[Freesurfer] Estimate of number of manual edits and time to complete in 100subject sample

[Schumman Resonance]

This is a question for the FS community in general,

I gather there is variability around this, but rather than an exact number
and time, I was hoping for an estimate on how many scans would I expect to
require manual edits(any of the check points recommended in the tutorials)
as well as an estimate of the time it takes to go through them.

For the sake of the argument, take a sample of 100 subjects.

Thanks,

Kev
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Re: [Freesurfer] Longitudinal analysis of one timepoint

[Sarah Whittle]

Hi,

RE the below post, we have longitudinal data from three time points, but a 
number of participants have scans for only one or two time points. We've done 
all of the cross-sectional analysis (including a lot of manual editing) and are 
ready to run everything through the longitudinal stream. Our plan was to run 
sets of analyses for all of the possible combinations of longitudinal scans.

e.g., Time 1, Time 2, Time 3;
Time 1, Time 2;
Time 1, Time 3;
Time 2, Time 3

Obviously the new feature in version 5.2 (i.e., being able to run all images 
together, regardless of whether some time points are missing for some people) 
would be MUCH better. Is this possible to do using our 5.1 cross-sectionally 
processed images? Given the time we've put into manual editing, we really 
wouldn't want to have to run everything again through 5.2.

Thanks,

Sarah



Hi Henk-Jan,

to avoid bias between subjects with single time points and others, we
run them through the same steps. This way it is possible to include them
into the statistical analysis. (For this an artificial base is created
with the head in an upright and straight position).

This feature will be available in 5.2. Nothing with respect to
processing commands changes, you will simply pass only a single time
point to the -base and then run it with -long.
Nice and transparent :-).

Anyway, you probably should wait till 5.2. There is several programs
that changed for this to work. Also the current recon-all contains many
changes not related to this. If you absolutely cannot wait, let me know
and I'll take a look at how difficult it is to go back and adjust 5.1.

Best, Martin



On Tue, 2012-12-04 at 17:06 +, Westeneng, H.J. wrote:
> Hi Freesurfer experts,
>
>
>
> This week a read the article of Bernal-Rusiel et al. titled
> “Statistical analysis of longitudinal neuroimage data with Linear
> Mixed Effects models”. In this article you described the submission of
> single time-point scans to the longitudinal pipeline of Freesurfer.
> I’m very interested in how to do this. Your help will be appreciated.
>
>
>
> Thanks in advance,
>
>
>
> Henk-Jan
>
>
>
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Re: [Freesurfer] tkmedit segmentation color offset

[Douglas Greve]

Using mri_label2vol will work a little better than mri_vol2vol.
doug

On 3/5/13 8:41 PM, Bruce Fischl wrote:
you'll have to look at the help. It's pretty extensive since Doug 
wrote it :) Then you can use freeview to visualize the transformed 
intensity and aseg volumes


cheers
Bruce
On Tue, 5 Mar 2013, Natalie Han wrote:


Thanks for the quick reply. Can you elaborate a little bit how to use
mri_vol2vol to get what I want? what would be the final scipt for 
tkmedit

then?


On Tue, Mar 5, 2013 at 5:31 PM, Bruce Fischl 


wrote:
  Hi Natalie

  sorry, tkmedit won't do what you want. It's old and we are not
  developing it anymore. You can apply the transform using
  mri_vol2vol, just make sure to use nearest nbr interp for the
  aseg.

  cheers
  Bruce
  On Tue, 5 Mar 2013, Natalie Han wrote:

Hi, all,
I have a tkmedit display issue when I try to add
transformation to the main
volume, but the segmentation volume won't conform to
Talairach domain
accordingly. Here is the commandline

tkmedit subject norm.mgz  -main-transform
talairach.xfm -seg aseg.mgz

really appreciate any feedback on how to add
transformation on this
segmentation results.

Thanks.
Natalie




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Re: [Freesurfer] tkmedit segmentation color offset

[Bruce Fischl]

you'll have to look at the help. It's pretty extensive since Doug wrote 
it :) Then you can use freeview to visualize the transformed intensity 
and aseg volumes


cheers
Bruce
On Tue, 5 Mar 2013, Natalie Han wrote:


Thanks for the quick reply. Can you elaborate a little bit how to use
mri_vol2vol to get what I want? what would be the final scipt for tkmedit
then?


On Tue, Mar 5, 2013 at 5:31 PM, Bruce Fischl 
wrote:
  Hi Natalie

  sorry, tkmedit won't do what you want. It's old and we are not
  developing it anymore. You can apply the transform using
  mri_vol2vol, just make sure to use nearest nbr interp for the
  aseg.

  cheers
  Bruce
  On Tue, 5 Mar 2013, Natalie Han wrote:

Hi, all, 
I have a tkmedit display issue when I try to add
transformation to the main
volume, but the segmentation volume won't conform to
Talairach domain
accordingly. Here is the commandline

tkmedit subject norm.mgz  -main-transform
talairach.xfm -seg aseg.mgz

really appreciate any feedback on how to add
transformation on this
segmentation results. 

Thanks.
Natalie




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Re: [Freesurfer] tkmedit segmentation color offset

[Natalie Han]

Thanks for the quick reply. Can you elaborate a little bit how to use
mri_vol2vol to get what I want? what would be the final scipt for tkmedit
then?


