Re: [Freesurfer] Extraction of segmentation maps using mri_extract_label

[Douglas Greve]

FYI, these numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt

On 1/7/15 9:19 AM, Bruce Fischl wrote:

for left and right:
1. 2 and 42
2. 3 and 42
3. 10 and 49
4. 77/78/79
5. 11 and 50
6. 12 and 51
7. 13 and 52
8. We don't have a single one for all of cingulate and it depends on 
which parcellation you use. You should take the uniton of e.g. 1002 
and such (assuming you are using the aparc and not the a2009)


cheers
Bruce

On Wed, 7 Jan 2015, Ben Eliezer, Noam wrote:


Dear Freesurfer Gurus ---
I'm using mri_extract_label to extract segmentation masks, but a little
baffled as to which label numbers to use for each brain part.

The masks I need are:

1. Global white matter
2. Cortical Gray matter
3. Thalamus
4. WM-Hypointensity
5. Caudate nucleus
6. Putamen
7. Palidum
8. Entire cingulate gyrus

...the problem is each of these appear under many label numbers.
For example, the thalamus appears in label numbers: 9, 10, 48, 49, 
107, 116,

8001-8014.

Any suggestion how to decide which label numbers to use for each of the
above brain parts?

Thanks!
 --- Noam



--
Noam Ben-Eliezer, PhD
Adjunct Assistant Professor of Radiology
Center for Biomedical-Imaging
New-York University Medical School
noam.ben-elie...@nyumc.org









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Re: [Freesurfer] recon-all error

[Douglas Greve]

That probably is not a problem since  dicoms don't have to have a 
certain extension. To test, try running


mri_convert  4571157  test.mgh

To run this you must be in the folder where 4571157 is located




On 1/13/15 2:14 AM, Borzello, Mia wrote:

Hi Bruce,

Thanks for e-mail. I did a search on the dicom file, and it said there was no file (top 
part of image). However, I can get myself in the folder and the dicome 
"4571157" is in there. I'm wondering if it's a file type issue. The files 
aren't listed as 4571157.dcm for example- could that be the problem?

Thanks so much,
m

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, January 12, 2015 9:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error

Hi Mia

you need to run it with the full path of the dicom you are trying to give
to recon-all

cheers
Bruce
On Tue, 13 Jan 2015,
Borzello, Mia wrote:


Okay, just ran ls-l and don't see it- image attached.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, January 12, 2015 8:39 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error

does that dicom exist? Can you run ls -l on it?
On Sat, 10 Jan 2015,
Borzello, Mia wrote:


I just fixed that but I'm still getting an error. I attached a screenshot.

Thanks,
Mia

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Krieger, Donald N. 
[krieg...@upmc.edu]
Sent: Friday, January 09, 2015 5:39 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error

It looks like there's a typo in your recon-all command - there's a space between 
"-"  and autorecon3 .

Regards,

Don


Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text



-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
boun...@nmr.mgh.harvard.edu] On Behalf Of Borzello, Mia
Sent: Friday, January 09, 2015 5:30 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error

Yea I didn't see it in /autofs/space/huygens_001/users/mia/subjects.
I attached the output error for recon-all.

Thanks,
m

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-
boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, January 08, 2015 4:27 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error

did you look in

/autofs/space/huygens_001/users/mia/subjects

Can you send us the screen output of recon-all?

On Thu, 8 Jan 2015, Borzello,
Mia wrote:


I looked for that file and did not see a BI22_SurferOutput folder at all.

From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, January 08, 2015 2:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all error

Hi Mia

can you send us the recon-all.log? I don't think you included the
error message in your email so there isn't much for us to go on.

thanks
Bruce

On Thu, 8 Jan 2015, Borzello, Mia wrote:


Hi Freesurfers,

I'm wondering if you can help with the following error that occurred
when trying to create a reconstruction:

FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0

Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514

RedHat release: CentOS release 6.5 (Final)

Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64

NMR Center info (/space/freesurfer exists):

   machine: huygens

   SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects

   PWD: /autofs/space/huygens_001/users/mia/subjects

   ssh huygens
   setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects
   cd /autofs/space/huygens_001/users/mia/subjects


1)BI22
2)recon-all -autorecon1 -autorecon2 - autoreon3 -subject
BI22_SurferOutput
-

i/autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/DICOM_B

I19/4571
/4571157.dcm
3)recon-all -s  exited with ERRORS at Thu Jan  8 13:08:33 EST 2015


Thanks,
m



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Re: [Freesurfer] R: Fwd: fcseed-sess - segmentation fault

[Douglas Greve]

Have you run

fcseed-sess -s sessionid -cfg mean.L_Thalamus.config

That is what will create that file


On 1/13/15 6:50 PM, std...@virgilio.it wrote:

Hi list

I'm running

preproc-sess -s Sess01 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd 
rest -per-run


fcseed-config -segid 10 -fcname L_Thalamus.dat -fsd rest -mean -cfg 
mean.L_Thalamus.config


Create nuisance variables:
fcseed-config -wm -fcname wm.dat -fsd bold -pca -cfg wm.config
fcseed-sess -s sessionid -cfg wm.config
fcseed-config -vcsf -fcname vcsf.dat -fsd bold -pca -cfg vcsf.config
fcseed-sess -s sessionid -cfg vcsf.config

mkanalysis-sess -analysis fc.lthalseed.surf.lh -surface fsaverage lh 
-fwhm 5 -notask -taskreg L_Thalamus.dat 1 -nuisreg vcsf.dat 5 -nuisreg 
wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run


selxavg3-sess -s Sess01 -a fc.lthalseed.surf.lh


$Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $

/Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m

/Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m

/Applications/freesurfer/matlab/MRIread.m

-

outtop = /Applications/freesurfer/subjects/FUNCTIONAL_DATA

Extension format = nii.gz

ERROR: cannot find volume matching 
/Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/L_Thalamus.dat


ERROR: loading nonpar reg 
/Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/L_Thalamus.dat


--

ERROR: fast_selxavg3() failed\n



What's happen?

Thanks in advanced


Stefano


Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 9-gen-2015 17.30
A: "Freesurfer@nmr.mgh.harvard.edu"
Ogg: [Freesurfer] Fwd:  fcseed-sess - segmentation fault


Having both Thalamus and Thalamus-Proper creates all kinds of confusion.
Is there a reason to have both?

9   Left-Thalamus   0   118 14  0
10  Left-Thalamus-Proper0   118 14  0

 Forwarded Message 
Subject: [Freesurfer] fcseed-sess - segmentation fault
Date: Thu, 8 Jan 2015 20:57:46 +0100 (CET)
From: std...@virgilio.it
Reply-To: std...@virgilio.it, Freesurfer support list

To: freesurfer@nmr.mgh.harvard.edu



Hi list,


I'm running FAST on resting state data.


After


fcseed-config -segid 9 -fcname L_Thalamus.dat -fsd rest -mean -cfg
mean.L_Thalamus.config


and


fcseed-sess -s Sess01 -cfg mean.L_Thalamus.config


gives this error:



Loading
/Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/tmp.fcseed-sess.55885/mask.nii.gz

Loading
/Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/fmcpr.nii.gz

Voxel Volume is 64.5752 mm^3

Generating list of segmentation ids

Found   1 segmentations

Computing statistics for each segmentation

   0   1  0   0.000

MRIalloc(0, 1, 1): bad parm


Reporting on   0 segmentations

Computing spatial average of each frame


Writing to
/Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/rest/001/tmp.fcseed-sess.55885/avgwf.mgh

Segmentation fault



Thanks in advance,



Stefano



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Re: [Freesurfer] FreeSurferOutputVolume

[Douglas Greve]

Try this instead

mri_label2vol --seg ${mgz_file} --temp 001.nii --regheader ${mgz_file} 
--o ${cut1}.nii





On 1/13/15 3:22 PM, Zhuang, Xiaowei wrote:


Hi,

I am a new user of freesurfer, mainly for hippocampus segmentation.

The output of my command: recon-all -i ${subject}.nii -subject 
${subject} -all -hippo-subfields


will give me all the subfields in Hippocampus and in .mgz format base 
on my input T1(${subject}.nii file).


And after this, I am doing a mri_convert:  mri_convert 
--out_orientation RAS -rt nearest --reslice_like $SUBJECTS_DIR/001.nii 
-it mgz ${mgz_file} -ot nii $NIIDIR/${cut1}.nii


Which will give me all the output hippocampal subregions in .nii format.

