiv8DahDeUMtd6pNWEUHJagvmUDsyMHXbd1pm-XmpTmfa1RXkgkyaVwFfLwauPMJh4WFhchF7wz1ikJ8evtbLmu13H0jH_fCDLhFjkQlIHGSX4u1iiBtVtWcQQBc3tYacYBQNS-ly18qBzxa6Ebq21iyHPLMQ5lsZwvlRZoZl9d53xxdrTkwCPcwwkvO1szKIQ/https%3A%2F%2Fcl.linkedin.com%2Fin%2Fgonzalorojascosta

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Re: [Freesurfer] TRACULA Question

2022-01-31 Thread Salar Dini, Elaheh

External Email - Use Caution

Hello,

I just wanted to follow-up on my last message. I will be thankful if you can 
respond at the earliest time of your convince.

Thanks and all the best,
Ela


From: Salar Dini, Elaheh 
Sent: Wednesday, January 26, 2022 2:29 PM
To: Freesurfer support list 
Subject: Re: TRACULA Question

Dear Anastasia,

Thank you so much for the response. Interestingly, when I try to open the two 
reconstructed brains at the same time, they don't overlay. Am I correct to 
assume then that we have to run recon-all using version 7.2.0? I'm providing a 
screenshot of the simultaneously opened MRIs in the attached drobox link: 
https://secure-web.cisco.com/1bjk0NdGOMfB6NKhn2KCWf4-haQCa6trjJc5Dj8D-7w7B2nCg1-9bCYFoObeg-FKdiZ0K5m0NqSSLrnIzXO79u-CQU5shRDBG0Z7MgcVtK8VWNJDEmlhDaMYOYcQ6IJhpyardGx585fAsOAdkOJ1ASMP0BDRepX9eYnqhS5ggrbxrNU--n8q_hi3KLnbCO1S5XyaCqpiherGch4qFrDY-tBHECwynH7N6-dHMrSnRUJ4F9OOih-e1FS3lC90fOV_3aRjSHa-GYyuo0vcIVXvQ6S6BkFNeLoL6efZ8m0oi5zUpZTHCWYYC0JR1PKZ44jVoDg1CcbFvmdk5UuhypdFqgg/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fc2gsp8h8jj7c93d%2FScreen%2520Shot%25202022-01-26%2520at%25201.40.23%2520PM.png%3Fdl%3D0
[https://secure-web.cisco.com/11NJ9pbqdzx2Q5us6cqdu7nTaM2_6gYeDmh7ymNpTqdpM7cpQMi0p_coWb7WZa_HQR_is9cTXkzVuIBzs5aVIl02cmlWbuxkgJvXI9sp4f5keV2j1OPXAokycdUShU0fyEHEkq2ohUgbrsId4fIKZqNJ24NtJEalDjbG7fzAcpfCmEtqmsTpHpYQt8YkPLnRnNUzTJoyB5qsCARaGp5zr8V2KeJfP-yaItltEqIhRhnaWcBFN4PmMj85S-GeRbKi_la5gxXqpXtzeldXq4N2LRv9z3syj0WP0eYSfQysnyeSllAR07pKGa4_D3jWfqE5dnfD7eyk4BZtG96y20JaHvg/https%3A%2F%2Fwww.dropbox.com%2Ftemp_thumb_from_token%2Fs%2Fc2gsp8h8jj7c93d%3Fpreserve_transparency%3DFalse%26size%3D1200x1200%26size_mode%3D4
Screen Shot 2022-01-26 at 1.40.23 
PM.png
Shared with Dropbox
http://secure-web.cisco.com/1bv3dovP1EOZNFOeqrtWA8pUKqnru7Uv5k31_AUBNQ_-1tBg63HCQ5joG-b6eOCKBKD-WzPRAgXl2dZvwyct_yq4U2UJjBmFqWY8wgfdSyvZDWbHHGeX0Yi6IJ7Ma857BnAa47EZHT-bVKU2HypxNs67QnDBsHOq39xsd7I83F0e9yrp1u2bAxzylK55The71NmJ3PX0NeXyiStMBvUK6jzR02HFNP3YoPQ8FhPpEO7uOMohdb0HHJYUMGXIkqXx3cl4HemT9WOVGKi5zYtQdeRxKZiiiKkaaHsl14oalAqc8qx60qmKfaXZKfvhQnXCgeig94owfq7Jk-RMZLerBFA/http%3A%2F%2Fwww.dropbox.com



If yes, this brings me to another question: if the missing voxels from the 
BET.MASK are limited to ventricles or gray matter, and we don't correct these 
missing voxels, is TRACULA still able to run with precision and provide us with 
an accurate result? Since TRACULA is a probabilistic method and use prior 
knowledge of positions of anatomical structures with respect to each other, I 
wasn't sure that white matter reconstruction won't be affected by missing 
voxels in ventricle or gray matter. Our missing voxels in Alzheimer's Disease 
Patients are usually limited to ventricles or in extreme cases gray matter. If 
it is not affecting the white matter reconstruct and extracted metrics, we can 
skip the step that we manually fix the BET. Mask. If you suggest going ahead 
and manually correct the missing voxels from the BET mask, we will do it.

Thank you




From: Yendiki, 
Anastasia
Sent:  Wed, 19 Jan 2022 19:57:32

Re: [Freesurfer] TRACULA Question

2022-01-26 Thread Salar Dini, Elaheh

External Email - Use Caution

Dear Anastasia,

Thank you so much for the response. Interestingly, when I try to open the two 
reconstructed brains at the same time, they don't overlay. Am I correct to 
assume then that we have to run recon-all using version 7.2.0? I'm providing a 
screenshot of the simultaneously opened MRIs in the attached drobox link: 
https://secure-web.cisco.com/1VHfD0Q3rypPafcUSw5pqIJs_awOmpRgYIzZGpsZZ3nHObzY0DUphIFO_BZkMVkJKl6kkmgeiyZbiKaxtLVhBFbPEMY33VaESl1stGZ5ZndrkXQ9_B-tjVx9nHZB2trbLZXPNv8gqnf6HKpzx20lqldBiDnxY2_ryUh9ut9KjAuoqG34BzftD_Ha2D51lt-KCnNnSCJT9YUQHOjFyeJHmVJCZQaiNOSyRXBRy5Rnou4t4ez5Sv76pddU9IMSGIw4wT8KhwUXf0RNOKYiAqdykH4wmBxKN6jhT4vF6YUuyhcj42IDJbI6JsnpdCQz-dhWqDJhQWyzM60tq7FEzMBjd4w/https%3A%2F%2Fwww.dropbox.com%2Fs%2Fc2gsp8h8jj7c93d%2FScreen%2520Shot%25202022-01-26%2520at%25201.40.23%2520PM.png%3Fdl%3D0
[https://secure-web.cisco.com/12qznXChPnk4lzoVX7jSXmhfrfg5tLxhxLFwAdR8shTWygDtZ73LoT4q6ZqCkshyIkt3qyOR6J-OEspAolJZSxO1ufCq0JU13ZEV0Gl-mwWyXgUcLvsf297_vjr8FHX3VmyClFSlKrEBiAAQnL49l0zrsehh5USiaZ1v_IogFhlTkKsqViRT2dE1h6sJroA3LvysG5Zju-9B-VYe5FsiCq-fD4GL3_MlnuhUvBy5eLkh3y29ZmoJ0oiYuo9s8NCXBgaK-2Y6TRuQg842lvkAtJt9x44BHYZMtb8azO_4XX7zptEtonElbMit7W_fFwn2wAdqeuP8Gujrh2rNs2ge0JQ/https%3A%2F%2Fwww.dropbox.com%2Ftemp_thumb_from_token%2Fs%2Fc2gsp8h8jj7c93d%3Fpreserve_transparency%3DFalse%26size%3D1200x1200%26size_mode%3D4
Screen Shot 2022-01-26 at 1.40.23 
PM.png
Shared with Dropbox
http://secure-web.cisco.com/1po5cpn46Uk2_2A6IsDZeYNjWTbfbavOoIL00gd11MMpHtRvOhC_lHt-13qMZKHWZBvtgDHaUvMm9KaOfkG6bkMp6lTIlqdQdZSeZ7SLAFYUucjvn2UWfPgXa_Dp5VsxvsvbTmqhROmz7aM7ZlHvxdvGhq5meLfyW4C53a8GoaI57UKGmSaZSwPK7Vl2Op6yFwaeOrwUP6XMSY3bWXyMXoUn6fIgXb9-azK1AF6UkYOEA9slsG4HXVcb7Cn_U10D7ESzsMY_UW3dojGNRdjBk-nr6VoAYSKf_i9XJM3yxWwfuLvvpnfJff7XuTauPAg9wNLIjKEQPe_Myw_4ECFRVYA/http%3A%2F%2Fwww.dropbox.com



If yes, this brings me to another question: if the missing voxels from the 
BET.MASK are limited to ventricles or gray matter, and we don't correct these 
missing voxels, is TRACULA still able to run with precision and provide us with 
an accurate result? Since TRACULA is a probabilistic method and use prior 
knowledge of positions of anatomical structures with respect to each other, I 
wasn't sure that white matter reconstruction won't be affected by missing 
voxels in ventricle or gray matter. Our missing voxels in Alzheimer's Disease 
Patients are usually limited to ventricles or in extreme cases gray matter. If 
it is not affecting the white matter reconstruct and extracted metrics, we can 
skip the step that we manually fix the BET. Mask. If you suggest going ahead 
and manually correct the missing voxels from the BET mask, we will do it.

Thank you




From: Yendiki, 
Anastasia
Sent:  Wed, 19 Jan 2022 19:57:32 
-0800
Subject: Re: TRACULA Question




Hi Ela - When you overlay the aparc+aseg from 6.0 and

Re: [Freesurfer] TRACULA Question

2022-01-19 Thread Yendiki, Anastasia

Hi Ela - When you overlay the aparc+aseg from 6.0 and the one from 7.2, is 
there a notable difference? Is there any chance that the brain is cut off? The 
error happened in the anterior commissure, that's a tract that does goes fairly 
close to the ventral surface of the brain, and in the part of the log file 
where the error happens I see some strange negative coordinates in the z 
direction.

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Salar Dini, Elaheh 

Sent: Tuesday, January 18, 2022 4:55 PM
To: Freesurfer support list 
Subject: [Freesurfer] TRACULA Question


External Email - Use Caution

Dear Anastasia,
I have run trac -all -prep in 2 different conditions:
a) prerequisite recon-all step was done using freesurfer 7.2.0
b) prerequisite recon-all step was done using freesurfer 6

The first time everything ran smoothly without an error, but when we used 
aparc+aseg resulted from running recon -all using version 6 of freesurfer, we 
got the following error for which I also attach the log file to this message: 
Segmentation fault (core dumped)

My question is that if I'm correct to assume that we can't run trac-all -prep 
using structural MRI segmentation done by previous versions of freesurfer? The 
reason I'm asking this is that I have a data from 100 subjects with Alzheimer's 
Disease. We have been collecting this data over the past 4 years and have done 
the recon -all step using freesurfer 6 for all of them as we acquired them. If 
trac-all can't use those segmentation, we have to do this step again for all 
these 100 subjects.

I appreciate your help and insight.
Ela

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Re: [Freesurfer] Tracula question

2019-10-17 Thread Alan Francis

External Email - Use Caution

Thanks Anastasia. That is exactly what happened and we have fixed it.

best,

Alan

On Tue, Oct 15, 2019 at 5:37 PM Yendiki, Anastasia 
wrote:

> Hi Alan - It looks like it may be due to a mismatch between the
> bvals/bvecs files and the number of volumes in your DWI data. I think it's
> expecting to find a b=0 volume as the 64th volume, but your DWI nifti has
> only 63 volumes.
>
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alan Francis <
> alandarkene...@gmail.com>
> *Sent:* Tuesday, October 15, 2019 10:26:32 AM
> *To:* Freesurfer 
> *Subject:* [Freesurfer] Tracula question
>
>
> External Email - Use Caution
>
> Dear Anastasia -
>
> I tried running tracula preproc. However, it gave me an error message.
> Could you please shed some light on this?
>
> Thank you,
>
> Alan
>
> [airhunger:JC_DTI] (nmr-stable6-env) trac-all -prep -c dmrirc-esq-14-hc
> INFO: SUBJECTS_DIR is /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC
> INFO: Diffusion root is /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC
> Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/stable6
> trac-preproc -c
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/dmrirc.local
> -log
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/trac-all.log
> -cmd
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/trac-all.cmd
> #-
> /usr/local/freesurfer/stable6/bin/trac-preproc
> #-
> #@# Image corrections Tue Oct 15 10:01:10 EDT 2019
> mri_convert --bvec-voxel
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz
> mri_convert.bin --bvec-voxel
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.996936, 0.0343122, -0.0703008)
> j_ras = (0.0173889, 0.973389, 0.228497)
> k_ras = (-0.0762703, -0.226574, 0.971003)
> writing to
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz...
> cp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/31916396_bvecs
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs
> cp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/31916396_bvals
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals
> mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.tmp
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs
> mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvals.tmp
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals
> orientLAS
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz
> INFO: input image orientation is LAS
> INFO: input image determinant is -18.7806
> mri_convert -oni 130 -onj 130 -onk 24 -oid -0.996936 0.0343122 -0.0703008
> -ojd 0.0173889 0.973389 0.228497 -okd -0.0762703 -0.226574 0.971003 -oc
> -0.761131 24.2246 -3.09646 -rt nearest
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz
> mri_convert.bin -oni 130 -onj 130 -onk 24 -oid -0.996936 0.0343122
> -0.0703008 -ojd 0.0173889 0.973389 0.228497 -okd -0.0762703 -0.226574
> 0.971003 -oc -0.761131 24.2246 -3.09646 -rt nearest
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz
>
> normalizing out_i_direction: (-0.996936, 0.0343122, -0.0703008) ->
> (-0.996936, 0.0343122, -0.0703008)
> normalizing out_j_direction: (0.0173889, 0.973389, 0.228497) ->
> (0.0173889, 0.973389, 0.228497)
> normalizing out_k_direction: (-0.0762703, -0.226574, 0.971003) ->
> (-0.0762703, -0.226574, 0.971003)
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.996936, 0.0343122, -0.0703008)
> j_ras = (0.0173889, 0.973389, 0.228497)
> k_ras = (-0.0762703, -0.226574, 0.971003)
> Reslicing using nearest
> writing to
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz...
> INFO: found
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals,
> copying
> INFO: found
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs,
> converting to LAS
> mv -f
> /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.bvecs
>

Re: [Freesurfer] Tracula question

2019-10-15 Thread Yendiki, Anastasia

Hi Alan - It looks like it may be due to a mismatch between the bvals/bvecs 
files and the number of volumes in your DWI data. I think it's expecting to 
find a b=0 volume as the 64th volume, but your DWI nifti has only 63 volumes.

