Re: [Freesurfer] Zero angle for retinotopy

[Mohamed Abdelhack]

Does this mean that the zero angle is the one where the wedge starts
rotating in the experiment?
Does this apply to eccentricity experiment also (In my lab's protocol it
doesn't start from zero)?

On Sat, Feb 6, 2016 at 2:20 AM, dgw  wrote:

> Hi,
>
> I know Doug is away, so he may correct me later, but I believe it
> doesn't matter, as long as it is consistent across runs, and you know
> what it is. It will just determine where the angle 0 activity goes (in
> a color map etc.). The way FS-FAST does the mapping it just may mean
> your colors don't line up with others.
>
> hth
> d
>
> On Thu, Feb 4, 2016 at 11:52 PM,   wrote:
> > Dear all,
> >
> >
> >
> > I am wondering about what the zero angle for retinotopy corresponds to in
> > retinotopy analysis. I mean corresponding to the wedge being at zero
> angle
> > in circular coordinate map (horizontal) or vertical up?
> >
> >
> >
> > Thank you,
> >
> > Best,
> >
> >
> >
> >
> > ___
> > 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
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] Planum temporale measurement

[Christophe Destrieux]

Hi Adam,
sorry for the delay in my answer

The aparc.a2009s is based on the anatomical rules we published in Neuroimage in 
2010:
- There are 2 separate labels : one is sulcal, for the posterior part of the 
lateral fissure (Lat_Fis-post),  the other one is gyral,  for the planum 
temporale (G_temp_sup-Plan_tempo)
- I’m not quite sure to understand the second part of the question : in my mind 
the lateral fissure can be divided in 3 segments (anterior, middle, posterior), 
and the posterior one is more or less ascending. There was only a single label  
(Lat_Fis-post) for the posterior segment of the lateral fissure

I hope it helps
— 
Christophe Destrieux, 
Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de 
Tours 
Service de Neurochirurgie 
Laboratoire d’Anatomie, Faculté de Médecine, 10 Bd Tonnellé - 37032 Tours - 
France 
Bureau: +33 2 47 36 61 36 | Fax +33 2 47 36 62 07 | Mel Bureau: 
christophe.destri...@univ-tours.fr
Web : http://www.u930.tours.inserm.fr/  









> Le 5 févr. 2016 à 01:19, Adam David Felton  a 
> écrit :
> 
> Hello,
> 
> I checked the listserv history, but couldn't find an answer to my question:
> 
> With the 2009 parcellation scheme, 1) does the planum temporale parcellation 
> include the posterior ascending ramus (which Destrieux et al. 2010 seems to 
> imply) and 2) does the planum temporale include the posterior descending 
> ramus?
> 
> 
> 
> Thank you!
> 
> 
> 
> 
> Adam
> ___
> 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


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] To use a ROI.label as seed in FS-FAST

[stdp82]

Hi list,

I would like to use as seed in FS-FAST a ROI.label which I have drawn on a 
cluster in tksurfer.How can I do it?Should I use mri_label2vol?
Thanks.
Stefano



___
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] FreeSurfer group analysis: mri_glmfit-sim

[Silas]

Dear FS team,


I'm currently making a group analysis using the "command-line" group analysis 
stream in freesurfer.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng

[https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]

FsTutorial/GroupAnalysisDng - Free Surfer 
Wiki
surfer.nmr.mgh.harvard.edu
Introduction. This tutorial is designed to introduce you to the "command-line" 
group analysis stream in FreeSurfer (as opposed to QDEC which is GUI-driven), 
including ...



1) I would like to do a surface based analysis where i'm only investigating a 
certain area or label - instead of doing a whole brain analysis. This can be 
done by introducing --label surface_area_of_interest.label when running 
mri_glmfit. Would this (in theory) give me different results from doing a whole 
brain analysis - or would it just exclude the results from outside the label? 
And how about after clusterwise correction for multiple comparisons?

-> is there a better way to do this than following the command-line group 
analysis stream in freesurfer?