The thing is the output nii files share a different orientation with 
my input T1 file, is there a way for me to keep them the same?


Sincerely thanks for answering this questionI really appreciate 
any reponse.


Best,

Xiaowei.

===

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Re: [Freesurfer] Freesurfer Calculation of Vertex-Wise Area

[Douglas Greve]

The computation is pretty simple, it is just the average of the area of 
the surrounding triangle. Is that what you mean or do you mean the 
mapping of said area to the average space?

doug



On 1/15/15 11:37 PM, Bronwyn Overs wrote:

Dear Mailing List,

I would like to understand how freesurfer calculates the surface area 
at each voxel to be used in the GLM procedure. Is there a key methods 
paper that describes this process, and can this method be explained in 
simple terms?

--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to 
the NeuRA Magazine 




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Re: [Freesurfer] vertex-wise covariate for gyrification index

[Douglas Greve]

That's fine. mri_glmfit-sim has a little anxiety when it finds 
mri_glmfit options it does not recognize.
doug

On 1/26/15 5:00 PM, angela.fav...@unipd.it wrote:
> Hi Doug,
> thank you for this hint.
> I have included --pvr in my mri_glmfit command using a stack of cortical
> thickness maps of the same hemisphere (and same subjects in the same
> order). I also added a column in my design matrix. It seems to work. Only
> when I use the mri_glmfit-sim command, this message appears:
>
> WARNING: unrecognized mri_glmfit cmd option --pvr
>
> WARNING: unrecognized mri_glmfit cmd option /qdec/lh_LGI_vtw/thick.mgh
>
> but everything seems to work anyway (and clusters of differences do not
> disappear!!).
> Is it all correct?
>
> Thank you for your help!
>
> Angela
>
>
>> QDEC does not allow it, but you can do it with mri_glmfit with the --pvr
>> option. Run mri_glmfit with --help to get more info.
>> doug
>>
>> On 01/25/2015 11:16 AM, angela.fav...@unipd.it wrote:
>>> Hi all,
>>> I wrote a paper about gyrification in a sample of malnourished patients.
>>> I
>>> found only little overlap between maps of significantly rediced cortical
>>> thickness and maps of significantly reduced gyrification index (in
>>> comparison to a group of healthy controls).
>>> One of the reviewer raised the question that this is not sufficient to
>>> demonstrate that reduced gyrification is not due to reduced cortical
>>> thickness (or GM volume) and suggest to perform a between group analysis
>>> using cortical thickness (or volume) maps as vertex-wise covariates.
>>> Is it possible to perform this type of analysis? I believe that QDEC
>>> does
>>> not allow it
>>>
>>> Thank you
>>>
>>> Angela
>>>
>>>
>>>
>>>
>>>
 Hi Maria

 it's really hard to say - you'll need to try it out. There aren't
 strong
 prior constraints on skull shape, but if the shape of the brain is too
 different, things may degrade

 Bruce


 On Fri, 23 Jan 2015, Maria Holland wrote:

> Hi all,
> I am starting a project analyzing patients with cranial deformities.
> How
> robust is the automatic cortical reconstruction process - i.e., would
> it
> be
> able to handle deformed skulls?  Similar to this picture:
>
> http://upload.wikimedia.org/wikipedia/commons/1/1f/Single_suture_synostosis
> .png
>
> I am also wondering about the possibility of getting information about
> the
> intermediate steps of the local gyrification calculation.  Like, could
> we
> get information on the pial and outer pial surface paths on each
> individual
> slice, before that information is turned into a 3D surface?
>
> Thanks for your help!
>
> ~ Maria
>
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>>>
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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
>> 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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>
>
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Re: [Freesurfer] extracting pvalues

[Douglas Greve]

what do you mean? Just a list of values? the column, row, slice as well?

On 1/26/15 4:02 PM, Hirsch, Gabriella wrote:


Hi FreeSurfer experts,

Is there a way to extract significant pvalues from sig.mgh files 
(Obtained from the  GroupAnalysisDng tutorial)?


I've looked online but having trouble. Somehow mris_covert isn't working.

Thanks!

Gabriella



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Re: [Freesurfer] Extract mean time series from parcellated region

[Douglas Greve]

what do you mean you can't get them? The program fails? It produces 0s?

On 1/26/15 3:48 PM, sabin khadka wrote:

Hi FS user,

I am trying to extract time series of fmri rest data of certain 
parcellated regions (both cortical and subcortical). for that I am 
doing following


# bbregister --s  --mov  --init-fsl --reg 
register.dat --bold
# mri_label2vol --aparc+aseg --subject  --temp  
--fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz
# mri_vol2vol --mov test1.nii.gz --targ  
--reg register.dat --o test2.nii.gz
# mri_segstats --seg  --id caudate> --in test2.nii.gz --avgwf 
I am not able to get the mean time series values. Could anyone tell me 
what I am missing?

Cheers,
Sabin Khadka


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Re: [Freesurfer] Extract mean time series from parcellated region

[Douglas Greve]

It all looks correct. How many frames does test2.nii.gz have? Try 
running mri_info test2.nii.gz to see


On 1/27/15 9:05 AM, sabin khadka wrote:
Hi Doug- The command doesn't error out but it just give me one value. 
I was assuming the following command would give me value in  time 
series x mean value in text file. Am I following correct 
strategy/commands?

Cheers,
Sabin Khadka


*From:* Douglas Greve 
*To:* sabin khadka ; Freesurfer Support List 


*Sent:* Monday, January 26, 2015 5:33 PM
*Subject:* Re: [Freesurfer] Extract mean time series from parcellated 
region



what do you mean you can't get them? The program fails? It produces 0s?



On 1/26/15 3:48 PM, sabin khadka wrote:

Hi FS user,

I am trying to extract time series of fmri rest data of certain 
parcellated regions (both cortical and subcortical). for that I am 
doing following


# bbregister --s  --mov  --init-fsl --reg 
register.dat --bold
# mri_label2vol --aparc+aseg --subject  --temp  
--fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz
# mri_vol2vol --mov test1.nii.gz --targ  
--reg register.dat --o test2.nii.gz
# mri_segstats --seg  --id caudate> --in test2.nii.gz --avgwf 
I am not able to get the mean time series values. Could anyone tell 
me what I am missing?

Cheers,
Sabin Khadka



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Re: [Freesurfer] Converting dicom images to nifti

[Douglas Greve]

Hi Pradeep, I don't think that we can convert that either. Sorry.
doug

On 1/27/15 7:18 AM, pradeep mahato wrote:

Hi experts,

I am trying to convert dicom images namely 00A0,00A1,00A2 
[ No file extension ] etc. These are generated by Philips machine. I 
used dcm2nii, it does not give correct result. It gives warning : this 
software will only convert the first slice of this multislice lossless 
compressed JPEG . In one thread I read that dicom images from Philips 
scanner are oriented differently.


I tried to use dcmunpack method, but I am not able to save the 
converted image.

I used dcmunpack -src . Please share the correct procedure.

In one of the subjects I have very less number of images:30. Is it 
necessary to have more dicom images to have a better brain mri image . 
If yes, what should be the optimal number of images


Thanking You

Pradeep Kumar Mahato


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Re: [Freesurfer] Extraction of T2 map statistics-per-segment

[Douglas Greve]

On 1/27/15 2:11 AM, Ben Eliezer, Noam wrote:

Hello ---

I'm trying to extract quantitative T2 values for different brain segments.
I've converted my T2 set of DICOMs to .mgz format using mri_convert 
and loaded them into freeview.
>> mri_convert -it siemens_dicom -ot mgz 
T2_maps_Dir/slice_1_T2_map.dcm T2_in_mgz.mgz


After loading T2_in_mgz.mgz to Freeview the T2 maps seem to coincide 
very well with the segmentation maps (aseg+aparc-in-rawavg.mgz).


My questions are:

1. Should I have applied some pre-registration operation on the T2 
maps before loading them into freeview,
or does the fact that they coincide with the segmentation maps mean 
that I don't need to apply any registration?
Since they are in the same session, they will be pretty close in 
registration, it just depends on how much the subject moved between the 
two acquisitions. As a matter of course, I would run a registration on 
them (bbregister with --init-header). This subject may not have moved 
much but it is no guarantee that others won't move more.