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alan Francis 

Sent: Tuesday, October 15, 2019 10:26:32 AM
To: Freesurfer 
Subject: [Freesurfer] Tracula question


External Email - Use Caution

Dear Anastasia -

I tried running tracula preproc. However, it gave me an error message. Could 
you please shed some light on this?

Thank you,

Alan

[airhunger:JC_DTI] (nmr-stable6-env) trac-all -prep -c dmrirc-esq-14-hc
INFO: SUBJECTS_DIR is /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC
INFO: Diffusion root is /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/stable6
trac-preproc -c 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/dmrirc.local -log 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/trac-all.log -cmd 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/trac-all.cmd
#-
/usr/local/freesurfer/stable6/bin/trac-preproc
#-
#@# Image corrections Tue Oct 15 10:01:10 EDT 2019
mri_convert --bvec-voxel 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996936, 0.0343122, -0.0703008)
j_ras = (0.0173889, 0.973389, 0.228497)
k_ras = (-0.0762703, -0.226574, 0.971003)
writing to 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz...
cp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/31916396_bvecs 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs
cp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/31916396_bvals 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals
mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.tmp 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs
mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvals.tmp 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals
orientLAS 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -18.7806
mri_convert -oni 130 -onj 130 -onk 24 -oid -0.996936 0.0343122 -0.0703008 -ojd 
0.0173889 0.973389 0.228497 -okd -0.0762703 -0.226574 0.971003 -oc -0.761131 
24.2246 -3.09646 -rt nearest 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 130 -onj 130 -onk 24 -oid -0.996936 0.0343122 -0.0703008 
-ojd 0.0173889 0.973389 0.228497 -okd -0.0762703 -0.226574 0.971003 -oc 
-0.761131 24.2246 -3.09646 -rt nearest 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.996936, 0.0343122, -0.0703008) -> (-0.996936, 
0.0343122, -0.0703008)
normalizing out_j_direction: (0.0173889, 0.973389, 0.228497) -> (0.0173889, 
0.973389, 0.228497)
normalizing out_k_direction: (-0.0762703, -0.226574, 0.971003) -> (-0.0762703, 
-0.226574, 0.971003)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.996936, 0.0343122, -0.0703008)
j_ras = (0.0173889, 0.973389, 0.228497)
k_ras = (-0.0762703, -0.226574, 0.971003)
Reslicing using nearest
writing to 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz...
INFO: found 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals, copying
INFO: found 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs, 
converting to LAS
mv -f 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.bvecs 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs
mv -f 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.bvals 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvals
eddy_correct 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz 
/autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz 0
processing

Re: [Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

2018-11-19 Thread Yendiki, Anastasia

Hi June - Circling back to this to see if it was resolved. If you're just using 
the publicly available data, there should be 3x96 directions, with 3 different 
b-values. Which set of 96 are you using?


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of June Kang 

Sent: Saturday, November 3, 2018 7:35:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Question-How the threshold in final merged 
tracts are defined?


External Email - Use Caution

It’s just huge data collected from general population. Some data can have 
motion artifact, but I couldn’t find any special points in the protocol.

http://protocols.humanconnectome.org/HCP/3T/imaging-protocols.html

J.


On Nov 4, 2018, at 4:21 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi June - Not in principle, any number of directions > 30 should be compatible. 
Is there anything else that's different about this data, e.g., SNR, motion, 
population with more morphological variability, etc.?

a.y

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of June Kang mailto:cn...@korea.ac.kr>>
Sent: Saturday, November 3, 2018 12:24:54 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Question-How the threshold in final merged 
tracts are defined?

External Email - Use Caution

Thanks, Professor Anastasia,

I am testing HCP data with 96 directions.
There are really frequent failure for right cingulum-angular bundle and right 
uncinate fasciculus (more than 25%), which not happened with my own 
64-direction data with Siemens Trio.

Is there any known issue or recommended modification of the pipeline for HCP 
data or data with more directions?

Bests,
J.


On Nov 2, 2018, at 10:44 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

They are not random, they are 20% of the maximum value. If you want to generate 
stats at a different threshold, you can find the dmri_pathstats command line in 
trac-all.log and add the --pthr option (the default 20% would be --pthr .2).

On Nov 1, 2018 9:01 PM, June Kang mailto:cn...@korea.ac.kr>> 
wrote:
External Email - Use Caution

In the visualization step of Tracula processing, freeview -tv 
merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), 
which make them look like the reconstruction-failed ones.
The tracts failed to reconstruction usually show threshold of 300 (not 
changeable) with tiny rounded cylinder shape.
In successfully reconstructed tracts with very high threshold, it looks ok, 
when I adjust threshold to the similar value from contralateral one.

Is there any reason for this extremely high threshold? or it’s just randomly 
set values?

Bests,
J.


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Re: [Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

2018-11-03 Thread June Kang

External Email - Use Caution

It’s just huge data collected from general population. Some data can have 
motion artifact, but I couldn’t find any special points in the protocol.

http://protocols.humanconnectome.org/HCP/3T/imaging-protocols.html 
<http://protocols.humanconnectome.org/HCP/3T/imaging-protocols.html>

J.


> On Nov 4, 2018, at 4:21 AM, Yendiki, Anastasia  
> wrote:
> 
> Hi June - Not in principle, any number of directions > 30 should be 
> compatible. Is there anything else that's different about this data, e.g., 
> SNR, motion, population with more morphological variability, etc.?
> 
> a.y
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of June Kang 
> mailto:cn...@korea.ac.kr>>
> Sent: Saturday, November 3, 2018 12:24:54 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tracula Question-How the threshold in final merged 
> tracts are defined?
>  
> External Email - Use Caution
> Thanks, Professor Anastasia,
> 
> I am testing HCP data with 96 directions.
> There are really frequent failure for right cingulum-angular bundle and right 
> uncinate fasciculus (more than 25%), which not happened with my own 
> 64-direction data with Siemens Trio.
> 
> Is there any known issue or recommended modification of the pipeline for HCP 
> data or data with more directions?
> 
> Bests,
> J.
> 
> 
>> On Nov 2, 2018, at 10:44 AM, Yendiki, Anastasia > <mailto:ayend...@mgh.harvard.edu>> wrote:
>> 
>> They are not random, they are 20% of the maximum value. If you want to 
>> generate stats at a different threshold, you can find the dmri_pathstats 
>> command line in trac-all.log and add the --pthr option (the default 20% 
>> would be --pthr .2).
>> 
>> On Nov 1, 2018 9:01 PM, June Kang > <mailto:cn...@korea.ac.kr>> wrote:
>> External Email - Use Caution
>> 
>> In the visualization step of Tracula processing, freeview -tv 
>> merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), 
>> which make them look like the reconstruction-failed ones.
>> The tracts failed to reconstruction usually show threshold of 300 (not 
>> changeable) with tiny rounded cylinder shape.
>> In successfully reconstructed tracts with very high threshold, it looks ok, 
>> when I adjust threshold to the similar value from contralateral one.
>> 
>> Is there any reason for this extremely high threshold? or it’s just randomly 
>> set values?
>> 
>> Bests,
>> J.
>> 
>> 
>> ___
>> Freesurfer mailing list
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> ___
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Re: [Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

2018-11-03 Thread Yendiki, Anastasia

Hi June - Not in principle, any number of directions > 30 should be compatible. 
Is there anything else that's different about this data, e.g., SNR, motion, 
population with more morphological variability, etc.?


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of June Kang 

Sent: Saturday, November 3, 2018 12:24:54 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Question-How the threshold in final merged 
tracts are defined?


External Email - Use Caution

Thanks, Professor Anastasia,

I am testing HCP data with 96 directions.
There are really frequent failure for right cingulum-angular bundle and right 
uncinate fasciculus (more than 25%), which not happened with my own 
64-direction data with Siemens Trio.

Is there any known issue or recommended modification of the pipeline for HCP 
data or data with more directions?

Bests,
J.


On Nov 2, 2018, at 10:44 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

They are not random, they are 20% of the maximum value. If you want to generate 
stats at a different threshold, you can find the dmri_pathstats command line in 
trac-all.log and add the --pthr option (the default 20% would be --pthr .2).

On Nov 1, 2018 9:01 PM, June Kang mailto:cn...@korea.ac.kr>> 
wrote:
External Email - Use Caution

In the visualization step of Tracula processing, freeview -tv 
merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), 
which make them look like the reconstruction-failed ones.
The tracts failed to reconstruction usually show threshold of 300 (not 
changeable) with tiny rounded cylinder shape.
In successfully reconstructed tracts with very high threshold, it looks ok, 
when I adjust threshold to the similar value from contralateral one.

Is there any reason for this extremely high threshold? or it’s just randomly 
set values?

Bests,
J.


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Re: [Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

2018-11-03 Thread June Kang

External Email - Use Caution

Thanks, Professor Anastasia,

I am testing HCP data with 96 directions.
There are really frequent failure for right cingulum-angular bundle and right 
uncinate fasciculus (more than 25%), which not happened with my own 
64-direction data with Siemens Trio.

Is there any known issue or recommended modification of the pipeline for HCP 
data or data with more directions?

Bests,
J.


> On Nov 2, 2018, at 10:44 AM, Yendiki, Anastasia  
> wrote:
> 
> They are not random, they are 20% of the maximum value. If you want to 
> generate stats at a different threshold, you can find the dmri_pathstats 
> command line in trac-all.log and add the --pthr option (the default 20% would 
> be --pthr .2).
> 
> On Nov 1, 2018 9:01 PM, June Kang  > wrote:
> External Email - Use Caution
> 
> In the visualization step of Tracula processing, freeview -tv 
> merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), 
> which make them look like the reconstruction-failed ones.
> The tracts failed to reconstruction usually show threshold of 300 (not 
> changeable) with tiny rounded cylinder shape.
> In successfully reconstructed tracts with very high threshold, it looks ok, 
> when I adjust threshold to the similar value from contralateral one.
> 
> Is there any reason for this extremely high threshold? or it’s just randomly 
> set values?
> 
> Bests,
> J.
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
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Re: [Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

2018-11-01 Thread Yendiki, Anastasia

They are not random, they are 20% of the maximum value. If you want to generate 
stats at a different threshold, you can find the dmri_pathstats command line in 
trac-all.log and add the --pthr option (the default 20% would be --pthr .2).

On Nov 1, 2018 9:01 PM, June Kang  wrote:
External Email - Use Caution

In the visualization step of Tracula processing, freeview -tv 
merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), 
which make them look like the reconstruction-failed ones.
The tracts failed to reconstruction usually show threshold of 300 (not 
changeable) with tiny rounded cylinder shape.
In successfully reconstructed tracts with very high threshold, it looks ok, 
when I adjust threshold to the similar value from contralateral one.

Is there any reason for this extremely high threshold? or it’s just randomly 
set values?

Bests,
J.


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Re: [Freesurfer] TRACULA question

2017-12-25 Thread Yendiki, Anastasia

Hi Gabriela - When you define a list of items in the config file, i.e., 
anything between two parentheses "( ... )", the items in the list need to be on 
the same line, or, if you want to split them across multiple lines, there has 
to be a backslash "\" at the end of each of the intermediate lines. See the 
example config file:


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


Best,


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Figueiro Longo, Maria 
Gabriela 
Sent: Wednesday, December 6, 2017 5:18:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA question

Hi,

I am trying to run TRACULA and I am having the same error, after reviewing my 
directory and the configuration file:

"ERROR: run list is longer than subject list"

The number of inputs is the same number of subjects. I've read some old emails 
with similar errors but none of the suggested solutions worked for me.

Following a copy of my configuration file.