2) When running mri_glmfit-sim i'm investigating the output ending with 
-voxel.mgh - how do i interpret the results of this file? When investigating 
the file in freeview what is the meaning of the units when configuring the 
overlay?


Best, Silas
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] Paired analysis FSFAST

[Douglas Greve]

When you run isxconcat-sess add -paired-diff. This will compute 1-2 for 
each subject. You can then run mri_glmfit. With that FSGD file, your 
contrast should be 1 not 1 0

doug


On 2/6/16 11:17 AM, Thục Trinh wrote:

Hello,

I'm working on group analysis in fMRI activation using FSFAST. I tend 
to test whether any significant changed in fMRI activation within 
group across two time points ( pre-training vs post). I ran first 
level already.  I still confuse about the concat data and the 
mri_glmfit command. Here are the command lines, I'm wondering if it 
runs exactly what I want it to do.


--  idlist

Input NCP140005_1
Input NCP140005_2
Input NCP140012_1
Input NCP140012_2
Input NCP140071_1
Input NCP140071_2
Input NCP140079_1
Input NCP140079_2
Input NCP140082_1
Input NCP140082_2
Input NCP140543_1
Input NCP140543_2
Input NCP140556_1
Input NCP140556_2
Input NCP140558_1
Input NCP140558_2

-- concat data
isxconcat-sess -sf idlist -analysis work.sm5.lh -contrast con-v-arrow 
-o group2


-- FSGD file

GroupDescriptorFile 1
Title Con-arrow Gr2
Class Defi
Input NCP140005 Defi
Input NCP140012 Defi
Input NCP140071 Defi
Input NCP140079 Defi
Input NCP140082 Defi
Input NCP140543 Defi
Input NCP140556 Defi
Input NCP140558 Defi

-- run glm analyisis

mri_glmfit --glmdir lh.paired.gr2-diff --y ces.nii  --fsgd 
con-arrow_group2.fsgd --C mean.mat


-- content in matrix contrast
 C = [ 1 0 ]

Thank you,
Trinh


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


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


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

Re: [Freesurfer] To use a ROI.label as seed in FS-FAST

[Douglas Greve]

Use mri_label2vol to convert the label into a volume in the anatomical 
space and store it in $SUBJECTS_DIR/subject/mri. Make sure to use 
--fill-ribbon if the label is surface-based. When running fcseed-config, 
specify the volume with the -seg option and use -segid 1


On 2/7/16 3:16 PM, std...@virgilio.it wrote:


Hi list,

I would like to use as seed in FS-FAST a ROI.label which I have
drawn on a cluster in tksurfer.
How can I do it?
Should I use mri_label2vol?

Thanks.

Stefano




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


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


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

Re: [Freesurfer] spot checking results

[Douglas Greve]

Even on the same operating system they will be different because there 
is stuff in the header that will change. Use mri_diff (volumes, 
segmentations, and surface overlays) or mris_diff for surfaces to check 
whether they are different.

On 2/5/16 11:55 PM, dgw wrote:
> Don,
>
> Running FreeSurfer on two different versions of any operating system
> will not produce the same results. If you want the same results, you
> must use exactly the same version of an operating system for all of an
> analysis.
>
> hth
> d
>
> On 2/5/16 8:29 PM, Krieger, Donald N. wrote:
>> Dear List,
>>
>> I have run recon-all –all on the same scan on two different machines
>> likely running two different versions of Linux but in any case the runs
>> were done with different numbers of cores.
>>
>> I  haven’t done anything fancy to compare that the results are identical
>> except for some spot checks of individual files with md5sum.
>>
>> label/lh.BA4a.label shows up the same on both.
>>
>> mri/wmparc.mgz does not.
>>
>> Your comments would be welcome.
>>
>> Is there something about the non-ascii files, e.g. wmparc.mgz, which
>> would make them show different checksums, e.g. inclusion of a processing
>> time or some such?
>>
>> Do you have experience or suggestions for convincing ourselves that we
>> are getting the same answers on different machines?
>>
>> ???
>>
>> Thanks - Don
>>
>>
>>
>> ___
>> 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
>
>

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

Re: [Freesurfer] tkregister2 - horizontal and coronal inverted in the functional only

[Douglas Greve]

On 2/5/16 12:49 PM, Ilaria Sani wrote:

Dear All,

I have a functional and a T1 registered, but they are not in 
anatomical coordinates.
Do you mean neither are in the "conformed" 256^3, 1mm^3 FreeSurfer 
coordinates?

