date:20170625

[Freesurfer] freesurfer@nmr.mgh.harvard.edu

2017-06-25 Thread 糜超

Hi,
I am preprocessing my fMRI data acquired with Philips. when I using the command 
'dcmunpack -src . -targ sess01 -run 101 bold nii f.nii .'
The error occurred likes below:
Found 31 total files.
Found 12 unique series: 0 101 301 401 501 601 701 801 901 1001 1101 1201
Subject xxx
Date xxx
Time 110223
Institution x.
0 Survey unknown unknown unknown unknown unknown unknown ./PS_0002
101 Survey unknown unknown unknown unknown unknown 140 ./XX_0003
301 T1W_3D_TFE_ref unknown unknown unknown unknown unknown 190 ./IM_0004
401 FE_EPI unknown unknown unknown unknown unknown 2835 ./XX_0007
501 FE_EPI_EX1 unknown unknown unknown unknown unknown 2835 ./IM_0008
601 FE_EPI_EX2 unknown unknown unknown unknown unknown 2835 ./IM_0011
701 FE_EPI_EX3 unknown unknown unknown unknown unknown 2835 ./IM_0013
801 FE_EPI_EX4 unknown unknown unknown unknown unknown 2835 ./XX_0016
901 FE_EPI_EX5 unknown unknown unknown unknown unknown 2835 ./XX_0018
1001 FE_EPI_EX6 unknown unknown unknown unknown unknown 2835 ./IM_0019
1101 FE_EPI_EX7 unknown unknown unknown unknown unknown 2835 ./XX_0022
1201 FE_EPI_EX8 unknown unknown unknown unknown unknown 2835 ./XX_0024
mri_convert ./XX_0003 ./bold/101/f.nii --nskip 0 --ndrop 0 
nskip = 0
ndrop = 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from ./XX_0003...
Starting DICOMRead2()
dcmfile = ./XX_0003
dcmdir = .
WARNING: tag image orientation not found in ./XX_0003
Ref Series No = 101
ERROR: bits = 0 not supported.


My os is Linux 16.04 and the Freesurfer's version is 5.3.





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Re: [Freesurfer] Regarding_ Midbrain_misalignment

2017-06-25 Thread Dr Sampada Sinha

Thanks Dr Fischl, I will surely try that. Appreciate all your help at the
busy time of this year!

Thanks and regards,

Sam

On Sun, Jun 25, 2017 at 8:12 PM, Bruce Fischl 
wrote:

> Hi Sampada
>
> it's the eve of HBM and a lot of people are traveling or preparing to
> travel, so our response time may be longer!
>
> As for your problem, you might try mri_vol2vol instead of mri_convert. If
> you run it with --help and search for 'talairach' you will find a lot of
> useful stuff, including this example:
>
> mri_vol2vol --help
> .
> .
> .
> 3. Apply an MNI transform to data by resampling the anatomical orig.mgz
> into talairach space using bert/mri/transforms/talairach.xfm:
>
> First, check that the talairach.xfm is correct (this is basically the same
> thing as 'tkregister2 --s bert --fstal' in Example 2:
>
>  cd bert/mri
>  tkregister2 --targ orig.mgz \
>  --mov $FREESURFER_HOME/average/mni305.cor.mgz \
>  --xfm transforms/talairach.xfm --reg /tmp/reg
>
>  Now resample
>  mri_vol2vol --mov orig.mgz \
>  --targ $FREESURFER_HOME/average/mni305.cor.mgz \
>  --xfm transforms/talairach.xfm  \
>  --o orig-in-mni305.mgz
>
>  Now test the resampling:
>  tkregister2 --mov orig-in-mni305.mgz \
> --targ $FREESURFER_HOME/average/mni305.cor.mgz \
> --reg /tmp/reg --regheader
>
>
>
> note that you can just specify the output file as
> mdd_brainstem.mni305.nii.gz and it will be saved in nifti. No need for an
> additional step
>
> cheers
> Bruce
>
>
>
>
> On Sun, 25 Jun 2017, Dr Sampada Sinha wrote:
>
> Hello Dr Greve,
>>
>> Will you please let me know if the above said process I did to overlay
>> brainstorm mask on colin atlas is correct?
>>
>> Thanks and regards,
>>
>> Sam
>>
>>
>>
>> On Tue, Jun 20, 2017 at 8:47 PM, Dr Sampada Sinha <
>> drsampadasi...@gmail.com> wrote:
>>   Thanks Dr Douglas for your reply. Following is the list of command
>> I used to generate brainstem mask.
>>  *  I first created from average subject directory, mask of brainstem
>> using mri_binarize command:
>> mri_binarize --match 16 --i aseg.mgz --o hc_brainstem.mgz
>>  *  Then converted to mni305 space using mri_convert command:
>> mri_convert mdd_brainstem.mgz mdd_brainstem.mni305.mgz --apply_transform
>> transforms/talairach.xfm -oc 0 0 0 --conform
>>  *  Converted the .mgz to nii.gz with command:
>>
>> mri_convert mdd_brainstem.mni305.mgz mdd_brainstem.mni305.nii.gz
>>
>> Finally overlaid it on the mni_colin_t1hires atlas using mango.
>>
>> Thanks and regards,
>>
>> Sam
>>
>>
>> On Tue, Jun 20, 2017 at 7:59 PM, Douglas Greve 
>> wrote:
>>
>>   how was it created?
>>
>>
>>   On 6/20/17 9:41 AM, Dr Sampada Sinha wrote:
>>   Dear freesurfer experts,
>>
>> I am trying to over brainstem mask of my patients' group on
>> mmi_colin_t1hires atlas. I had no problems in overlaying thalamus or
>> amygdala mask, but somehow
>> the midbrain mask is shifted from the actual place (please see
>> attachment). Can you please let me know how do I correct this error?
>>
>> Thanks for all your help.
>>
>> Kind regards,
>>
>> Sam
>>
>> --
>> Dr Sampada Sinha
>> Research medical scientist (B)
>> Department of Geriatric Mental Health (DGMH)
>> King George Medical University
>> Lucknow-226003 , Uttar Pradesh
>> India
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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.
>>
>>
>>
>>
>> --
>> Dr Sampada Sinha
>> Research medical scientist (B)
>> Department of Geriatric Mental Health (DGMH)
>> King George Medical University
>> Lucknow-226003, Uttar Pradesh
>> India
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> Dr Sampada Sinha
>> Research medical scientist (B)
>> Department of Geriatric Mental Health (DGMH)
>> King George Medical University
>> Lucknow-226003, Uttar Pradesh
>> India
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
> ___
> 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

Re: [Freesurfer] Regarding_ Midbrain_misalignment

2017-06-25 Thread Bruce Fischl


Hi Sampada

it's the eve of HBM and a lot of people are traveling or preparing to 
travel, so our response time may be longer!


As for your problem, you might try mri_vol2vol instead of mri_convert. If 
you run it with --help and search for 'talairach' you will find a lot of 
useful stuff, including this example:


mri_vol2vol --help
.
.
.
3. Apply an MNI transform to data by resampling the anatomical orig.mgz
into talairach space using bert/mri/transforms/talairach.xfm:

First, check that the talairach.xfm is correct (this is basically the same
thing as 'tkregister2 --s bert --fstal' in Example 2:

 cd bert/mri
 tkregister2 --targ orig.mgz \
 --mov $FREESURFER_HOME/average/mni305.cor.mgz \
 --xfm transforms/talairach.xfm --reg /tmp/reg

 Now resample
 mri_vol2vol --mov orig.mgz \
 --targ $FREESURFER_HOME/average/mni305.cor.mgz \
 --xfm transforms/talairach.xfm  \
 --o orig-in-mni305.mgz

 Now test the resampling:
 tkregister2 --mov orig-in-mni305.mgz \
--targ $FREESURFER_HOME/average/mni305.cor.mgz \
--reg /tmp/reg --regheader



note that you can just specify the output file as 
mdd_brainstem.mni305.nii.gz and it will be saved in nifti. No need for an 
additional step


cheers
Bruce




On Sun, 25 Jun 2017, Dr Sampada Sinha wrote:


Hello Dr Greve,

Will you please let me know if the above said process I did to overlay 
brainstorm mask on colin atlas is correct?