2. How can I extract mean T2 values for different segments? (not the 
usual volume-per-segment)

Use mri_segstats. Run with --help to get examples
doug



Much obliged!
 --- Noam




--
Noam Ben-Eliezer, PhD
Adjunct Assistant Professor of Radiology
Center for Biomedical-Imaging
New-York University Medical School
noam.ben-elie...@nyumc.org 




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Re: [Freesurfer] Extraction of T2 map statistics-per-segment

[Douglas Greve]

First off, I would use --init-header instead of --init-spm. Probably 
won't make a difference, but it is safer in this case. Second, look at 
the registration in tkregister (bbregister prints out the command line, 
you can just cut and paste).

doug

ps. Please remember to post the list instead of directly to us. thanks!



On 1/27/15 11:23 AM, Ben Eliezer, Noam wrote:

Hi Doug —

My apologies for the confusion. Please ignore the commands set below.
There is only one set of commands that I tried.

It’s:

>> mri_convert -it siemens_dicom -ot mgz 
SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm 
T2_siemens.mgz
>> bbregister --s subj01 --mov T2_siemens.mgz   --reg 
T2_siemens_regMat.dat   --init-spm --t2
>> mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz 
--interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat 
--no-save-reg
>> mri_segstats --seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum 
T2_siemens_stats.stats --seg-erode 1


But as I wrote below — loading the registered T2 map 
T2_siemens_reg.mgz into Freeview shows that it’s incorrectly 
registered on the segmentation maps.


Thanks and sorry for the confusion,
 — Noam


On Jan 27, 2015, at 5:07 PM, Ben Eliezer, Noam 
mailto:noam.ben-elie...@nyumc.org>> wrote:



Hi Doug —

Thank you for the prompt reply!

I have indeed tried using bbregister (and consult the -- help) but I 
am probably not using it correctly.


I’ve tried two set of commands:

>> mri_convert -it siemens_dicom -ot mgz 
SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm 
T2_siemens.mgz
>> bbregister --s subj01--mov T2_siemens.mgz --reg 
T2_siemens_regMat.dat   --init-spm --t2
>> mri_segstats —seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum 
T2_siemens_stats.stats --seg-erode 1


or,
>> mri_convert -it siemens_dicom -ot mgz 
SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm 
T2_siemens.mgz
>> mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz 
--interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat 
--no-save-reg
>> mri_segstats --seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz --sum 
T2_siemens_stats.stats --seg-erode 1


Both set of commands age the same statistics values, yet, in both 
cases the registration seemed wrong, when running:

>>tkregister2 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat —surf

so I am not sure if the values I get are ok….

Also, when loading the registered T2 maps (T2_siemens_reg.mgz) into 
Freeview they did not coincide with my aseg+aparc.mgz or 
aseg+aparc-in-rawavg.mgz


Any help would be highly appreciated!

Best!
Noam




On 1/27/15 2:11 AM, Ben Eliezer, Noam wrote:

Hello ---

I'm trying to extract quantitative T2 values for different brain segments.

I've converted my T2 set of DICOMs to .mgz format using
mri_convert and loaded them into freeview. >> mri_convert -it
siemens_dicom -ot mgz T2_maps_Dir/slice_1_T2_map.dcm
T2_in_mgz.mgz After loading T2_in_mgz.mgz to Freeview the T2 maps
seem to coincide very well with the segmentation maps
(aseg+aparc-in-rawavg.mgz).

My questions are:

1. Should I have applied some pre-registration operation on the
T2 maps before loading them into freeview, or does the fact that
they coincide with the segmentation maps mean that I don't need
to apply any registration?

Since they are in the same session, they will be pretty close in 
registration, it just depends on how much the subject moved between 
the two acquisitions. As a matter of course, I would run a 
registration on them (bbregister with --init-header). This subject 
may not have moved much but it is no guarantee that others won't move 
more.


2. How can I extract mean T2 values for different segments? (not
the usual volume-per-segment)

Use mri_segstats. Run with --help to get examples
doug

Much obliged!
  --- Noam




--
Noam Ben-Eliezer, PhD
Adjunct Assistant Professor of Radiology
Center for Biomedical-Imaging
New-York University Medical School
noam.ben-elie...@nyumc.org    







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Re: [Freesurfer] Converting dicom images to nifti

[Douglas Greve]

If you run it with --help there will be lots of documentation and 
examples. It will not be able to convert the multiframe dicom files though


On 1/27/15 12:24 PM, pradeep mahato wrote:


Please tell how to use dcmunpack. Any help converting dicom to nii.

On Jan 27, 2015 9:03 PM, "Douglas Greve" <mailto:gr...@nmr.mgh.harvard.edu>> wrote:



Hi Pradeep, I don't think that we can convert that either. Sorry.
doug

On 1/27/15 7:18 AM, pradeep mahato wrote:

Hi experts,

I am trying to convert dicom images namely
00A0,00A1,00A2 [ No file extension ] etc. These are
generated by Philips machine. I used dcm2nii, it does not give
correct result. It gives warning : this software will only
convert the first slice of this multislice lossless compressed
JPEG . In one thread I read that dicom images from Philips
scanner are oriented differently.

I tried to use dcmunpack method, but I am not able to save the
converted image.
I used dcmunpack -src . Please share the correct procedure.

In one of the subjects I have very less number of images:30. Is
it necessary to have more dicom images to have a better brain mri
image . If yes, what should be the optimal number of images

Thanking You

Pradeep Kumar Mahato


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Re: [Freesurfer] Extract mean time series from parcellated region

[Douglas Greve]

That label2vol command maps the aseg into the epi space to create test1 
so it will only have 1 frame. The epi never comes  into play there 
except as a geometry template. If you want to extract a time course from 
the epi, then map it to the anatomical space with that vol2vol command 
using the epi as the --mov, then run mri_segstats. That label2vol 
command is not necessary.


doug


On 1/27/15 12:13 PM, sabin khadka wrote:
Hi doug. I now see the problem. When I run mri_info the test1.nii.gz 
and test2.nii.gz both have only 1 frame. But when I run
# mri_label2vol --aparc+aseg --subject  --temp  
--fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz
# mri_vol2vol --mov test1.nii.gz --targ  
--reg register.dat --o test2.nii.gz
EPI.nii.gz is 4D image with 210 frames. How can I get test1.nii.gz and 
test2.nii.gz in 4D format? Should be something basic but I could not 
figure out how.


I appreciate your help!!
Cheers,
Sabin Khadka


*From:* Douglas Greve 
*To:* sabin khadka ; Freesurfer support list 


*Sent:* Tuesday, January 27, 2015 10:31 AM
*Subject:* Re: [Freesurfer] Extract mean time series from parcellated 
region



It all looks correct. How many frames does test2.nii.gz have? Try 
running mri_info test2.nii.gz to see




On 1/27/15 9:05 AM, sabin khadka wrote:
Hi Doug- The command doesn't error out but it just give me one value. 
I was assuming the following command would give me value in  time 
series x mean value in text file. Am I following correct 
strategy/commands?

Cheers,
Sabin Khadka


*From:* Douglas Greve  
<mailto:gr...@nmr.mgh.harvard.edu>
*To:* sabin khadka  
<mailto:sabink...@yahoo.com>; Freesurfer Support List 
 <mailto:freesurfer@nmr.mgh.harvard.edu>

*Sent:* Monday, January 26, 2015 5:33 PM
*Subject:* Re: [Freesurfer] Extract mean time series from parcellated 
region



what do you mean you can't get them? The program fails? It produces 0s?



On 1/26/15 3:48 PM, sabin khadka wrote:

Hi FS user,

I am trying to extract time series of fmri rest data of certain 
parcellated regions (both cortical and subcortical). for that I am 
doing following


# bbregister --s  --mov  --init-fsl --reg 
register.dat --bold
# mri_label2vol --aparc+aseg --subject  --temp  
--fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz
# mri_vol2vol --mov test1.nii.gz --targ  
--reg register.dat --o test2.nii.gz
# mri_segstats --seg  --id caudate> --in test2.nii.gz --avgwf 
I am not able to get the mean time series values. Could anyone tell 
me what I am missing?

Cheers,
Sabin Khadka



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Re: [Freesurfer] Extraction of T2 map statistics-per-segment

[Douglas Greve]

On 1/27/15 12:38 PM, Ben Eliezer, Noam wrote:

Thanks Doug.

