[Freesurfer] recon-all and local Gyrification Index

[Ankita Chatterjee]

Hello,
I ran several recon-all processes on raw T1 MRI data. I was trying to run
recon-all -lgi as per the instructions from this paper -
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/ but it fails with an
error that Matlab is required. So, my question is if local GI is already
computed by running recon-all? Or, do I need to get MatLab? Since I don't
have MatLab, any other workarounds?

Thanks!
Ankita
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[Faeze Vedaei]

Hi,

Thank you so much for assistant me in the process. I could do that. It
worked. Thanks

Faezeh Vedaei

On Wed, Mar 2, 2016 at 6:15 PM, Faeze Vedaei  wrote:

> Hi
>
> Thank you so much for your help. I just got your meaning. I created new
> LUT file by just changing randomly the RBG values for each 13 specific
> regions and opened the annot file in tksurfer. And the strange issue is
> that just for paracentral I used your values I had paracentral in tksurfer
> GUI name, but for the rest of the regions I saw that problem I had before!
> (the region's names were not the names in .ctab file). So, what do you
> think about?
>
> Regards,
> Faeze
>
> On Wed, Mar 2, 2016 at 2:59 PM, Faeze Vedaei 
> wrote:
>
>> Hi,
>>
>> Thank you for your response. sorry, I could not understand what you mean.
>> How you found 23 230 60 values for paracentral region? I mean. Are these
>> from Freesurfer LUT?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Tue, Mar 1, 2016 at 9:33 PM, Faeze Vedaei 
>> wrote:
>>
>>> Thank you for your response. It is better to explain my question that
>>> the coordinates for paracentral in .ctab file is '63 100 60', that you
>>> changed these to '23 230 60' in your new version. My question is that how
>>> you applied such this change on the RBG values for this region?
>>>
>>> Regards,
>>> Faezeh
>>>
>>> On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei 
>>> wrote:
>>>
 Thank you so much for you response. I should say that I know about what
 you are saying. My issue is that I have these 4 columns in my LUT file. Why
 and how can I change the numbers (RGB values) to create new LUT?

 Bests,
 Faezeh

 On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei 
 wrote:

> Hi,
>
> Thank you so much for you descriptions. I checked out the link you
> just sent me. Because I do not have many experiences working with
> Freesurfer, I really could not understand about how I can do such this
> revising in LUT file. Can you explain more about this? I truly appreciate
> your time and help.
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei 
> wrote:
>
>> Hi,
>>
>> I really appreciate you for help me in this process. May you clarify
>> me from which pattern you changed the RGB values for that region? How I 
>> can
>> change the coordinates for the others?
>>
>> Regards,
>> Faezeh Vedaei
>>
>>
>> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei 
>> wrote:
>>
>>> Hi,
>>>
>>> I should let you know that, it works! It shows paracentral name in
>>> tksurfer. So, how I have to revise my .ctab file to get the right 
>>> result?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
>>> wrote:
>>>
 Hi,

 Thank you for your response. I just used the command you suggested
 to use by just a change in calling .ctab LUT file. I used the path:
 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by 
 just
 calling aparc.annot.a2009s.ctab. It is strange that I created annot 
 file
 for lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
 G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
 opinion?

 Regards,
 Faezeh Vedaei

 On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei <
 faezeved...@gmail.com> wrote:

> Hi,
>
>
> Here is the text format of those files.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei <
> faezeved...@gmail.com> wrote:
>
>> Hi
>>
>> Thank you so much for your response. I attached here three files
>> including the command lines, LUT file , and the list of names I want 
>> to get
>> and what the result is actually. I'd appreciate if you look at them 
>> and let
>> me know what is wrong with that.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei <
>> faezeved...@gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I checked again to arrange the labels in the order of LUT file,
>>> but the result has not changed. Can you help me more how I can fix 
>>> this
>>> problem? Thank you so much for your time and help.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei <
>>> faezeved...@gmail.com> wrote:
>>>
 Hi,

Re: [Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

[R Edgar]

On 3 March 2016 at 13:22, Francis Tyson Thomas
 wrote:

> Also, it looks like development for GPU usage has been halted for now and so
> I was trying to use the CUDA 5 for getting it working under ubuntu 14.04. I
> have been not successful that as the cuda device isn't getting selected. Do
> you have any recommendations on that?

I have recently started looking at the CUDA port again, although I'm
making no promises as to the amount of time I'll have to spend on it.
This said I've got mri_ca_register running with CUDA 7.5 on my
machine. On my E3 Xeon with a K1200, I can run mri_ca_register with
the test dataset in about 9 minutes.

Are you compiling from source? I had to tamper a bit with the
configure script before compiling CUDA was enabled again. I don't have
access to the right machine at the moment, but as I recall, there was
a line
with_cuda=""
which I had to comment out, since it was overriding the path to the
machine's CUDA installation which I was passing on the command line.
There are a few other minor bug fixes and performance improvements for
GPU code which I've submitted for Zeke; no new kernels yet, I'm
afraid.

If you could give me some more details about what you're doing, I may
be able to help.

Just the standard warning: the GPU results will be different from the
CPU results on the same inputs. We've been kicking around some ideas
recently to quantify how different (and to devise input datasets where
the correct answers are unambiguous).

Regards,

Richard
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Re: [Freesurfer] conflicting Monte Carlo simulation results...

[Douglas N Greve]

yes, that is the right file

On 03/03/2016 02:20 PM, Karl Liu wrote:
> Dear Doug,
> Thank you for your clarification. It sounds the right way for 
> correction is:
>
> mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ 
> --cwp  0.05\ --2spaces
>
>
>
> One last question: Is the resulting 
> "cache.th40.neg.sig.cluster.summary" the right file to look for 
> post-correction cluster information? The (old) manual said results 
> should be stored in a files starting with "mc-z", but the 
> "cachesummary" file is the only summary file FS produces after 
> running the script above...
>
>
>
> thank you.
>
>
>
> Karl
>
>
>
> 
> In the first command you only used 5 samples in your simulation. If you
> read the "Notes" section below the command, you'll see that this should
> be something like 5000. Only 5 was used because it would take very long
> to run. In general, you don't need to run the simulation because it has
> already been run and the data tabulated (this is what is accessed in the
> 2nd command line).
> On 03/02/2016 10:03 PM, Karl Liu wrote:
> >
> > Dear Freesurfer experts:
> >
> >
> > I ran into a confusing problem when applying Monte Carlo simulation to
> > control for multiple comparisons. I am using the buckner data from
> > tutorial dataset.
> >
> >
> > I first tried the simulation based on Freesurfer;s 2012 manual:
> >
> > (http://www.freesurfer.net/pub/docs/tarballs_for_courses/FreeSurferTutorial-2012.pdf)
> >
> >
> > mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4
> > mc-z.negative \ --sim-sign neg --cwpvalthresh 0.05\ --overwrite
> >
> >
> > This produced a "mc-z.negative.sig.cluster.summary". In this text, no
> > clusters survived correction.
> >
> >
> > Later on, I applied on a slightly different script, based on
> > Freesurfer tutorial
> >
> > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ClusterwiseCorrectionforMultipleComparisons)
> >
> >
> > mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \
> > --cwp  0.05\ --2spaces
> >
> >
> >  It produced a "cache.th40.neg.sig.cluster.summary" this time. But
> > according to this result, 22 clusters survived.
> >
> >
> > Now I am quite confused, because both corrections have the same
> > voxel-wise (p=0.001) and cluster-wise (p=0.05) threshold. Where the
> > drastic discrepancies come from and which result is more reliable?
> >
> >
> >  Many thinks in advance.
> >
> > Best,
> >
> > Karl
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -- 
> 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:https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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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 
> erro
>
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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] error in mc-sess

[Douglas N Greve]