Thanks for the help,
Gabriela



setenv SUBJECTS_DIR /autofs/cluster/guptagp/gabi/Volume

set dtroot = /autofs/cluster/guptagp/gabi/Output

set subjlist = (3LT043_s1_170520
3LT043_s2_170715
3LT043_s3_170829
3LT044_s1_170526
3LT044_s2_170607
3LT044_s3_170822
3LT046_s1_170609
3LT046_s2_170620
3LT046_s3_170929 )

set baselist = (3LT043
3LT043
3LT043
3LT044
3LT044
3LT044
3LT046
3LT046
3LT046 )

set dcmlist = ( /autofs/cluster/guptagp/gabi/Diffusion/3LT043_s1_170520.nii.gz
/autofs/cluster/guptagp/gabi/Diffusion/3LT043_s2_170715.nii.gz
/autofs/cluster/guptagp/gabi/Diffusion/3T043_s3_170829.nii.gz
/autofs/cluster/guptagp/gabi/Diffusion/3LT044_s1_170526.nii.gz
/autofs/cluster/guptagp/gabi/Diffusion/3LT044_s2_170607.nii.gz
/autofs/cluster/guptagp/gabi/Diffusion/3LT044_s3_170822.nii.gz
/autofs/cluster/guptagp/gabi/Diffusion/3LT046_s1_17060.nii.gz
/autofs/cluster/guptagp/gabi/Diffusion/3LT046_s2_170620.nii.gz
/autofs/cluster/guptagp/gabi/Diffusion/3LT046_s3_170929.nii.gz )

set bvallist = (/autofs/cluster/guptagp/gabi/Diffusion/3LT043_s1_170520.bvals
/autofs/cluster/guptagp/gabi/Diffusion/3LT043_s2_170715.bvals
/autofs/cluster/guptagp/gabi/Diffusion/3LT043_s3_170829.bvals
/autofs/cluster/guptagp/gabi/Diffusion/3LT044_s1_170526.bvals
/autofs/cluster/guptagp/gabi/Diffusion/3LT044_s2_170607.bvals
/autofs/cluster/guptagp/gabi/Diffusion/3LT044_s3_170822.bvals
/autofs/cluster/guptagp/gabi/Diffusion/3LT046_s1_17060.bvals
/autofs/cluster/guptagp/gabi/Diffusion/3LT046_s2_170620.bvals
/autofs/cluster/guptagp/gabi/Diffusion/3LT046_s3_170929.bvals )

set bveclist = ( 
/autofs/cluster/guptagp/gabi/Diffusion/3LT043_s1_170520.voxel_space.bvecs
/autofs/cluster/guptagp/gabi/Diffusion/3LT043_s2_170715.voxel_space.bvecs
/autofs/cluster/guptagp/gabi/Diffusion/3LT043_s3_170829.voxel_space.bvecs
/autofs/cluster/guptagp/gabi/Diffusion/3LT044_s1_170526.voxel_space.bvecs
/autofs/cluster/guptagp/gabi/Diffusion/3LT044_s2_170607.voxel_space.bvecs
/autofs/cluster/guptagp/gabi/Diffusion/3LT044_s3_170822.voxel_space.bvecs
/autofs/cluster/guptagp/gabi/Diffusion/3LT046_s1_17060.voxel_space.bvecs
/autofs/cluster/guptagp/gabi/Diffusion/3LT046_s2_170620.voxel_space.bvecs

/autofs/cluster/guptagp/gabi/Diffusion/3LT046_s3_170929.voxel_space.bvecs )


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Re: [Freesurfer] TRACULA question- pathstats not loading

2015-12-15 Thread Anastasia Yendiki

Hi Noa - If you're still having this issue, please send the complete 
trac-all.log file and your configuration file. It's impossible to guess 
what goes wrong without seeing the full output.

Best,
a.y

On Fri, 30 Oct 2015, Golan, Noa wrote:

> Hi,
> I am currently analyzing DTI data and I am having issues with one file in 
> particular. When I run the tracheal -path -c step, all of the files are 
> generated except the pathstats text files.
>
> Any thoughts?
>
> Thanks!
> Noa
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>
>
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Re: [Freesurfer] Tracula Question

2014-12-18 Thread Anastasia Yendiki



Hi Emily - One should be a symbolic link to the other, so they should be 
the exact same file.


a.y

On Tue, 16 Dec 2014, Emily Louise Belleau wrote:



__
Hello,

I was wondering what the difference was between the dwi.nii.gz and thd 
data.nii.gz files.

I know based on the website description that the dwi.nii.gz file is the DWI 
after all corrections have been made but I was unsure about
the data.nii.gz file.

I am trying a different program that does local tractography and was wondering 
whether to feed in the dwi.nii.gz or the data.nii.gz files
to calculate the diffusion tensors?

Thanks,

Emily

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Re: [Freesurfer] TRACULA question

2013-10-10 Thread Anastasia Yendiki


Hi Lars - Just like you have to do before you run any freesurfer programs, 
you'll have to run a script that comes with freesurfer and sets up all the 
necessary environment variables. See:
http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration

Hope this helps,
a.y

PS: Please send emails about tracula usage to the freesurfer list (cc'd 
here) and not to me personally. This makes sure the answers get archived 
so that people can search for answers to common questions. Thanks!

On Thu, 10 Oct 2013, Lars M. Rimol wrote:

 Dear Dr. Yendiki,
 
 I am trying to learn how to do Tracula analyses and was wondering about one
 thing:
 
 According to the tutorial, all I need to do is set up the various
 configuration files. However, when I try to run the example data set, with
 
 trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial
 
 it complains: FSLDIR: Undefined variable.
 
 FSL dir doesn't seem to be defined in any of the configuration files
 provided in the tutorial. Is it necessary to install FSL in order to use
 Tracula? And where do I set the FSLDIR variable?
 
 
 
 
 Thank you!
 
 
 
 yours,
 
 Dr. Lars M. Rimol
 

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Re: [Freesurfer] Tracula question

2013-08-07 Thread Anastasia Yendiki


Yes, please attach the dmrirc and trac-all.log. Thanks!

a.y

On Wed, 7 Aug 2013, Alan Francis wrote:

 Hi Anastasia:
 
 For one brain I got this error message :
 
 csh::alanf@cerebro 
 [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
  : trac-all -prep
 -c 
 /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107
 
 Too many ('s.
 ERROR: must specify as many DWI dicoms as subjects
 
 I tried specifying the exact number of DWI dicoms but it is not working. 
 Should I send you my dmrirc for this brain?
 
 thanks,
 
 Alan
 

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Re: [Freesurfer] Tracula question

2013-08-07 Thread Alan Francis

Thank you Anastasia. Another brain had a different problem: Here is the
trac-all log:

mri_concat --i
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
--mean --o
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/lowb.nii.gz
niiRead(): error opening file
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
ninputs = 1
Checking inputs
ERROR: reading
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz
Linux cerebro 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed Aug 7 13:01:21 EDT 2013

thanks so much,

Alan

On Wed, Aug 7, 2013 at 1:11 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

Hi Alan - Try removing the \ character from the end of the dcmlist
definition. That's a change of line character.

a.y

On Wed, 7 Aug 2013, Alan Francis wrote:

Hi Anastasia:

Here is the trac-all log. Please find attached the dmrirc file.

csh::alanf@cerebro [/autofs/space/dali_003/users/**
BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons] : trac-all -prep
-c /autofs/space/dali_003/users/**BW_project_DTI/FreeSurfer_5.3_**
Data/diffusion_recons/dmrirc-**107

Too many ('s.
ERROR: must specify as many DWI dicoms as subjects

Thank you so much.

Alan

On Wed, Aug 7, 2013 at 12:32 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

Yes, please attach the dmrirc and trac-all.log. Thanks!

a.y

On Wed, 7 Aug 2013, Alan Francis wrote:

Hi Anastasia:

For one brain I got this error message :

csh::alanf@cerebro
[/autofs/space/dali_003/users/**
BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons] : trac-all
-prep
-c /autofs/space/dali_003/users/**
BW_project_DTI/FreeSurfer_5.3_**Data/diffusion_recons/dmrirc-**107

Too many ('s.
ERROR: must specify as many DWI dicoms as subjects

I tried specifying the exact number of DWI dicoms but it is
not working. Should I send you my
dmrirc for this brain?

thanks,

Alan

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Re: [Freesurfer] Tracula question

2013-08-07 Thread Anastasia Yendiki

Please attach the file trac-all.log. I can't tell what's going on just by
looking at the end of it.

On Wed, 7 Aug 2013, Alan Francis wrote:

Thank you Anastasia. Another brain had a different problem: Here is the
trac-all log:

trac-preproc exited with ERRORS at Wed Aug 7 13:01:21 EDT 2013

thanks so much,

Alan

On Wed, Aug 7, 2013 at 1:11 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

Hi Alan - Try removing the \ character from the end of the dcmlist
definition. That's a change of line
character.

a.y

On Wed, 7 Aug 2013, Alan Francis wrote:

Hi Anastasia:

Here is the trac-all log. Please find attached the dmrirc file.

csh::alanf@cerebro

[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: trac-all
-prep
-c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107

Too many ('s.
ERROR: must specify as many DWI dicoms as subjects

Thank you so much.

Alan

On Wed, Aug 7, 2013 at 12:32 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

Yes, please attach the dmrirc and trac-all.log. Thanks!

a.y

On Wed, 7 Aug 2013, Alan Francis wrote:

Hi Anastasia:

For one brain I got this error message :

csh::alanf@cerebro
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons]
: trac-all
-prep
-c

/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107

Too many ('s.
ERROR: must specify as many DWI dicoms as subjects

I tried specifying the exact number of DWI dicoms but
it is not working. Should I
send you my
dmrirc for this brain?

thanks,

Alan

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Re: [Freesurfer] Tracula question

2013-08-07 Thread Alan Francis

Hi Anastasia:

Here is the trac-all log. Thanks so much:


csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons]
: trac-all -prep -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-106
INFO: SUBJECTS_DIR is
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons
INFO: Diffusion root is
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
trac-preproc -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/dmrirc.local
-log
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/trac-all.log
-cmd
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/trac-all.cmd
#-
/usr/local/freesurfer/stable5_3_0//bin/trac-preproc
#-
#@# Image corrections Wed Aug  7 13:16:17 EDT 2013
mri_convert
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_121245216000-21-01DIFFUSIONHighResValeraBI106s021a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
mri_convert
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_121245216000-21-01DIFFUSIONHighResValeraBI106s021a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_121245216000-21-01DIFFUSIONHighResValeraBI106s021a001.nii...
TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.63925e-05, 3.62902e-06)
j_ras = (1.67894e-05, 0.976296, 0.21644)
k_ras = (0, -0.21644, 0.976296)
writing to
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz...
cp
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons/bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvecs
cp
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons/bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvals
flip4fsl
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -6.8719
fslswapdim
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
x y z
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
INFO: found
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvals,
converting to FSL format
INFO: found
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvecs,
converting to FSL format
mv -f
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.mghdti.bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/bvecs
mv -f
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.mghdti.bvals
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/bvals
eddy_correct
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi.nii.gz
0
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0001
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0002
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0003
processing
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0004
processing

Re: [Freesurfer] Tracula question

2013-08-07 Thread Anastasia Yendiki



It looks like there may be something wrong with the bval file. Are you 
using a different one for this particular subject?


On Wed, 7 Aug 2013, Alan Francis wrote:


Hi Anastasia:

Here is the trac-all log. Thanks so much:


csh::alanf@cerebro
[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons]
 : trac-all
-prep -c 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-106
INFO: SUBJECTS_DIR is 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons
INFO: Diffusion root is 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0
trac-preproc -c
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/dmrirc.local
 -log
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/trac-all.log
 -cmd
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/scripts/trac-all.cmd
#-
/usr/local/freesurfer/stable5_3_0//bin/trac-preproc
#-
#@# Image corrections Wed Aug  7 13:16:17 EDT 2013
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_12124
5216000-21-01DIFFUSIONHighResValeraBI106s021a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
mri_convert/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_12124
5216000-21-01DIFFUSIONHighResValeraBI106s021a001.nii
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading 
from/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/Diffusion_Recons/20080928_12124
5216000-21-01DIFFUSIONHighResValeraBI106s021a001.nii...
TR=7570.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.63925e-05, 3.62902e-06)
j_ras = (1.67894e-05, 0.976296, 0.21644)
k_ras = (0, -0.21644, 0.976296)
writing to
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz...
cp 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons/bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvecs
cp 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons/bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvals
flip4fsl 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -6.8719
fslswapdim 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.nii.gz
x y z 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
INFO: found
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvals,
converting to FSL format
INFO: found
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig.mghdti.bvecs,
converting to FSL format
mv 
-f/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.mghdti.bvecs
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/bvecs
mv 
-f/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.mghdti.bvals
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/bvals
eddy_correct
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_orig_flip.nii.gz
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi.nii.gz
 0
processing 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp
processing 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0001
processing 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0002
processing 
/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_tmp0003
processing

Re: [Freesurfer] tracula question

2012-10-05 Thread Anastasia Yendiki



Hola Fernando - Please send questions about tracula to the freesurfer list 
and not me personally, so that all users may benefit.