On Tue, Mar 5, 2013 at 5:31 PM, Bruce Fischl wrote:

> Hi Natalie
>
> sorry, tkmedit won't do what you want. It's old and we are not developing
> it anymore. You can apply the transform using mri_vol2vol, just make sure
> to use nearest nbr interp for the aseg.
>
> cheers
> Bruce
>
> On Tue, 5 Mar 2013, Natalie Han wrote:
>
>  Hi, all,
>> I have a tkmedit display issue when I try to add transformation to the
>> main
>> volume, but the segmentation volume won't conform to Talairach domain
>> accordingly. Here is the commandline
>>
>> tkmedit subject norm.mgz  -main-transform talairach.xfm -seg aseg.mgz
>>
>> really appreciate any feedback on how to add transformation on this
>> segmentation results.
>>
>> Thanks.
>> Natalie
>>
>>
>>
>
> 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
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Re: [Freesurfer] tkmedit segmentation color offset

[Bruce Fischl]

Hi Natalie

sorry, tkmedit won't do what you want. It's old and we are not developing 
it anymore. You can apply the transform using mri_vol2vol, just make sure 
to use nearest nbr interp for the aseg.


cheers
Bruce
On Tue, 5 Mar 2013, Natalie Han 
wrote:



Hi, all, 
I have a tkmedit display issue when I try to add transformation to the main
volume, but the segmentation volume won't conform to Talairach domain
accordingly. Here is the commandline

tkmedit subject norm.mgz  -main-transform talairach.xfm -seg aseg.mgz

really appreciate any feedback on how to add transformation on this
segmentation results. 

Thanks.
Natalie

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[Freesurfer] tkmedit segmentation color offset

[Natalie Han]

Hi, all,

I have a tkmedit display issue when I try to add transformation to the main
volume, but the segmentation volume won't conform to Talairach domain
accordingly. Here is the commandline

tkmedit subject norm.mgz  -main-transform talairach.xfm -seg aseg.mgz

really appreciate any feedback on how to add transformation on this
segmentation results.

Thanks.
Natalie
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[Freesurfer] FreeSurfer 5.2 TRACULA and FSL 5

[Sean Hatton]

Hi all,

I have installed FreeSurfer 5.2 to take advantage of improvements in TRACULA. 
When I run trac-all -bedp I get an error:

 .../freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected

Looking at the programming it is faulting on line 131 where it is checking the 
FSL version. 

 fslver=(`cat $FSLDIR/etc/fslversion | sed 's/\./ /g'`)

Is this syntax correct? Is TRACULA compatible with FSL 5+?


Sean Hatton
Brain and Mind Research Institute
University of Sydney 
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Re: [Freesurfer] Can I skip some folders to install freesurfer

[Nick Schmansky]

DJ,

Agreed that the distribution has gotten bloated.  In future releases I'd
like to change it to not include most of the data and to have recon-all
or other utilities print a 'wget' command to use to download the data
when needed.

I've updated the ReleaseNotes section with a list of some directories of
stuff that is not used in the default stream.  So deletion depends on
whether you or your local user-base will ever need these, which can be
tough to predict:

  * freesurfer/average/mult-comp-cor - Correction for Multiple
Comparisons pre-calc - 1.3G
  * freesurfer/subjects/fsaverage? - fsaverage at other iso-levels -
310M 
  * freesurfer/subjects/fsaverage_sym - symmetric fsaverage for
contra-lateral surface mapping - 197M 
  * freesurfer/subjects/cvs_avg* - CVS Combined Volume and Surface
registration target - 531M 
  * freesurfer/trctrain - Tracula training set - 886M

These files in total are about 3GB.

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

Nick


On Tue, 2013-03-05 at 13:43 -0600, Dian Jiao wrote:
> Hi,
> 
> 
> I was trying to install Freesurfer on a HPC cluster. It seems to be a
> pretty large distribution, ~4.3 GB after unpacking. I wonder if all
> the subfolders are needed for running freesurfer or is there any
> folders could be skipped. Thanks in advance.
> 
> 
> DJ
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[Freesurfer] Post-doctoral research fellow position in neuroimage analysis at MGH/Harvard Medical School

[Mert Rory Sabuncu]

A post-doctoral research fellow position is available in the Laboratory for 
Computational Neuroimaging (with PI's Bruce Fischl and Mert Sabuncu) at the 
Massachusetts General Hospital, Athinoula A. Martinos Center for Biomedical 
Imaging and the Department of Radiology at Harvard Medical School.

Responsibilities: The position will involve developing novel computational 
image processing and statistical analysis tools for longitudinal neuroimaging 
studies. A minimum commitment of two years is required. Salary will be 
competitive and commensurate with experience.

Requirements: The candidate should have:

• A PhD in computer science, electrical engineering, statistics or a related 
field
• Research experience in image processing and/or computational image analysis, 
preferably in biomedical applications
• Excellent oral and written communication skills using the English language.
• Strong organizational skills
• The ability to work independently within the research lab on assigned 
projects as well as the ability to work well with others on a research team
• Strong coding skills (e.g. in Matlab, Python, C/C++, Unix scripting)

There is no formal application deadline and candidates are encouraged to apply 
as soon as possible. The search will continue until position is filled. 
The start date can be as soon as possible (latest Fall 2013, but preferably 
sooner).

Please email Mert Sabuncu (msabu...@nmr.mgh.harvard.edu with subject line 
"Longitudinal Post-doc application" ) with questions and/or applications. To 
apply please send a cover letter, CV and the names/contact information of 3 
people who could provide letters of reference.

---
Mert Rory Sabuncu
Assistant Professor of Radiology
A.A. Martinos Center for Biomedical Imaging
MGH/Harvard Medical School

Research Affiliate 
Computer Science and Artificial Intelligence Lab, MIT

http://people.csail.mit.edu/msabuncu
Google Scholar Page








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[Freesurfer] mris_flatten_cuda

[James Gao]

Hi,
I'd like to use mris_flatten_cuda to accelerate the flattening process.
However, it seems that the code doesn't handle ripped vertices correctly.
mris_flatten by itself works correctly, but attempts to run
mris_flatten_cuda results in thousands of "PANIC: RIPFLAG IS NOT SUPPORTED
!" messages. The result is a completely folded surface.

Peering through the code, it seems that the MRISremoveRipped command is
being run (line 236 in mris_flatten.c), but somehow doesn't operate
correctly. Is there any way to get the cuda version to run correctly, or is
that not supported at this time?

-James Gao

-- 
University of California - Berkeley
Vision Science Graduate Group
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[Freesurfer] Can I skip some folders to install freesurfer

[Dian Jiao]

Hi,

I was trying to install Freesurfer on a HPC cluster. It seems to be a
pretty large distribution, ~4.3 GB after unpacking. I wonder if all the
subfolders are needed for running freesurfer or is there any folders could
be skipped. Thanks in advance.