On 03/03/2016 02:46 PM, Ji Won Bang wrote:
> Thanks for your reply. It works.
>
> I have 1 more general question.
>
> When running: mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_day1
>
> I get 2 files (template.log & template.nii.gz) under the functional 
> subdirectory(bold_day1) and under each run(001, 002 etc).
>
> When I run: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_day1 -per-run
>
> Does that command use the template for motion correction that was 
> created under each run? Not the one under the functional subdirectory?
It uses the one under each run.
>
> My understanding of mktemplate-sess and mc-sess is that 
> mktemplate-sess produces the template per each run (saves the template 
> file under each run) and/or the template per session(?) (saves the 
> template file under the functional subdirectory).
>
> Then mc-sess utilizes the template for motion correction.
> If I use -per-run, mc-sess utilizes the template file created per each 
> run and if I use -per-session, mc-see utilizes the template file 
> created per session(file under the functional subdirectory).
>
> Is my understanding correct?
Yes
>
> Thanks a lot!
>
> Best,
> Ji Won
>
> 2016-03-03 12:36 GMT-05:00 Douglas N Greve  >:
>
> you have to use -per-run not -per-session
>
>
> On 03/03/2016 12:27 PM, Ji Won Bang wrote:
> > The command I used is:
> >
> > mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
> >
> > mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-session
> >
> > Thank you.
> >
> > Best,
> > Ji Won
> >
> >
> >
> > 2016-03-03 12:22 GMT-05:00 Ji Won Bang  
> > >>:
> >
> > Dear. freesurfer experts.
> >
> > Hi. I'm using freesurfer version 5.3.0.
> >
> > I tried mc-sess onto runs that have different number of slices.
> >
> > However, due to this different number of slices in different
> runs,
> > mc-sess gives an error.
> >
> > I expected that running mc-sess in freesurfer version 5.3.0
> would
> > handle this issue.
> >
> > If you can share your idea to fix this problem, that would be a
> > great help.
> >
> > Thank you!
> >
> > Best,
> > Ji Won
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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.
>
>
>
>
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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] error in mc-sess

[Ji Won Bang]

Thanks for your reply. It works.

I have 1 more general question.

When running: mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_day1

I get 2 files (template.log & template.nii.gz) under the functional
subdirectory(bold_day1) and under each run(001, 002 etc).

When I run: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_day1 -per-run

Does that command use the template for motion correction that was created
under each run? Not the one under the functional subdirectory?

My understanding of mktemplate-sess and mc-sess is that mktemplate-sess
produces the template per each run (saves the template file under each run)
and/or the template per session(?) (saves the template file under the
functional subdirectory).

Then mc-sess utilizes the template for motion correction.
If I use -per-run, mc-sess utilizes the template file created per each run
and if I use -per-session, mc-see utilizes the template file created per
session(file under the functional subdirectory).

Is my understanding correct?

Thanks a lot!

Best,
Ji Won

2016-03-03 12:36 GMT-05:00 Douglas N Greve :

> you have to use -per-run not -per-session
>
>
> On 03/03/2016 12:27 PM, Ji Won Bang wrote:
> > The command I used is:
> >
> > mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
> >
> > mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-session
> >
> > Thank you.
> >
> > Best,
> > Ji Won
> >
> >
> >
> > 2016-03-03 12:22 GMT-05:00 Ji Won Bang  > >:
> >
> > Dear. freesurfer experts.
> >
> > Hi. I'm using freesurfer version 5.3.0.
> >
> > I tried mc-sess onto runs that have different number of slices.
> >
> > However, due to this different number of slices in different runs,
> > mc-sess gives an error.
> >
> > I expected that running mc-sess in freesurfer version 5.3.0 would
> > handle this issue.
> >
> > If you can share your idea to fix this problem, that would be a
> > great help.
> >
> > Thank you!
> >
> > Best,
> > Ji Won
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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.
>
>
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] conflicting Monte Carlo simulation results...

[Karl Liu]

Dear Doug, Thank you for your clarification. It sounds the right way for 
correction is:mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4
neg \ --cwp  0.05\ --2spaces

One last question: Is the resulting "cache.th40.neg.sig.cluster.summary"
the right file to look for post-correction cluster information? The (old) 
manual said
results should be stored in a files starting with "mc-z", but the
"cachesummary" file is the only summary file FS produces after
running the script above...

thank you.

Karl


In the first command you only used 5 samples in your simulation. If you 
read the "Notes" section below the command, you'll see that this should 
be something like 5000. Only 5 was used because it would take very long 
to run. In general, you don't need to run the simulation because it has 
already been run and the data tabulated (this is what is accessed in the 
2nd command line).On 03/02/2016 10:03 PM, Karl Liu wrote:
>
> Dear Freesurfer experts:
>
>
> I ran into a confusing problem when applying Monte Carlo simulation to 
> control for multiple comparisons. I am using the buckner data from 
> tutorial dataset.
>
>
> I first tried the simulation based on Freesurfer;s 2012 manual:
>
> (http://www.freesurfer.net/pub/docs/tarballs_for_courses/FreeSurferTutorial-2012.pdf)
>
>
> mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 
> mc-z.negative \ --sim-sign neg --cwpvalthresh 0.05\ --overwrite
>
>
> This produced a "mc-z.negative.sig.cluster.summary". In this text, no 
> clusters survived correction.
>
>
> Later on, I applied on a slightly different script, based on 
> Freesurfer tutorial
>
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ClusterwiseCorrectionforMultipleComparisons)
>
>
> mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ 
> --cwp  0.05\ --2spaces
>
>
>  It produced a "cache.th40.neg.sig.cluster.summary" this time. But 
> according to this result, 22 clusters survived.
>
>
> Now I am quite confused, because both corrections have the same 
> voxel-wise (p=0.001) and cluster-wise (p=0.05) threshold. Where the 
> drastic discrepancies come from and which result is more reliable?
>
>
>  Many thinks in advance.
>
> Best,
>
> Karl
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] AAL atlas question

[pfotiad]

Hi Doug,

Thanks for your response!

Panos

> I would recon the mni152 (or whatever space the AAL atlas is in), map
> the AAL ROIs onto the surface (vol2surf), then use mri_surf2surf to
> transfer them to the individual.
>
> On 02/29/2016 06:37 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi FS community,
>>
>> I have recon-ed a set of subjects and I was interested in also obtaining
>> structural info (cortical thickness, gray matter volume, surface area
>> etc.) based on a different atlas than the ones FS is using, and in
>> particular the AAL atlas.
>>
>> I was wondering whether my approach would be the correct one or whether
>> there is another (better and more accurate) approach:
>>
>> 1) Convert the AAL atlas into a surface (with mri_vol2surf) from the MNI
>> space into the native subjects' space,
>> 2) Use mris_anatomical_stats to calculate the structural stats
>>
>> Sorry for the potentially trivial question, and thank you for your time!
>>
>> Best,
>> Panos
>>
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
> --
> 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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>
>
>

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[Freesurfer] OpenMP and GPU implementation in freesurfer 6 beta

[Francis Tyson Thomas]

Hi,

I have been working on speeding up the the hippocampal segmentation in
freesurfer 6 beta and I have been playing around with both -openmp and
-use-gpu flags. I noticed that freesurfer does seem to make use of all the
threads in freesurfer 6 irrespective of passing the -openmp flag or not. Is
that the right behaviour. I found this by analysing the cpu usage in both
the cases.

Also, it looks like development for GPU usage has been halted for now and
so I was trying to use the CUDA 5 for getting it working under ubuntu
14.04. I have been not successful that as the cuda device isn't getting
selected. Do you have any recommendations on that?

And lastly, there is the itkthreads option available to
-hippocampal-subfields-T1, so can I combine all three or two of these
options to minimize the execution time - like GPU and itkthreads or GPU,
OPENMP and itkthreads?

