Re: [Freesurfer] Unpacking DWI Data

[Emily Louise Belleau]

Got it, this is fantastic, thanks!


Emily


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Barbara Kreilkamp 

Sent: Sunday, September 18, 2016 5:54:48 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Unpacking DWI Data


Hi Emily,


Yes, Osirix Lite should be sufficient, I think it works by picking File-import 
and then File-export-export DICOMs (decompression is sometimes helpful). It 
should be straightforward, just have a go at it.

Hope it helps.


Best wishes,
Barbara

On 19/09/2016 00:36, Emily Louise Belleau wrote:

Hi Barbara,


Thank you so much! I have downloaded Osirix Lite, since regular Osirix costs a 
pretty penny!


So, once I have imported the dicoms, is it simply a matter of exporting them 
onto my hardrive where I would like them to be?


Thanks so much!


Emily


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Barbara Kreilkamp 

Sent: Sunday, September 18, 2016 3:21:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Unpacking DWI Data


Hi Emily,


I've never tried to use unpacksdcmdir but you may try the Osirix tool, it 
allows you to read in a dicom folder and save a new folder with subfolders 
according to the sequences that were run. At the same time you can also 
anonymize your data.


Does this help?

Best wishes,

Barbara

On 17/09/2016 22:17, Emily Louise Belleau wrote:

Hello Freesurfer Experts,


Our research team has recently collected data from Martinos Center. The entire 
scanning protocol (including anatomical, functional runs, DWI) is in one 
directory.


Therefore I have been using unpacksdcmdir to tell me what runs go with each 
scanning sequence. I have had no trouble unpacking the functional and 
anatomical runs. I have had difficulties unpacking the DWI data.  I have been 
recently warned that unpackdcmdir does not correctly unpack DWI data. Is there 
a work around or another tool I could use? It seems that most tools are for 
unpacking per run (dcmtonii), and would not work in my situation where all 
scans are in one folder?


The runs that say "err" which typically indicated something is missing in the 
scan appear to be unpacking. However, it does say on the terminal that there is 
an error but attempting to unpack anyway.

Some of the runs that say "ok" in the scan log are not unpacking properly.  
Additionally, we are finding that  when we unpack on of the DWI sequences we 
used, we get bvec and bval files. However, we do not when we unpack a different 
DWI sequence we also ran we do not get  the corresponding bvec and bval files.

The command I am using, where I put related runs into related folders:

unpacksdcmdir -src dicomdir -targ  targetdir -fsfast \

  -run 2 bold nii f.nii  \

  -run 3 bold nii f.nii  \

  -run 4 bold nii f.nii  \

  -run 5 bold nii f.nii  \

  -run 6 bold nii f.nii  \

  -run 8 3danat mgz  001.mgz \

  -run 9 3danat mgz  001.mgz




Any help would be great appreciated! Thanks!




Rmily



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Re: [Freesurfer] Unpacking DWI Data

[Barbara Kreilkamp]

Hi Emily,


Yes, Osirix Lite should be sufficient, I think it works by picking 
File-import and then File-export-export DICOMs (decompression is 
sometimes helpful). It should be straightforward, just have a go at it.


Hope it helps.


Best wishes,
Barbara


On 19/09/2016 00:36, Emily Louise Belleau wrote:


Hi Barbara,


Thank you so much! I have downloaded Osirix Lite, since regular Osirix 
costs a pretty penny!



So, once I have imported the dicoms, is it simply a matter of 
exporting them onto my hardrive where I would like them to be?



Thanks so much!


Emily


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Barbara 
Kreilkamp 

*Sent:* Sunday, September 18, 2016 3:21:00 PM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] Unpacking DWI Data

Hi Emily,


I've never tried to use unpacksdcmdir but you may try the Osirix tool, 
it allows you to read in a dicom folder and save a new folder with 
subfolders according to the sequences that were run. At the same time 
you can also anonymize your data.



Does this help?

Best wishes,

Barbara


On 17/09/2016 22:17, Emily Louise Belleau wrote:


Hello Freesurfer Experts,


Our research team has recently collected data from Martinos Center. 
The entire scanning protocol (including anatomical, functional runs, 
DWI) is in one directory.



Therefore I have been using unpacksdcmdir to tell me what runs go 
with each scanning sequence. I have had no trouble unpacking the 
functional and anatomical runs. I have had difficulties unpacking the 
DWI data.  I have been recently warned that unpackdcmdir does not 
correctly unpack DWI data. Is there a work around or another tool I 
could use? It seems that most tools are for unpacking per run 
(dcmtonii), and would not work in my situation where all scans are in 
one folder?



The runs that say "err" which typically indicated something is 
missing in the scan appear to be unpacking. However, it does say on 
the terminal that there is an error but attempting to unpack anyway.