DJ
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Re: [Freesurfer] FIR analysis, time window question

[Douglas N Greve]

yes, my mistake
doug
On 03/05/2013 01:30 PM, Cesar Echavarria wrote:
> Also, did you mean ' fir 4 26'  in your previous response? since the 
> TimeWindow parameter should include the 'PreStimulus' time
> (I just want to double check since this is crucial to my question)
>
> Cesar
>
>
> On Tue, Mar 5, 2013 at 1:00 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> If you presented the stimulus for 10sec, then you should set the
> time window to include about 12 sec after stimulus offset. If your
> stimulus is 10 secand you want the time window to start 4 sec
> prior to onset and go 12 sec after onset, then you will need a
> time window of 4+10+12=26sec, so it would be --fir 4 22. You have
> to model the return to baseline even if you are not interested
> init. Try that and get back to me if it does not work.
> doug
>
>
> On 03/05/2013 12:43 PM, Cesar Echavarria wrote:
>
> Hi Doug,
>
> As you can see from the attached image (time course on x-axis,
> normalized BOLD response on y-axis) the signal peak occurs
> earlier than expected if I were to consider the first frame to
> be -4 sec relative to stimulus onset.
>  In our experiment we presented a stimulus for 10 seconds, and
> we wanted to see the time course of the BOLD response while
> the stimulus was on. We also wanted to see the response of the
> aftereffect due to the stimulus separately which is why we are
> interested only in the 10 seconds the stimulus is on.
>
> Thanks,
>
> Cesar
>
>
> On Tue, Mar 5, 2013 at 12:27 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
> Hi Cesar, for your case, it would correspond to 4sec prior to
> stimulus onset (the TR that goes from -4 to -3 sec). What
> seems to
> be wrong? The last frame would be the TR that goes from
> +9sec to
> +10 sec. Not related to your question, but Is 10 sec post
> stimulus
> long enough?
> doug
>
>
>
> On 03/05/2013 11:53 AM, Cesar E Echavarria wrote:
>
>
> Hi Freesurfers,
>
> I did an FIR analysis to get the BOLD response over
> time, the
> following way
>
> mkanalysis-sess -analysis Afterimage_FIR2.rh -surface
> self rh
> -native
> -fwhm 5 -paradigm ShapeAE_New.par -event-related
> -polyfit 1
> -mcextreg -TR
> 1.000 -nconditions 8 -force -fsd bold  -fir 4 14
>
> I then generated the relevant contrasts, ran the
> funcroi-config command,
> and the func-roi-table-sess command to create 14 files
> for my
> ROI, each
> containing the signal value at 14 different time points.
>
> i.e.
> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c
> condition1
> -map cespct
> -o ROI/frame0 -frame 0
>
> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c
> condition1
> -map cespct
> -o ROI/frame1 -frame 1
>
> .
> .
> .
> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c
> condition1
> -map cespct
> -o ROI/frame13 -frame 13
>
>
>
> My question is this:
>
> To what time point (relative to stimulus onset) does
> the value
> in the
> frame0 file correspond?
>
> As I understand it, the first 4 frame values should
> correspond
> to activity
> pre-stimulus. However, this expectation is not
> corroborated by
> the timing
> and pattern of the BOLD response I am observing.
>
> I would appreciate any guidance on this issue.
>
> Thanks,
>
> Cesar Echavarria
>
>
>
> -- Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
>  >
> Phone Number: 617-724-2358 
> >
> Fax: 617-726-7422   >
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> 
> FileDrop:
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> 

Re: [Freesurfer] FIR analysis, time window question

[Douglas N Greve]

Hi Cesar, you cannot really do the analysis you want to do, it is 
mathematically impossible. If you do not expect a response from one of 
the conditions, then you could code it as 0. Alternatively, you can 
consider both conditions as a single 20 sec event and get the FIR for 
that event out to 28 sec. If you don't have to have an FIR analysis, you 
can assume a shape to the HRF and do the usual statistics on it.
doug

On 03/05/2013 01:21 PM, Cesar Echavarria wrote:
> Does the post-stimulus period have to be as long as 12 seconds? With 
> such a long time window I get the following error when running 
> selxavg3-sess:
>
> XCond = 1.47995e+18 (normalized)
> ERROR: design is ill-conditioned
>
> To clarify: in our design we have 10 seconds of condition 1 followed 
> immediately after with 10 seconds of condition 2 followed by 10 
> seconds of fixation.
> Given, this what would be the limit on how much post-stimulus time we 
> should include in our time window?
>
> Thanks again,
> Cesar
>
>
> On Tue, Mar 5, 2013 at 1:00 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> If you presented the stimulus for 10sec, then you should set the
> time window to include about 12 sec after stimulus offset. If your
> stimulus is 10 secand you want the time window to start 4 sec
> prior to onset and go 12 sec after onset, then you will need a
> time window of 4+10+12=26sec, so it would be --fir 4 22. You have
> to model the return to baseline even if you are not interested
> init. Try that and get back to me if it does not work.
> doug
>
>
> On 03/05/2013 12:43 PM, Cesar Echavarria wrote:
>
> Hi Doug,
>
> As you can see from the attached image (time course on x-axis,
> normalized BOLD response on y-axis) the signal peak occurs
> earlier than expected if I were to consider the first frame to
> be -4 sec relative to stimulus onset.
>  In our experiment we presented a stimulus for 10 seconds, and
> we wanted to see the time course of the BOLD response while
> the stimulus was on. We also wanted to see the response of the
> aftereffect due to the stimulus separately which is why we are
> interested only in the 10 seconds the stimulus is on.
>
> Thanks,
>
> Cesar
>
>
> On Tue, Mar 5, 2013 at 12:27 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
> Hi Cesar, for your case, it would correspond to 4sec prior to
> stimulus onset (the TR that goes from -4 to -3 sec). What
> seems to
> be wrong? The last frame would be the TR that goes from
> +9sec to
> +10 sec. Not related to your question, but Is 10 sec post
> stimulus
> long enough?
> doug
>
>
>
> On 03/05/2013 11:53 AM, Cesar E Echavarria wrote:
>
>
> Hi Freesurfers,
>
> I did an FIR analysis to get the BOLD response over
> time, the
> following way
>
> mkanalysis-sess -analysis Afterimage_FIR2.rh -surface
> self rh
> -native
> -fwhm 5 -paradigm ShapeAE_New.par -event-related
> -polyfit 1
> -mcextreg -TR
> 1.000 -nconditions 8 -force -fsd bold  -fir 4 14
>
> I then generated the relevant contrasts, ran the
> funcroi-config command,
> and the func-roi-table-sess command to create 14 files
> for my
> ROI, each
> containing the signal value at 14 different time points.
>
> i.e.
> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c
> condition1
> -map cespct
> -o ROI/frame0 -frame 0
>
> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c
> condition1
> -map cespct
> -o ROI/frame1 -frame 1
>
> .
> .
> .
> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c
> condition1
> -map cespct
> -o ROI/frame13 -frame 13
>
>
>
> My question is this:
>
> To what time point (relative to stimulus onset) does
> the value
> in the
> frame0 file correspond?
>
> As I understand it, the first 4 frame values should
> correspond
> to activity
> pre-stimulus. However, this expectation is not
> corroborated by
> the timing
> and pattern of the BOLD response I am observing.
>
> I would appreciate any guidance on this issue.
>
> Thanks,
>
> Cesar Echavarria
>
>
>