Also the v6 beta is no longer available on your website. Is there any
particular reason as to why it was removed and can I continue using the
copy that I have for hippocampal segmentation ?

Thanks,
Tyson
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Re: [Freesurfer] Qdec-statistical map

[Douglas N Greve]

yes

On 03/03/2016 01:06 PM, John Anderson wrote:
> This si Great!!! Thanks Doug. One more question:
> What is the correct input in the command mri_surfcluster. Is it the 
> image "sig.mgh" ?
>
> Bests,
> John
> *Sent:* Thursday, March 03, 2016 at 12:47 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec-statistical map
> You will have to extract clusters (mri_surfcluster) to create an
> annotation, then use mri_segstats with the --annot option and specifying
> the y.mgh file as input and the output using something like --avgwf
> output.txt (also add --exludeid 0). The output will have a row for each
> frame in y.mgh (ie, each subject) and a column for each cluster
>
> On 03/03/2016 12:43 PM, John Anderson wrote:
> > Hi Doug,
> > How can I use this statistical map ( e.g. as a mask) to calculate the
> > mean cortical thickness only in the areas of significant differnce
> > between the groups for every subject?
> > Bests,
> > John
> > *Sent:* Thursday, March 03, 2016 at 12:37 PM
> > *From:* "Douglas N Greve" 
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] Qdec-statistical map
> > not sure what you mean. the statistical map will have a single value,
> > not a value for each subject
> >
> > On 03/03/2016 12:31 PM, John Anderson wrote:
> > > Dear FS experts,
> > > I am using Qdec to study the differnce in cortical thicnkess between
> > > two groups.
> > > Qdec is running a GLM analysis. This will output a statistical map
> > > (sig.mgh) for the differnce between the groups in cortical thicnkess.
> > > How can I extract the numbers of cortical thickness for every
> > > subject (depending on the order of subjects in Qdec table) from this
> > > statistical map ?
> > > Bests,
> > > John
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
> > 
> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > 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.
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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] Qdec-statistical map

[John Anderson]

This si Great!!! Thanks Doug. One more question:

What is the correct input in the command mri_surfcluster. Is it the image "sig.mgh" ?

 


 

Bests,
John 


 

Sent: Thursday, March 03, 2016 at 12:47 PM
From: "Douglas N Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec-statistical map

You will have to extract clusters (mri_surfcluster) to create an
annotation, then use mri_segstats with the --annot option and specifying
the y.mgh file as input and the output using something like --avgwf
output.txt (also add --exludeid 0). The output will have a row for each
frame in y.mgh (ie, each subject) and a column for each cluster

On 03/03/2016 12:43 PM, John Anderson wrote:
> Hi Doug,
> How can I use this statistical map ( e.g. as a mask) to calculate the
> mean cortical thickness only in the areas of significant differnce
> between the groups for every subject?
> Bests,
> John
> *Sent:* Thursday, March 03, 2016 at 12:37 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec-statistical map
> not sure what you mean. the statistical map will have a single value,
> not a value for each subject
>
> On 03/03/2016 12:31 PM, John Anderson wrote:
> > Dear FS experts,
> > I am using Qdec to study the differnce in cortical thicnkess between
> > two groups.
> > Qdec is running a GLM analysis. This will output a statistical map
> > (sig.mgh) for the differnce between the groups in cortical thicnkess.
> > How can I extract the numbers of cortical thickness for every
> > subject (depending on the order of subjects in Qdec table) from this
> > statistical map ?
> > Bests,
> > John
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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.
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
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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] "wm" boundaries and stats

[Krieger, Donald N.]

Thanks very much, Doug.
I could always hope.

> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Thursday, March 03, 2016 12:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] "wm" boundaries and stats
> 
> Hi Don, there is not an easy way to get this information. You can use
> mri_binarize to create a surface of each ROI, something like
> 
> mri_binarize --i wmparc.mgz --match 3013 --surf lh.wm.lingual
> 
> Use this version of mri_binarize
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
> 
> but doing the other things you want is a real programming job
> 
> doug
> 
> 
> On 03/01/2016 09:29 AM, Krieger, Donald N. wrote:
> >
> > Freesurfer provides 34 ctx label volumes on each side of the brain
> > with adjacent wm labels.
> >
> > The boundary between each ctx volume and the co-named adjacent wm
> > volume is a third "white" label.
> >
> > I would like to extract a few pieces of information from the analogous
> > boundary between each wm volume and those adjacent volumes to it which
> > are not the co-named ctx volume.
> >
> > For instance many wm volumes share a boundary with the unsegmented
> > white matter.
> >
> > Some share a boundary with sub-cortical structures.
> >
> > Here are some of the information I would like to extract.
> >
> > What do you think?
> >
> > What are the xyz coordinates of the complete boundary surrounding each
> > wm volume and what is the name of the adjacent volume for each point
> > on the boundary?
> >
> > I understand that for the boundary between the ctx volume and the
> > adjacent wm volume, the white label provides this information.
> >
> > What is the percentage and area of the complete boundary surrounding a
> > wm volume which is adjacent to the co-named ctx volume.?
> >
> > What are the names of the other volumes with which each wm volume
> > shares a boundary and what is the percentage and area of the boundary
> > shared with each?
> >
> > For each point within a wm volume, are the nearest points on the wm
> > boundary adjacent to the co-named ctx volume or are some adjacent to
> > unsegmented white matter or sub-cortical structures?
> >
> > More generally, is a particular few mm voxel surrounded by gray matter
> > and so is likely primarily composed primarily of relatively short
> > range fibers or is it adjacent to the deep white matter (unsegmented)
> > and likely composed of a mix of relatively short range fibers and long
> > range "en passage" fibers.
> >
> > It is this last question which most closely gets at the ideas I wish
> > to explore.
> >
> > We are able to measure electric current in the white matter with mm
> > resolution from the MEG.
> >
> > The mix of local and "en passage" fibers should effect the direction
> > of the electric currents in the white matter and I can measure that.
> >
> > The distance scale is at the edge of that provided by DTI-derived
> > tractography so we may be able to meld these measurements with those.
> >
> > Your thoughts would be welcome on what is already there in freesurfer
> > that will help with this and what you think might be a good direction
> > to proceed to develop what we need from what is there.
> >
> > Thanks - Don
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> --
> 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
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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
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Re: [Freesurfer] v5.3 fsaverage (accidentally) in v5.1 directory

[Douglas N Greve]

If it affects anything, it would only affect the BA labels. If the BA 
labels did not change between 5.1 and 5.3, I don't think it would affect 
anything.


On 03/03/2016 12:41 PM, Adam Martersteck wrote:
> Hi Freesurfer team,
>
> *Short question: *Will (accidentally) using the fsaverage v5.3 subject 
> in our v5.1 directory influence our reconstructions?