I’ve made two changes to the set of commands.

*1.* Following your suggestion, I’ve shifted from --init-spm to 
--init-header and now tkregister2 shows that the registration is OK.


>>tkregister2 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat —surf
Thanks!


*2.* When loading the result of vol2vol command (T2_siemens_reg.mgz):
  >> mri_vol2vol --mov T2_siemens.mgz --targ 
subj01/mri/aparc+aseg-in-rawavg.mgz --interp nearest --o 
T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg
into freeview the maps are rotated 90-deg in-plane and 90-deg through 
plane versus the segmentation maps — in short they do not match in 
orientation.


I’ve solved this by changing from using aseg+aparc-in-rawavg.mgz to 
aseg+aparg.mgz
>> mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz 
--interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat 
--no-save-reg


_Question1:_ Is that a correct approach? not to use the rawavg 
coordinate system?
Oh, I did not see that. Yes, that is the problem. If you want to use the 
rawavg coordinate system, then you'll have to create another 
registration file because the one that you have only goes between the T2 
and the conformed 256 1mm space. Let me know if that is what you want.


—

Now, I re- gather statistics using:
>> mri_segstats --seg $FSsubjDIR/mri/aparc+aseg.mgz --id 2 7 41 46 
--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i T2_siemens_reg.mgz 
--sum T2_siemens_stats.stats --seg-erode 1


and get the following values:
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev 
Min Max Range
  1   2125567   125567.0  Left-Cerebral-White-Matter   97.9045
68.8609 0.  4000.  4000.
  2   7 1083310833.0  Left-Cerebellum-White-Matter   1.1878
14.7193 0.   608.   608.
  3  41130433   130433.0  Right-Cerebral-White-Matter   96.1764
60.0490 0.  4000.  4000.
  4  46 1155111551.0  Right-Cerebellum-White-Matter   1.2395  
  15.3000 0.   453.   453.


_Question 2:_
Is there any way to verify that these values are accurate…?
(I am a little worried by the large standard deviation values)
Yes, I see what you mean. Is the T2 whole brain? Have you tried it 
without --seg-erode?


Thanks again for the prompt replies,
 — Noam



On Jan 27, 2015, at 6:02 PM, Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>> wrote:




First off, I would use --init-header instead of --init-spm. Probably 
won't make a difference, but it is safer in this case. Second, look 
at the registration in tkregister (bbregister prints out the command 
line, you can just cut and paste).

doug

ps. Please remember to post the list instead of directly to us. thanks!



On 1/27/15 11:23 AM, Ben Eliezer, Noam wrote:

Hi Doug —

My apologies for the confusion. Please ignore the commands set below.
There is only one set of commands that I tried.

It’s:

>> mri_convert -it siemens_dicom -ot mgz 
SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm 
T2_siemens.mgz
>> bbregister --s subj01 --mov T2_siemens.mgz   --reg 
T2_siemens_regMat.dat --init-spm --t2
>> mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz 
--interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat 
--no-save-reg
>> mri_segstats --seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 
--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i 
T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1


But as I wrote below — loading the registered T2 map 
T2_siemens_reg.mgz into Freeview shows that it’s incorrectly 
registered on the segmentation maps.


Thanks and sorry for the confusion,
 — Noam


On Jan 27, 2015, at 5:07 PM, Ben Eliezer, Noam 
mailto:noam.ben-elie...@nyumc.org>> wrote:



Hi Doug —

Thank you for the prompt reply!

I have indeed tried using bbregister (and consult the -- help) but 
I am probably not using it correctly.


I’ve tried two set of commands:

>> mri_convert -it siemens_dicom -ot mgz 
SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm 
T2_siemens.mgz
>> bbregister --s subj01--mov T2_siemens.mgz   --reg 
T2_siemens_regMat.dat --init-spm --t2
>> mri_segstats —seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 
--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i 
T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1


or,
>> mri_convert -it siemens_dicom -ot mgz 
SEMC_siemens_T2maps/1.3.12.2.1107.5.2.19.45219.2014072207350934197931766.dcm 
T2_siemens.mgz
>> mri_vol2vol --mov T2_siemens.mgz --targ 
subj01/mri/aparc+aseg.mgz --interp nearest --o T2_siemens_reg.mgz 
--reg T2_siemens_regMat.dat --no-save-reg
>> mri_segstats --seg subj01/mri/aparc+aseg.mgz --id 2 7 41 46 
--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i 
T2_siemens_reg.mgz --sum T2_siemens_stats.st

Re: [Freesurfer] Extraction of T2 map statistics-per-segment

[Douglas Greve]

It is finding 0s in the T2 (the range is 0-4000). I'm not sure about the 
4000, but the 0s indicate that something is strange with that image. How 
was it created?


On 1/27/15 1:22 PM, Ben Eliezer, Noam wrote:
— I (think that) I am not really interested in converting into rawavg 
coordinate system, but just need to register my T2 maps to the 
segmentation maps.

So, I guess that aseg+aparc.mgz will suffice in my case

— Regarding the mean +- std values:
Yes - the T2 maps are whole brain. could that account for the large STD?

I have tried running it w/o --seg-erode.… the mean values stay similar 
yet, the standard-deviation increases significantly.
I’ve also tried erode=2 pixels, which gave identical results to 
erode=1 pixel.


With erode (2 pixels):
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev 
Min Max Range
  1   2125567   125567.0  Left-Cerebral-White-Matter   97.9045
68.8609 0.  4000.  4000.
  2   7 1083310833.0  Left-Cerebellum-White-Matter   1.1878
14.7193 0.   608.   608.
  3  41130433   130433.0  Right-Cerebral-White-Matter   96.1764
60.0490 0.  4000.  4000.
  4  46 1155111551.0  Right-Cerebellum-White-Matter   1.2395  
  15.3000 0.   453.   453.


With erode (1 pixel):
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev 
Min Max Range
  1   2125567   125567.0  Left-Cerebral-White-Matter 97.9045
68.8609 0.  4000.  4000.
  2   7 1083310833.0  Left-Cerebellum-White-Matter 1.1878
14.7193 0.   608.   608.
  3 41130433   130433.0  Right-Cerebral-White-Matter 96.1764
60.0490 0.  4000.  4000.
  4 46 1155111551.0  Right-Cerebellum-White-Matter 1.2395
15.3000 0.   453.   453.


Without erode:
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev 
Min Max Range
  1   2193533   193533.0  Left-Cerebral-White-Matter   99.1265   
125.6069 0.  4000.  4000.
  2   7 1779417794.0  Left-Cerebellum-White-Matter   7.2259
65.3060 0.  4000.  4000.
  3  41197895   197895.0  Right-Cerebral-White-Matter   96.9839   
115.9002 0.  4000.  4000.
  4  46 1799917999.0  Right-Cerebellum-White-Matter   6.0798  
  88.1490 0.  4000.  4000.


It’s indeed encouraging that using the erode option decreases the STD, 
but I’m still wondering whether there a way to validate accuracy of 
the values.


Thanks!
 Noam


On Jan 27, 2015, at 6:50 PM, Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>> wrote:




On 1/27/15 12:38 PM, Ben Eliezer, Noam wrote:

Thanks Doug.

I’ve made two changes to the set of commands.

*1.* Following your suggestion, I’ve shifted from --init-spm to 
--init-header and now tkregister2 shows that the registration is OK.


>>tkregister2 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat —surf
Thanks!


*2.* When loading the result of vol2vol command (T2_siemens_reg.mgz):
  >> mri_vol2vol --mov T2_siemens.mgz --targ 
subj01/mri/aparc+aseg-in-rawavg.mgz --interp nearest --o 
T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg
into freeview the maps are rotated 90-deg in-plane and 90-deg 
through plane versus the segmentation maps — in short they do not 
match in orientation.


I’ve solved this by changing from using aseg+aparc-in-rawavg.mgz to 
aseg+aparg.mgz
>> mri_vol2vol --mov T2_siemens.mgz --targ subj01/mri/aparc+aseg.mgz 
--interp nearest --o T2_siemens_reg.mgz --reg T2_siemens_regMat.dat 
--no-save-reg


_Question1:_ Is that a correct approach? not to use the rawavg 
coordinate system?
Oh, I did not see that. Yes, that is the problem. If you want to use 
the rawavg coordinate system, then you'll have to create another 
registration file because the one that you have only goes between the 
T2 and the conformed 256 1mm space. Let me know if that is what you want.