Re: [Freesurfer] FIR analysis, time window question

[Cesar Echavarria]

Also, did you mean ' fir 4 26'  in your previous response? since the
TimeWindow parameter should include the 'PreStimulus' time
(I just want to double check since this is crucial to my question)

Cesar


On Tue, Mar 5, 2013 at 1:00 PM, Douglas N Greve
wrote:

>
> If you presented the stimulus for 10sec, then you should set the time
> window to include about 12 sec after stimulus offset. If your stimulus is
> 10 secand you want the time window to start 4 sec prior to onset and go 12
> sec after onset, then you will need a time window of 4+10+12=26sec, so it
> would be --fir 4 22. You have to model the return to baseline even if you
> are not interested init. Try that and get back to me if it does not work.
> doug
>
>
> On 03/05/2013 12:43 PM, Cesar Echavarria wrote:
>
>> Hi Doug,
>>
>> As you can see from the attached image (time course on x-axis, normalized
>> BOLD response on y-axis) the signal peak occurs earlier than expected if I
>> were to consider the first frame to be -4 sec relative to stimulus onset.
>>  In our experiment we presented a stimulus for 10 seconds, and we wanted
>> to see the time course of the BOLD response while the stimulus was on. We
>> also wanted to see the response of the aftereffect due to the stimulus
>> separately which is why we are interested only in the 10 seconds the
>> stimulus is on.
>>
>> Thanks,
>>
>> Cesar
>>
>>
>> On Tue, Mar 5, 2013 at 12:27 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu 
>> >
>> wrote:
>>
>> Hi Cesar, for your case, it would correspond to 4sec prior to
>> stimulus onset (the TR that goes from -4 to -3 sec). What seems to
>> be wrong? The last frame would be the TR that goes from +9sec to
>> +10 sec. Not related to your question, but Is 10 sec post stimulus
>> long enough?
>> doug
>>
>>
>>
>> On 03/05/2013 11:53 AM, Cesar E Echavarria wrote:
>>
>>
>> Hi Freesurfers,
>>
>> I did an FIR analysis to get the BOLD response over time, the
>> following way
>>
>> mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh
>> -native
>> -fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1
>> -mcextreg -TR
>> 1.000 -nconditions 8 -force -fsd bold  -fir 4 14
>>
>> I then generated the relevant contrasts, ran the
>> funcroi-config command,
>> and the func-roi-table-sess command to create 14 files for my
>> ROI, each
>> containing the signal value at 14 different time points.
>>
>> i.e.
>> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1
>> -map cespct
>> -o ROI/frame0 -frame 0
>>
>> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1
>> -map cespct
>> -o ROI/frame1 -frame 1
>>
>> .
>> .
>> .
>> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1
>> -map cespct
>> -o ROI/frame13 -frame 13
>>
>>
>>
>> My question is this:
>>
>> To what time point (relative to stimulus onset) does the value
>> in the
>> frame0 file correspond?
>>
>> As I understand it, the first 4 frame values should correspond
>> to activity
>> pre-stimulus. However, this expectation is not corroborated by
>> the timing
>> and pattern of the BOLD response I am observing.
>>
>> I would appreciate any guidance on this issue.
>>
>> Thanks,
>>
>> Cesar Echavarria
>>
>>
>>
>> -- Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
>> > >
>> Phone Number: 617-724-2358 
>> Fax: 617-726-7422 
>>
>> Bugs: 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>> 
>> 
>> >
>> FileDrop: 
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>> 
>> 
>> >
>>
>> Outgoing:
>> 
>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/
>>
>>
>>
>>
>> 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-ma

Re: [Freesurfer] FIR analysis, time window question

[Cesar Echavarria]

Does the post-stimulus period have to be as long as 12 seconds? With such a
long time window I get the following error when running selxavg3-sess:

XCond = 1.47995e+18 (normalized)
ERROR: design is ill-conditioned

To clarify: in our design we have 10 seconds of condition 1 followed
immediately after with 10 seconds of condition 2 followed by 10 seconds of
fixation.
Given, this what would be the limit on how much post-stimulus time we
should include in our time window?