>
> *Long question:* Our server has 2 different freesurfer environments. A 
> recon was accidentally run on a single v5.1 subject in the v5.1 
> directory with freesurfer version 5.3. During the “balabels” stage of 
> autorecon3, because FS 5.3 couldn’t find the perirhinal label – it 
> deleted our 5.1 symlink and replaced it with the correct 5.3 symlink. 
> We realized it had happened and correct the subject, but didn’t catch 
> that the symlink had been changed.
>
> We have run multiple (hundreds) of brains through v5.1 since then – 
> with the v5.3 fsaverage in the v5.1 directory.
>
> A cursory glance over the release notes from 5.1 to 5.3 makes me think 
> nothing has fundamentally changed – only new files have been added to 
> fsaverage 5.3 (e.g. cortical parcellation networks). No new GCA atlas 
> or anything that would change how FS 5.1 reconstructs the brain?
>
> Thanks for any thoughts!
> Adam
>
>
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-- 
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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] Qdec-statistical map

[Douglas N Greve]

You will have to extract clusters (mri_surfcluster) to create an 
annotation, then use mri_segstats with the --annot option and specifying 
the y.mgh file as input and the output using something like --avgwf 
output.txt (also add --exludeid 0). The output will have a row for each 
frame in y.mgh (ie, each subject) and a column for each cluster

On 03/03/2016 12:43 PM, John Anderson wrote:
> Hi Doug,
> How can I use this statistical map ( e.g. as a mask) to calculate the 
> mean cortical thickness only in the areas of significant differnce 
> between the groups for every subject?
> Bests,
> John
> *Sent:* Thursday, March 03, 2016 at 12:37 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec-statistical map
> not sure what you mean. the statistical map will have a single value,
> not a value for each subject
>
> On 03/03/2016 12:31 PM, John Anderson wrote:
> > Dear FS experts,
> > I am using Qdec to study the differnce in cortical thicnkess between
> > two groups.
> > Qdec is running a GLM analysis. This will output a statistical map
> > (sig.mgh) for the differnce between the groups in cortical thicnkess.
> > How can I extract the numbers of cortical thickness for every
> > subject (depending on the order of subjects in Qdec table) from this
> > statistical map ?
> > Bests,
> > John
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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Re: [Freesurfer] "wm" boundaries and stats

[Douglas N Greve]

Hi Don, there is not an easy way to get this information. You can use 
mri_binarize to create a surface of each ROI, something like

mri_binarize --i wmparc.mgz --match 3013 --surf lh.wm.lingual

Use this version of mri_binarize
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize

but doing the other things you want is a real programming job

doug


On 03/01/2016 09:29 AM, Krieger, Donald N. wrote:
>
> Freesurfer provides 34 ctx label volumes on each side of the brain 
> with adjacent wm labels.
>
> The boundary between each ctx volume and the co-named adjacent wm 
> volume is a third “white” label.
>
> I would like to extract a few pieces of information from the analogous 
> boundary between each wm volume and those adjacent volumes to it which 
> are not the co-named ctx volume.
>
> For instance many wm volumes share a boundary with the unsegmented 
> white matter.
>
> Some share a boundary with sub-cortical structures.
>
> Here are some of the information I would like to extract.
>
> What do you think?
>
> What are the xyz coordinates of the complete boundary surrounding each 
> wm volume and what is the name of the adjacent volume for each point 
> on the boundary?
>
> I understand that for the boundary between the ctx volume and the 
> adjacent wm volume, the white label provides this information.
>
> What is the percentage and area of the complete boundary surrounding a 
> wm volume which is adjacent to the co-named ctx volume.?
>
> What are the names of the other volumes with which each wm volume 
> shares a boundary and what is the percentage and area of the boundary 
> shared with each?
>
> For each point within a wm volume, are the nearest points on the wm 
> boundary adjacent to the co-named ctx volume or are some adjacent to 
> unsegmented white matter or sub-cortical structures?
>
> More generally, is a particular few mm voxel surrounded by gray matter 
> and so is likely primarily composed primarily of relatively short 
> range fibers or is it adjacent to the deep white matter (unsegmented) 
> and likely composed of a mix of relatively short range fibers and long 
> range “en passage” fibers.
>
> It is this last question which most closely gets at the ideas I wish 
> to explore.
>
> We are able to measure electric current in the white matter with mm 
> resolution from the MEG.
>
> The mix of local and “en passage” fibers should effect the direction 
> of the electric currents in the white matter and I can measure that.
>
> The distance scale is at the edge of that provided by DTI-derived 
> tractography so we may be able to meld these measurements with those.
>
> Your thoughts would be welcome on what is already there in freesurfer 
> that will help with this and what you think might be a good direction 
> to proceed to develop what we need from what is there.
>
> Thanks – Don
>
>
>
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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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Re: [Freesurfer] Qdec-statistical map

[John Anderson]

Hi Doug,

How can I use this statistical map ( e.g. as a mask) to calculate the mean cortical thickness only in the areas of significant differnce between the groups for every subject?

 

Bests,
John 


 

Sent: Thursday, March 03, 2016 at 12:37 PM
From: "Douglas N Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec-statistical map

not sure what you mean. the statistical map will have a single value,
not a value for each subject

On 03/03/2016 12:31 PM, John Anderson wrote:
> Dear FS experts,
> I am using Qdec to study the differnce in cortical thicnkess between
> two groups.
> Qdec is running a GLM analysis. This will output a statistical map
> (sig.mgh) for the differnce between the groups in cortical thicnkess.
> How can I extract the numbers of cortical thickness for every
> subject (depending on the order of subjects in Qdec table) from this
> statistical map ?
> Bests,
> John
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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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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[Freesurfer] v5.3 fsaverage (accidentally) in v5.1 directory

[Adam Martersteck]

 Hi Freesurfer team,

*Short question: *Will (accidentally) using the fsaverage v5.3 subject in
our v5.1 directory influence our reconstructions?

*Long question:* Our server has 2 different freesurfer environments. A
recon was accidentally run on a single v5.1 subject in the v5.1 directory
with freesurfer version 5.3. During the “balabels” stage of autorecon3,
because FS 5.3 couldn’t find the perirhinal label – it deleted our 5.1
symlink and replaced it with the correct 5.3 symlink. We realized it had
happened and correct the subject, but didn’t catch that the symlink had
been changed.

We have run multiple (hundreds) of brains through v5.1 since then – with
the v5.3 fsaverage in the v5.1 directory.

A cursory glance over the release notes from 5.1 to 5.3 makes me think
nothing has fundamentally changed – only new files have been added to
fsaverage 5.3 (e.g. cortical parcellation networks). No new GCA atlas or
anything that would change how FS 5.1 reconstructs the brain?

Thanks for any thoughts!
Adam
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Re: [Freesurfer] error in mc-sess

[Douglas N Greve]

what is your command line? You have to use -per-run and not -per-session

On 03/03/2016 12:22 PM, Ji Won Bang wrote:
> Dear. freesurfer experts.
>
> Hi. I'm using freesurfer version 5.3.0.
>
> I tried mc-sess onto runs that have different number of slices.
>
> However, due to this different number of slices in different runs, 
> mc-sess gives an error.
>
> I expected that running mc-sess in freesurfer version 5.3.0 would 
> handle this issue.
>
> If you can share your idea to fix this problem, that would be a great 
> help.
>
> Thank you!
>
> Best,
> Ji Won
>
>
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Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Douglas N Greve]

All the values are between 0 and 1, so I suspect this is a map of 
p-values, not a map of -log10(p). Is that right? If so, convert it to 
-log10(p) and rerun. You can do this in matlab with
p = MRIread('rh_time.mgh');
sig = p;
sig.vol = -log10(abs(p.vol));
MRIwrite(sig,'sig.mgh');