I put the anatomical in the desired position by using tkregister2.
Was the T1 used to generate the FS results? If so,  why do you need to 
get it into FS coordinates? If not, then use bbregister to create the 
registration file, then use mri_vol2vol to map it into FS space.
I was hoping to use the output reg file to re-position the functional 
as well.
Use bbregister to register the functional to FS coordinates, then again 
use mri_vol2vol.


I got an unexpected output!
The functional looks reoriented BUT, coronal is horizontal, horizontal 
is coronal and sagittal is 90deg rotated.


How did it happen and how can I fix the problem?

Thanks,
Ilaria




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


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


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

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 27492.1

[Douglas Greve]

Try multiplying the covariate by 100 (after subtracting the mean).

On 2/5/16 8:28 AM, Nabin Koirala wrote:
I did that but it still does not work, it is almost the same error 
except the condno is now 15521.8 before it was 27492.1, though I am 
not sure if that tells something about the error. Could it be 
something else ?

Thank you.

Regards,
Nabin

On Thu, Feb 4, 2016 at 5:59 PM, Douglas Greve 
> wrote:


I'm not sure what the difference is. Compute the mean of the 2nd
column, then subtract that number from the values in the 2nd column.
doug


On 2/2/16 7:30 AM, Nabin Koirala wrote:

Thank you for your response . Sorry but for my understanding,
should i substract the mean from the data (demean) or you mean to
remove the value which is equal to the mean ?

Thank you.

Regards,
Nabin

On Mon, Feb 1, 2016 at 5:21 PM, Douglas N Greve
> wrote:

Try removing the mean from your covariate

On 01/30/2016 01:31 PM, Nabin Koirala wrote:
> Dear Freesurfer forum,
>
> 'I am trying to run qdec analysis for a group of subjects
to see if
> correlation exists but I am getting this error only for this
>  particular set of data but could not figure out what is
exactly wrong
> with it. Your suggestion would be greatly appreciated.
>
> Following is the terminal output for the process:
> ..
> Saving design matrix to
/g/f/h/s/freesurfer/subjects/qdec/Untitled/Xg.dat
> Normalized matrix condition is 27492.1
> Design matrix --
>  1.000   0.408;
>  1.000   0.417;
>  1.000   0.417;
>  1.000   0.405;
>  1.000   0.412;
>  1.000   0.412;
>  1.000   0.411;
>  1.000   0.417;
>  1.000   0.405;
>  1.000   0.406;
>  1.000   0.402;
>  1.000   0.419;
>  1.000   0.413;
>  1.000   0.413;
> 
> ERROR: matrix is ill-conditioned or badly scaled, condno =
27492.1
> 
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
> If you seek help with this problem, make sure to send:
>   1. Your command line:
> mri_glmfit --y
/g/f/h/s/freesurfer/subjects/qdec/Untitled/y.mgh
> --fsgd /g/f/h/s/freesurfer/subjects/qdec/Untitled/qdec.fsgd
dods
> --glmdir /g/f/h/s/freesurfer/subjects/qdec/Untitled --surf
fsaverage
> lh --label
/g/f/h/s/freesurfer/subjects/fsaverage/label/lh.aparc.label
> --C
>

/g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
> --C
>

/g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-alpha1-Cor.mat
>
>   2. The FSGD file (if using one)
>   3. And the design matrix above
> Error in Analyze: command failed: mri_glmfit --y
> /g/f/h/s/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd
> /g/f/h/s/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods
--glmdir
> /g/f/h/s/freesurfer/subjects/qdec/Untitled --surf fsaverage
lh --label
> /g/f/h/s/freesurfer/subjects/fsaverage/label/lh.aparc.label --C
>

/g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
> --C
>

/g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-alpha1-Cor.mat
>
> Many thanks in advance.
>
> Regards,
> Nabin
>
>
> ___
> 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

Re: [Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN

[Douglas Greve]

Can you send me the Xtmp.mat file?