Thanks again,
Cesar


On Tue, Mar 5, 2013 at 1:00 PM, Douglas N Greve
wrote:

>
> If you presented the stimulus for 10sec, then you should set the time
> window to include about 12 sec after stimulus offset. If your stimulus is
> 10 secand you want the time window to start 4 sec prior to onset and go 12
> sec after onset, then you will need a time window of 4+10+12=26sec, so it
> would be --fir 4 22. You have to model the return to baseline even if you
> are not interested init. Try that and get back to me if it does not work.
> doug
>
>
> On 03/05/2013 12:43 PM, Cesar Echavarria wrote:
>
>> Hi Doug,
>>
>> As you can see from the attached image (time course on x-axis, normalized
>> BOLD response on y-axis) the signal peak occurs earlier than expected if I
>> were to consider the first frame to be -4 sec relative to stimulus onset.
>>  In our experiment we presented a stimulus for 10 seconds, and we wanted
>> to see the time course of the BOLD response while the stimulus was on. We
>> also wanted to see the response of the aftereffect due to the stimulus
>> separately which is why we are interested only in the 10 seconds the
>> stimulus is on.
>>
>> Thanks,
>>
>> Cesar
>>
>>
>> On Tue, Mar 5, 2013 at 12:27 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu 
>> >
>> wrote:
>>
>> Hi Cesar, for your case, it would correspond to 4sec prior to
>> stimulus onset (the TR that goes from -4 to -3 sec). What seems to
>> be wrong? The last frame would be the TR that goes from +9sec to
>> +10 sec. Not related to your question, but Is 10 sec post stimulus
>> long enough?
>> doug
>>
>>
>>
>> On 03/05/2013 11:53 AM, Cesar E Echavarria wrote:
>>
>>
>> Hi Freesurfers,
>>
>> I did an FIR analysis to get the BOLD response over time, the
>> following way
>>
>> mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh
>> -native
>> -fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1
>> -mcextreg -TR
>> 1.000 -nconditions 8 -force -fsd bold  -fir 4 14
>>
>> I then generated the relevant contrasts, ran the
>> funcroi-config command,
>> and the func-roi-table-sess command to create 14 files for my
>> ROI, each
>> containing the signal value at 14 different time points.
>>
>> i.e.
>> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1
>> -map cespct
>> -o ROI/frame0 -frame 0
>>
>> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1
>> -map cespct
>> -o ROI/frame1 -frame 1
>>
>> .
>> .
>> .
>> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1
>> -map cespct
>> -o ROI/frame13 -frame 13
>>
>>
>>
>> My question is this:
>>
>> To what time point (relative to stimulus onset) does the value
>> in the
>> frame0 file correspond?
>>
>> As I understand it, the first 4 frame values should correspond
>> to activity
>> pre-stimulus. However, this expectation is not corroborated by
>> the timing
>> and pattern of the BOLD response I am observing.
>>
>> I would appreciate any guidance on this issue.
>>
>> Thanks,
>>
>> Cesar Echavarria
>>
>>
>>
>> -- Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
>> > >
>> Phone Number: 617-724-2358 
>> Fax: 617-726-7422 
>>
>> Bugs: 
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>> 
>> 
>> >
>> FileDrop: 
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>> 
>> 
>> >
>>
>> Outgoing:
>> 
>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/
>>
>>
>>
>>
>> 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
>

Re: [Freesurfer] FIR analysis, time window question

[Douglas N Greve]

If you presented the stimulus for 10sec, then you should set the time 
window to include about 12 sec after stimulus offset. If your stimulus 
is 10 secand you want the time window to start 4 sec prior to onset and 
go 12 sec after onset, then you will need a time window of 
4+10+12=26sec, so it would be --fir 4 22. You have to model the return 
to baseline even if you are not interested init. Try that and get back 
to me if it does not work.
doug

On 03/05/2013 12:43 PM, Cesar Echavarria wrote:
> Hi Doug,
>
> As you can see from the attached image (time course on x-axis, 
> normalized BOLD response on y-axis) the signal peak occurs earlier 
> than expected if I were to consider the first frame to be -4 sec 
> relative to stimulus onset.
>  In our experiment we presented a stimulus for 10 seconds, and we 
> wanted to see the time course of the BOLD response while the stimulus 
> was on. We also wanted to see the response of the aftereffect due to 
> the stimulus separately which is why we are interested only in the 10 
> seconds the stimulus is on.
>
> Thanks,
>
> Cesar
>
>
> On Tue, Mar 5, 2013 at 12:27 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Cesar, for your case, it would correspond to 4sec prior to
> stimulus onset (the TR that goes from -4 to -3 sec). What seems to
> be wrong? The last frame would be the TR that goes from +9sec to
> +10 sec. Not related to your question, but Is 10 sec post stimulus
> long enough?
> doug
>
>
>
> On 03/05/2013 11:53 AM, Cesar E Echavarria wrote:
>
>
> Hi Freesurfers,
>
> I did an FIR analysis to get the BOLD response over time, the
> following way
>
> mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh
> -native
> -fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1
> -mcextreg -TR
> 1.000 -nconditions 8 -force -fsd bold  -fir 4 14
>
> I then generated the relevant contrasts, ran the
> funcroi-config command,
> and the func-roi-table-sess command to create 14 files for my
> ROI, each
> containing the signal value at 14 different time points.
>
> i.e.
> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1
> -map cespct
> -o ROI/frame0 -frame 0
>
> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1
> -map cespct
> -o ROI/frame1 -frame 1
>
> .
> .
> .
> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1
> -map cespct
> -o ROI/frame13 -frame 13
>
>
>
> My question is this:
>
> To what time point (relative to stimulus onset) does the value
> in the
> frame0 file correspond?
>
> As I understand it, the first 4 frame values should correspond
> to activity
> pre-stimulus. However, this expectation is not corroborated by
> the timing
> and pattern of the BOLD response I am observing.
>
> I would appreciate any guidance on this issue.
>
> Thanks,
>
> Cesar Echavarria
>
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
>
> 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.
>
>
>
>
> -- 
> Cesar Echavarria
> Brain & Cognitive Science
> MIT 2012

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] question stats

[Douglas N Greve]

Hi Joost, I'm a little lost. Are you doing the initial mri_glmfit 
analysis on thickness or CT?
doug