On 03/03/2016 12:34 PM, Jennifer Legault wrote:
> Absolutely,  here it is attached.  Thank you for looking into this.
>
> Best,
>
> Jen
>
> On Thu, Mar 3, 2016 at 12:24 PM, Douglas N Greve 
> > wrote:
>
> Can you send me rh_time_spval.mgh?
>
>
>
> On 03/01/2016 04:42 PM, Jennifer Legault wrote:
> > Hi Doug,
> >
> > Thank you for responding.  I actually realized what was the
> matter (I
> > had specified the path for fsaverage which led to the error; this is
> > no longer an issue so long as I use "--subject fsaverage" instead of
> > "--subject /path/fsaverage."
> >
> > Here is the command I've been running for mri_surfcluster:
> >
> > mri_surfcluster --subject fsaverage --hemi rh --in
> > /path/rh_time_spval.mgh --csd
> >
> 
> /usr/global/freesurfer/5.3.0/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm01/pos/th40/mc-z.csd
> > --cwpvalthresh 0.0001 --fdr .05 --no-fixmni --annot aparc --sign pos
> > --o /path/rh_time_cluster_cwp0001.mgh  --cwsig
> > /path/rh_time_cluster_mni_cwp0001.mgh --sum
> > /path/rh_time_cluster_mni_sum
> >
> >
> > I do consistently have an issue though where the final output
> seems to
> > be inaccurate (even with CWP of p<.0001 and FDR correction, I
> receive
> > over 800 significant clusters).  I am assuming this is a problem
> with
> > the LME multivariate analysis script, although I am not exactly sure
> > which part of the script needs to be changed. Attached is a
> > screenshot of the output (visualized with freeview), as well as the
> > matlab script and the qdec file (with fsid, fsid-base, MRI (time),
> > group, and eTIV as columns).  This script is geared towards
> examining
> > changes in the brain after cognitive training lasting 2-3 weeks.  If
> > you have the time to look over this and let me know of any
> > recommendations you have, it would be greatly appreciated.
> >
> > Best,
> >
> > Jennifer Legault
> >
> > On Tue, Mar 1, 2016 at 3:27 PM, Douglas N Greve
> > >
> wrote:
> >> can you send your command line and terminal output?
> >>
> >> On 02/25/2016 01:52 PM, Jennifer Legault wrote:
> >>> Hi Douglas,
> >>>
> >>> Thank you for all your help.  When I say "volume" I do mean the FS
> >>> thickness*area measure.  I ran the mri_glmfit with --osgm and
> for the
> >>> FWHM received the value of .925737. Assuming that this rounds
> up to 1,
> >>> I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to
> >>> find the CSD file and I selected the fwhm01 csd file.
> >>>
> >>> I then ran the mri_surfcluster command, however, I got the
> following
> >>> error:
> >>>
> >>> ERROR: you have specified srcsubjid=fsaverage on cmdline, but
> >>> CSD file was created with fsaverage
> >>>
> >>> Any suggestions you have would be appreciated.
> >>>
> >>> Best,
> >>>
> >>> Jen
> >>>
> >>> On Thu, Feb 11, 2016 at 1:32 PM, Douglas N Greve
> >>> 
>  >> wrote:
> >>>
> >>>  by "volume" do you mean a VBM-type analysis or do you
> mean the volume
> >>>  that comes out of FS (thickness*area)? If you are going
> to use a
> >>>  clusterwise correction, then you have to have a FWHM
> measurement. You
> >>>  can try analyzing it in mri_glmfit with --osgm just to
> get the
> >>>  FWHM out
> >>>  of it.
> >>>
> >>>  You should be able to output a .mgh file instead of a .w file
> >>>
> >>>
> >>>  On 02/11/2016 01:07 PM, Jennifer Legault wrote:
> >>>  > That's very useful, thank you. In terms of FWHM, I am
> examining
> >>>  gray
> >>>  > matter volume, not cortical thickness, and was
> previously instructed
> >>>  > by Martin Reuter not to smooth these data.  Do you think it
> >>>  would make
> >>>  > sense then to just use the fwhm01?  And in terms of the
> voxel-wise
> >>>  > threshold, is there a commonly used value for GM volume
> data?  I am
> >>>  > still new to freesurfer and I appreciate any feedback.
> >>>  >
> >>>  > For visualization, after I run the mri_surfcluster the
> only outputs
> >>>  > are a summary file and a .w file, and freeview doesn't
> 

Re: [Freesurfer] Qdec-statistical map

[Douglas N Greve]

not sure what you mean. the statistical map will have a single value, 
not a value for each subject

On 03/03/2016 12:31 PM, John Anderson wrote:
> Dear FS experts,
> I am using Qdec to study the differnce in cortical thicnkess between 
> two groups.
> Qdec is running a GLM analysis. This will output a statistical map 
> (sig.mgh) for the differnce between the groups in cortical thicnkess.
> How can I extract the numbers of cortical thickness for every 
> subject (depending on the order of subjects in Qdec table) from this 
> statistical map ?
> Bests,
> John
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] error in mc-sess

[Douglas N Greve]

you have to use -per-run not -per-session


On 03/03/2016 12:27 PM, Ji Won Bang wrote:
> The command I used is:
>
> mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
>
> mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-session
>
> Thank you.
>
> Best,
> Ji Won
>
>
>
> 2016-03-03 12:22 GMT-05:00 Ji Won Bang  >:
>
> Dear. freesurfer experts.
>
> Hi. I'm using freesurfer version 5.3.0.
>
> I tried mc-sess onto runs that have different number of slices.
>
> However, due to this different number of slices in different runs,
> mc-sess gives an error.
>
> I expected that running mc-sess in freesurfer version 5.3.0 would
> handle this issue.
>
> If you can share your idea to fix this problem, that would be a
> great help.
>
> Thank you!
>
> Best,
> Ji Won
>
>
>
>
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Re: [Freesurfer] conflicting Monte Carlo simulation results...

[Douglas N Greve]

In the first command you only used 5 samples in your simulation. If you 
read the "Notes" section below the command, you'll see that this should 
be something like 5000. Only 5 was used because it would take very long 
to run. In general, you don't need to run the simulation because it has 
already been run and the data tabulated (this is what is accessed in the 
2nd command line).

On 03/02/2016 10:03 PM, Karl Liu wrote:
>
> Dear Freesurfer experts:
>
>
> I ran into a confusing problem when applying Monte Carlo simulation to 
> control for multiple comparisons. I am using the buckner data from 
> tutorial dataset.
>
>
> I first tried the simulation based on Freesurfer;s 2012 manual:
>
> (http://www.freesurfer.net/pub/docs/tarballs_for_courses/FreeSurferTutorial-2012.pdf)
>
>
> mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 
> mc-z.negative \ --sim-sign neg --cwpvalthresh 0.05\ --overwrite
>
>
> This produced a "mc-z.negative.sig.cluster.summary". In this text, no 
> clusters survived correction.
>
>
> Later on, I applied on a slightly different script, based on 
> Freesurfer tutorial
>
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ClusterwiseCorrectionforMultipleComparisons)
>
>
> mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ 
> --cwp  0.05\ --2spaces
>
>
>  It produced a "cache.th40.neg.sig.cluster.summary" this time. But 
> according to this result, 22 clusters survived.
>
>
> Now I am quite confused, because both corrections have the same 
> voxel-wise (p=0.001) and cluster-wise (p=0.05) threshold. Where the 
> drastic discrepancies come from and which result is more reliable?
>
>
>  Many thinks in advance.
>
> Best,
>
> Karl
>
>
>
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[Freesurfer] Qdec-statistical map

[John Anderson]

Dear FS experts,

I am using Qdec to study the differnce in cortical thicnkess between two groups.

Qdec is running a GLM analysis. This will output a statistical map (sig.mgh) for the differnce between the groups in cortical thicnkess.

How can I extract the numbers of cortical thickness for every subject (depending on the order of subjects in Qdec table) from this statistical map ?
 

Bests,
John 
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Re: [Freesurfer] Problem with mriconvert

[Douglas N Greve]

Do you have write permission to that folder? Is the disk full?