On 2/2/16 6:40 PM, Mcnorgan, Christopher wrote:
> Hi,
> I'm attempting an inaugural run through the FS pipeline on some event-related 
> data collected over 6 runs. I'm not sure if this makes any difference, but 
> the experiment is self-paced, and the events are of varying duration (it's a 
> lexical decision task, and participants can take up to 4 seconds to respond 
> but typically respond between 600 - 800ms, with an exponentially-decreasing 
> jittered ITI between trials).
>
> When I run selxavg3-sess on this single participant, the following error is 
> generated:
>
> /**
> Saving X matrix to /home/kali/fMRI/LDT/1001_001/bold/LDT.sm6.lh/Xtmp.mat
> Error using svd
> Input to SVD must not contain NaN or Inf.
>
> Error in cond (line 35)
>  s = svd(A);
>
> Error in fast_selxavg3 (line 279)
>XCond = cond(XtX);
>   
>>> --
> ERROR: fast_selxavg3() failed\n
> ***/
>
> If I open up the generated .mat file, I see the several rows/columns of the 
> XtX matrix are indeed populated with NaN. We tried running the 
> mkanalysis-sess a couple different ways, getting the same error, though our 
> different parameter selections for mkanalysis-sess lead to different XtX 
> matrices, so I suspect that this might be the source of the problem. 
> Unfortunately, I have no insight into what the root of the problem might be. 
> The .par files used have the event durations set to the reaction times for 
> each trial, and the -refeventdur value is set to the mean reaction time
>
> Thanks for any help anyone might be able to give me
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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


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

Re: [Freesurfer] FreeSurfer group analysis: mri_glmfit-sim

[Douglas Greve]

On 2/7/16 1:34 PM, Silas wrote:


Dear FS team,


I'm currently making a group analysis using the "command-line" group 
analysis stream in freesurfer.


https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng



FsTutorial/GroupAnalysisDng - Free Surfer Wiki 


surfer.nmr.mgh.harvard.edu
Introduction. This tutorial is designed to introduce you to the 
"command-line" group analysis stream in FreeSurfer (as opposed to QDEC 
which is GUI-driven), including ...



1) I would like to do a surface based analysis where i'm only 
investigating a certain area or label - instead of doing a whole brain 
analysis. This can be done by introducing --label 
surface_area_of_interest.label when running mri_glmfit. Would this (in 
theory) give me different results from doing a whole brain analysis - 
or would it just exclude the results from outside the label?


No. However, if your activation is near the boundary of the ROI, then 
you may want to constrain the spatial smoothing to be within the ROI.


And how about after clusterwise correction for multiple comparisons?

If your new ROI is much smaller than whole hemisphere, then you will 
need to generate new correction tables (otherwise it won't help to 
constrain it to an ROI). To do this, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo


-> is there a better way to do this than following the command-line 
group analysis stream in freesurfer?



No



2) When running mri_glmfit-sim i'm investigating the output ending 
with -voxel.mgh - how do i interpret the results of this file? When 
investigating the file in freeview what is the meaning of the units 
when configuring the overlay?


This is the voxel-wise correction for multiple comparisons. The value of 
the voxel (and overlay config units) are -log10(p), where p is the 
p-value corrected for multiple comparisons. So p=.01 means 2.



Best, Silas



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


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


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

Re: [Freesurfer] Fw: Gray matter intensity

[Douglas Greve]

Load them as an overlay in freeview or tksurfer. There should be 
examples on the wiki.