On 03/05/2013 03:31 AM, j janssen wrote:
> Hi Doug,
>
> using mri_glmfit with DODS and mri_glmfit-sim with a fsgd-file and 
> contrast (attached) that looks like (2 discrete factors: 1 with 2 
> levels (diagnosis) and 1 with 4 levels (Site) and 1 continuous 
> covariate (age)):
> GroupDescriptorFile 1
> Title AGE-subj
> Class PatSite1
> Class PatSite2
> Class PatSite3
> Class PatSite4
> Class ConSite1
> Class ConSite2
> Class ConSite3
> Class ConSite4
> variables Age
> Input $FSGDID PatSite1 12.8
> ..
> Input $FSGDID PatSite2 9.3
> ..
> Input $FSGDID PatSite3 15.1
> ..
> Input $FSGDID PatSite4 10
> ..
> Input $FSGDID ConSite1 7.6
> ..
> Input $FSGDID ConSite2 8.9
> ..
> Input $FSGDID ConSite3 10.2
> ..
> Input $FSGDID ConSite4 14
> ..
>
> mri_glmfit --y lh.justmen.NOTmatched.CT.fwhm10.mgh --fsgd 
> fsgd_justmen_NOTmatched_only_age.txt --C contrast_justmen_DODS_GxA.mtx 
> --surf fsaverage lh --cortex --glmdir 
> lh.justmen.NOTmatched.all.GRxAge.CT.fwhm10
>
> for the contrast attached (which i thought is the interaction between 
> diagnosis and age, independent of 'Site') i found 3 clusters using 
> mri_glmfit-sim (attached). i saved these clusters as labels and 
> transformed them to native space (cluster appeared in the correct 
> location in native space):
> mri_label2label --srclabel cluster-001.label --srcsubject fsaverage 
> --trgsubject $subject --trglabel $subject_cluster-001.label 
> --regmethod surface --hemi lh
>
> and extracted mean CT from the cluster in native space:
> mris_anatomical_stats -l  $subject_cluster-001.label -t lh.thickness 
> -b -f $subject_cluster-001.stats $subject
>
> i plotted mean thickness for each cluster against age but did *not* 
> see an interaction between groups. even though this is mean thickness 
> for the cluster on non-smoothed native space thickness i would have 
> expected to see some interaction but the slopes for both groups are 
> almost parallel. any thoughts? i can provide more info if needed.
> -joost
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Some basic cortical thickness questions

[Douglas N Greve]

On 03/05/2013 12:13 AM, Rongxiang Tang wrote:
> Dear All,
>
> I have some basic questions about groups analysis for cortical 
> thickness, and I looked over the list and tutorial, but still have 
> questions.
> I have two groups, experimental and control, and both were tested 
> before and after training...
> I plan to use qdec to run the group analysis, and I finished the 
> recon-all, and -qcache processing for each subject.
> My question is that:
>
> 1.Is it necessary to select a ROI prior to my cortical thickness 
> analysis?
no
> 2.For the .dat text file, which stats (for cortical thickness) output 
> should I use for the continuous factors such as left hemi thickness, 
> right hemi thickness?
If you want to use the thickness as an dependent variable (sounds like 
you do), then do not put thickness in the .dat file.
doug
>
> Thanks,
> Catherine
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] mprage resolution for surfaces/thicknes?

[Inati, Souheil (NIH/NIMH) [E]]

Thanks Bruce.  FYI, I got a couple of other emails off list.  One of them 
reminded me that the original ADNI protocol had this resolution.
Cheers,
Souheil


On Mar 5, 2013, at 9:50 AM, Bruce Fischl wrote:

> Hi Souheil
> 
> our standard acquisition used to be 1.33x1x1 so I don't think there 
> should be any problem (although it has been a long time since we used to 
> get those - 1.5T and single channel)
> 
> cheers
> Bruce
> On Tue, 5 Mar 2013, Inati, Souheil 
> (NIH/NIMH) [E] wrote:
> 
>> A colleague has some mprage scans collected on a 3T sagittally 1mmx1mm in 
>> plane, 1.3mm thick.  The SNR and CNR are pretty good.  I figured I'd ping 
>> the list to see if anyone have any experience running scans with the 
>> slightly thickish voxels through the recon-all pipeline.  Anything I ought 
>> to look out for in particular?
>> 
>> Thanks,
>> Souheil
>> 
>> 
>> Souheil Inati, PhD
>> Staff Scientist, Functional MRI Facility
>> NIMH/NIH/DHHS
>> souheil.in...@nih.gov
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>> 
>> 
>> 
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> 
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Re: [Freesurfer] qdec/other options

[Douglas N Greve]

That is correct (though you might not want to use Bonferroni as it is a 
little harsh). QDEC will do the same thing. It provides a GUI but is 
less flexible.
doug


On 03/05/2013 07:59 AM, std...@virgilio.it wrote:
> Hi list,
>
> I'm performing cortical thickness on three group of subject. I have 
> also three covariates (age, gender and educational level).
>
> I'm doing:
>
> 1-built a .fsgd file
> 2-mris_preproc
> 3-mri_surf2surf
> 4-mri_glmfit
> 5-Bonferroni correction
>
> Are those processes correct?
>
> Alternatively should I use qdec option? In this way, when should I use it?
>
> Thank you very much,
>
>
> Stefano
>
>
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-- 
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] FIR analysis, time window question

[Douglas N Greve]

Hi Cesar, for your case, it would correspond to 4sec prior to stimulus 
onset (the TR that goes from -4 to -3 sec). What seems to be wrong? The 
last frame would be the TR that goes from +9sec to +10 sec. Not related 
to your question, but Is 10 sec post stimulus long enough?
doug