Some of the runs that say "ok" in the scan log are not unpacking 
properly.  Additionally, we are finding that  when we unpack on of 
the DWI sequences we used, we get bvec and bval files. However, we do 
not when we unpack a different DWI sequence we also ran we do not 
get  the corresponding bvec and bval files.


The command I am using, where I put related runs into related folders:
unpacksdcmdir -src dicomdir -targ  targetdir -fsfast \
  -run 2 bold nii f.nii  \
  -run 3 bold nii f.nii  \
  -run 4 bold nii f.nii  \
  -run 5 bold nii f.nii  \
  -run 6 bold nii f.nii  \
  -run 8 3danat mgz  001.mgz \
  -run 9 3danat mgz  001.mgz
Any help would be great appreciated! Thanks!
Rmily


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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
dispose of the e-mail.




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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Unpacking DWI Data

[Emily Louise Belleau]

Hi Barbara,


Thank you so much! I have downloaded Osirix Lite, since regular Osirix costs a 
pretty penny!


So, once I have imported the dicoms, is it simply a matter of exporting them 
onto my hardrive where I would like them to be?


Thanks so much!


Emily


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Barbara Kreilkamp 

Sent: Sunday, September 18, 2016 3:21:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Unpacking DWI Data


Hi Emily,


I've never tried to use unpacksdcmdir but you may try the Osirix tool, it 
allows you to read in a dicom folder and save a new folder with subfolders 
according to the sequences that were run. At the same time you can also 
anonymize your data.


Does this help?

Best wishes,

Barbara

On 17/09/2016 22:17, Emily Louise Belleau wrote:

Hello Freesurfer Experts,


Our research team has recently collected data from Martinos Center. The entire 
scanning protocol (including anatomical, functional runs, DWI) is in one 
directory.


Therefore I have been using unpacksdcmdir to tell me what runs go with each 
scanning sequence. I have had no trouble unpacking the functional and 
anatomical runs. I have had difficulties unpacking the DWI data.  I have been 
recently warned that unpackdcmdir does not correctly unpack DWI data. Is there 
a work around or another tool I could use? It seems that most tools are for 
unpacking per run (dcmtonii), and would not work in my situation where all 
scans are in one folder?


The runs that say "err" which typically indicated something is missing in the 
scan appear to be unpacking. However, it does say on the terminal that there is 
an error but attempting to unpack anyway.

Some of the runs that say "ok" in the scan log are not unpacking properly.  
Additionally, we are finding that  when we unpack on of the DWI sequences we 
used, we get bvec and bval files. However, we do not when we unpack a different 
DWI sequence we also ran we do not get  the corresponding bvec and bval files.

The command I am using, where I put related runs into related folders:

unpacksdcmdir -src dicomdir -targ  targetdir -fsfast \

  -run 2 bold nii f.nii  \

  -run 3 bold nii f.nii  \

  -run 4 bold nii f.nii  \

  -run 5 bold nii f.nii  \

  -run 6 bold nii f.nii  \

  -run 8 3danat mgz  001.mgz \

  -run 9 3danat mgz  001.mgz




Any help would be great appreciated! Thanks!




Rmily



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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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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Longitudinal surface analysis of PET data

[Matthieu Vanhoutte]

Hi Martin,

Thanks for your answer. However, it seems to me that cortical thickness follow 
a particular process with the recon-all -long process, isn’t it ? Is there any 
resample onto average time subject then other operation following ?

Best regards,
Matthieu

> Le 18 sept. 2016 à 16:26, Martin Reuter  a écrit 
> :
> 
> Hi Matthieu,
> 
> I never used PET data, but once you manage to resample you pet data onto the 
> surface, you will have a file similar to the thickness file for each 
> subjects. Instead of thickness it holds you PET information. From that point 
> on everything should be identical to the thickness analysis.
> 
> So this is really more a question how to get your PET data sampled onto the 
> surface. If no one else replies, write that into the subject line and repost. 
> 
> Best, Martin
> 
> 
>> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte 
>>  wrote:
>> 
>> Dear Freesurfer’s experts,
>> 
>> I would like to use the longitudinal mixed-effects model for surface PET 
>> analysis. Although I could find all the process to follow the longitudinal 
>> analysis of cortical thickness, I couldn’t resolve the steps/commands to 
>> apply successively to coregistered PET data on T1 MRI.
>> 
>> Could you precise me the process and commands to use for PET longitudinal 
>> analysis ?
>> 
>> Many thanks in advance !
>> 
>> Best regards,
>> Matthieu
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 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
> 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] Dev builds not found

[Leila Reddy]

Hi Bruce,Thanks for your reply. 