On 2/4/16 10:04 PM, Sabrina Yu wrote:
> Hi Doug,
>
> Thank you for taking the time to answer, I really appreciate it! I have 
> completed this step for all subjects, and created the lh.wm.mgh and rh.wm.mgh 
> files. What should be the next step for creating those maps? Unsure on how to 
> overlay the mgh files.
>
> Thanks,
> Sabrina
>> On Feb 4, 2016, at 4:48 PM, Douglas Greve  wrote:
>>
>> Hi Sabrina, sorry, I was working on a grant, and now I'm out of town
>> until Monday. I can try to push you forward on this now, but I have to
>> be brief. Those images where made from data created with the pctsurfcon
>> scriopt. If you run it with --help, you will get some docs on it. This
>> is already run by default with output {lr}h.w-g.pct.mgh which is the
>> GM/WM intensity in Figure 1. This script will also create the GM and WM
>> intensity files but deletes them by default. You can re-run it and
>> specify the temporary folder with --tmp, and those files will be in
>> there. I don't know what they will be called but hopefully it will be
>> obvious.
>>
>> doug
>>
>> On 2/4/16 2:14 PM, Sabrina Yu wrote:
>>> Hi sorry, haven't heard back yet from Freesurfers. Just following up on how 
>>> to generate gray matter & white matter intensity maps overlaid onto brain 
>>> like in Salat paper.
>>>
>>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57
>>>
>>> Figure 1 (c). The mean maps of signal intensity.
>>>
>>> Thanks!
>>> 
>>> From: Sabrina Yu
>>> Sent: Thursday, January 28, 2016 10:51 AM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>>>
>>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57
>>>
>>> Figure 1 (c). The mean maps of signal intensity.
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Douglas N Greve 
>>> 
>>> Sent: Thursday, January 28, 2016 10:47 AM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>>>
>>> which figure(s) in particular?
>>>
>>> On 01/28/2016 01:41 PM, Sabrina Yu wrote:
 Hi,

 Sorry for bringing this thread up again. Referring back to the figure in 
 the Salat paper, what map do I load as an overlay to get the intensity 
 maps? How do I generate these maps?

 Thank you,
 Sabrina

 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
  on behalf of Douglas N Greve 
 
 Sent: Monday, December 21, 2015 10:08 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Fw: Gray matter intensity

 freeview or tksurfer. Load the relevant map as an overlay

 On 12/21/2015 12:57 PM, Sabrina Yu wrote:
> Hello,
>
> Thank you for the very helpful replies! I have another quick question. 
> Which commands would I use to generate images like the ones  in Figure 1 
> (C) generated in the Salat paper 
> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?
>
> Thank you
> Sabrina
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Tuesday, December 15, 2015 10:10 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>
> On 12/15/2015 01:00 PM, Sabrina Yu wrote:
>> Hi,
>>
>>
>> Just following up on my previous email (see below) as I have not yet
>> heard back. I also have another question regarding the lh.wm.mgh and
>> rh.wm.mgh generated by pctsurfcon. How do I view these as surface
>> overlays on T1 brain scans?
>>
> If you want to view them on a volume instead of a surface, you can use
> mri_surf2vol
>> Thank you very much.
>>
>>
>>
>> 
>> *From:* Sabrina Yu
>> *Sent:* Thursday, December 10, 2015 2:47 PM
>> *To:* Freesurfer support list
>> *Subject:* Gray matter intensity
>>
>> Hello,
>>
>>
>>
>> I have been following the instructions in this email thread:
>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.
>> 
>>  And
>> have successfully gotten the wm-gm signal intensity contrast, but
>> now have a few questions regarding signal intensity for white matter
>> and gray matter intensity.
>>
>>
>> 1) Does the wmparc.stats contain mean white matter intensity 

Re: [Freesurfer] Volume analysis in native space vs. mni305 space

[Douglas Greve]

Right. FSFAST uses "three spaces": lh (surface), rh (surface), and 
subcortical (volume). To prevent voxels from being counted twice, we 
mask cortical voxels out of the volume-based analysis.


On 2/5/16 11:29 AM, Rodriguez-Thompson, Anais wrote:

Hi FreeSurfer experts,

I'm writing to follow up on an email I sent on Monday.

I'm working in 5.3 and switching over to running my 1st level analysis 
in fsaverage. I noticed that when visualizing the volume output from 
the mni305 analysis in tkmedit, there is only activation in 
subcortical regions and none in cortical regions.