This issue will be resolved in the next version. For now, if you're on a 
unix system that doesn't have the jot command, you'll just have to specify 
the runlist in your configuration file, even if you want to process all 
subjects on your list. So if you have 5 subjects for example:

set runlist = (1 2 3 4 5)

Hope this helps,
a.y

On Fri, 5 Oct 2012, Fernando Ventrice wrote:


Dear Anastasia Yendiki,
I have been trying to use TRACULA and I think I'm doing something wrong. 
Because it keeps on giving me this error (I tried within tcsh and bash):

fventrice@xubuntu1204x64fleni:~$ trac-all -prep -c 
${TUTORIAL_DATA}/diffusion_tutorial/scripts/dmrirc_single_subject
jot: Command not found.
INFO: SUBJECTS_DIR is 
/media/LEVIATAN01/LaboINEBA/testing_TRACULA/diffusion_recons
INFO: Diffusion root is 
/media/LEVIATAN01/LaboINEBA/testing_TRACULA/diffusion_tutorial
Actual FREESURFER_HOME /home/fventrice/CONTAINER_FLENI/Programs/freesurfer

I use freesurfer and fsl perfectly well. I have also tried with the new version 
of trac-all. But keeps on giving the same error.
Best regards and thanks!
Fernando Ventrice

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Re: [Freesurfer] TRACULA Question

2012-09-28 Thread Anastasia Yendiki


Hi Gabor - The info that tracula uses is which aparc+aseg labels each 
pathway neighbors at each point along its trajectory. It learns this 
information from the 33 subjects in the atlas, where the pathways were 
labeled manually, and then applies that knowledge to reconstruct the 
pathways in your subject.

As long as the aparc+aseg of your subject is consistent with the ones in 
the atlas, you're fine. But if you think that the version you used to 
generate your aparc+aseg, and the latest version, that the aparc+aseg's in 
the atlas were generated with, have significant differences, this *may* be 
a problem. The extent of the problem will depend on how often the 
problematic label occurs next to one of the 18 pathways that tracula 
reconstructs and how different the label is b/w the versions. A small 
diference will probably not affect tracula at all.

Your aparc+aseg's were generated with freesurfer 4.5, and there was no 
tracula atlas generated with that version of aparc+aseg's.

Hope this helps,
a.y

On Fri, 28 Sep 2012, Gabor Perlaki wrote:

 Dear Anastasia,

 Thanks a lot your answer. My fear is that the pars triangular
 segmentation also seems bad, because it is right lateralized in most
 of our analyzed data. Here is the post about this issue:
 https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024541.html

 Is it also OK with Tracula?

 Thank you in advance,
 Gabor

 2012/9/27 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu:

 Hi Gabor - Tracula doesn't use the BA labels, only the labels in the
 aparc+aseg. I hope this answers your question.

 a.y


 On Sun, 16 Sep 2012, Gabor Perlaki wrote:

 Dear Anastasia,

 Earlier I was posted an issue about BA44/pars triangular:
 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23706.html

 Because TRACULA also uses the cortical parcellation it may be
 important to handle this issue somehow. Is it handled in TRACULA
 analysis? Does it affect the result of WM-volumes?

 Thank you for your answer,
 Gabor
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Re: [Freesurfer] TRACULA Question

2012-09-27 Thread Anastasia Yendiki


Hi Gabor - Tracula doesn't use the BA labels, only the labels in the 
aparc+aseg. I hope this answers your question.

a.y

On Sun, 16 Sep 2012, Gabor Perlaki wrote:

 Dear Anastasia,

 Earlier I was posted an issue about BA44/pars triangular:
 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23706.html

 Because TRACULA also uses the cortical parcellation it may be
 important to handle this issue somehow. Is it handled in TRACULA
 analysis? Does it affect the result of WM-volumes?

 Thank you for your answer,
 Gabor
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Re: [Freesurfer] Tracula question

2012-08-23 Thread Anastasia Yendiki



Hi Natalia - I'd need to see at which point in the processing the error 
occurs, since this is a very generic error message. Can you please include 
your trac-all.log and dmrirc?


Thanks,
a.y

On Thu, 23 Aug 2012, Natalia Sánchez wrote:


Hi Anastasia!I finally made tracula -prep work without errors, using the 1mm
T1 MNI template (i tried using the 2mm one but the vertices for registering
white matter came out as NaN). However, I was not able to get bedpost to
work. After looking at other posts on the FS archive, I think the reason why
-bedp does not work is because of my FSL version. I tried running bedpost on
FSL and then just copying those files on my dmri.bedpost folder and using
those files for reconstructing the white matter tracts. However, I get a
Segmentation Fault error. Do you have any idea what this error may mean?

My dpath folder is empty and I my trac-all.log file has no errors related to
-path

Thanks!

 

-- Natalia Sánchez
    PhD Candidate
    Departments of Biomedical Engineering 
    Physical Therapy and Human Movement Sciences    Northwestern University
    645 North Michigan Ave, Suite 1100
    Chicago, IL 60611




On Fri, Aug 10, 2012 at 5:05 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  Hi Natalia - This is an error that will occur if lowb_brain_mask
  does not exist. The command that generates lowb_brain_mask is
  bet - can you find that line in the log file and run it
  directly on the command line and see if you get an error?

  On a separate note, have you opted to use a DWI mask instead of
  an anatomical mask by setting usemaskanat = 0? If not, then it
  may be that it's trying to use the DWI mask b/c it can't find
  the anatomicals, in which case I'd check if SUBJECTS_DIR has
  been set properly and a freesurfer recon of the same subject
  exists there. But this is a separate
  issue than the DWI mask not being generated.

  Hope this helps,
  a.y

  On Fri, 10 Aug 2012, Natalia Sánchez wrote:

  The required files were not generated. 

  the error occurs at 

  
rh.slft_PP_roi2.flt.nii.gz--bmask/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/low
  b_brain
  
_mask.flt.nii.gz--fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_F
  A.fl
  t.nii.gz --ncpts 5 --trunc --debug
  ERROR: fio_pushd:
  /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni
  ERROR: Must specify brain mask volume for output subject

  does the brain mask have to be input manually in the
  configuration file, or
  is this part of the pre-processing? since I set the bet
  thr to 0.23 in the
  config file i thought the brain mask was also created
  during the
  preprocessing stage. Attached is my log file.

  I am familiar with FSL but I am using Free surfer since i
  think automating
  the entire process, including tracking is a great
  advantage, but I'm just
  starting to get the hang of it

  Thanks!



  -- Natalia Sánchez
      PhD Candidate
      Departments of Biomedical Engineering 
      Physical Therapy and Human Movement Sciences  
   Northwestern University
      645 North Michigan Ave, Suite 1100
      Chicago, IL 60611




  On Fri, Aug 10, 2012 at 4:28 PM, Anastasia Yendiki
  ayend...@nmr.mgh.harvard.edu wrote:
        dtifit_FA.fl
        t.nii.gz






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Re: [Freesurfer] Tracula question

2012-08-23 Thread Anastasia Yendiki



Can you please check that the x-y-z dimensions of the bedpostx output 
files are the same as the dimensions of the DWIs?


On Thu, 23 Aug 2012, Natalia Sánchez wrote:


Thanks for your response!Attached are the requested files

The error occurs here are shown on my terminal: 
Loading b-values 
from/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmri/bv
als
Loading gradients 
from/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmri/bv
ecs
Segmentation fault 
Darwin dhcp-165-124-9-141.phystherapy.northwestern.edu 10.8.0 Darwin Kernel
Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011;
root:xnu-1504.15.3~1/RELEASE_I386 i386


-- Natalia Sánchez
    PhD Candidate
    Departments of Biomedical Engineering 
    Physical Therapy and Human Movement Sciences    Northwestern University
    645 North Michigan Ave, Suite 1100
    Chicago, IL 60611




On Thu, Aug 23, 2012 at 1:48 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  Hi Natalia - I'd need to see at which point in the processing
  the error occurs, since this is a very generic error message.
  Can you please include your trac-all.log and dmrirc?

  Thanks,
  a.y

  On Thu, 23 Aug 2012, Natalia Sánchez wrote:

Hi Anastasia!I finally made tracula -prep work
without errors, using the 1mm
T1 MNI template (i tried using the 2mm one but the
vertices for registering
white matter came out as NaN). However, I was not
able to get bedpost to
work. After looking at other posts on the FS
archive, I think the reason why
-bedp does not work is because of my FSL version. I
tried running bedpost on
FSL and then just copying those files on my
dmri.bedpost folder and using
those files for reconstructing the white matter
tracts. However, I get a
Segmentation Fault error. Do you have any idea
what this error may mean?

My dpath folder is empty and I my trac-all.log file
has no errors related to
-path

Thanks!

 

-- Natalia Sánchez
    PhD Candidate
    Departments of Biomedical Engineering 
    Physical Therapy and Human Movement Sciences  
 Northwestern University
    645 North Michigan Ave, Suite 1100
    Chicago, IL 60611




On Fri, Aug 10, 2012 at 5:05 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

      Hi Natalia - This is an error that will occur
if lowb_brain_mask
      does not exist. The command that generates
lowb_brain_mask is
      bet - can you find that line in the log file
and run it
      directly on the command line and see if you
get an error?

      On a separate note, have you opted to use a
DWI mask instead of
      an anatomical mask by setting usemaskanat = 0?
If not, then it
      may be that it's trying to use the DWI mask
b/c it can't find
      the anatomicals, in which case I'd check if
SUBJECTS_DIR has
      been set properly and a freesurfer recon of
the same subject
      exists there. But this is a separate
      issue than the DWI mask not being generated.

      Hope this helps,
      a.y

      On Fri, 10 Aug 2012, Natalia Sánchez wrote:

      The required files were not generated. 

      the error occurs at 

     
rh.slft_PP_roi2.flt.nii.gz--bmask/Users/Natalia/Desktop/freesurfer/subjects
/Justin/cJD/dlabel/mni/low
      b_brain
     
_mask.flt.nii.gz--fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/d
mri/mni/dtifit_F
      A.fl
      t.nii.gz --ncpts 5 --trunc --debug
      ERROR: fio_pushd:
     
/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni
      ERROR: Must specify brain mask volume for
output subject

      does the brain mask have to be input manually
in the
      configuration file, or
      is this part of the pre-processing? since I
set the bet
      thr to 0.23 in the
      config file i thought the brain mask was also
created
      during the
      preprocessing stage. Attached is my log file.

      I am familiar with FSL but I am using Free
surfer since i
      think automating
      the entire process, including tracking is a
great

Re: [Freesurfer] Tracula question

2012-08-23 Thread Anastasia Yendiki



This probably means that bedpostx didn't process all the slices in your 
DWIs. Someone else reported something like that recently, not sure what 
may be causing it, but since it's independent of trac-all, I'd check on 
the FSL list archives.



On Thu, 23 Aug 2012, Natalia Sánchez wrote:


they are not. The z dimension of the bedpost images is 52 (from FSL) and for
the dmri FS images it is 72. 

-- Natalia Sánchez
    PhD Candidate
    Departments of Biomedical Engineering 
    Physical Therapy and Human Movement Sciences    Northwestern University
    645 North Michigan Ave, Suite 1100
    Chicago, IL 60611




On Thu, Aug 23, 2012 at 2:08 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  Can you please check that the x-y-z dimensions of the bedpostx
  output files are the same as the dimensions of the DWIs?

  On Thu, 23 Aug 2012, Natalia Sánchez wrote:

  Thanks for your response!Attached are the requested files

  The error occurs here are shown on my terminal: 
  Loading 
b-valuesfrom/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmr
  i/bv
  als
  Loading 
gradientsfrom/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmr
  i/bv
  ecs
  Segmentation fault 
  Darwin dhcp-165-124-9-141.phystherapy.northwestern.edu
  10.8.0 Darwin Kernel
  Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011;
  root:xnu-1504.15.3~1/RELEASE_I386 i386


  -- Natalia Sánchez
      PhD Candidate
      Departments of Biomedical Engineering 
      Physical Therapy and Human Movement Sciences  
   Northwestern University
      645 North Michigan Ave, Suite 1100
      Chicago, IL 60611




  On Thu, Aug 23, 2012 at 1:48 PM, Anastasia Yendiki
  ayend...@nmr.mgh.harvard.edu wrote:

        Hi Natalia - I'd need to see at which point in the
  processing
        the error occurs, since this is a very generic error
  message.
        Can you please include your trac-all.log and dmrirc?

        Thanks,
        a.y

        On Thu, 23 Aug 2012, Natalia Sánchez wrote:

              Hi Anastasia!I finally made tracula -prep work
              without errors, using the 1mm
              T1 MNI template (i tried using the 2mm one but
  the
              vertices for registering
              white matter came out as NaN). However, I was
  not
              able to get bedpost to
              work. After looking at other posts on the FS
              archive, I think the reason why
              -bedp does not work is because of my FSL
  version. I
              tried running bedpost on
              FSL and then just copying those files on my
              dmri.bedpost folder and using
              those files for reconstructing the white
  matter
              tracts. However, I get a
              Segmentation Fault error. Do you have any
  idea
              what this error may mean?

              My dpath folder is empty and I my trac-all.log
  file
              has no errors related to
              -path

              Thanks!

               

              -- Natalia Sánchez
                  PhD Candidate
                  Departments of Biomedical Engineering 
                  Physical Therapy and Human Movement
  Sciences  
               Northwestern University
                  645 North Michigan Ave, Suite 1100
                  Chicago, IL 60611




              On Fri, Aug 10, 2012 at 5:05 PM, Anastasia
  Yendiki
              ayend...@nmr.mgh.harvard.edu wrote:

                    Hi Natalia - This is an error that will
  occur
              if lowb_brain_mask
                    does not exist. The command that
  generates
              lowb_brain_mask is
                    bet - can you find that line in the
  log file
              and run it
                    directly on the command line and see if
  you
              get an error?

                    On a separate note, have you opted to
  use a
              DWI mask instead of
                    an anatomical mask by setting
  usemaskanat = 0?
              If not, then it
                    may be that it's trying to use the DWI
  mask
              b/c it can't find
                    the anatomicals, in which case I'd check
  if
              SUBJECTS_DIR has
                    been set properly and a freesurfer recon
  of
              the same subject
                    exists there. But this is a separate
                    issue than the DWI mask not being
  generated.