Does anyone on the list have access to the tar file of the latest dev build 
that they could put on some other site or in a public Dropbox folder? I totally 
changed my system and don't have a working version of Freesurfer/FS-FAST 
anymore and am pretty much stuck. Otherwise, do you think I should try to 
install an older version of perl? 
Sorry to cause you trouble,Thanks,
Leila___
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Unpacking DWI Data

[Barbara Kreilkamp]

Hi Emily,


I've never tried to use unpacksdcmdir but you may try the Osirix tool, 
it allows you to read in a dicom folder and save a new folder with 
subfolders according to the sequences that were run. At the same time 
you can also anonymize your data.



Does this help?

Best wishes,

Barbara


On 17/09/2016 22:17, Emily Louise Belleau wrote:


Hello Freesurfer Experts,


Our research team has recently collected data from Martinos Center. 
The entire scanning protocol (including anatomical, functional runs, 
DWI) is in one directory.



Therefore I have been using unpacksdcmdir to tell me what runs go with 
each scanning sequence. I have had no trouble unpacking the functional 
and anatomical runs. I have had difficulties unpacking the DWI data. 
 I have been recently warned that unpackdcmdir does not correctly 
unpack DWI data. Is there a work around or another tool I could use? 
It seems that most tools are for unpacking per run (dcmtonii), and 
would not work in my situation where all scans are in one folder?



The runs that say "err" which typically indicated something is missing 
in the scan appear to be unpacking. However, it does say on the 
terminal that there is an error but attempting to unpack anyway.


Some of the runs that say "ok" in the scan log are not unpacking 
properly.  Additionally, we are finding that  when we unpack on of the 
DWI sequences we used, we get bvec and bval files. However, we do not 
when we unpack a different DWI sequence we also ran we do not get  the 
corresponding bvec and bval files.


The command I am using, where I put related runs into related folders:
unpacksdcmdir -src dicomdir -targ  targetdir -fsfast \
  -run 2 bold nii f.nii  \
  -run 3 bold nii f.nii  \
  -run 4 bold nii f.nii  \
  -run 5 bold nii f.nii  \
  -run 6 bold nii f.nii  \
  -run 8 3danat mgz  001.mgz \
  -run 9 3danat mgz  001.mgz
Any help would be great appreciated! Thanks!
Rmily


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contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] optseq2 downloading pb

[Alexandre Obert]

Dear all,

I would like to download optseq2 from 
https://surfer.nmr.mgh.harvard.edu/optseq/ it remains unavailable for 
several days.
Is there any other way to obtain it ?

Regards,

Alexandre Obert

-- 
Alexandre OBERT
Doctorant en Psychologie Cognitive
Université de Reims Champagne-Ardenne
Laboratoire C2S : Cognition, Santé, Socialisation (EA6291)
57, rue Pierre Taittinger - 51096 Reims Cedex - France
http://www.univ-reims.fr/C2S

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[Freesurfer] mris_calc cluster infos

[Nick Corriveau Lecavalier]

Hi Freesurfer team,


I have a 2 Group (MCI, CTL) x 2 (Time1, Time2) protocol. As suggested in an 
earlier discussion, I measured the rate atrophy for each group between my two 
time points. Then I applied the clusterwise correction for multiple comparison, 
which give a lot of information about each group (for example, number of 
clusters, # of voxels, regions where there's a significant difference).


Then I used mris_calc to compute the difference between my groups.


My question is: Is there a way to obtain the same informations on the group 
difference? Since mris_calc doesn't have a .log as output, I can't compute 
mris_glmfit-sim on it and I cannot get any infos on the cluster summary.


Regards,


Nick Corriveau-Lecavalier, B.Sc. (Hons.)
Étudiant au Ph.D. recherche/intervention, option neuropsychologie clinique
Coordonateur à la recherche, Association étudiante des cycles supérieurs en 
psychologie de l'Université de Montréal (AÉCSPUM)
Université de Montréal
Centre de recherche de l'Institut universitaire de gériatrie de Montréal, 
bureau M7819
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Re: [Freesurfer] Longitudinal surface analysis of PET data

[Martin Reuter]

Hi Matthieu,

I never used PET data, but once you manage to resample you pet data onto the 
surface, you will have a file similar to the thickness file for each subjects. 
Instead of thickness it holds you PET information. From that point on 
everything should be identical to the thickness analysis.

So this is really more a question how to get your PET data sampled onto the 
surface. If no one else replies, write that into the subject line and repost. 

Best, Martin


> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte  
> wrote:
> 
> Dear Freesurfer’s experts,
> 
> I would like to use the longitudinal mixed-effects model for surface PET 
> analysis. Although I could find all the process to follow the longitudinal 
> analysis of cortical thickness, I couldn’t resolve the steps/commands to 
> apply successively to coregistered PET data on T1 MRI.
> 
> Could you precise me the process and commands to use for PET longitudinal 
> analysis ?
> 
> Many thanks in advance !
> 
> Best regards,
> Matthieu
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 


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