I read in the FreeSurfer release notes for 5.1 that fsfast "now masks 
the volume-based analysis to include only subcortical areas."


I just wanted to confirm that we are not seeing cortical activation in 
the volume due to it being masked out.


Again, my commands are:
Pre-processing: preproc-sess -s GDDA001 -surface fsaverage lhrh 
-mni305 -fwhm 5 -per-run -d $SUBJECTS_DIR -fsd bold -so siemens
Mkanalysis: mkanalysis-sess -analysis 
SIRP_LoadRegression_Stable5.3_012616_sm5_mni305 -mni305 2 -fwhm 5 
-paradigm slopepar -event-related -fsd bold -runlistfile runlistfile 
-tpef tpef_1.5mm.txt -timewindow 20 -TER 2 -nconditions 9 -gammafit 
2.25 1.25 -refeventdur 2 -per-run -TR 2 -stc siemens -force


Thanks,
Anais

On Feb 1, 2016, at 12:40 PM, Rodriguez-Thompson, Anais 
> wrote:



Hi FreeSurfer experts,

I'm in the process of switching over our first-level analyses from 
being run in native space to being run in fsaverage/mni305 space. 
Looking at the first-levels on an individual subject level, the 
volume analyses look fairly different (cortical signal especially is 
lost in the mni305 analysis). I've attached a couple of slides with 
images comparing the two volume analyses.


My commands for the mni305 analysis are...

Pre-processing: preproc-sess -s GDDA001 -surface fsaverage lhrh 
-mni305 -fwhm 5 -per-run -d $SUBJECTS_DIR -fsd bold -so siemens
Mkanalysis: mkanalysis-sess -analysis 
SIRP_LoadRegression_Stable5.3_012616_sm5_mni305 -mni305 2 -fwhm 5 
-paradigm slopepar -event-related -fsd bold -runlistfile runlistfile 
-tpef tpef_1.5mm.txt -timewindow 20 -TER 2 -nconditions 9 -gammafit 
2.25 1.25 -refeventdur 2 -per-run -TR 2 -stc siemens -force
Mkcontrast: mkcontrast-sess -analysis 
SIRP_LoadRegression_Stable5.3_012616_sm5_mni305 -contrast 2vFix -a 2 -c 0


My commands for the native space analysis are...

Preprocessing: preproc-sess -s GDDA001 -fwhm 5 -per-run -d 
$SUBJECTS_DIR -fsd bold
Mkanalysis: mkanalysis-sess -analysis 
SIRP_LoadRegression_Stable5_050514 -TR 2 -paradigm slopepar 
-event-related -runlistfile runlistfile -tpef tpef_1.5mm.txt -native 
-fwhm 5 -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 
-refeventdur 2
Mkcontrast: mkcontrast-sess -analysis 
SIRP_LoadRegression_Stable5_050514 -contrast 2vFix -a 2 -c 0


I have a couple of questions regarding the differences between the 
two analyses. First, why is so much of the signal robustness from the 
native space volume analysis lost in the mni305 analysis? Second, why 
are the voxel sizes so different between the two analyses (with the 
native space analysis having a much larger voxel size)?


Thanks,
Anais

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



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


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


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

Re: [Freesurfer] generate .mgz file from DICOM

[Douglas Greve]

It looks like there is a lot of information missing from the dicom file. 
Did it come directly from the scanner? Or was it transformed in some 
way? Anonymized?


On 2/4/16 5:06 PM, Kan Ding wrote:


Hi,
I am having trouble to generate .mgz file from DICOM. However, I was 
able to run the same code with NIFTI file. What did I do wrong? Thanks 
for your help. Kan