On 03/02/2016 11:12 AM, Óscar Soto Angona wrote:
> Hello,
>
> We are medicine students who are using freesurfer for research. We had 
> been using freesurfer in Ubuntu 12.02 without encountering any 
> trouble; recently we updated to 14.04.
>
> Now, when we attempt to convert a mgz file to nii using mriconvert, we 
> have an error regarding failure to write the files .nii
>
> The command we are using is as follows:
>
> mri_convert 
> ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_cortical_seg.mgz
>  
> ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090_cortical_seg.nii
>
>
> The error message we find is this one:
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from 
> /home/psa/datos_MRI_cerebral/estructural/Freesurfer_seg_cortical_resultado/C2090_cortical_seg.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, -4.74975e-08, 0)
> j_ras = (0, 0, -1)
> k_ras = (1.21072e-08, 1, 0)
> writing to 
> ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii...
> niiWrite(): error opening file 
> ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii
> ERROR: failure writing 
> ../estructural/Freesurfer_segmentacion_cortical_resultado/C2090.nii
>
>
> We really could use your help, since we can't find any solution in the 
> Internet. Thanks in advance for your attention.
>
>
> Regards,
>
>
> Óscar and Alba
>
>
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Re: [Freesurfer] error in mc-sess

[Ji Won Bang]

The command I used is:

mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_retino

mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-session

Thank you.

Best,
Ji Won



2016-03-03 12:22 GMT-05:00 Ji Won Bang :

> Dear. freesurfer experts.
>
> Hi. I'm using freesurfer version 5.3.0.
>
> I tried mc-sess onto runs that have different number of slices.
>
> However, due to this different number of slices in different runs, mc-sess
> gives an error.
>
> I expected that running mc-sess in freesurfer version 5.3.0 would handle
> this issue.
>
> If you can share your idea to fix this problem, that would be a great help.
>
> Thank you!
>
> Best,
> Ji Won
>
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Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Douglas N Greve]

Can you send me rh_time_spval.mgh?



On 03/01/2016 04:42 PM, Jennifer Legault wrote:
> Hi Doug,
>
> Thank you for responding.  I actually realized what was the matter (I
> had specified the path for fsaverage which led to the error; this is
> no longer an issue so long as I use "--subject fsaverage" instead of
> "--subject /path/fsaverage."
>
> Here is the command I've been running for mri_surfcluster:
>
> mri_surfcluster --subject fsaverage --hemi rh --in
> /path/rh_time_spval.mgh --csd
> /usr/global/freesurfer/5.3.0/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm01/pos/th40/mc-z.csd
> --cwpvalthresh 0.0001 --fdr .05 --no-fixmni --annot aparc --sign pos
> --o /path/rh_time_cluster_cwp0001.mgh  --cwsig
> /path/rh_time_cluster_mni_cwp0001.mgh --sum
> /path/rh_time_cluster_mni_sum
>
>
> I do consistently have an issue though where the final output seems to
> be inaccurate (even with CWP of p<.0001 and FDR correction, I receive
> over 800 significant clusters).  I am assuming this is a problem with
> the LME multivariate analysis script, although I am not exactly sure
> which part of the script needs to be changed.  Attached is a
> screenshot of the output (visualized with freeview), as well as the
> matlab script and the qdec file (with fsid, fsid-base, MRI (time),
> group, and eTIV as columns).  This script is geared towards examining
> changes in the brain after cognitive training lasting 2-3 weeks.  If
> you have the time to look over this and let me know of any
> recommendations you have, it would be greatly appreciated.
>
> Best,
>
> Jennifer Legault
>
> On Tue, Mar 1, 2016 at 3:27 PM, Douglas N Greve
>  wrote:
>> can you send your command line and terminal output?
>>
>> On 02/25/2016 01:52 PM, Jennifer Legault wrote:
>>> Hi Douglas,
>>>
>>> Thank you for all your help.  When I say "volume" I do mean the FS
>>> thickness*area measure.  I ran the mri_glmfit with --osgm and for the
>>> FWHM received the value of .925737. Assuming that this rounds up to 1,
>>> I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to
>>> find the CSD file and I selected the fwhm01 csd file.
>>>
>>> I then ran the mri_surfcluster command, however, I got the following
>>> error:
>>>
>>> ERROR: you have specified srcsubjid=fsaverage on cmdline, but
>>> CSD file was created with fsaverage
>>>
>>> Any suggestions you have would be appreciated.
>>>
>>> Best,
>>>
>>> Jen
>>>
>>> On Thu, Feb 11, 2016 at 1:32 PM, Douglas N Greve
>>> > wrote:
>>>
>>>  by "volume" do you mean a VBM-type analysis or do you mean the volume
>>>  that comes out of FS (thickness*area)? If you are going to use a
>>>  clusterwise correction, then you have to have a FWHM measurement. You
>>>  can try analyzing it in mri_glmfit with --osgm just to get the
>>>  FWHM out
>>>  of it.
>>>
>>>  You should be able to output a .mgh file instead of a .w file
>>>
>>>
>>>  On 02/11/2016 01:07 PM, Jennifer Legault wrote:
>>>  > That's very useful, thank you.  In terms of FWHM, I am examining
>>>  gray
>>>  > matter volume, not cortical thickness, and was previously instructed
>>>  > by Martin Reuter not to smooth these data.  Do you think it
>>>  would make
>>>  > sense then to just use the fwhm01?  And in terms of the voxel-wise
>>>  > threshold, is there a commonly used value for GM volume data?  I am
>>>  > still new to freesurfer and I appreciate any feedback.
>>>  >
>>>  > For visualization, after I run the mri_surfcluster the only outputs
>>>  > are a summary file and a .w file, and freeview doesn't accept this
>>>  > format.  Is it possible to have a cluster-wise corrected map (a
>>>  > sig.cluster.mgh file) as they do for the Clusterwise Correction for
>>>  > Multiple Comparisons tutorial here
>>>  >
>>>  ?
>>>  >
>>>  >
>>>  > Best,
>>>  >
>>>  > Jen
>>>  >
>>>  > On Thu, Feb 11, 2016 at 11:39 AM, Douglas N Greve
>>>  > 
>>>  >>  >> wrote:
>>>  >
>>>  >
>>>  >
>>>  > On 02/11/2016 11:19 AM, Jennifer Legault wrote:
>>>  > > Thank you for your response.  Do I need to run the glm_fit-sim
>>>  > command
>>>  > > to make the csd file?  I feel this would be inappropriate
>>>  for my
>>>  > data
>>>  > > since I already ran the LME model.
>>>  > No, look in
>>>  $FREESURFER_HOME/average/mult-comp-cor/fsaverage. You will
>>>  > need the FWHM though
>>>  > >
>>>  > > Second, is there an argument to make an output file that
>>>  can be
>>>  > > visualized via freeview?  In other words, how can I view
>>>  my cluster
>>>

[Freesurfer] error in mc-sess

[Ji Won Bang]

Dear. freesurfer experts.

Hi. I'm using freesurfer version 5.3.0.

I tried mc-sess onto runs that have different number of slices.

However, due to this different number of slices in different runs, mc-sess
gives an error.

I expected that running mc-sess in freesurfer version 5.3.0 would handle
this issue.

If you can share your idea to fix this problem, that would be a great help.

Thank you!

Best,
Ji Won
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Re: [Freesurfer] How to find the difference between to different fMRI datasets?