—

Now, I re- gather statistics using:
>> mri_segstats --seg $FSsubjDIR/mri/aparc+aseg.mgz --id 2 7 41 46 
--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i 
T2_siemens_reg.mgz --sum T2_siemens_stats.stats --seg-erode 1


and get the following values:
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev 
Min Max Range
  1   2125567   125567.0 Left-Cerebral-White-Matter
97.904568.8609   0.  4000.  4000.
  2   7 1083310833.0 Left-Cerebellum-White-Matter   
1.187814.7193   0.   608.   608.
  3  41130433   130433.0 Right-Cerebral-White-Matter   
96.176460.0490   0.  4000.  4000.
  4  46 1155111551.0 Right-Cerebellum-White-Matter  
1.239515.3000   0.   453.   453.


_Question 2:_
Is there any way to verify that these values are accurate…?
(I am a little worried by the large standard deviation values)
Yes, I see what you mean. Is the T2 wh

Re: [Freesurfer] retinotopy in subject volumetric space

[Douglas Greve]

Ugh, that's weird, I don't know what's going on with that. I'll have to 
dig into it more.


On 1/27/15 1:26 PM, Benjamin Zimmerman wrote:

Hello,

When I try your recommended code, I am able to get the data back into 
volumetric space, but one hemisphere's cortex is significantly thinner 
than the other. If I do mri_surf2vol separately on each hemisphere, I 
don't have this problem. It seems to occur only if I try merging the 
two files. I assume that this is because I am using the volume that I 
am merging to as a template instead of inputting the template 
directly. Do you have any ideas how to solve this problem?


Thanks for your help,

Ben







On Wed, Dec 24, 2014 at 2:57 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:



I don't think we have a tool to display the color wheel in a
volume. FreeView might be able to do it. For the color wheel in
tksurfer, you are looking at the angle file (one for eccen and one
for polar), so you would map them. You can run mri_surf2vol
something like

mri_surf2vol --surfval lh.angle.nii.gz --identity yoursubject
--hemi lh --template path/orig.mgz --fillribbon --o vol.angle.mgz
mri_surf2vol --surfval rh.angle.nii.gz --identity yoursubject
--hemi rh  --fillribbon --merge vol.angle.mgz --o vol.angle.mgz

doug


On 12/18/14 1:24 PM, Benjamin Zimmerman wrote:

I mean the individual's anatomical volumetric space.

On Thu, Dec 18, 2014 at 11:53 AM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>>
wrote:


What do you mean by the individual's volumetric space? The
anatomical
space or the functional space?


On 12/16/2014 05:18 PM, Benjamin Zimmerman wrote:
> Thanks for the advice. I thought I would like to use
mri_surf2vol, but
> I am a little confused about the parameters and how they
relate to
> what the retinotopy analysis outputs.
>
> To be explicit, I want to view the real.nii.gz and
imag.nii.gz files
> in an individual's volumetric space. I can load these as
overlays to
> the inflated surface using tksurfer  
inflated.
> Then I can configure the overlay to use a color wheel color
scale and
> display as complex to see the retinotopic mapping.
>
> I'm not sure how I would go about using mri_surf2vol to
recreate this
> map in volumetric space. Should I just use real.nii.gz and
imag.nii.gz
> as surfval? Where is the registration file outputted in a
retinotopy
> analysis?
>
> Thank you for any more help that you can provide,
>
> Ben
>
> On Mon, Dec 15, 2014 at 3:26 PM, dgw mailto:dgwake...@gmail.com>
> <mailto:dgwake...@gmail.com <mailto:dgwake...@gmail.com>>> wrote:
>
> Hi Ben,
>
> You should be able to map it back with mri_surf2vol. I
haven't done
> this, but the wiki page looks fairly detailed:
> http://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol
>
> HTH
> D
>
> On Mon, Dec 15, 2014 at 3:43 PM, Benjamin Zimmerman
> mailto:benjamin.zimmerm...@gmail.com>
> <mailto:benjamin.zimmerm...@gmail.com
<mailto:benjamin.zimmerm...@gmail.com>>> wrote:
> > Hi all,
> >
> > FsFast has an excellent individual retinotopy
analysis that
> allows me to see
> > phase data on the inflated surface of the brain. Is
there a way
> to view the
> > results of the retinotopy analysis in the subject's
original
> volumetric
> > space rather than on the subject's surface space?
> >
> > Thank you for any help,
> >
> > Ben
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto: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
> 

Re: [Freesurfer] Extraction of T2 map statistics-per-segment

[Douglas Greve]

On 1/27/15 1:56 PM, Ben Eliezer, Noam wrote:
The maps were generated by Siemens scanner, fitting a multi-spin-echo 
protocol.


I see your point, though. The values should not range between 0 to 
4000. The latter 4000 value is the background out-of-brain map value.
But when looking at the T2_siemens_reg.mgz, overlaid on the 
aparc+aseg.mgz in freeview, the white matter (segment #2) seems well 
within the brain, and does not include any parts that have value = 0 
or 4000.


_Question 1_: is it possible to look at the actual set of values that 
are used to calculate these mean and STD result?
This would probably give some hint as to the large std. Perhaps there 
are small number of outliers that contribute to the large variation?

You can use matlab, something like
t2 = MRIread('T2_siemsn_reg.mgz');
seg = MRIread('aparc+aseg.mgz');
ind = find(seg.vol == 17); % left hippo
t2hip = t2.vol(ind);

See $FREESURFER_HOME/FreeSurferColorLUT.txt for a list of segmentation 
numbers


_Question 2_: (just to put my mind at rest): if both tkregister2 and 
freeview show show that the maps register accurately on the 
segmentation data, does it mean that mri_segstats masks the T2 maps 
correctly?
I’m asking this because if the segmentation masks are off by, e.g., 
90-degree, it would cause to a large number of values=4000 to be 
included in the mean/std values.

It should. You can also try
tkmedit -f t2file.mgz -seg  aparc+aseg.mgz




Thanks!
 — Noam

On Jan 27, 2015, at 7:30 PM, Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>> wrote:




It is finding 0s in the T2 (the range is 0-4000). I'm not sure about 
the 4000, but the 0s indicate that something is strange with that 
image. How was it created?


On 1/27/15 1:22 PM, Ben Eliezer, Noam wrote:
— I (think that) I am not really interested in converting into 
rawavg coordinate system, but just need to register my T2 maps to 
the segmentation maps.

So, I guess that aseg+aparc.mgz will suffice in my case

— Regarding the mean +- std values:
Yes - the T2 maps are whole brain. could that account for the large STD?

I have tried running it w/o --seg-erode.… the mean values stay 
similar yet, the standard-deviation increases significantly.
I’ve also tried erode=2 pixels, which gave identical results to 
erode=1 pixel.


With erode (2 pixels):
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev 
Min Max Range
  1   2125567   125567.0 Left-Cerebral-White-Matter
97.904568.8609   0.  4000.  4000.
  2   7 1083310833.0 Left-Cerebellum-White-Matter   
1.187814.7193   0.   608.   608.
  3  41130433   130433.0 Right-Cerebral-White-Matter   
96.176460.0490   0.  4000.  4000.
  4  46 1155111551.0 Right-Cerebellum-White-Matter  
1.239515.3000   0.   453.   453.


With erode (1 pixel):
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev 
Min Max Range
  1   2125567   125567.0 Left-Cerebral-White-Matter
97.904568.8609   0.  4000.  4000.
  2   7 1083310833.0 Left-Cerebellum-White-Matter   
1.187814.7193   0.   608.   608.
  3  41130433   130433.0 Right-Cerebral-White-Matter   
96.176460.0490   0.  4000.  4000.
  4  46 1155111551.0 Right-Cerebellum-White-Matter  
1.239515.3000   0.   453.   453.


Without erode:
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev 
Min Max Range
  1   2193533   193533.0 Left-Cerebral-White-Matter
99.1265   125.6069   0.  4000.  4000.
  2   7 1779417794.0 Left-Cerebellum-White-Matter   
7.225965.3060   0.  4000.  4000.
  3  41197895   197895.0 Right-Cerebral-White-Matter   
96.9839   115.9002   0.  4000.  4000.
  4  46 1799917999.0 Right-Cerebellum-White-Matter  
6.079888.1490   0.  4000.  4000.