NUA502608:300T1 kding$ ls

3010-0.dcm3010-27.dcm

3010-1.dcm3010-28.dcm

3010-10.dcm3010-29.dcm

3010-100.dcm3010-3.dcm

3010-101.dcm3010-30.dcm

3010-102.dcm3010-31.dcm

3010-103.dcm3010-32.dcm

3010-104.dcm3010-33.dcm

3010-105.dcm3010-34.dcm

3010-106.dcm3010-35.dcm

3010-107.dcm3010-36.dcm

3010-108.dcm3010-37.dcm

3010-109.dcm3010-38.dcm

3010-11.dcm3010-39.dcm

3010-110.dcm3010-4.dcm

3010-111.dcm3010-40.dcm

3010-112.dcm3010-41.dcm

3010-113.dcm3010-42.dcm

3010-114.dcm3010-43.dcm

3010-115.dcm3010-44.dcm

3010-116.dcm3010-45.dcm

3010-117.dcm3010-46.dcm

3010-118.dcm3010-47.dcm

3010-119.dcm3010-48.dcm

3010-12.dcm3010-49.dcm

3010-120.dcm3010-5.dcm

3010-121.dcm3010-50.dcm

3010-122.dcm3010-51.dcm

3010-123.dcm3010-52.dcm

3010-124.dcm3010-53.dcm

3010-125.dcm3010-54.dcm

3010-126.dcm3010-55.dcm

3010-127.dcm3010-56.dcm

3010-128.dcm3010-57.dcm

3010-129.dcm3010-58.dcm

3010-13.dcm3010-59.dcm

3010-130.dcm3010-6.dcm

3010-131.dcm3010-60.dcm

3010-132.dcm3010-61.dcm

3010-133.dcm3010-62.dcm

3010-134.dcm3010-63.dcm

3010-135.dcm3010-64.dcm

3010-136.dcm3010-65.dcm

3010-137.dcm3010-66.dcm

3010-138.dcm3010-67.dcm

3010-139.dcm3010-68.dcm

3010-14.dcm3010-69.dcm

3010-140.dcm3010-7.dcm

3010-141.dcm3010-70.dcm

3010-142.dcm3010-71.dcm

3010-143.dcm3010-72.dcm

3010-144.dcm3010-73.dcm

3010-145.dcm3010-74.dcm

3010-146.dcm3010-75.dcm

3010-147.dcm3010-76.dcm

3010-148.dcm3010-77.dcm

3010-149.dcm3010-78.dcm

3010-15.dcm3010-79.dcm

3010-150.dcm3010-8.dcm

3010-151.dcm3010-80.dcm

3010-152.dcm3010-81.dcm

3010-153.dcm3010-82.dcm

3010-154.dcm3010-83.dcm

3010-155.dcm3010-84.dcm

3010-156.dcm3010-85.dcm

3010-157.dcm3010-86.dcm

3010-158.dcm3010-87.dcm

3010-159.dcm3010-88.dcm

3010-16.dcm3010-89.dcm

3010-160.dcm3010-9.dcm

3010-17.dcm3010-90.dcm

3010-18.dcm3010-91.dcm

3010-19.dcm3010-92.dcm

3010-2.dcm3010-93.dcm

3010-20.dcm3010-94.dcm

3010-21.dcm3010-95.dcm

3010-22.dcm3010-96.dcm

3010-23.dcm3010-97.dcm

3010-24.dcm3010-98.dcm

3010-25.dcm3010-99.dcm

3010-26.dcm

NUA502608:300T1 kding$ recon-all -i 3010-0.dcm -s 300

Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /Users/kding/desktop/data/TBIE/TBIET1/300T1

Actual FREESURFER_HOME /Applications/freesurfer

Darwin nua502608.dhcp.swmed.org 14.5.0 Darwin Kernel Version 14.5.0: 
Tue Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64


/Users/kding/desktop/data/TBIE/TBIET1/300T1/300

\n mri_convert 
/Users/kding/desktop/data/TBIE/TBIET1/300T1/3010-0.dcm 
/Users/kding/desktop/data/TBIE/TBIET1/300T1/300/mri/orig/001.mgz \n


mri_convert /Users/kding/desktop/data/TBIE/TBIET1/300T1/3010-0.dcm 
/Users/kding/desktop/data/TBIE/TBIET1/300T1/300/mri/orig/001.mgz


$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from /Users/kding/desktop/data/TBIE/TBIET1/300T1/3010-0.dcm...