                    Hope this helps,
                    a.y

                    On Fri, 10 Aug 2012, Natalia Sánchez

Re: [Freesurfer] Tracula question

2012-08-10 Thread Anastasia Yendiki



Do these files that it's trying to load exist? If not, the actual error 
happened earlier, when they were being generated. Looking at the entire 
trac-all.log instead of just the end might shed some light on this.


On Fri, 10 Aug 2012, Natalia Sánchez wrote:


Hi!I am running tracula for the first time and I am encountering the
following error:

Loading brain mask of output subject 
from/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/lowb_brain
_mask.flt.nii.gz
niiRead(): error opening 
file/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/lowb_brain
_mask.flt.nii.gz
Loading FA map of output subject 
from/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_FA.fl
t.nii.gz
niiRead(): error opening 
file/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_FA.fl
t.nii.gz
Segmentation fault 
Darwin dhcp-165-124-9-95.phystherapy.northwestern.edu 10.8.0 Darwin Kernel
Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011;
root:xnu-1504.15.3~1/RELEASE_I386 i386

trac-preproc exited with ERRORS at Fri Aug 10 16:19:17 CDT 2012


what file is lowb_brain_mask.flt.nii.gz? should this have been created
during tracula or is this file my nodiff image?

Thanks!


-- Natalia Sánchez
    PhD Candidate
    Departments of Biomedical Engineering 
    Physical Therapy and Human Movement Sciences    Northwestern University
    645 North Michigan Ave, Suite 1100
    Chicago, IL 60611



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Re: [Freesurfer] Tracula question

2012-08-10 Thread Anastasia Yendiki



Hi Natalia - This is an error that will occur if lowb_brain_mask does not 
exist. The command that generates lowb_brain_mask is bet - can you find 
that line in the log file and run it directly on the command line and see 
if you get an error?


On a separate note, have you opted to use a DWI mask instead of an 
anatomical mask by setting usemaskanat = 0? If not, then it may be that 
it's trying to use the DWI mask b/c it can't find the anatomicals, in 
which case I'd check if SUBJECTS_DIR has been set properly and a 
freesurfer recon of the same subject exists there. But this is a separate

issue than the DWI mask not being generated.

Hope this helps,
a.y

On Fri, 10 Aug 2012, Natalia Sánchez wrote:


The required files were not generated. 

the error occurs at 

rh.slft_PP_roi2.flt.nii.gz 
--bmask/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/lowb_brain
_mask.flt.nii.gz 
--fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_FA.fl
t.nii.gz --ncpts 5 --trunc --debug
ERROR: fio_pushd:
/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni
ERROR: Must specify brain mask volume for output subject

does the brain mask have to be input manually in the configuration file, or
is this part of the pre-processing? since I set the bet thr to 0.23 in the
config file i thought the brain mask was also created during the
preprocessing stage. Attached is my log file.

I am familiar with FSL but I am using Free surfer since i think automating
the entire process, including tracking is a great advantage, but I'm just
starting to get the hang of it

Thanks!



-- Natalia Sánchez
    PhD Candidate
    Departments of Biomedical Engineering 
    Physical Therapy and Human Movement Sciences    Northwestern University
    645 North Michigan Ave, Suite 1100
    Chicago, IL 60611




On Fri, Aug 10, 2012 at 4:28 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
  dtifit_FA.fl
  t.nii.gz



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Re: [Freesurfer] TRACULA question: pathstats.overall.txt

2012-06-28 Thread Anastasia Yendiki


Hi Minjie - These commonly used measures are provided for your 
convenience. You can always use the reconstructed path distribution volume 
path.pd.nii.gz, thresholded or not, as a mask to average your measurement 
of choice.

a.y

On Thu, 28 Jun 2012, Minjie Wu wrote:

 Dear TRACULA Developer  User,

 I am wondering if it is possible to add other DTI measurements to the
 pathstats.overall.txt along with those DTI parameters already included
 (FA, MD, AD, RD)?

 Thank you very much.
 Minjie
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] TRACULA question: pathstats.overall.txt

2012-06-28 Thread Minjie Wu

Dear Dr. Yendiki,

Thank you very much for your quick response. To calculate the weighted
DTI measure, per your previous emails, we would need to normalize
path.pd.nii.gz, right? If this is the case, we could use the following
equation correct for weighted measurement:

dti_para (DTI parameter image)
path_pd (path.pd.nii.gz)

sum(dti_para.*path_pd))/sum(path_pd)

Thank you very much.

Minjie




On Thu, Jun 28, 2012 at 11:05 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

 Hi Minjie - These commonly used measures are provided for your convenience.
 You can always use the reconstructed path distribution volume
 path.pd.nii.gz, thresholded or not, as a mask to average your measurement of
 choice.

 a.y


 On Thu, 28 Jun 2012, Minjie Wu wrote:

 Dear TRACULA Developer  User,

 I am wondering if it is possible to add other DTI measurements to the
 pathstats.overall.txt along with those DTI parameters already included
 (FA, MD, AD, RD)?

 Thank you very much.
 Minjie
 ___
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer





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

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Re: [Freesurfer] TRACULA question: pathstats.overall.txt

2012-06-28 Thread Anastasia Yendiki


Yes, if you wanted to do a weighted average of your measure. Or you could 
just theshold and binarize path.pd and use it a simple ROI to do an 
unweighted average.

On Thu, 28 Jun 2012, Minjie Wu wrote:

 Dear Dr. Yendiki,

 Thank you very much for your quick response. To calculate the weighted
 DTI measure, per your previous emails, we would need to normalize
 path.pd.nii.gz, right? If this is the case, we could use the following
 equation correct for weighted measurement:

 dti_para (DTI parameter image)
 path_pd (path.pd.nii.gz)

 sum(dti_para.*path_pd))/sum(path_pd)

 Thank you very much.

 Minjie




 On Thu, Jun 28, 2012 at 11:05 AM, Anastasia Yendiki
 ayend...@nmr.mgh.harvard.edu wrote:

 Hi Minjie - These commonly used measures are provided for your convenience.
 You can always use the reconstructed path distribution volume
 path.pd.nii.gz, thresholded or not, as a mask to average your measurement of
 choice.

 a.y


 On Thu, 28 Jun 2012, Minjie Wu wrote:

 Dear TRACULA Developer  User,

 I am wondering if it is possible to add other DTI measurements to the
 pathstats.overall.txt along with those DTI parameters already included
 (FA, MD, AD, RD)?

 Thank you very much.
 Minjie
 ___
 Freesurfer mailing list
 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
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Re: [Freesurfer] TRACULA question: pathstats.byvoxel.txt

2012-02-20 Thread Minjie Wu

Hi Priti,

Thank you very much for the detailed instructions. The tracts with
empty pathstat.byvoxel.txt files are slfp, slft, and unc tracts.
After your email, I have checked all 10+ subjects with such problems.
They all share similar motion problems (the parietal or temporal part
of brain is cut due to motion), which may be why TRACULA is not
working.

The other issue is with fmajor. For many subjects (almost 1/3 of
overall subjects), the fiber tracking for fmajor (path.pd.nii.gz)
looks like a single fiber (or 2,3 fibers) instead of a bundle of
fibers.  The volume from pathstats.overall.txt (195 voxels) is
significantly lower than the mean fmajor volume (1000 voxels) from the
population (see attached file). These brain images are complete (no
cutting issue at fmajor). Also I have checked the FA-MNI
co-registration, and the registration seems to be accurate.  Any idea
of how to avoid this problem will be really appreciated.

Thanks,
Minjie




[minjiewu@ccmfsl1 fmajor_PP_avg33_mni_bbr]$ more pathstats.overall.txt
# Title Pathway Statistics
#
# generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats
# cvs_version
# cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc
/ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr
--dtbase /ccm/pavuluri/rest/DTI/data/20191/dmri/dtifit --path
fmajor --subj 20191 --out
/ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt
--outvox 
/ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr/pathstats
.byvoxel.txt
# sysname Linux
# hostname ccmfsl2.psych.uic.edu
# machine x86_64
# user minjiewu
# anatomy_type pathway
#
# subjectname 20191
# pathwayname fmajor
#
Count 1000
Volume 195
Len_Min 136
Len_Max 179
Len_Avg 149.767
Len_Center 164
AD_Avg 0.00145274
AD_Avg_Weight 0.00149492
AD_Avg_Center 0.00165127
RD_Avg 0.000615351
RD_Avg_Weight 0.00058665
RD_Avg_Center 0.000529699
MD_Avg 0.00089448
MD_Avg_Weight 0.000889406
MD_Avg_Center 0.000903556
FA_Avg 0.475963
FA_Avg_Weight 0.507926
FA_Avg_Center 0.610243






On Wed, Feb 15, 2012 at 9:25 AM, Priti Srinivasan
rspr...@nmr.mgh.harvard.edu wrote:
 Hi Minjie,

 The pathstats.byvoxel.txt gives the statistics of the higest probability
 streamline of the posterior distribution of the tract and the
 pathstats.overall.txt gives you average diffusion values for the whole
 tract.

 Please refer to the following:

 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics

 Your pathstats.overall.txt does not look right. For instance the center
 streamline's length (Len_Center = 0). Did you open the posterior
 probability distribution of this tract?

 You can use the following command to do the same:

 freeview path/to/your/data/dpath/path.pd.nii.gz

 If it does not look right then something probably went wrong during the
 path reconstruction. If you can send us your trac-all.log, we can check
 for anything that went wrong.

 Hope this is helpful.,

 Priti


 Hello Tracula Developer  User,

 I found a few subjects have pathstat.overall.txt information but with
 blank voxel information in pathstats.byvoxel.txt. For such tracts,
 they usually len_min = len_max = len_avg. Anyone know what happened
 for the fiber tracking? Is it possible to extract the byvoxel
 information along the tract?

 Thanks,
 Minjie

 For example:

 [minjiewu@ccmfsl1 data]$ more
 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt
 # Title Pathway Statistics
 #
 # generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats
 # cvs_version
 # cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc
 /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr
 --dtbase /ccm/pavuluri/rest/DTI/data/223
 31/dmri/dtifit --path rh.slfp --subj 22331 --out
 /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt
 --outvox /ccm/pavuluri/rest/DTI/data/
 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.byvoxel.txt
 # sysname Linux
 # hostname ccmfsl2.psych.uic.edu
 # machine x86_64
 # user minjiewu
 # anatomy_type pathway
 #
 # subjectname 22331
 # pathwayname rh.slfp
 #
 Count 1000
 Volume 86
 Len_Min 86
 Len_Max 86
 Len_Avg 86
 Len_Center 0
 AD_Avg 0.00112029
 AD_Avg_Weight 0.00112029
 AD_Avg_Center nan
 RD_Avg 0.000783836
 RD_Avg_Weight 0.000783836
 RD_Avg_Center nan
 MD_Avg 0.000895987
 MD_Avg_Weight 0.000895987
 MD_Avg_Center nan
 FA_Avg 0.264347
 FA_Avg_Weight 0.264347
 FA_Avg_Center nan
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 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the e-mail
 contains patient information, please contact the Partners Compliance HelpLine 
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 error
 but does not contain patient information, please

Re: [Freesurfer] TRACULA question: pathstats.byvoxel.txt

2012-02-20 Thread Anastasia Yendiki


Hi Minjie - There was no attachment to your email. The fmajor issue that 
you're describing sounds like an initialization issue. That single curve 
that you describe is where the algorithm starts at and b/c something is 
wrong with it, it doesn't move from there. Does the curve seem to go into 
a low anisotropy area? Can you rerun the dmri_paths command for just one 
of these fmajor paths with --debug and send us the log.txt file?

Thanks!
a.y

On Mon, 20 Feb 2012, Minjie Wu wrote:

 Hi Priti,

 Thank you very much for the detailed instructions. The tracts with
 empty pathstat.byvoxel.txt files are slfp, slft, and unc tracts.
 After your email, I have checked all 10+ subjects with such problems.
 They all share similar motion problems (the parietal or temporal part
 of brain is cut due to motion), which may be why TRACULA is not
 working.

 The other issue is with fmajor. For many subjects (almost 1/3 of
 overall subjects), the fiber tracking for fmajor (path.pd.nii.gz)
 looks like a single fiber (or 2,3 fibers) instead of a bundle of
 fibers.  The volume from pathstats.overall.txt (195 voxels) is
 significantly lower than the mean fmajor volume (1000 voxels) from the
 population (see attached file). These brain images are complete (no
 cutting issue at fmajor). Also I have checked the FA-MNI
 co-registration, and the registration seems to be accurate.  Any idea
 of how to avoid this problem will be really appreciated.

