date:20170629

[Freesurfer] content of "subjects_dir"

2017-06-29 Thread Schumman Resonance

Dear free surfer community,

Silly question here. I note the default "subjects_dir" in freesurfer
contains a bunch of directories and files.

If I set the environment so that my "subjects_dir" is not the default
location, do I need to move any of the files in the original location to
the new one?

I hope this makes sense.

Thanks,

Kev
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[Freesurfer] viewing mri_glmfit FDR corrected results

2017-06-29 Thread marco mcsweeney

Dear FreeSurfer experts,

I ran my group analysis using mri_glmfit and found a number of significant
clusters showing cortical thickness differences between 2 groups. I used
tksurfer to visualize the results and used FDR to correct for multiple
comparisons.

My question is about how do I correctly get the FDR corrected results
showing cluster number, size, MNI coordinates etc. as I would if I used
QDEC?

I have searched through the archives and have found what looks like the
answer, but I'm not convinced that the method I used is correct.

I used

1) mri_glmfit-sim --glmdir lh.group_diff.glmdir --cache 1.3 abs
--cwpvalthresh .99

and

2) less lh.group_diff.glmdir/contrast.txt/cache.th13.abs.sig.cluster.summary

However when I visualize the FDR corrected results with tksurfer or
freeview I can see a couple of clusters not listed in the summary. Am I
missing something?

Thank you so much in advance.

Any help or advice would be greatly appreciated.

Best wishes

Marco
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Re: [Freesurfer] Using asegstats2table for gtm.stats.dat?

2017-06-29 Thread miracle ozzoude

Hello Elijah,

I want to extract this values like you did. How do I use the script doug
recommended?

Thanks
Paul

On Wed, Jun 21, 2017 at 11:47 AM, Elijah Mak 
wrote:

> Thanks Doug! It works!
>
> Best Wishes,
> Elijah
>
> On 21 June 2017 at 16:09:29, Douglas N Greve (gr...@nmr.mgh.harvard.edu)
> wrote:
>
> use this script
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/gtmstats2table
>
>
>
> On 06/21/2017 10:53 AM, Elijah Mak wrote:
> > Hi Freesurfer Team
> >
> > Apologies for bumping this thread up again. I am wondering if is there
> > is a way to extract the ROI stats in gtm.stats.dat after mri_gtmpvc
> > (using a similar approach such as asegstats2table)?
> >
> > Thanks for your help!
> >
> > Best Wishes,
> > Elijah
> >
> >
> >
> > On 16 June 2017 at 16:53:33, Elijah Mak (fk...@medschl.cam.ac.uk
> > ) wrote:
> >
> >> Hi Unix experts,
> >>
> >> I am trying to extract the PVC-ed values from gtm.stats.dat for every
> >> subject. Is there a fast way to do this using a similar workflow with
> >> asegstats2table? Thanks.
> >>
> >> Best Wishes,
> >> Elijah
> >
> >
> > ___
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 <(617)%20724-2358>
> Fax: 617-726-7422 <(617)%20726-7422>
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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[Freesurfer] Question mri_glmfit fwhm smoothing

2017-06-29 Thread Van Der Deijl, Rosanne

Hi,

I have a question about mri_glmfit. As an input, you give e.g. the stacked
thickness data from all subjects, smoothed with a certain fwhm. But then as an
output file, it gives an fwhm.dat file, which, at least in my case, contains
another smoothing level.

I noticed this because I ran mri_glmfit-sim forclusterwise multiple comparison
correction, which gives me the error:

ERROR: cannot find
/usr/local/freesurfer/stable6/average/mult-comp-cor/fsaverage/rh/cortex/fwhm33/abs/th13/mc-z.csd

As input I gave data smoothed to 25fwhm, and not fwhm33, as it seems to think.
But indeed, in the fwhm.dat file it gives fwhm = 32.940499.

I read in the tutorial that the fwhm.dat file contains the average FWHM of the
residual.
But still my questions are:
- what this means
- why mri_glmfit-sim would need this number, and whether/how I can run the
mult. comparison correction on the 25fwhm-smoothed data.

Thank you in advance!