On 03/05/2013 11:53 AM, Cesar E Echavarria wrote:
>
> Hi Freesurfers,
>
> I did an FIR analysis to get the BOLD response over time, the following way
>
> mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh -native
> -fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1 -mcextreg -TR
> 1.000 -nconditions 8 -force -fsd bold  -fir 4 14
>
> I then generated the relevant contrasts, ran the funcroi-config command,
> and the func-roi-table-sess command to create 14 files for my ROI, each
> containing the signal value at 14 different time points.
>
> i.e.
> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct
> -o ROI/frame0 -frame 0
>
> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct
> -o ROI/frame1 -frame 1
>
> .
> .
> .
> funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct
> -o ROI/frame13 -frame 13
>
>
>
> My question is this:
>
> To what time point (relative to stimulus onset) does the value in the
> frame0 file correspond?
>
> As I understand it, the first 4 frame values should correspond to activity
> pre-stimulus. However, this expectation is not corroborated by the timing
> and pattern of the BOLD response I am observing.
>
> I would appreciate any guidance on this issue.
>
> Thanks,
>
> Cesar Echavarria
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] processing 2 dti's from 1 experiment

[Anastasia Yendiki]

Hi Jon - I mean concatenating them:

mri_concat --i dwi1.nii.gz dwi2.nii.gz --o dwi.nii.gz
cat bvecs1.txt bvecs2.txt > bvecs.txt
cat bvals1.txt bvals2.txt > bvals.txt

Make sure though this doesn't leave any blank lines in between the two 
sets of bvecs/bvals in the concatenated text files.

Hope this helps,
a.y

On Tue, 5 Mar 2013, Jon Wieser wrote:

> HI Anastasia,
> The two data sets have the same bvecs table, but the bvals differ, one set is 
> 800 and the other is 1000.
> can you be more specific as to how I would merge the two datasets? or you 
> talking about putting all the
> dicom files from both sets into one directory, or do you mean something else?
> we have one anatomical set
>
> Jon
>
> - Original Message -
> From: "Anastasia Yendiki" 
> To: "Jon Wieser" 
> Cc: "freesurfer" 
> Sent: Monday, March 4, 2013 5:17:31 PM
> Subject: Re: [Freesurfer] processing 2 dti's from 1 experiment
>
>
> Hi Jon - You can try merging the DWIs, gradient tables, and b-value files
> from the 2 scans and specifying the merged version in the config file as
> if this were a single scan. I haven't tried this myself, so do let me know
> if this works!
>
> If in addition to 2 DWIs you also had 2 anatomicals, you could try the new
> longitudinal option, which reconstructs tracts from multiple data sets at
> once. With only one anatomical, this would require some mild hacks but
> could still be done in principle (again, never tried it).
>
> Or you could try quantifying which of the two DWI scans has the least
> motion of the 2 and only use that one.
>
> Hope this helps,
> a.y
>
> On Mon, 4 Mar 2013, Jon Wieser wrote:
>
>> hello,
>>
>> we have acquired dti scans  on a subject during a FMRI experiment.  is it 
>> possible to process both dti's with tracule to get an average of the 2 dti's?
>> If so, how do I setup the config file for this?
>> Thanks
>> Jon
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>>
>>
>
>
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[Freesurfer] FIR analysis, time window question

[Cesar E Echavarria]

Hi Freesurfers,

I did an FIR analysis to get the BOLD response over time, the following way

mkanalysis-sess -analysis Afterimage_FIR2.rh -surface self rh -native
-fwhm 5 -paradigm ShapeAE_New.par -event-related -polyfit 1 -mcextreg -TR
1.000 -nconditions 8 -force -fsd bold  -fir 4 14

I then generated the relevant contrasts, ran the funcroi-config command,
and the func-roi-table-sess command to create 14 files for my ROI, each
containing the signal value at 14 different time points.

i.e.
funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct
-o ROI/frame0 -frame 0

funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct
-o ROI/frame1 -frame 1

.
.
.
funcroi-table-sess -sf sessid -roi Labels/rh.V1 -c condition1 -map cespct
-o ROI/frame13 -frame 13



My question is this:

To what time point (relative to stimulus onset) does the value in the
frame0 file correspond?

As I understand it, the first 4 frame values should correspond to activity
pre-stimulus. However, this expectation is not corroborated by the timing
and pattern of the BOLD response I am observing.

I would appreciate any guidance on this issue.

Thanks,

Cesar Echavarria
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Re: [Freesurfer] mprage resolution for surfaces/thicknes?

[Bruce Fischl]

Hi Souheil

our standard acquisition used to be 1.33x1x1 so I don't think there 
should be any problem (although it has been a long time since we used to 
get those - 1.5T and single channel)

cheers
Bruce
On Tue, 5 Mar 2013, Inati, Souheil 
(NIH/NIMH) [E] wrote:

> A colleague has some mprage scans collected on a 3T sagittally 1mmx1mm in 
> plane, 1.3mm thick.  The SNR and CNR are pretty good.  I figured I'd ping the 
> list to see if anyone have any experience running scans with the slightly 
> thickish voxels through the recon-all pipeline.  Anything I ought to look out 
> for in particular?
>
> Thanks,
> Souheil
>
> 
> Souheil Inati, PhD
> Staff Scientist, Functional MRI Facility
> NIMH/NIH/DHHS
> souheil.in...@nih.gov
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>
>
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[Freesurfer] mprage resolution for surfaces/thicknes?

[Inati, Souheil (NIH/NIMH) [E]]

A colleague has some mprage scans collected on a 3T sagittally 1mmx1mm in 
plane, 1.3mm thick.  The SNR and CNR are pretty good.  I figured I'd ping the 
list to see if anyone have any experience running scans with the slightly 
thickish voxels through the recon-all pipeline.  Anything I ought to look out 
for in particular?

Thanks,
Souheil


Souheil Inati, PhD
Staff Scientist, Functional MRI Facility
NIMH/NIH/DHHS
souheil.in...@nih.gov
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Re: [Freesurfer] image resolution

[Bruce Fischl]

Hi Carolina

you can probabbly get reasonable asegs out of it, but  I don't think
surfaces will work since your 5 or 6 mm is larger than the spacing between 
many adjacent gyri.


cheers
Bruce


On Tue, 5 Mar 2013, carolina.mr wrote:


Hello,
Someone asked me if it is possible to process T1 images with a 5mm slice /
1mm gap with FreeSurfer. Is it feasible to analyse? The person who asked
used ITK tools to interpolate the images and reconstructed an isotropic
voxel. I do not know if the post processed image with ITK can be validated
to obtain trustable volumetric measurements of cortical tickness with
Freesurfer...
 