 Thanks,
 Minjie




 [minjiewu@ccmfsl1 fmajor_PP_avg33_mni_bbr]$ more pathstats.overall.txt
 # Title Pathway Statistics
 #
 # generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats
 # cvs_version
 # cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc
 /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr
 --dtbase /ccm/pavuluri/rest/DTI/data/20191/dmri/dtifit --path
 fmajor --subj 20191 --out
 /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt
 --outvox 
 /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr/pathstats
 .byvoxel.txt
 # sysname Linux
 # hostname ccmfsl2.psych.uic.edu
 # machine x86_64
 # user minjiewu
 # anatomy_type pathway
 #
 # subjectname 20191
 # pathwayname fmajor
 #
 Count 1000
 Volume 195
 Len_Min 136
 Len_Max 179
 Len_Avg 149.767
 Len_Center 164
 AD_Avg 0.00145274
 AD_Avg_Weight 0.00149492
 AD_Avg_Center 0.00165127
 RD_Avg 0.000615351
 RD_Avg_Weight 0.00058665
 RD_Avg_Center 0.000529699
 MD_Avg 0.00089448
 MD_Avg_Weight 0.000889406
 MD_Avg_Center 0.000903556
 FA_Avg 0.475963
 FA_Avg_Weight 0.507926
 FA_Avg_Center 0.610243






 On Wed, Feb 15, 2012 at 9:25 AM, Priti Srinivasan
 rspr...@nmr.mgh.harvard.edu wrote:
 Hi Minjie,

 The pathstats.byvoxel.txt gives the statistics of the higest probability
 streamline of the posterior distribution of the tract and the
 pathstats.overall.txt gives you average diffusion values for the whole
 tract.

 Please refer to the following:

 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics

 Your pathstats.overall.txt does not look right. For instance the center
 streamline's length (Len_Center = 0). Did you open the posterior
 probability distribution of this tract?

 You can use the following command to do the same:

 freeview path/to/your/data/dpath/path.pd.nii.gz

 If it does not look right then something probably went wrong during the
 path reconstruction. If you can send us your trac-all.log, we can check
 for anything that went wrong.

 Hope this is helpful.,

 Priti


 Hello Tracula Developer  User,

 I found a few subjects have pathstat.overall.txt information but with
 blank voxel information in pathstats.byvoxel.txt. For such tracts,
 they usually len_min = len_max = len_avg. Anyone know what happened
 for the fiber tracking? Is it possible to extract the byvoxel
 information along the tract?

 Thanks,
 Minjie

 For example:

 [minjiewu@ccmfsl1 data]$ more
 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt
 # Title Pathway Statistics
 #
 # generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats
 # cvs_version
 # cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc
 /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr
 --dtbase /ccm/pavuluri/rest/DTI/data/223
 31/dmri/dtifit --path rh.slfp --subj 22331 --out
 /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt
 --outvox /ccm/pavuluri/rest/DTI/data/
 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.byvoxel.txt
 # sysname Linux
 # hostname ccmfsl2.psych.uic.edu
 # machine x86_64
 # user minjiewu
 # anatomy_type pathway
 #
 # subjectname 22331
 # pathwayname rh.slfp
 #
 Count 1000
 Volume 86
 Len_Min 86
 Len_Max 86
 Len_Avg 86
 Len_Center 0
 AD_Avg 0.00112029
 AD_Avg_Weight 0.00112029
 AD_Avg_Center nan
 RD_Avg 0.000783836
 RD_Avg_Weight 0.000783836
 RD_Avg_Center nan
 MD_Avg 0.000895987
 MD_Avg_Weight 0.000895987
 MD_Avg_Center nan
 FA_Avg 0.264347
 FA_Avg_Weight 0.264347
 FA_Avg_Center nan

Re: [Freesurfer] TRACULA question: pathstats.byvoxel.txt

2012-02-20 Thread Minjie Wu

Thanks Anastasia! The pathstats.allvoxel.txt was pasted at the end of
this email as in the previous one.

I will rerun  dmri_paths command for the fmajor path and will send you
the log.txt file.

Thanks,
Minjie


[minjiewu@ccmfsl1 fmajor_PP_avg33_mni_bbr]$ more pathstats.overall.txt
# Title Pathway Statistics
#
# generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats
# cvs_version
# cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc
/ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr
--dtbase /ccm/pavuluri/rest/DTI/data/20191/dmri/dtifit --path
fmajor --subj 20191 --out
/ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt
--outvox 
/ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr/pathstats
.byvoxel.txt
# sysname Linux
# hostname ccmfsl2.psych.uic.edu
# machine x86_64
# user minjiewu
# anatomy_type pathway
#
# subjectname 20191
# pathwayname fmajor
#
Count 1000
Volume 195
Len_Min 136
Len_Max 179
Len_Avg 149.767
Len_Center 164
AD_Avg 0.00145274
AD_Avg_Weight 0.00149492
AD_Avg_Center 0.00165127
RD_Avg 0.000615351
RD_Avg_Weight 0.00058665
RD_Avg_Center 0.000529699
MD_Avg 0.00089448
MD_Avg_Weight 0.000889406
MD_Avg_Center 0.000903556
FA_Avg 0.475963
FA_Avg_Weight 0.507926
FA_Avg_Center 0.610243
On Mon, Feb 20, 2012 at 9:08 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

 Hi Minjie - There was no attachment to your email. The fmajor issue that
 you're describing sounds like an initialization issue. That single curve
 that you describe is where the algorithm starts at and b/c something is
 wrong with it, it doesn't move from there. Does the curve seem to go into a
 low anisotropy area? Can you rerun the dmri_paths command for just one of
 these fmajor paths with --debug and send us the log.txt file?

 Thanks!
 a.y


 On Mon, 20 Feb 2012, Minjie Wu wrote:

 Hi Priti,

 Thank you very much for the detailed instructions. The tracts with
 empty pathstat.byvoxel.txt files are slfp, slft, and unc tracts.
 After your email, I have checked all 10+ subjects with such problems.
 They all share similar motion problems (the parietal or temporal part
 of brain is cut due to motion), which may be why TRACULA is not
 working.

 The other issue is with fmajor. For many subjects (almost 1/3 of
 overall subjects), the fiber tracking for fmajor (path.pd.nii.gz)
 looks like a single fiber (or 2,3 fibers) instead of a bundle of
 fibers.  The volume from pathstats.overall.txt (195 voxels) is
 significantly lower than the mean fmajor volume (1000 voxels) from the
 population (see attached file). These brain images are complete (no
 cutting issue at fmajor). Also I have checked the FA-MNI
 co-registration, and the registration seems to be accurate.  Any idea
 of how to avoid this problem will be really appreciated.

 Thanks,
 Minjie




 [minjiewu@ccmfsl1 fmajor_PP_avg33_mni_bbr]$ more pathstats.overall.txt
 # Title Pathway Statistics
 #
 # generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats
 # cvs_version
 # cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc
 /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr
 --dtbase /ccm/pavuluri/rest/DTI/data/20191/dmri/dtifit --path
 fmajor --subj 20191 --out

 /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt
 --outvox
 /ccm/pavuluri/rest/DTI/data/20191/dpath/fmajor_PP_avg33_mni_bbr/pathstats
 .byvoxel.txt
 # sysname Linux
 # hostname ccmfsl2.psych.uic.edu
 # machine x86_64
 # user minjiewu
 # anatomy_type pathway
 #
 # subjectname 20191
 # pathwayname fmajor
 #
 Count 1000
 Volume 195
 Len_Min 136
 Len_Max 179
 Len_Avg 149.767
 Len_Center 164
 AD_Avg 0.00145274
 AD_Avg_Weight 0.00149492
 AD_Avg_Center 0.00165127
 RD_Avg 0.000615351
 RD_Avg_Weight 0.00058665
 RD_Avg_Center 0.000529699
 MD_Avg 0.00089448
 MD_Avg_Weight 0.000889406
 MD_Avg_Center 0.000903556
 FA_Avg 0.475963
 FA_Avg_Weight 0.507926
 FA_Avg_Center 0.610243






 On Wed, Feb 15, 2012 at 9:25 AM, Priti Srinivasan
 rspr...@nmr.mgh.harvard.edu wrote:

 Hi Minjie,

 The pathstats.byvoxel.txt gives the statistics of the higest probability
 streamline of the posterior distribution of the tract and the
 pathstats.overall.txt gives you average diffusion values for the whole
 tract.

 Please refer to the following:

 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics

 Your pathstats.overall.txt does not look right. For instance the center
 streamline's length (Len_Center = 0). Did you open the posterior
 probability distribution of this tract?

 You can use the following command to do the same:

 freeview path/to/your/data/dpath/path.pd.nii.gz

 If it does not look right then something probably went wrong during the
 path reconstruction. If you can send us your trac-all.log, we can check
 for anything that went wrong.

 Hope this is helpful.,

 Priti


 Hello Tracula Developer  User,

Re: [Freesurfer] TRACULA question: pathstats.byvoxel.txt

2012-02-15 Thread Priti Srinivasan

Hi Minjie,

The pathstats.byvoxel.txt gives the statistics of the higest probability
streamline of the posterior distribution of the tract and the
pathstats.overall.txt gives you average diffusion values for the whole
tract.

Please refer to the following:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics

Your pathstats.overall.txt does not look right. For instance the center
streamline's length (Len_Center = 0). Did you open the posterior
probability distribution of this tract?

You can use the following command to do the same:

freeview path/to/your/data/dpath/path.pd.nii.gz

If it does not look right then something probably went wrong during the
path reconstruction. If you can send us your trac-all.log, we can check
for anything that went wrong.

Hope this is helpful.,

Priti


 Hello Tracula Developer  User,

 I found a few subjects have pathstat.overall.txt information but with
 blank voxel information in pathstats.byvoxel.txt. For such tracts,
 they usually len_min = len_max = len_avg. Anyone know what happened
 for the fiber tracking? Is it possible to extract the byvoxel
 information along the tract?

 Thanks,
 Minjie

 For example:

 [minjiewu@ccmfsl1 data]$ more
 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt
 # Title Pathway Statistics
 #
 # generating_program /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats
 # cvs_version
 # cmdline /ccm/pavuluri/imgsw/freesurfer/bin/dmri_pathstats --intrc
 /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr
 --dtbase /ccm/pavuluri/rest/DTI/data/223
 31/dmri/dtifit --path rh.slfp --subj 22331 --out
 /ccm/pavuluri/rest/DTI/data/22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt
 --outvox /ccm/pavuluri/rest/DTI/data/
 22331/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.byvoxel.txt
 # sysname Linux
 # hostname ccmfsl2.psych.uic.edu
 # machine x86_64
 # user minjiewu
 # anatomy_type pathway
 #
 # subjectname 22331
 # pathwayname rh.slfp
 #
 Count 1000
 Volume 86
 Len_Min 86
 Len_Max 86
 Len_Avg 86
 Len_Center 0
 AD_Avg 0.00112029
 AD_Avg_Weight 0.00112029
 AD_Avg_Center nan
 RD_Avg 0.000783836
 RD_Avg_Weight 0.000783836
 RD_Avg_Center nan
 MD_Avg 0.000895987
 MD_Avg_Weight 0.000895987
 MD_Avg_Center nan
 FA_Avg 0.264347
 FA_Avg_Weight 0.264347
 FA_Avg_Center nan
 ___
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Tracula Question, step 2

2011-11-10 Thread Shannon Buckley

Hi Anastasia, 

I checked the brain mask and it looks good. We are using FSLv4.1.4. I 
take it that we are due for an upgrade? Is there a minimum version number that 
we should be using in order for bedpostx to run smoothly? 

Thanks again, 
~SB

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] 
Sent: Wednesday, November 09, 2011 4:57 PM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: RE: [Freesurfer] Tracula Question, step 2


Hi Shannon - Which version of FSL do you have? Older versions didn't use 
to save the mean_dsamples.nii.gz, but that was a while ago.

How quickly it runs depends on the size of the brain mask, so I'd check 
that that's ok too.

a.y

On Wed, 9 Nov 2011, Shannon Buckley wrote:

 Hi Anastasia,

   It turns out that I was NOT able to run the original bedpostx on our 
 cluster, so thank you for pointing me in the right direction! In case other 
 users experience a similar problem, this is what we did to get the ball 
 rolling on our grid:

   We found the fsl_sub_seychelles and fsl_sub scripts where the 
 default q-names were identified. We modified the files (changing long and 
 short.q to reflect the naming convention used here) and ran the original 
 bedpostx. The preproc and datacheck functions worked perfectly. The bedpostx 
 function SEEMED to have launched fine, but we hit another snag...

   The program finished far too quickly for it to have worked properly (an 
 hour, tops), and when I try to run the next -prep step I get the following 
 error, which confirms that suspicion:

 _+_+_+_+_+_+_+_+_+_+_
 Loading BEDPOST parameter samples from 
 /cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX
 niiRead(): error opening file 
 /cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
 ERROR: Could not read 
 /cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
 Linux paris 2.6.18-194.11.1.el5 #1 SMP Tue Aug 10 19:05:06 EDT 2010 x86_64 
 x86_64 x86_64 GNU/Linux

 trac-paths exited with ERRORS at Wed Nov  9 16:18:53 PST 2011

 Word too long.
 +_+_+_+_+_+_+_+_+_+_+_


   I have to confess I'm not familiar with the word too long error. In 
 any case, bedpostx seems to fail to produce the requisite files for -prep 
 (mean_dsamples.nii.gz). Since I'm not sure what the inputs would be for 
 creating such a file, I'm including my ls output for our dmri.bedpostX path.

 _+_+_+_+_+_+_+_+_+_+_+

 [vhasfcbuckls@paris dmri.bedpostX]$ ls
 bvals dyads2.nii.gz   mean_ph2samples.nii.gz
 merged_ph2samples.nii.gz
 bvecs error.log   mean_th1samples.nii.gz
 merged_th1samples.nii.gz
 cancellogsmean_th2samples.nii.gz
 merged_th2samples.nii.gz
 commands.txt  mean_f1samples.nii.gz   merged_f1samples.nii.gz   
 monitor
 dmri.bedpostX.nii.gz  mean_f2samples.nii.gz   merged_f2samples.nii.gz   
 nodif_brain_mask.nii.gz
 dyads1.nii.gz mean_ph1samples.nii.gz  merged_ph1samples.nii.gz  xfms
 [vhasfcbuckls@paris dmri.bedpostX]$
 +_+_+_+_+_+_+_+_+_+_


   Do you have any advice for getting passed this step? We are fairly in 
 the dark with this function over here, so any help / hints you can provide 
 would be wonderful. Please let me know if you need more information.