- Rose

Commands:
mri_glmfit:
mri_glmfit --fsgd $CALMGREY/CALM_FSGD.txt dods --C CALMlong_contrast1.mat --C
CALMlong_contrast2.mat --C CALMlong_contrast3.mat --C CALMlong_contrast4.mat
--glmdir rh.CALMlong.thickness-spc.fwhm25 --y
rh.CALMlong.thickness-spc.stack.fwhm25.mgh --cortex --surf fsaverage rh

mri_glmfit-sim:
mri_glmfit-sim --glmdir rh.CALMlong.thickness-spc.fwhm0 --cache 1.3 neg --cwp
--2spaces

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[Freesurfer] Subject with missing fMRI data

2017-06-29 Thread Sadie Marvel

Hi List,


I am currently doing a group analysis of 26 subjects, one of which has missing 
fMRI data where the signal cuts off through parts of the occipital and temporal 
lobes. I was wondering if freesurfer has any way of dealing with this, such as 
multiple imputation, or other methods of filling the missing data. 
Alternatively, is there a way to only use the portions of the brain that have 
data when doing mri_glmfit? Does freesurfer do this automatically?


Thanks.
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Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

2017-06-29 Thread Corinna Bauer

Great, thank you!

Best,

Corinna

On Thu, Jun 29, 2017 at 12:09 AM, Thomas Yeo  wrote:

> Hi Corinna,
>
> You can download here: https://www.dropbox.com/s/yj1gbpmpgho7wtm/Yeo_
> JNeurophysiol11_SplitLabels.zip?dl=0
>
> Regards,
> Thomas
>
>
> On Thu, Jun 29, 2017 at 5:45 AM, Corinna Bauer 
> wrote:
>
>> Dear Dr. Yeo,
>>
>> Our research group is currently trying to segment the Yeo atlas into
>> separate labels, but just came across this thread which indicates that you
>> have already done this. Would you be willing to re-share the link to your
>> previously extracted individual labels from your 7 and 17 networks?
>>
>> Thank you!
>>
>> Corinna
>>
>> On Thu, May 14, 2015 at 4:54 AM, Thomas Yeo 
>> wrote:
>>
>>> Hi Annie,
>>>
>>> I have previously extracted individual regions from the 7 and 17
>>> networks. You can download them here
>>> (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol
>>> 11_SplitLabels.zip?dl=0).
>>> Please see the README in the folder for more explanations. There
>>> should be a precuneus DMN region.
>>>
>>> The 17 networks consist of 114 regions that have been previously
>>> published:
>>>
>>> 1) Krienen et al., Reconfigurable state-dependent functional coupling
>>> modes cluster around a core functional architecture. Philosophical
>>> Transactions of the Royal Society B, 369:20130526, 2014
>>>
>>> 2) Yeo et al., Functional connectivity during rested wakefulness
>>> predicts vulnerability to sleep deprivation. Neuroimage 111:147-158,
>>> 2015
>>>
>>> Hope this helps.
>>>
>>> Cheers,
>>> Thomas
>>>
>>> On Thu, May 14, 2015 at 3:08 PM, 陳昱潔  wrote:
>>> > Hello Dr. Yeo,
>>> >
>>> > Thank you for your previous help and reply. We've worked out the way to
>>> > switch the resolution of parcellation and successfully extracted the
>>> > anatomical information using your mask derived from iFC work.
>>> >
>>> > However, we came across a new problem to apply the cortical mask and
>>> need
>>> > your kind help again. We aim to conduct a seed-based analysis to
>>> investigate
>>> > structural covariance based on the network defined by iFC, and find
>>> your
>>> > work of cortical parcellation conceptually perfectly suit our research
>>> > question. Based on the current approach, however, it seemed that we
>>> could
>>> > only extract the anatomical information from the whole well-defined
>>> network,
>>> > but not the specific hub within the network (e.g., the anatomical
>>> > information of the precuneus from the DMN). We wonder if you have any
>>> > suggestion to resolve our problem, ie, to be specific, is there any
>>> way to
>>> > only extract the discrete hub information rather than the whole
>>> network?
>>> >
>>> > We really appreciate your generous help. Thank you very much.
>>> >
>>> > p.s. This email would also forward to my senior colleague, Dr.
>>> Hsiang-Yuan
>>> > Lin, who is a child and adolescent psychiatrist doing imaging research
>>> in
>>> > Taiwan.
>>> >
>>> >
>>> > 2015-05-13 19:15 GMT+08:00 陳昱潔 :
>>> >>
>>> >> Hi Professor Yeo :
>>> >>
>>> >> Thank you for helping us so much!
>>> >> After mris_anatomical_stat I tried aparcstats2table to extract the
>>> table.
>>> >> But I failed with generating the table.
>>> >>
>>> >>
>>> >> Best wishes,
>>> >> Annie
>>> >>
>>> >> 2015-05-12 8:29 GMT-04:00 Thomas Yeo :
>>> >>
>>> >>> Hi Annie,
>>> >>>
>>> >>> I assume this means 5202 is your subject ID? Maybe you should check
>>> if
>>> >>> /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Network
>>> s_N1000.annot
>>> >>> exist?
>>> >>>
>>> >>> If so, you can run mris_anatomical_stats to generate statistics for
>>> >>> the parcellation.
>>> >>>
>>> >>> Cheers,
>>> >>> Thomas
>>> >>>
>>> >>> On Tue, May 12, 2015 at 6:29 PM, 陳昱潔  wrote:
>>> >>> > Hi Professor Yeo :
>>> >>> > After I rechecked the directory and run again mri_surf2surf
>>> >>> > I got the result:
>>> >>> > "Saving target data
>>> >>> > Converting to target annot
>>> >>> > Saving to target annot
>>> >>> >
>>> >>> > /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Network
>>> s_N1000.annot"
>>> >>> > The file of 5202/label didn't come out with
>>> >>> > lh.Yeo2011_7Networks_N1000.annot
>>> >>> > But it seems succeed, right?
>>> >>> > How can I get the stat of this parcellation ?
>>> >>> >
>>> >>> > Thank you very much!
>>> >>> >
>>> >>> > Best wishes,
>>> >>> > Annie
>>> >>> >
>>> >>> > 2015-05-12 6:06 GMT-04:00 Thomas Yeo :
>>> >>> >
>>> >>> >> Hi Annie,
>>> >>> >>
>>> >>> >> mri_surf2surf is complaining that it cannot write out the
>>> annotation.
>>> >>> >>
>>> >>> >> Just to clarify, is your subject called test_run_allindex? In
>>> other
>>> >>> >> words, is the variable s equal to test_run_allindex?
>>> >>> >>
>>> >>> >> Does the directory "/home/annie/test_run_allindex/label/" exist?
>>> If
>>> >>> >> not, then you first need to