What is your experience on that?
 
Thank you,
Carolina
 

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[Freesurfer] image resolution

[carolina.mr]

Hello,
Someone asked me if it is possible to process T1 images with a 5mm slice / 1mm gap with FreeSurfer. Is it feasible to analyse? The person who asked used ITK tools to interpolate the images and reconstructed an isotropic voxel. I do not know if the post processed image with ITK can be validated to obtain trustable volumetric measurements of cortical tickness with Freesurfer...
 
What is your experience on that?
 
Thank you,
Carolina
 
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Re: [Freesurfer] A question regarding high FA values when running DTI script

[Rotem Saar]

2013/3/5 Rotem Saar 

> Hi
>
> Attached is some pictures that might help ? Is this what you meant ?
> Looking at this again - something is weird but I can't say what...
> I can ZIP the data of one subject and send it to you but I don't feel
> comfortable asking you to personally examine it...
> Hopefully the upcoming course will shed some light on these problems...
>
> thanks
>
> Rotem
>
> 2013/2/26 Bruce Fischl 
>
>> Hi Rotem
>>
>> that's always a problem with FA estimation (the partial volume stuff I
>> mean). It's hard to diagnose this without seeing some images. Can you send
>> some of the registration?
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Tue, 26 Feb 2013, Rotem Saar wrote:
>>
>>  Hi Bruce,
>>>
>>> Thanks for your answer and sorry about the delay in mine.
>>> Registration seems fine, but I came up with some questions regarding it -
>>>
>>> 1) When testing the registration, using the "compare" button, I can see
>>> both the diffusion and what is suppose to be the anatomical slices - but why
>>> do the anatomical data it smoothed and doesn't look like a clear
>>> anatomical image ? can this be related ? maybe i did something wrong ?
>>>
>>> 2) Another thing I thought about was that the corpuse-callosum values
>>> are very high, but values for the ventricles are really low - so that even
>>> really small shifts in the registration can bring to a situation that
>>> values in the ventricles are higher than expected. Do u suggest manual
>>> intervention in registration that will mainly follow the mid-sagittal
>>> slice ? I don't mean ignoring the others, but mainly test the fit according
>>> the
>>> mid-sagittal slice.
>>>
>>> If u have any other ideas for why this is happening - I would appreciate
>>> it if u share them with me in order to think of a solution.
>>>
>>> Thanks !
>>>
>>> Rotem
>>>
>>> 2013/2/18 Bruce Fischl 
>>>   Hi Rotem
>>>
>>>   that does sound high. Have you checked the registation between
>>> your diffusion data and the anatomicals?
>>>
>>>   cheers
>>>   Bruce
>>>
>>>
>>>   On Mon, 18 Feb 2013, Rotem Saar wrote:
>>>
>>> Hi all,
>>>
>>> I run into somthing that seems odd to me and wanted to
>>> consult -
>>> I run the following script for getting the FA values from my
>>> DTI scans:
>>>
>>> 1) dt_recon --i /usr/local/freesurfer/**
>>> subjects/FOLDER-NAME/DTI/**I1.dcm
>>> --s FOLDER-NAME --o 
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI
>>> --b
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/**
>>> bvals.bval
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/**
>>> bvecs.bvec
>>> 2) tkregister2 --s fsaverage --surf white --reg
>>> 
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/fa-**tal.nii.reg
>>> --mov
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/fa-**
>>> tal.nii
>>> 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg
>>> wmparc.mgz -reg
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/**register.dat
>>> -overlay
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/fa.**nii
>>> -fthresh 0.2 -fmax 1
>>> 4) mri_vol2vol --mov /usr/local/freesurfer/**
>>> subjects/FOLDER-NAME/DTI/fa.**nii
>>> --targ /usr/local/freesurfer/**
>>> subjects/FOLDER-NAME/mri/orig.**mgz --s
>>> FOLDER-NAME --interp nearest --o
>>> 
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/fa_**FOLDER-NAME.nii
>>> --reg
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/**
>>> register.dat
>>> 5) tkregister2 --mov
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/fa_**marsal.nii
>>> --targ
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/mri/orig.**mgz
>>> --reg
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/fa_**
>>> FOLDER-NAME.nii.reg
>>> 6) mri_segstats --seg
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/mri/**wmparc.mgz
>>> --ctab
>>> $FREESURFER_HOME/**FreeSurferColorLUT.txt --i
>>> 
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/DTI/fa_**FOLDER-NAME.mask.nii
>>> --sum
>>> /usr/local/freesurfer/**subjects/FOLDER-NAME/stats/**
>>> all_stats_fa_FOLDER-NAME
>>>
>>>
>>> I got a table with all the FA values, for each segment, but
>>> I suspect a
>>> problem: I think that the values are too high (I set the
>>> threshold to
>>> 0.2-1), am I right ?
>>> I'm attaching the table I got, and to be specific, I'm very
>>> much interested
>>> in the Corpus-Colosseum values, which are high (not
>>> surprising) but when I
>>> wanted to validate with some other structures, like the
>>> "left putamen" I saw
>>> 0.53 which is to my opinion too high ?
>>> I would really appreciate if you can have a look at the
>>> table I attached
>>> 

[Freesurfer] qdec.table

[Varghese Chikku]

All,
I have completed  base and long runs for qdec longitudinal analysis.Now I
am struggling to make qdec.table.dat.How can I do this.
Tx
chikku
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[Freesurfer] qdec/other options

[stdp82]

Hi list,
I'm performing cortical thickness on three group of subject. I have also three 
covariates (age, gender and educational level). 
I'm doing:
1-built a .fsgd file2-mris_preproc3-mri_surf2surf4-mri_glmfit5-Bonferroni 
correction
Are those processes correct? 
Alternatively should I use qdec option? In this way, when should I use it?
Thank you very much,

Stefano ___
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