 Thanks again for your help and patience,

 ~Shannon B.
 -Original Message-
 From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
 Sent: Thursday, November 03, 2011 7:39 AM
 To: shannon.buck...@radiology.ucsf.edu
 Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
 Subject: Re: [Freesurfer] Tracula Question, step 2


 Hi Shannon - Does the original bedpostx run fine on your cluster? You'd
 probably have to edit that to get it to work, it's not made to work on
 every possible cluster. Bedpostx_seychelles is the modified version that
 tracula calls that I've modified from the original FSL version so that it
 runs on our clusters.

 In either case, trac-all is meant to always be run from the command line,
 whether you're on a personal computer (where is runs jobs serially) or a
 cluster (where it submits them as jobs using qsub). But probably some
 editing will be needed as I said.

 Hope this helps,
 a.y

 On Wed, 2 Nov 2011, Shannon Buckley wrote:


 Hi Anastasia,



 I am trying to run Tracula for the first time in our lab and
 I’m getting errors during step 2 that seem to involve how the program wants
 to be launched via grid. I’ve attached the configuration file I’m using and
 the error message is below...


 


 $trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI/Tracula.sh

 Using Freesurfer version 5.1.



   Subjects Directory is /cind/00/PPMI/Freesurfer/Tracula/

   Sessions Directory is /home/vhasfcbuckls/sessions



 INFO

Re: [Freesurfer] Tracula Question, step 2

2011-11-10 Thread Anastasia Yendiki



That should be the latest version, so I'm not sure why the file was not 
saved. I'll have ro refer you to the FSL list for further support with 
running bedpost.


On Thu, 10 Nov 2011, Shannon Buckley wrote:


Hi Anastasia,

I checked the brain mask and it looks good. We are using
FSLv4.1.4. I take it that we are due for an upgrade? Is there a
minimum version number that we should be using in order for
bedpostx to run smoothly?

Thanks again,
~SB

-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Wednesday, November 09, 2011 4:57 PM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: RE: [Freesurfer] Tracula Question, step 2


Hi Shannon - Which version of FSL do you have? Older versions didn't use
to save the mean_dsamples.nii.gz, but that was a while ago.

How quickly it runs depends on the size of the brain mask, so I'd check
that that's ok too.

a.y

On Wed, 9 Nov 2011, Shannon Buckley wrote:


Hi Anastasia,

It turns out that I was NOT able to run the original bedpostx on our 
cluster, so thank you for pointing me in the right direction! In case other 
users experience a similar problem, this is what we did to get the ball rolling 
on our grid:

We found the fsl_sub_seychelles and fsl_sub scripts where the 
default q-names were identified. We modified the files (changing long and short.q to reflect the 
naming convention used here) and ran the original bedpostx. The preproc and datacheck functions 
worked perfectly. The bedpostx function SEEMED to have launched fine, but we hit another snag...

The program finished far too quickly for it to have worked properly (an hour, 
tops), and when I try to run the next -prep step I get the following error, 
which confirms that suspicion:

_+_+_+_+_+_+_+_+_+_+_
Loading BEDPOST parameter samples from 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX
niiRead(): error opening file 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
ERROR: Could not read 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
Linux paris 2.6.18-194.11.1.el5 #1 SMP Tue Aug 10 19:05:06 EDT 2010 x86_64 
x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Wed Nov  9 16:18:53 PST 2011

Word too long.
+_+_+_+_+_+_+_+_+_+_+_


I have to confess I'm not familiar with the word too long error. In any case, 
bedpostx seems to fail to produce the requisite files for -prep (mean_dsamples.nii.gz). Since I'm 
not sure what the inputs would be for creating such a file, I'm including my ls output 
for our dmri.bedpostX path.

_+_+_+_+_+_+_+_+_+_+_+

[vhasfcbuckls@paris dmri.bedpostX]$ ls
bvals dyads2.nii.gz   mean_ph2samples.nii.gz
merged_ph2samples.nii.gz
bvecs error.log   mean_th1samples.nii.gz
merged_th1samples.nii.gz
cancellogsmean_th2samples.nii.gz
merged_th2samples.nii.gz
commands.txt  mean_f1samples.nii.gz   merged_f1samples.nii.gz   monitor
dmri.bedpostX.nii.gz  mean_f2samples.nii.gz   merged_f2samples.nii.gz   
nodif_brain_mask.nii.gz
dyads1.nii.gz mean_ph1samples.nii.gz  merged_ph1samples.nii.gz  xfms
[vhasfcbuckls@paris dmri.bedpostX]$
+_+_+_+_+_+_+_+_+_+_


Do you have any advice for getting passed this step? We are fairly in 
the dark with this function over here, so any help / hints you can provide 
would be wonderful. Please let me know if you need more information.

Thanks again for your help and patience,

~Shannon B.
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, November 03, 2011 7:39 AM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: Re: [Freesurfer] Tracula Question, step 2


Hi Shannon - Does the original bedpostx run fine on your cluster? You'd
probably have to edit that to get it to work, it's not made to work on
every possible cluster. Bedpostx_seychelles is the modified version that
tracula calls that I've modified from the original FSL version so that it
runs on our clusters.

In either case, trac-all is meant to always be run from the command line,
whether you're on a personal computer (where is runs jobs serially) or a
cluster (where it submits them as jobs using qsub). But probably some
editing will be needed as I said.

Hope this helps,
a.y

On Wed, 2 Nov 2011, Shannon Buckley wrote:



Hi Anastasia,



I am trying to run Tracula for the first time in our lab and
I’m getting errors during step 2 that seem to involve how the program wants
to be launched via grid. I’ve attached the configuration file I’m using and
the error message is below...





$trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI

Re: [Freesurfer] Tracula Question, step 2

2011-11-09 Thread Shannon Buckley

Hi Anastasia, 

It turns out that I was NOT able to run the original bedpostx on our 
cluster, so thank you for pointing me in the right direction! In case other 
users experience a similar problem, this is what we did to get the ball rolling 
on our grid: 

We found the fsl_sub_seychelles and fsl_sub scripts where the 
default q-names were identified. We modified the files (changing long and 
short.q to reflect the naming convention used here) and ran the original 
bedpostx. The preproc and datacheck functions worked perfectly. The bedpostx 
function SEEMED to have launched fine, but we hit another snag...  

The program finished far too quickly for it to have worked properly (an 
hour, tops), and when I try to run the next -prep step I get the following 
error, which confirms that suspicion: 

_+_+_+_+_+_+_+_+_+_+_
Loading BEDPOST parameter samples from 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX
niiRead(): error opening file 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
ERROR: Could not read 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
Linux paris 2.6.18-194.11.1.el5 #1 SMP Tue Aug 10 19:05:06 EDT 2010 x86_64 
x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Wed Nov  9 16:18:53 PST 2011

Word too long.
+_+_+_+_+_+_+_+_+_+_+_


I have to confess I'm not familiar with the word too long error. In 
any case, bedpostx seems to fail to produce the requisite files for -prep 
(mean_dsamples.nii.gz). Since I'm not sure what the inputs would be for 
creating such a file, I'm including my ls output for our dmri.bedpostX path. 

_+_+_+_+_+_+_+_+_+_+_+

[vhasfcbuckls@paris dmri.bedpostX]$ ls
bvals dyads2.nii.gz   mean_ph2samples.nii.gz
merged_ph2samples.nii.gz
bvecs error.log   mean_th1samples.nii.gz
merged_th1samples.nii.gz
cancellogsmean_th2samples.nii.gz
merged_th2samples.nii.gz
commands.txt  mean_f1samples.nii.gz   merged_f1samples.nii.gz   monitor
dmri.bedpostX.nii.gz  mean_f2samples.nii.gz   merged_f2samples.nii.gz   
nodif_brain_mask.nii.gz
dyads1.nii.gz mean_ph1samples.nii.gz  merged_ph1samples.nii.gz  xfms
[vhasfcbuckls@paris dmri.bedpostX]$
+_+_+_+_+_+_+_+_+_+_


Do you have any advice for getting passed this step? We are fairly in 
the dark with this function over here, so any help / hints you can provide 
would be wonderful. Please let me know if you need more information. 

Thanks again for your help and patience, 

~Shannon B.
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] 
Sent: Thursday, November 03, 2011 7:39 AM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: Re: [Freesurfer] Tracula Question, step 2


Hi Shannon - Does the original bedpostx run fine on your cluster? You'd 
probably have to edit that to get it to work, it's not made to work on 
every possible cluster. Bedpostx_seychelles is the modified version that 
tracula calls that I've modified from the original FSL version so that it 
runs on our clusters.

In either case, trac-all is meant to always be run from the command line, 
whether you're on a personal computer (where is runs jobs serially) or a 
cluster (where it submits them as jobs using qsub). But probably some 
editing will be needed as I said.

Hope this helps,
a.y

On Wed, 2 Nov 2011, Shannon Buckley wrote:

 
 Hi Anastasia,
 
  
 
 I am trying to run Tracula for the first time in our lab and
 I’m getting errors during step 2 that seem to involve how the program wants
 to be launched via grid. I’ve attached the configuration file I’m using and
 the error message is below...
 
 
 
 
 
 $trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI/Tracula.sh
 
 Using Freesurfer version 5.1.
 
  
 
   Subjects Directory is /cind/00/PPMI/Freesurfer/Tracula/
 
   Sessions Directory is /home/vhasfcbuckls/sessions
 
  
 
 INFO: SUBJECTS_DIR is /cind/07/PPMI/Freesurfer/subjects
 
 INFO: Diffusion root is /cind/00/PPMI/Freesurfer/Tracula
 
 Actual FREESURFER_HOME /cind/01/apps/freesurfer/64bit/freesurfer5.1
 
 ln 
 -sf/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dlabel/diff/anat_brain_
 mask.bbr.nii.gz/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/nodif_brain_mask.n
 ii.gz
 
 ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/dwi.nii.gz
 /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/data.nii.gz
 
 WARN: Running FSL's bedbost locally - this might take a while
 
 WARN: It is recommended to run this step on a cluster
 
 bedpostx_seychelles /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri
 
 subjectdir is /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri
 
 Making bedpostx directory structure

Re: [Freesurfer] Tracula Question, step 2

2011-11-09 Thread Anastasia Yendiki



Hi Shannon - Which version of FSL do you have? Older versions didn't use 
to save the mean_dsamples.nii.gz, but that was a while ago.


How quickly it runs depends on the size of the brain mask, so I'd check 
that that's ok too.


a.y

On Wed, 9 Nov 2011, Shannon Buckley wrote:


Hi Anastasia,

It turns out that I was NOT able to run the original bedpostx on our 
cluster, so thank you for pointing me in the right direction! In case other 
users experience a similar problem, this is what we did to get the ball rolling 
on our grid:

We found the fsl_sub_seychelles and fsl_sub scripts where the 
default q-names were identified. We modified the files (changing long and short.q to reflect the 
naming convention used here) and ran the original bedpostx. The preproc and datacheck functions 
worked perfectly. The bedpostx function SEEMED to have launched fine, but we hit another snag...

The program finished far too quickly for it to have worked properly (an hour, 
tops), and when I try to run the next -prep step I get the following error, 
which confirms that suspicion:

_+_+_+_+_+_+_+_+_+_+_
Loading BEDPOST parameter samples from 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX
niiRead(): error opening file 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
ERROR: Could not read 
/cind/07/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri.bedpostX/mean_dsamples.nii.gz
Linux paris 2.6.18-194.11.1.el5 #1 SMP Tue Aug 10 19:05:06 EDT 2010 x86_64 
x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Wed Nov  9 16:18:53 PST 2011

Word too long.
+_+_+_+_+_+_+_+_+_+_+_


I have to confess I'm not familiar with the word too long error. In any case, 
bedpostx seems to fail to produce the requisite files for -prep (mean_dsamples.nii.gz). Since I'm 
not sure what the inputs would be for creating such a file, I'm including my ls output 
for our dmri.bedpostX path.

_+_+_+_+_+_+_+_+_+_+_+

[vhasfcbuckls@paris dmri.bedpostX]$ ls
bvals dyads2.nii.gz   mean_ph2samples.nii.gz
merged_ph2samples.nii.gz
bvecs error.log   mean_th1samples.nii.gz
merged_th1samples.nii.gz
cancellogsmean_th2samples.nii.gz
merged_th2samples.nii.gz
commands.txt  mean_f1samples.nii.gz   merged_f1samples.nii.gz   monitor
dmri.bedpostX.nii.gz  mean_f2samples.nii.gz   merged_f2samples.nii.gz   
nodif_brain_mask.nii.gz
dyads1.nii.gz mean_ph1samples.nii.gz  merged_ph1samples.nii.gz  xfms
[vhasfcbuckls@paris dmri.bedpostX]$
+_+_+_+_+_+_+_+_+_+_


Do you have any advice for getting passed this step? We are fairly in 
the dark with this function over here, so any help / hints you can provide 
would be wonderful. Please let me know if you need more information.