[Douglas N Greve]

Create a contrast between the two conditions

On 03/01/2016 01:27 AM, Silas wrote:
>
> Dear FreeSurfer team,
>
>
> Thank you for all your help so far!
>
>
> I would like to visualize the difference between two fMRI data sets.
>
> Data set1: Cortical activation during movement of a finger.
>
> Data set2: Cortical activation during movement of a finger different 
> from the first finger.
>
>
> How can i perform this operation?
>
>
> Best, Silas
>
>
>
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Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)

[Douglas N Greve]

I cannot replicate the error. What version of FS are you using? What 
happens if you run
  mri_glmfit --fsgd RPA-acc.fsgd
or
mri_glmfit --fsgd RPA-accGT.fsgd



On 02/29/2016 09:38 PM, Joseph Dien wrote:
> Hi,
> I’m having an fsgd error that has totally stumped me.  I’m trying to run 
> the following command to compute the second level statistics:
>
> mri_glmfit --surf fsaverage lh --y ces.nii.gz --wls cesvar.nii.gz  --nii.gz 
> --fsgd RPA-accGT.fsgd --glmdir conVinc_normAcc.wls --C main.mtx --C 
> normAcc.mtx
>
> I get the error message:
>
> Reading source surface /Volumes/Data2/RP1/freesurfer/fsaverage/surf/lh.white
> gdfReadHeader: reading RPA-accGT.fsgd
> FSGDF Format Error: file = RPA-accGT.fsgd, tag=Title
>
> I used the utility flip to make sure the file was in UNIX format (with 
> linefeeds).
> I then double-checked by reading in the binary codes with Matlab’s fread and 
> directly checking the ASCII numbers, which are indeed ASCII 10 (linefeed).
>
> Here is the contents of the fsgd file.
>
> GroupDescriptorFile 1
> Title RP1
> Class Main
> Variables LogoAcc NormAcc OrthAcc PhonAcc
> Input RPA903  Main0.750.790.770.62
> Input RPA906  Main0.810.810.830.74
> Input RPA907  Main0.871   0.840.83
> Input RPA908  Main0.910.930.950.89
> Input RPA909  Main0.740.950.720.72
> Input RPA910  Main0.850.960.810.79
> Input RPA912  Main0.750.780.730.73
> Input RPA914  Main0.7 0.850.830.81
> Input RPA915  Main0.850.890.750.83
> Input RPA916  Main0.840.920.870.72
> Input RPA917  Main0.830.930.920.83
> Input RPA918  Main0.870.910.790.85
> Input RPA919  Main0.860.960.910.88
> Input RPA920  Main0.840.920.870.84
> Input RPA921  Main0.870.920.880.85
> Input RPA922  Main0.8 0.9 0.9 0.72
>
> What’s really driving me to distraction is that a previous version of this 
> file (with a different set of participants) works fine.  I’m attaching both.  
> RPA-accGT.fsgd does not work and RPA-acc.fsgd does work.  Using Matlab’s 
> fread, the first 85 characters (first four lines) of both files are identical.
>
> I’m running on OS X 10.11.3.  I’m using FSFAST 5.20.  Matlab 2015b.
>
> Any help would be greatly appreciated!
>
> Joe
>
>
>
> 
>
> Joseph Dien, PhD
> Senior Research Scientist
> Maryland Neuroimaging Center
> University of Maryland, College Park
> E-mail: jdie...@mac.com
> Cell Phone: 202-297-8117
> http://joedien.com
>
>
>
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Re: [Freesurfer] AAL atlas question

[Douglas N Greve]

I would recon the mni152 (or whatever space the AAL atlas is in), map 
the AAL ROIs onto the surface (vol2surf), then use mri_surf2surf to 
transfer them to the individual.

On 02/29/2016 06:37 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS community,
>
> I have recon-ed a set of subjects and I was interested in also obtaining
> structural info (cortical thickness, gray matter volume, surface area
> etc.) based on a different atlas than the ones FS is using, and in
> particular the AAL atlas.
>
> I was wondering whether my approach would be the correct one or whether
> there is another (better and more accurate) approach:
>
> 1) Convert the AAL atlas into a surface (with mri_vol2surf) from the MNI
> space into the native subjects' space,
> 2) Use mris_anatomical_stats to calculate the structural stats
>
> Sorry for the potentially trivial question, and thank you for your time!
>
> Best,
> Panos
>
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>

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Re: [Freesurfer] Extract LGI at MaxVertex and extract effect-sizes in table format

[Douglas N Greve]

On 02/29/2016 02:38 AM, Bittner, Nora wrote:
>
> Dear FreeSurfer Experts,
>
> Sorry for reposting this massage again, but I still have two 
> questions, which you can hopefully answer to:
>
> 1)
>
> I calculated several analyses with LGI as my dependent variable, 
> resulting in several significant clusters.
>
> Now, I would like to extract the individual LGI value at the *maximum 
> vertex* of each significant cluster to plot it against my experimental 
> variables (instead of working with the mean LGI values of the clusters).
>
> What I tried so far is to use mri_segstats to extract the LGI at the 
> maximum vertex:
>
> mri_segstats --i $SUBJECTS_DIR/qdec/glm/y.mgh --crs vertexno 84367 0 0 
> --avgwf vertexno84367.dat
>
> where y.mgh is my input file from the glm and vertexno 84367 is the 
> maximum vertex of the cluster as reported in the cluster.summary-file.
>
> I found the command in the FS helpline documentation 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42655.html), 
> but regrettably 
> 
>  
> I get the following error message:
> “ERROR: Option –-crs unkown”
> In the fswiki I also couldn´t find the “mri_segstats - - crs option” 
> in the user description.
> Is there any other option or argument I can use in mri_segstats (or in 
> any other command) to extract the LGI value per person at the given 
> vertex?
Remember, you can always run commands with --help to get more info. If 
you run this command with --help, you will see:
--vox C R S
 replace seg with all 0s except at CRS

So use --vox, not --crs.
>
> 2)
>
> I would like to calculate effect sizes of my results. Therefore I used 
> fscalc:
>
> fscalc $SUBJECTS_DIR/qdec/glm/contrast/gamma.mgh div 
> $SUBJECTS_DIR/qdec/glm/rstd.mgh -o $SUBJECTS_DIR/qdec/ 
> glm/contrast/effectsize.mgh
> This worked fine and resulted in a surface overlay displaying the 
> effect sizes. Now, I would like to extract these effect sizes in 
> 'table' format. I tried to use mri-segstats:
>
> mri_segstats* --i effectsize.mgh --annot fsaverage lh aparc --avgwf 
> effectsize.dat
>
> I am not sure, if this gives me the correct results. Is this the right 
> command?
>
> I would really appreciate 
> 
>  
> your help.
>
Yes, that will give you the effect size averaged over each annotation
>
> Thank you in advance,
>
> Nora
>
>
>
> 
> 
> Forschungszentrum Juelich GmbH
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> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> 
> 
>
>
>
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Re: [Freesurfer] Reading values from overlays with PETcoreg

[Douglas N Greve]

No, not yet, though I recently had a need to do the same thing. It is 
pretty easy to do though. If you run mri_gtmpvc with --save-input, it 
will create a file called input.rescaled.nii.gz. Then you can run
mri_segstats --i input.rescaled.nii.gz --seg aux/seg.nii.gz --ctab 
aux/seg.ctab --avgwfvol nopvc.nii.gz

nopvc.nii.gz will be the same size as gtm.nii.gz with the same order of 
ROIs. Not that the ROI used to rescale in the gtmpvc command (251 for 
you) will not have a value of 1.0 in the nopvc.nii.gz, so if you want to 
compare, then you'll need to rescale yourself.