It’s indeed encouraging that using the erode option decreases the 
STD, but I’m still wondering whether there a way to validate 
accuracy of the values.


Thanks!
 Noam


On Jan 27, 2015, at 6:50 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:




On 1/27/15 12:38 PM, Ben Eliezer, Noam wrote:

Thanks Doug.

I’ve made two changes to the set of commands.

*1.* Following your suggestion, I’ve shifted from --init-spm to 
--init-header and now tkregister2 shows that the registration is OK.


>>tkregister2 --mov T2_siemens.mgz --reg T2_siemens_regMat.dat —surf
Thanks!


*2.* When loading the result of vol2vol command (T2_siemens_reg.mgz):
  >> mri_vol2vol --mov T2_siemens.mgz --targ 
subj01/mri/aparc+aseg-in-rawavg.mgz --interp nearest --o 
T2_siemens_reg.mgz --reg T2_siemens_regMat.dat --no-save-reg
into freeview the maps are rotated 90-deg in-plane and 90-deg 
through plane versus the segmentation maps — in short they do not 
match in orientation.

Re: [Freesurfer] Extraction of T2 map statistics-per-segment

[Douglas Greve]

mri_segstats also has a --mask option. It will exclude anything not in 
the mask. There are a few mask options like setting thresholds, etc

doug


On 1/28/15 4:17 PM, Ben Eliezer, Noam wrote:

Dear Doug —

Your suggestion worked perfectly.
I’ve loaded the segmentation data (aparc+aseg.mgz) and the registered 
T2 maps into MATLAB and was able to detect a few outliers that biased 
the standard-deviation of the statistics.


I’ll apply the same approach to collect statistics for the rest of the 
segments.


Thank you once again for all the help.

Noam


On Jan 27, 2015, at 11:39 PM, Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>> wrote:




On 1/27/15 1:56 PM, Ben Eliezer, Noam wrote:
The maps were generated by Siemens scanner, fitting a 
multi-spin-echo protocol.


I see your point, though. The values should not range between 0 to 
4000. The latter 4000 value is the background out-of-brain map value.
But when looking at the T2_siemens_reg.mgz, overlaid on the 
aparc+aseg.mgz in freeview, the white matter (segment #2) seems well 
within the brain, and does not include any parts that have value = 0 
or 4000.


_Question 1_: is it possible to look at the actual set of values 
that are used to calculate these mean and STD result?
This would probably give some hint as to the large std. Perhaps 
there are small number of outliers that contribute to the large 
variation?

You can use matlab, something like
t2 = MRIread('T2_siemsn_reg.mgz');
seg = MRIread('aparc+aseg.mgz');
ind = find(seg.vol == 17); % left hippo
t2hip = t2.vol(ind);

See $FREESURFER_HOME/FreeSurferColorLUT.txt for a list of 
segmentation numbers


_Question 2_: (just to put my mind at rest): if both tkregister2 and 
freeview show show that the maps register accurately on the 
segmentation data, does it mean that mri_segstats masks the T2 maps 
correctly?
I’m asking this because if the segmentation masks are off by, e.g., 
90-degree, it would cause to a large number of values=4000 to be 
included in the mean/std values.

It should. You can also try
tkmedit -f t2file.mgz -seg  aparc+aseg.mgz




Thanks!
 — Noam

On Jan 27, 2015, at 7:30 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:




It is finding 0s in the T2 (the range is 0-4000). I'm not sure 
about the 4000, but the 0s indicate that something is strange with 
that image. How was it created?


On 1/27/15 1:22 PM, Ben Eliezer, Noam wrote:
— I (think that) I am not really interested in converting into 
rawavg coordinate system, but just need to register my T2 maps to 
the segmentation maps.

So, I guess that aseg+aparc.mgz will suffice in my case

— Regarding the mean +- std values:
Yes - the T2 maps are whole brain. could that account for the 
large STD?


I have tried running it w/o --seg-erode.… the mean values stay 
similar yet, the standard-deviation increases significantly.
I’ve also tried erode=2 pixels, which gave identical results to 
erode=1 pixel.


With erode (2 pixels):
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean 
StdDev Min Max Range
  1   2125567   125567.0 Left-Cerebral-White-Matter
97.9045 68.8609 0.  4000.  4000.
  2   7 1083310833.0 Left-Cerebellum-White-Matter   
1.1878 14.7193 0.   608.   608.
  3  41130433   130433.0 Right-Cerebral-White-Matter   
96.1764 60.0490 0.  4000.  4000.
  4  46 1155111551.0 Right-Cerebellum-White-Matter  
1.2395 15.3000 0.   453.   453.


With erode (1 pixel):
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean 
StdDev Min Max Range
  1   2125567 125567.0  Left-Cerebral-White-Matter 97.9045
68.8609 0.  4000. 4000.
  2   7 10833 10833.0  Left-Cerebellum-White-Matter 1.1878
14.7193 0.   608. 608.
  3  41130433 130433.0  Right-Cerebral-White-Matter 96.1764
60.0490 0.  4000. 4000.
  4  46 11551 11551.0  Right-Cerebellum-White-Matter 1.2395
15.3000 0.   453. 453.


Without erode:
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean 
StdDev Min Max Range
  1   2193533   193533.0 Left-Cerebral-White-Matter
99.1265 125.6069 0.  4000.  4000.
  2   7 1779417794.0 Left-Cerebellum-White-Matter   
7.2259 65.3060 0.  4000.  4000.
  3  41197895   197895.0 Right-Cerebral-White-Matter   
96.9839 115.9002 0.  4000.  4000.
  4  46 1799917999.0 Right-Cerebellum-White-Matter  
6.0798 88.1490 0.  4000.  4000.


It’s indeed encouraging that using the erode option decreases the 
STD, but I’m still wondering whether there a way to validate 
accuracy of the values.


Thanks!
 Noam


On Jan 27, 2015, at 6:50 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:




On 1/27/15 12:38 PM, Ben Eliezer, Noam wrote:

Thanks Doug.

I’ve made two changes to the set of c

Re: [Freesurfer] missing raw.fsnr files

[Douglas Greve]

I have no idea what the problem is. You can have it exclude the fsnr 
maps by adding -no-anamaps, though there might be something else going 
on with the data. Can you give me the location of your data and 
SUBJECTS_DIR as well as the command line you ran and the full terminal  
output of the command line?


doug

On 1/29/15 2:33 PM, Baran, Bengi wrote:

Hi,

We're trying to run isxconcat -sess and ran into the following error:

ERROR: cannot determine format for stem /raw.fsnr

Apparently our individual subject analysis files do not include a 
raw.fsnr file instead we have fsnr.nii in all the contrast folders.


This error terminates isxconcat so we're unable to get the surface 
based ces.nii etc files


Any idea why that may be the case or is there any flag to remove this 
step?


Best,



Bengi Baran, Ph.D.
Post-Doctoral Fellow
Martinos Center for Biomedical Imaging
Harvard Medical School
Massachusetts General Hospital
149 13th Street
Charlestown Navy Yard
Charlestown, MA 02129
email: bba...@partners.org 
phone: 617-643-7964
fax: 617-726-4078
https://sleep.med.harvard.edu/people/trainees/1598/Bengi+Baran+MA+PhD



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

Re: [Freesurfer] average values per cluster

[Douglas Greve]

You should report the clusterwise p-value. The p-value that you have 
computed is not interpretable. If it did not come out significant, then 
it would be worrisome, but it is only a check and cannot be used for 
anything. What p-value did you get from SPSS? I'd be curious to know 
what the source of the descrpancy is since this has happened several 
times now.


doug

On 1/30/15 3:25 AM, maaike rive wrote:

Hi Douglas,

I used the matlab code and the p value is signifiant, although less so 
than the p-value I get from the clusterwise statistics (0.0027 vs 
0.00010). (Indeed I used an abs threshold for the 
clusterwise statistics).


Which p-value should I report?

Thanks,

Maaike


From: r_maa...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Thu, 29 Jan 2015 19:48:44 +0100
Subject: Re: [Freesurfer] average values per cluster

No not yet; I will do so!