Thanks again for your help and patience,

~Shannon B.
-Original Message-
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, November 03, 2011 7:39 AM
To: shannon.buck...@radiology.ucsf.edu
Cc: freesurfer@nmr.mgh.harvard.edu; Mensch, Henry
Subject: Re: [Freesurfer] Tracula Question, step 2


Hi Shannon - Does the original bedpostx run fine on your cluster? You'd
probably have to edit that to get it to work, it's not made to work on
every possible cluster. Bedpostx_seychelles is the modified version that
tracula calls that I've modified from the original FSL version so that it
runs on our clusters.

In either case, trac-all is meant to always be run from the command line,
whether you're on a personal computer (where is runs jobs serially) or a
cluster (where it submits them as jobs using qsub). But probably some
editing will be needed as I said.

Hope this helps,
a.y

On Wed, 2 Nov 2011, Shannon Buckley wrote:



Hi Anastasia,



I am trying to run Tracula for the first time in our lab and
I’m getting errors during step 2 that seem to involve how the program wants
to be launched via grid. I’ve attached the configuration file I’m using and
the error message is below...





$trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI/Tracula.sh

Using Freesurfer version 5.1.



  Subjects Directory is /cind/00/PPMI/Freesurfer/Tracula/

  Sessions Directory is /home/vhasfcbuckls/sessions



INFO: SUBJECTS_DIR is /cind/07/PPMI/Freesurfer/subjects

INFO: Diffusion root is /cind/00/PPMI/Freesurfer/Tracula

Actual FREESURFER_HOME /cind/01/apps/freesurfer/64bit/freesurfer5.1

ln 
-sf/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dlabel/diff/anat_brain_
mask.bbr.nii.gz/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/nodif_brain_mask.n
ii.gz

ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/dwi.nii.gz
/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/data.nii.gz

WARN: Running FSL's bedbost locally - this might take a while

WARN: It is recommended to run

Re: [Freesurfer] Tracula Question, step 2

2011-11-03 Thread Anastasia Yendiki

Hi Shannon - Does the original bedpostx run fine on your cluster? You'd
probably have to edit that to get it to work, it's not made to work on
every possible cluster. Bedpostx_seychelles is the modified version that
tracula calls that I've modified from the original FSL version so that it
runs on our clusters.

In either case, trac-all is meant to always be run from the command line,
whether you're on a personal computer (where is runs jobs serially) or a
cluster (where it submits them as jobs using qsub). But probably some
editing will be needed as I said.

Hope this helps,
a.y

On Wed, 2 Nov 2011, Shannon Buckley wrote:

Hi Anastasia,

I am trying to run Tracula for the first time in our lab and
I’m getting errors during step 2 that seem to involve how the program wants
to be launched via grid. I’ve attached the configuration file I’m using and
the error message is below...

$trac-all -bedp -c /cind/01/users/vhasfcbuckls/PPMI/Tracula.sh

Using Freesurfer version 5.1.

Subjects Directory is /cind/00/PPMI/Freesurfer/Tracula/

Sessions Directory is /home/vhasfcbuckls/sessions

INFO: SUBJECTS_DIR is /cind/07/PPMI/Freesurfer/subjects

INFO: Diffusion root is /cind/00/PPMI/Freesurfer/Tracula

Actual FREESURFER_HOME /cind/01/apps/freesurfer/64bit/freesurfer5.1

ln
-sf/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dlabel/diff/anat_brain_
mask.bbr.nii.gz/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/nodif_brain_mask.n
ii.gz

ln -sf /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/dwi.nii.gz
/cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri/data.nii.gz

WARN: Running FSL's bedbost locally - this might take a while

WARN: It is recommended to run this step on a cluster

bedpostx_seychelles /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri

subjectdir is /cind/00/PPMI/Freesurfer/Tracula/PPMI_088_S_3551m00/dmri

Making bedpostx directory structure

Queuing preprocessing stages

Unable to run job: Job was rejected because job requests unknown queue
short.q.

Exiting.

Queuing parallel processing stage

Unable to run job: Job was rejected because job requests unknown queue
long.q.

Exiting.

Queuing post processing stage

Unable to run job: denied: 60 is not a valid object name (cannot start
with a digit)

Job was rejected because job requests unknown queue long.q.

Exiting.

Although we DO have a grid, I am trying to test the program for feasibility
purposes, just on my own system’s terminal, since we aren’t sure how results
will look with our specific data set (3.0 Tesla Siemens, 64 directional DWI
@ b=1000, with 1 b0 image). We are very interested in performing
tractography in T1-space… I am open to running this over the grid, if that’s
really the best way to do it, but the problem is that I don’t see anywhere
to specify the name of the queue that should be used for launching the
program.

Can you please tell me how to launch this without using the so-called long.q
and short.q? We typically launch jobs to our grid using our “bash.linux.q”,
but I haven’t been able to locate a place in the configuration file, or any
switches to use in the cmd line, to specify that this queue should be used.
I tried specifically launching Tracula’s step 2 onto our bash.linux.q via
the cmd line using “qsub”, but received the same old error I had been
getting. I checked the data independently using “bedpostx_preproc.sh”, and
it appears that all the required data are set up properly. As far as I can
tell, the only issue we have is this inability to use the long.q and
short.q…

What do you think?

I’ve cc’d our IT specialist, Henry Mensch, who oversees our grid system in
case you need someone to chime-in with any specific information about how
our Linux systems are set-up.

Thanks very much for your time,

Shannon T. Buckley
SRA III - Supervisor
CIND, UCSF
4150 Clement St. (114M)
San Francisco, CA 94121
Phone: (415) 221-4810 x4251
Fax: (415) 386-3954

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Re: [Freesurfer] Tracula question: group analysis

2011-06-28 Thread Anastasia Yendiki


Hi Maryam - You could compare the different measures like FA or MD across 
subjects along the length of the pathway.

There will be a different number of points along the pathway for each 
subject, so you'd have to interpolate the data points from all your 
subjects to do a point by point comparison. This can be done in matlab for 
example, and hopefully there'll be a built-in command for this in the next 
release!

Hope this helps,
a.y

On Tue, 28 Jun 2011, Maryam Moteabbed wrote:

 Hello Tracula Developers  Users,

 I can follow how to use the diffusion measures from
 pathstats.overall.txt for each subject to run a group
 analysis on the tracts.

 On the other hand I noticed there is also the
 pathstats.byvoxel.txt which contains various
 diffusion measures in each voxel along the highest
 probability path. What are your suggested steps
 for analyzing this text file for group comparison?
 I am guessing developers had an analysis method
 in mind when they decided to print this file out.

 Thank you in advance for your help.

 Best,
 Mary
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Re: [Freesurfer] Tracula question: trac-all config file and number of B0 specification

2011-06-13 Thread Anastasia Yendiki



No, if usemaskanat = 1, then the diffusion mask that comes from applying 
bet to the lowb volume will not be used for tractography. A dilated 
version of aparc+aseg will be used as a mask instead, which is typically 
more reliable than trying to find the right bet threshold.


On Fri, 10 Jun 2011, Deryk S. Beal, Ph.D. wrote:


Hi Anastasia
If I have T1 data available in my FS subject directory and I have

Use brain mask extracted from T1 image instead of low-b diffusion image?#
Has no effect if there is no T1 data
# Default: 1 (yes)
#
set usemaskanat = 1

then will the B0 brain mask we spoke of below be used? 

Deryk


On Fri, Jun 10, 2011 at 10:46 AM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:

  Hi Deryk - This variable is only used to average lowb images to
  create a mask, so in your case you can set it to 2 and it'll
  just use the first 2 volumes from your nii file. Sorry for the
  confusion!

  a.y


On Fri, 10 Jun 2011, Deryk S. Beal, Ph.D. wrote:

  Dear Tracula Users

  Does Tracula assume that the number of B0 scans, specified
  in Step 7.3 of
  the config file tutorial (below), are the first X number
  of volumes in the
  4Dnii.gz file or will the Tracula routines know from the
  bvals file where
  the B0 scans are ordered in the file? For example, I have
  two runs of 16
  directions + 2 B0s each for each of my subjects. I have
  merged the two runs
  together and the resulting file has the volumes ordered
  such that the bvals
  are entered into Tracula as follows:

  0
  0
  1000
  1000
  1000
  etc
  0
  0
  1000
  1000
  1000
  etc 

  My question pertains to the following part of the Tracula
  config file:

  Step7.3: Specifying Number Of low-b Images The last step
  to set up if not
  using original DICOMs would be to specify the number of
  low-b images with
  the following variable:

  set nb0 = *No. of low-b images*
  Thank you in advance for your help.
  Cheers,
  Deryk

  Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO
  Speech-Language Pathologist
  C.I.H.R. Post Doctoral Research Fellow
  Department of Cognitive and Neural Systems Speech
  Laboratory
  Boston University, 677 Beacon Street, Boston, MA 02215 
  dsb...@bu.edu
  http://blogs.bu.edu/dsbeal/about/
  *
  This email may contain confidential and/or privileged
  information for the
  sole use of the intended recipient. Any review or
  distribution by others is
  strictly prohibited. If you have received this email in
  error, please
  contact the sender and delete all copies. Opinions,
  conclusions or other
  information expressed or contained in this email are not
  given or endorsed
  by the sender unless otherwise affirmed independently by
  the sender.




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Re: [Freesurfer] Tracula question: trac-all config file and number of B0 specification

2011-06-10 Thread Anastasia Yendiki



Hi Deryk - This variable is only used to average lowb images to create a 
mask, so in your case you can set it to 2 and it'll just use the first 2 
volumes from your nii file. Sorry for the confusion!


a.y

On Fri, 10 Jun 2011, Deryk S. Beal, Ph.D. wrote:


Dear Tracula Users

Does Tracula assume that the number of B0 scans, specified in Step 7.3 of
the config file tutorial (below), are the first X number of volumes in the
4Dnii.gz file or will the Tracula routines know from the bvals file where
the B0 scans are ordered in the file? For example, I have two runs of 16
directions + 2 B0s each for each of my subjects. I have merged the two runs
together and the resulting file has the volumes ordered such that the bvals
are entered into Tracula as follows:

0
0
1000
1000
1000
etc
0
0
1000
1000
1000
etc 

My question pertains to the following part of the Tracula config file:

Step7.3: Specifying Number Of low-b Images The last step to set up if not
using original DICOMs would be to specify the number of low-b images with
the following variable:

set nb0 = *No. of low-b images*
Thank you in advance for your help.
Cheers,
Deryk

Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO
Speech-Language Pathologist
C.I.H.R. Post Doctoral Research Fellow
Department of Cognitive and Neural Systems Speech Laboratory
Boston University, 677 Beacon Street, Boston, MA 02215 
dsb...@bu.edu
http://blogs.bu.edu/dsbeal/about/
*
This email may contain confidential and/or privileged information for the
sole use of the intended recipient. Any review or distribution by others is
strictly prohibited. If you have received this email in error, please
contact the sender and delete all copies. Opinions, conclusions or other
information expressed or contained in this email are not given or endorsed
by the sender unless otherwise affirmed independently by the sender.

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Re: [Freesurfer] Tracula question: trac-all config file and number of B0 specification

2011-06-10 Thread Deryk S. Beal, Ph.D.

Hi Anastasia

If I have T1 data available in my FS subject directory and I have

Use brain mask extracted from T1 image instead of low-b diffusion image?
# Has no effect if there is no T1 data
# Default: 1 (yes)
#
set usemaskanat = 1

then will the B0 brain mask we spoke of below be used?

Deryk


On Fri, Jun 10, 2011 at 10:46 AM, Anastasia Yendiki 
ayend...@nmr.mgh.harvard.edu wrote:


 Hi Deryk - This variable is only used to average lowb images to create a
 mask, so in your case you can set it to 2 and it'll just use the first 2
 volumes from your nii file. Sorry for the confusion!

 a.y


 On Fri, 10 Jun 2011, Deryk S. Beal, Ph.D. wrote:

  Dear Tracula Users

 Does Tracula assume that the number of B0 scans, specified in Step 7.3 of
 the config file tutorial (below), are the first X number of volumes in the
 4Dnii.gz file or will the Tracula routines know from the bvals file where
 the B0 scans are ordered in the file? For example, I have two runs of 16
 directions + 2 B0s each for each of my subjects. I have merged the two
 runs
 together and the resulting file has the volumes ordered such that the
 bvals
 are entered into Tracula as follows:

 0
 0
 1000
 1000
 1000
 etc
 0
 0
 1000
 1000
 1000
 etc

 My question pertains to the following part of the Tracula config file:

 Step7.3: Specifying Number Of low-b Images The last step to set up if not
 using original DICOMs would be to specify the number of low-b images with
 the following variable:

 set nb0 = *No. of low-b images*
 Thank you in advance for your help.
 Cheers,
 Deryk

 Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO
 Speech-Language Pathologist
 C.I.H.R. Post Doctoral Research Fellow
 Department of Cognitive and Neural Systems Speech Laboratory
 Boston University, 677 Beacon Street, Boston, MA 02215
 dsb...@bu.edu
 http://blogs.bu.edu/dsbeal/about/
 *
 This email may contain confidential and/or privileged information for the
 sole use of the intended recipient. Any review or distribution by others
 is
 strictly prohibited. If you have received this email in error, please
 contact the sender and delete all copies. Opinions, conclusions or other
 information expressed or contained in this email are not given or endorsed
 by the sender unless otherwise affirmed independently by the sender.




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

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