Thanks and regards,

Sam



On Tue, Jun 20, 2017 at 8:47 PM, Dr Sampada Sinha  
wrote:
  Thanks Dr Douglas for your reply. Following is the list of command I used 
to generate brainstem mask.
 *  I first created from average subject directory, mask of brainstem using 
mri_binarize command: 
mri_binarize --match 16 --i aseg.mgz --o hc_brainstem.mgz
 *  Then converted to mni305 space using mri_convert command:
mri_convert mdd_brainstem.mgz mdd_brainstem.mni305.mgz --apply_transform 
transforms/talairach.xfm -oc 0 0 0 --conform
 *  Converted the .mgz to nii.gz with command:
mri_convert mdd_brainstem.mni305.mgz mdd_brainstem.mni305.nii.gz

Finally overlaid it on the mni_colin_t1hires atlas using mango.

Thanks and regards,

Sam


On Tue, Jun 20, 2017 at 7:59 PM, Douglas Greve  
wrote:

  how was it created?


  On 6/20/17 9:41 AM, Dr Sampada Sinha wrote:
  Dear freesurfer experts,

I am trying to over brainstem mask of my patients' group on mmi_colin_t1hires 
atlas. I had no problems in overlaying thalamus or amygdala mask, but somehow
the midbrain mask is shifted from the actual place (please see attachment). Can 
you please let me know how do I correct this error?

Thanks for all your help.

Kind regards,

Sam

--
Dr Sampada Sinha
Research medical scientist (B)
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003 , Uttar Pradesh
India










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


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




--
Dr Sampada Sinha
Research medical scientist (B)
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003, Uttar Pradesh
India











--
Dr Sampada Sinha
Research medical scientist (B)
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003, Uttar Pradesh
India









___
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
dispose of the e-mail.

Re: [Freesurfer] Regarding_ Midbrain_misalignment

2017-06-25 Thread Dr Sampada Sinha

Hello Dr Greve,

Will you please let me know if the above said process I did to overlay
brainstorm mask on colin atlas is correct?

Thanks and regards,

Sam



On Tue, Jun 20, 2017 at 8:47 PM, Dr Sampada Sinha 
wrote:

> Thanks Dr Douglas for your reply. Following is the list of command I used
> to generate brainstem mask.
>
>- I first created from average subject directory, mask of brainstem
>using mri_binarize command:
>
> mri_binarize --match 16 --i aseg.mgz --o hc_brainstem.mgz
>
>- Then converted to mni305 space using mri_convert command:
>
> mri_convert mdd_brainstem.mgz mdd_brainstem.mni305.mgz --apply_transform
> transforms/talairach.xfm -oc 0 0 0 --conform
>
>- Converted the .mgz to nii.gz with command:
>
> mri_convert mdd_brainstem.mni305.mgz mdd_brainstem.mni305.nii.gz
>
> Finally overlaid it on the mni_colin_t1hires atlas using mango.
>
> Thanks and regards,
>
> Sam
>
>
> On Tue, Jun 20, 2017 at 7:59 PM, Douglas Greve 
> wrote:
>
>> how was it created?
>>
>> On 6/20/17 9:41 AM, Dr Sampada Sinha wrote:
>>
>> Dear freesurfer experts,
>>
>> I am trying to over brainstem mask of my patients' group on
>> mmi_colin_t1hires atlas. I had no problems in overlaying thalamus or
>> amygdala mask, but somehow the midbrain mask is shifted from the actual
>> place (please see attachment). Can you please let me know how do I correct
>> this error?
>>
>> Thanks for all your help.
>>
>> Kind regards,
>>
>> Sam
>>
>> --
>> Dr Sampada Sinha
>> Research medical scientist (B)
>> Department of Geriatric Mental Health (DGMH)
>> King George Medical University
>> Lucknow-226003
>> , Uttar Pradesh
>> India
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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.
>>
>>
>
>
> --
> Dr Sampada Sinha
> Research medical scientist (B)
> Department of Geriatric Mental Health (DGMH)
> King George Medical University
> Lucknow-226003
> , Uttar Pradesh
> India
>
>
>
>
>
>
>
>
>


-- 
Dr Sampada Sinha
Research medical scientist (B)
Department of Geriatric Mental Health (DGMH)
King George Medical University
Lucknow-226003
, Uttar Pradesh
India
___
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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Regarding_ Midbrain_misalignment

Re: [Freesurfer] Regarding_ Midbrain_misalignment

Re: [Freesurfer] Regarding_ Midbrain_misalignment

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