> Date: Thu, 29 Jan 2015 13:44:33 -0500
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] average values per cluster
>
>
> The t is correct. When the contrast matrix only has one row, then the F
> is just an unsigned t. I don't know anything about SPSS so I can't tell
> from what you have sent whether it is the same model or not. Try to get
> SPSS to output the design matrix. Did you try the matlab code below?
>
> On 01/29/2015 01:40 PM, maaike rive wrote:
> > Hi Douglas,
> >
> > I checked but as far as I see it I used the same models. I attached
> > the SPSS model and output as wel as the FSGD file and contrast file
> > (to test a diagnosis x age interaction). Now that I come to think of
> > it, I think the reason for the discrepant findings is that I used a
> > t-contrast instead of an F-contrast for the interaction in 
Freesurfer.

> > Apologies I did not think about this earlier. But maybe there is
> > something else I did completely wrong.
> >
> > What do you think?
> >
> > If it is indeed the t vs F contrast, than how should I specify that
> > the contrast is an F-contrast? Is it ok to just add another line to
> > the contrastfile (so
> > 0 0 0 0 0 0 0 0 1 1 1 1 -1 -1 -1 -1
> > 0 0 0 0 0 0 0 0 -1 -1 -1 -1 1 1 1 1)?
> >
> > Thanks again,
> >
> > Maaike
> >
> > > Date: Mon, 26 Jan 2015 11:23:59 -0500
> > > From: gr...@nmr.mgh.harvard.edu
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] average values per cluster
> > >
> > >
> > > We get these kind of reports occasionally. When I ask people to 
confirm

> > > that they use exactly the same design matrix in SPSS, I never hear
> > back,
> > > so I assume that it gets resolved. So please check. The other 
thing you

> > > can do is to run in matlab, something like
> > >
> > > cd glmdir/contrast
> > > X = load('Xg.dat');
> > > y = load('ocn.dat');
> > > C = load('C.dat');
> > > [beta rvar] = fast_glmfit(y,X);
> > > [F p] = fast_fratio(beta,X,rvar,C);
> > > p will be the p-value
> > >
> > > If you used an unsigned cluster-forming threshold (ie, abs), 
then it is
> > > possible that some of the voxels are pos and some are neg so 
that they

> > > average out
> > >
> > > doug
> > >
> > >
> > >
> > >
> > > On 01/26/2015 09:03 AM, maaike rive wrote:
> > > > Dear Freesurfer experts,
> > > >
> > > > Sorry to bother you again, but I have two more questions about
> > > > extracting (thickness/surface/GI) values from a certain cluster.
> > > >
> > > > As I understood, the abs.y.ocn.dat file gives the average values
> > for a
> > > > given significant cluster (e.g. a cluster where there is a
> > significant
> > > > AxB interaction).
> > > >
> > > > I may be completely misunderstanding things, but if I use these
> > values
> > > > in SPSS for further statistics and test the same interaction 
(AxB),

> > > > than according to SPSS this interaction is /not /significant
> > > > (corrected for the same covariates as in the FSGD file).
> > > >
> > > > Could you tell me what is going wrong here? I do not trust my
> > results now.
> > > >
> > > > Furthermore, is it possible (and if so, how?) to extract the 
average
> > > > values of exactly the same cluster, but in an independent 
group not

> > > > used in the analysis, for post-hoc comparisons in SPSS?
> > > >
> > > > Thanks,
> > > >
> > > > Maaike
> > > >
> > > >
> > > > ___
> > > > 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/

> > >
> > > _

Re: [Freesurfer] Mri_segstats

[Douglas Greve]

There is not a flag to control the printing format. However, you can 
multiply the values by a constant (--mul flag). Eg, you can multiply all 
values by 100 or divide by 100.
doug

On 1/30/15 11:42 AM, Alshikho, Mohamad J. wrote:
> Dear FS Experts,
> In order to generate the statistics using mri_segstats I ran the following 
> command line:
>
> mri_segstats --seg${in}/${i}/mri/aparc+aseg.mgz --ctab-default --i 
> ${insa}/${i}/fa.anat.nii --mask ${insa}/${i}//svs.anat.nii --sum 
> ${insa}/${i}/fa.summary.dat
>
> In the final report (fa.summary.dat ) I can see that mri_segstats generated 
> the results for FA with a decimal number and four digits after the point like 
> (0.3130) is there any flag can control the count of numbers after the (0.) in 
> order to increase or decrease the numbers?
>
> Thanks
> Mohamad
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>

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Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."

[Douglas Greve]

Can you run the following cmd and send me the terminal output?

mkcontrast -debug -anadir RM_hard_easy_fake_error -wcond 1. 
-.5000 -.5000 0 -sumconds -o 
RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave


On 1/30/15 12:15 PM, Karahanoglu, Fikret Isik wrote:
>
> Dear all,
>
> We are trying to make a new contrast for our GLM analysis, however we have 
> the following flag error.
>
> Is there any solution for this?
>
> Thank you
> isik
>
> [schnook:subjects] (nmr-stable53-env) mkcontrast-sess -an 
> RM_hard_easy_fake_error -co hard_v_fake+easy -a 1 -c 2 -c 3
> (standard_in) 1: syntax error
> INFO: Found 4 Non-Null Conditions
> INFO: Found  Delays
> Condition Weights: 1. -.5000 
> -.5000 0
> mkcontrast -anadir RM_hard_easy_fake_error -wcond 1. 
> -.5000 -.5000 0 -sumconds -o 
> RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
>$Id: mkcontrast,v 1.10.2.1 2011/09/27 15:56:27 greve Exp $
> (standard_in) 1: syntax error
> ERROR: Flag 1 unrecognized.
> -anadir RM_hard_easy_fake_error -wcond 1. 
> -.5000 -.5000 0 -sumconds -o 
> RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
> ERROR running mkcontrast
> mkcontrast -anadir RM_hard_easy_fake_error -wcond 1. 
> -.5000 -.5000 0 -sumconds -o 
> RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
> Fri Jan 30 12:07:42 EST 2015
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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Re: [Freesurfer] average values per cluster

[Douglas Greve]

>>>I told him it the model is a GLM with age, gender and state as 
covariates


This is not a sufficient description. Several design matrices could be 
derived from this description.


On 1/30/15 11:58 AM, maaike rive wrote:
The p value from SPSS is 0.156. I checked with a statistician, just to 
be sure, but he says the SPSS model is correct... (he doesn't know 
anything about freesurfer and FSGD files, but I told him it the model 
is a GLM with age, gender and state as covariates).


Date: Fri, 30 Jan 2015 11:46:37 -0500
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] average values per cluster


You should report the clusterwise p-value. The p-value that you have 
computed is not interpretable. If it did not come out significant, 
then it would be worrisome, but it is only a check and cannot be used 
for anything. What p-value did you get from SPSS? I'd be curious to 
know what the source of the descrpancy is since this has happened 
several times now.


doug

On 1/30/15 3:25 AM, maaike rive wrote:

Hi Douglas,

I used the matlab code and the p value is signifiant, although
less so than the p-value I get from the clusterwise statistics
(0.0027 vs 0.00010). (Indeed I used an abs threshold for the
clusterwise statistics).

Which p-value should I report?

Thanks,

Maaike


From: r_maa...@hotmail.com 
To: freesurfer@nmr.mgh.harvard.edu

Date: Thu, 29 Jan 2015 19:48:44 +0100
Subject: Re: [Freesurfer] average values per cluster

No not yet; I will do so!