Starting DICOMRead2()

dcmfile = /Users/kding/desktop/data/TBIE/TBIET1/300T1/3010-0.dcm

dcmdir = /Users/kding/desktop/data/TBIE/TBIET1/300T1

WARNING: tag ImageNumber not found in 
/Users/kding/desktop/data/TBIE/TBIET1/300T1/3010-0.dcm


WARNING: tag image orientation not found in 
/Users/kding/desktop/data/TBIE/TBIET1/300T1/3010-0.dcm


Ref Series No = 18976

ERROR: bits = 0 not supported.

Send email to freesurfer@nmr.mgh.harvard.edu 



Darwin nua502608.dhcp.swmed.org 14.5.0 Darwin Kernel Version 14.5.0: 
Tue Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64



recon-all -s 300 exited with ERRORS at Thu Feb  4 15:53:19 CST 2016


For more details, see the log file 
/Users/kding/desktop/data/TBIE/TBIET1/300T1/300/scripts/recon-all.log


To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 








UTSouthwestern

Medical 

Re: [Freesurfer] mri_vol2surf Averaging with exclusion of specific values

[Douglas Greve]

There is not a single command to do this, but there is a bit of a hack 
that will work assuming the value you don't want to include is 0. You 
will have to run mri_vol2surf multiple times using a different 
projection fraction, creating a different file for each. Then use 
mri_concat to concatenate the files into one multi-frame overlay. You 
can then use mri_glmfit, something like

mri_glmfit --surf yoursubject lh --y multiframefile.mgh --osgm 
--frame-mask multiframefile.mgh --o glmdir

The final overlay you want will be in glmdir/osgm/gamma.mgh




On 2/1/16 11:57 AM, Gardumi Anna (PSYCHOLOGY) wrote:
> Thank you for your reply.
>
> I am then a bit confused because I thought each surface value was the result 
> of a two-step procedure:
> 1) sampling of the values along the normal to the surface at the points 
> specified by the option --projfrac-avg min max del; with such values computed 
> according the chosen interpolation method (nearest by default or specified by 
> --interp nearest/trilinear);
> 2) averaging of the value obtained from point 1)
> Is this correct?
>
> What I would like is the following:
> 1) sampling along the normal at the nearest voxel to each point defined by 
> --projfrac-avg min max del  (I will obtain for example five values, let's say 
> [1 0 1 2 2])
> 2) averaging these values excluding from the mean points having a specific 
> value (e.g. 0 so that I would obtain as a mean value 1.5, and not 1.2)
>
> I hope this clarify my point.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: maandag 1 februari 2016 17:14
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_vol2surf Averaging with exclusion of specific 
> values
>
> By default, the projection is done using nearest neighbor "interpolation", so 
> there is no averaging. Is this what you mean?
>
> On 02/01/2016 09:53 AM, Gardumi Anna (PSYCHOLOGY) wrote:
>> Dear FreeSurfer expert,
>>
>> I would like to project my maps from the "original" functional space
>> (2.5mm iso, same format as COPE images from FSL) to inflated
>> FreeSurfer surfaces (created from 1.0mm MPRAGE image with recon-all
>> pipeline) excluding voxels with a specific value (e.g. 0) from the
>> averaging procedure of the projection. The reason for this is that I
>> have non-continuous maps (i.e. map values are defined only for some
>> voxels; voxels for which map value is not defined will have 0 as
>> value). Is there a way to perform the projection excluding voxels with
>> a specific value from the averaging of the projection?
>>
>> Thank you in advance for any help!
>>
>> Anna
>>
>> As complementary information:
>>
>> My maps have discrete values (between -10 and 10) and at the moment I
>> am using the following command:
>>
>> mri_vol2surf --mov DiscreteMap.nii --reg $REGMAT --hemi lh
>> --projfrac-avg 0 1 0.2 --interp nearest --o DiscreteMap
>> _InFS_projAvg02_SurfLh.mgh
>>
>> However, in this way the resulting surface map will have values biased
>> by including in the average also the 0 values which in reality
>> represents voxels not included in the map.
>>
>>
>>
>> ___
>> 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
>
>

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