[Freesurfer] Qdec error in analysis

2017-06-29 Thread AYUSHI SHUKLA

Hi,

I'm a new user of qdec and I'm trying to run a cortical thickness analysis
in qdec between Schizophrenic patients and healthy controls.
I have run "recon-all -i" and "recon-all -s  -qcache" on my data
and it says that this has run successfully without any errors.

But when I hit analyze on the qdec GUI, I get the following error-  "Error
in Analyze: Couldn't open
/Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz
or .mgh file."

I went through the old questions with the same issue, however I could not
figure a solution for my problem as when I check in the directory, the file
is present. I have tried to re-run recon-all and recon-all -s as well, but
it is still giving the same error. I was wondering if someone could help me
with this issue.


Warm Regards

Ayushi Shukla
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Re: [Freesurfer] CT DIOCMs

2017-06-29 Thread Bruce Fischl


Hi Jon

CT doesn't usually provide any gray/white contrast, so I don't think it 
can work. The dicom issue is a separate one. We should be able to read 
most dicoms, but of course this is the issue with an "evolving standard".


cheers
Bruce
On 
Wed, 28 Jun 2017, John Anderson wrote:



Dear Freesurfer experts,
I have T1 images acquired using CT scan not MRI. I have the following
questions please:
 1. "mri_convert" failed to convert the dicoms to nifti, so I used "dcm2nii"
part of mricron to convert the dicoms to nifti. I am wondering if there are
any tools in Freesurfer to convert CT scan dicoms to nii or mgz formats
2. Can this type of images be processed in Freesufrer using the traditional
pipeline for surfaces reconstruction. I mean using "recon-all"


Thank you for your guidance
Jon

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Re: [Freesurfer] Pial surface editing