On 02/24/2016 12:46 PM, Pradeep wrote:
> Hello Doug,
>
> I was wondering if there is a flag in the command  to obtain the SUVRs 
> for the same ROIs with out partial volume correction so that it would 
> be easier to compare.
>
> Thanks,
> Pradeep
>
> On Fri, Jan 29, 2016 at 1:30 PM, Pradeep  > wrote:
>
> It worked! Thank you!
> mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01 --seg
> gtmseg.mgz --reg output.lta --replace-file seg.replace251.list
> --rescale 251 --mgx 0.01 --o gtmpvcRcc.output
>
> On Fri, Jan 29, 2016 at 12:23 PM, Douglas N Greve
> > wrote:
>
> The problem is that --default-seg-merge merges the CC with WM,
> so you
> can't use that option, which means that you'll have to specify
> the rest
> of the default seg merge manually. You can do this with more
> --replace
> args or you can create a file. If you've been able to run
> mri_gtmpvc
> without the current replace, then it will create a replacement
> file in
> the aux folder. Get that, remove the 251 entry, and change the
> 252-255
> entries to point to 251
>
> On 01/29/2016 02:12 PM, Pradeep wrote:
> > Unfortunately, that did not fix the problem.
> >
> > Here is what I did
> > 1)gtmseg --s 128_S_0225_v06 --keep-cc # noerrors
> > 2)gtmseg --s 128_S_0225_v06 --keep-cc --no-xcerseg  # no errors
> >
> > 3)mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2
> 0.01 --seg
> > gtmseg.mgz --reg output.lta --default-seg-merge --replace
> 252 251
> > --replace 253 251 --replace 254 251 --replace 255 251 --mgx
> 0.01 --o
> > gtmpvcrcc.output
> > Loading input t12pet.nii.gz
> >   done loading input 1 frames
> > ERROR: item 251 appears as both source and target seg id in
> > replacement list
> >
> > $Id: mri_gtmpvc.c,v 1.52.2.5 2015/08/28 19:00:13 greve Exp $
> > setenv SUBJECTS_DIR /analysis/software_test/fs6pvc
> > cd /analysis/software_test/fs6pvc/128_S_0225_v06/mri
> > mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask PSF+2 0.01
> --seg
> > gtmseg.mgz --reg output.lta --default-seg-merge --replace
> 252 251
> > --replace 253 251 --replace 254 251 --replace 255 251 --mgx
> 0.01 --o
> > gtmpvcrcc.output
> > sysname  Linux
> > hostname
> > machine  x86_64
> > user
> > vgthresh   0.001000
> > nReplace   22
> > 0. 0. 0. 0. 0. 0.
> > 9 avail.processors, using 9
> > Creating output directory gtmpvcrcc.output
> > Loading seg for gtm gtmseg.mgz
> > Loading seg ctab gtmseg.ctab
> > Reading gtmseg.lta
> > Replacing 22
> > ERROR: CheckSegTissueType() no entry for seg 192
> > Failed tissue type check
> >
> > Thank you for looking into this,
> > Pradeep
> >
> >
> > On Fri, Jan 29, 2016 at 10:13 AM, Douglas N Greve
> >  
>  >> wrote:
> >
> > I think I see the problem. When you run gtmseg, you need
> to add
> > --keep-cc. You can rerun it using the previous command
> line, but add
> > --keep-cc and --no-xcerseg. The second option tells it
> not to redo the
> > extracerebral segmentation (which won't change with CC)
> >
> > On 01/29/2016 11:21 AM, Pradeep wrote:
> > > Thank you for the response.
> > >
> > > Here is my full command log with error
> > >
> > >
> > > $gtmseg --s 128_S_0225_v06 --keep-hypo --keep-cc
> > >
> > > $ mri_gtmpvc --i t12pet.nii.gz --psf 4 --auto-mask
> PSF+2 0.01 --seg
> > > gtmseg.mgz --reg output.lta --default-seg-merge --mgx
> 0.01 --o
> > > gtmpvccc.output
> > > Loading input t12pet.nii.gz
> >  

Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

[Douglas N Greve]

Sorry, I'm still having a problem following what you are trying to do. 
You have a 3x3 functional design (3 levels of reward, 3 levels of risk), 
and you want to look for an interaction between reward and risk?


On 02/24/2016 12:10 PM, Afzal, Afsana wrote:
> Hi Doug,
>
> Upon reviewing the repeated measures ANOVA tutorial on the Freesurfer 
> website I was able to revise the fsgd file (below) to what I now think 
> is more accurate.
>
> I'm treating each observation of a condition (risk-reward pairing) and 
> indicating that each of those observations belong to the same subject 
> (Subject1, Subject2, etc).
>
> GroupDescriptorFile 1
> Class Subject1
> Class Subject2
> VariableshRisk-vs-lRisk hRisk-vs-mRisk
> Input Subject1-lRsk_lRwd Subject1 -1  0
> Input Subject1-lRsk_mRwd Subject1 -1 0
> Input Subject1-lRsk_hRwd Subject1 -10
> Input Subject1-mRsk_lRwd Subject1 0-1
> Input Subject1-mRsk_mRwd Subject1 0-1
> Input Subject1-mRsk_hRwd Subject1 0-1
> Input Subject1-hRsk_lRwd Subject1 11
> Input Subject1-hRsk_mRwd Subject1 11
> Input Subject1-hRsk_hRwd Subject1 11
>
> Input Subject2-lRsk_lRwd Subject1 -10
> Input Subject2-lRsk_mRwd Subject1 -10
> Input Subject2-lRsk_hRwd Subject1 -10
> Input Subject2-mRsk_lRwd Subject1 0-1
> Input Subject2-mRsk_mRwd Subject1 0-1
> Input Subject2-mRsk_hRwd Subject1 0-1
> Input Subject2-hRsk_lRwd Subject1 11
> Input Subject2-hRsk_mRwd Subject1 11
> Input Subject2-hRsk_hRwd Subject1 11
>
>
> Please let me know if you think this design looks more correct given 
> the observations per subject.
>
> Thanks for your help,
> Afsana
>
> __
> Afsana Afzal
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana 
> [aaf...@mgh.harvard.edu]
> Sent: Monday, February 22, 2016 2:34 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST
>
> Hi,
>
> Sorry about the lack of clarification.
>
> Yes, it's a functional study. Each of the classes is a subject. I 
> basically want to compute the main effect of risk at the group level 
> (i.e. High Risk minus Low Risk) but there are multiple observations 
> per risk level since there are three different reward levels within 
> each risk level (low Reward, med Reward, high Reward).
> I was thinking of setting up all the risk-reward conditions as active 
> (=1s) in the fsgd file and then subtracting the conditions using the 
> contrast matrices below to get the main effect of Risk.
>
> Please let me know if that makes a bit more sense.
>
> Thanks for your help,
> Afsana
>
> __
> Afsana Afzal
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, February 22, 2016 12:16 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST
>
> I'm having a hard time deciphering what you are doing. Is this a
> functional study? What are the 5 classes? Why are there all 1s
> regardless of risk or reward level?
>
> On 02/19/2016 10:52 AM, Afzal, Afsana wrote:
> > Hi,
> >
> > I'm analyzing a decision making task with a 3x3 condition matrix:
> > pairings of low, medium, high levels of risk with low, medium, high
> > levels of reward.
> >
> > I've set up the following FSGD file to do a repeated
> > measures/within-subject ANOVA:
> >
> > GroupDescriptorFile 1
> > Class hc001
> > Class hc002
> > Class hc003
> > Class hc004
> > Class hc005
> > Variables lRsk_lRwd lRsk_mRwd lRsk_hRwd mRsk_lRwd
> > mRsk_mRwd mRsk_hRwd hRsk_lRwd hRsk_mRwd hRsk_hRwd
> > Input hc001 hc001 1 1 1 1 1 1
> > 1 1 1
> > Input hc002 hc002 1 1 1 1 1 1
> > 1 1 1
> > Input hc003 hc003 1 1 1 1 1 1
> > 1 1 1
> > Input hc004 hc004 1 1 1 1 1 1
> > 1 1 1
> > Input hc005 hc005 1 1 1 1 1 1
> > 1 1 1
> >
> > I've also created the following contrast matrices:
> >
> > Con1: Does difference between highRisk andLowRisk differ from 0?
> > 0 0 0 0 0 -1 -1 -1 0 0 0 1 1 1
> >
> > Con2: Does difference between highRisk andMedRisk differ from 0?
> > 0 0 0 0 0 0 0 0 -1 -1 -1 1 1 1
> >
> > Is this an appropriate way of setting up the ANOVA?
> >
> > Thanks for your help,
> >
> > Afsana
> > __
> > *Afsana Afzal*
> > Clinical Research Coordinator
> > Massachusetts General Hospital
> > Division