> Date: Thu, 29 Jan 2015 13:44:33 -0500
> From: gr...@nmr.mgh.harvard.edu 
> To: freesurfer@nmr.mgh.harvard.edu

> Subject: Re: [Freesurfer] average values per cluster
>
>
> The t is correct. When the contrast matrix only has one row,
then the F
> is just an unsigned t. I don't know anything about SPSS so I
can't tell
> from what you have sent whether it is the same model or not. Try
to get
> SPSS to output the design matrix. Did you try the matlab code below?
>
> On 01/29/2015 01:40 PM, maaike rive wrote:
> > Hi Douglas,
> >
> > I checked but as far as I see it I used the same models. I
attached
> > the SPSS model and output as wel as the FSGD file and contrast
file
> > (to test a diagnosis x age interaction). Now that I come to
think of
> > it, I think the reason for the discrepant findings is that I
used a
> > t-contrast instead of an F-contrast for the interaction in
Freesurfer.
> > Apologies I did not think about this earlier. But maybe there is
> > something else I did completely wrong.
> >
> > What do you think?
> >
> > If it is indeed the t vs F contrast, than how should I specify
that
> > the contrast is an F-contrast? Is it ok to just add another
line to
> > the contrastfile (so
> > 0 0 0 0 0 0 0 0 1 1 1 1 -1 -1 -1 -1
> > 0 0 0 0 0 0 0 0 -1 -1 -1 -1 1 1 1 1)?
> >
> > Thanks again,
> >
> > Maaike
> >
> > > Date: Mon, 26 Jan 2015 11:23:59 -0500
> > > From: gr...@nmr.mgh.harvard.edu

> > > To: freesurfer@nmr.mgh.harvard.edu

> > > Subject: Re: [Freesurfer] average values per cluster
> > >
> > >
> > > We get these kind of reports occasionally. When I ask people
to confirm
> > > that they use exactly the same design matrix in SPSS, I
never hear
> > back,
> > > so I assume that it gets resolved. So please check. The
other thing you
> > > can do is to run in matlab, something like
> > >
> > > cd glmdir/contrast
> > > X = load('Xg.dat');
> > > y = load('ocn.dat');
> > > C = load('C.dat');
> > > [beta rvar] = fast_glmfit(y,X);
> > > [F p] = fast_fratio(beta,X,rvar,C);
> > > p will be the p-value
> > >
> > > If you used an unsigned cluster-forming threshold (ie, abs),
then it is
> > > possible that some of the voxels are pos and some are neg so
that they
> > > average out
> > >
> > > doug
> > >
> > >
> > >
> > >
> > > On 01/26/2015 09:03 AM, maaike rive wrote:
> > > > Dear Freesurfer experts,
> > > >
> > > > Sorry to bother you again, but I have two more questions about
> > > > extracting (thickness/surface/GI) values from a certain
cluster.
> > > >
> > > > As I understood, the abs.y.ocn.dat file gives the average
values
> > for a
> > > > given significant cluster (e.g. a cluster where there is a
> > significant
> > > > AxB interaction)

Re: [Freesurfer] average values per cluster

[Douglas Greve]

It depends on the actual covariates and whether you used DOSS or DODS. 
The default is DODS, which is a full interaction model. Assuming that 
state is a categorical variable with 2 levels, you'd have 4 regressors 
(gender by state) + 4 more regressors (gender by state by age). If the 
SPSS model did not have 8 regressors, then it is not the same.


doug

On 1/30/15 1:26 PM, maaike rive wrote:

How should I have described the model?


Date: Fri, 30 Jan 2015 13:09:40 -0500
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] average values per cluster

>>>I told him it the model is a GLM with age, gender and state as 
covariates


This is not a sufficient description. Several design matrices could be 
derived from this description.


On 1/30/15 11:58 AM, maaike rive wrote:

The p value from SPSS is 0.156. I checked with a statistician,
just to be sure, but he says the SPSS model is correct... (he
doesn't know anything about freesurfer and FSGD files, but I told
him it the model is a GLM with age, gender and state as covariates).

Date: Fri, 30 Jan 2015 11:46:37 -0500
From: gr...@nmr.mgh.harvard.edu 
To: freesurfer@nmr.mgh.harvard.edu

Subject: Re: [Freesurfer] average values per cluster


You should report the clusterwise p-value. The p-value that you
have computed is not interpretable. If it did not come out
significant, then it would be worrisome, but it is only a check
and cannot be used for anything. What p-value did you get from
SPSS? I'd be curious to know what the source of the descrpancy is
since this has happened several times now.

doug

On 1/30/15 3:25 AM, maaike rive wrote:

Hi Douglas,

I used the matlab code and the p value is signifiant, although
less so than the p-value I get from the clusterwise statistics
(0.0027 vs 0.00010). (Indeed I used an abs threshold for the
clusterwise statistics).

Which p-value should I report?

Thanks,

Maaike


From: r_maa...@hotmail.com 
To: freesurfer@nmr.mgh.harvard.edu

Date: Thu, 29 Jan 2015 19:48:44 +0100
Subject: Re: [Freesurfer] average values per cluster

No not yet; I will do so!

> Date: Thu, 29 Jan 2015 13:44:33 -0500
> From: gr...@nmr.mgh.harvard.edu

> To: freesurfer@nmr.mgh.harvard.edu

> Subject: Re: [Freesurfer] average values per cluster
>
>
> The t is correct. When the contrast matrix only has one row,
then the F
> is just an unsigned t. I don't know anything about SPSS so I
can't tell
> from what you have sent whether it is the same model or not.
Try to get
> SPSS to output the design matrix. Did you try the matlab
code below?
>
> On 01/29/2015 01:40 PM, maaike rive wrote:
> > Hi Douglas,
> >
> > I checked but as far as I see it I used the same models. I
attached
> > the SPSS model and output as wel as the FSGD file and
contrast file
> > (to test a diagnosis x age interaction). Now that I come
to think of
> > it, I think the reason for the discrepant findings is that
I used a
> > t-contrast instead of an F-contrast for the interaction in
Freesurfer.
> > Apologies I did not think about this earlier. But maybe
there is
> > something else I did completely wrong.
> >
> > What do you think?
> >
> > If it is indeed the t vs F contrast, than how should I
specify that
> > the contrast is an F-contrast? Is it ok to just add
another line to
> > the contrastfile (so
> > 0 0 0 0 0 0 0 0 1 1 1 1 -1 -1 -1 -1
> > 0 0 0 0 0 0 0 0 -1 -1 -1 -1 1 1 1 1)?
> >
> > Thanks again,
> >
> > Maaike
> >
> > > Date: Mon, 26 Jan 2015 11:23:59 -0500
> > > From: gr...@nmr.mgh.harvard.edu

> > > To: freesurfer@nmr.mgh.harvard.edu

> > > Subject: Re: [Freesurfer] average values per cluster
> > >
> > >
> > > We get these kind of reports occasionally. When I ask
people to confirm
> > > that they use exactly the same design matrix in SPSS, I
never hear
> > back,
> > > 

Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."

[Douglas Greve]

sorry, can you send me your mkanalysis-sess command line as well? You 
can find it in the analysis.info file in the analysis folder

On 1/30/15 12:15 PM, Karahanoglu, Fikret Isik wrote:
>
> Dear all,
>
> We are trying to make a new contrast for our GLM analysis, however we have 
> the following flag error.
>
> Is there any solution for this?
>
> Thank you
> isik
>
> [schnook:subjects] (nmr-stable53-env) mkcontrast-sess -an 
> RM_hard_easy_fake_error -co hard_v_fake+easy -a 1 -c 2 -c 3
> (standard_in) 1: syntax error
> INFO: Found 4 Non-Null Conditions
> INFO: Found  Delays
> Condition Weights: 1. -.5000 
> -.5000 0
> mkcontrast -anadir RM_hard_easy_fake_error -wcond 1. 
> -.5000 -.5000 0 -sumconds -o 
> RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
>$Id: mkcontrast,v 1.10.2.1 2011/09/27 15:56:27 greve Exp $
> (standard_in) 1: syntax error
> ERROR: Flag 1 unrecognized.
> -anadir RM_hard_easy_fake_error -wcond 1. 
> -.5000 -.5000 0 -sumconds -o 
> RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
> ERROR running mkcontrast
> mkcontrast -anadir RM_hard_easy_fake_error -wcond 1. 
> -.5000 -.5000 0 -sumconds -o 
> RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
> Fri Jan 30 12:07:42 EST 2015
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] FREESURFER_HOME: Undefined variable. - path issue?

[Douglas Greve]

The sudo is causing it to run under a different user (root) which means 
that it opens a new shell that does not have the proper environment set. 
Why are you running it as root? If you set SUBJECTS_DIR to something 
other than


 /Applications/freesurfer/subjects you won't have to run as root

doug


On 1/30/15 1:43 PM, Tyler Good wrote:

Hi all,

I've seen very similar questions posted, but I haven't seen one with a 
response.


I just installed freesurfer onto a mac os x.  I did the following steps:

export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
and got this output:
 freesurfer-Darwin-lion-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/subjects
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /Users/Tyler/fsl
after working through the installation testing commands with no issue (qdec, 
recon-all --help, tkmedit, tksurfer), I tried to perform the following command:

sudo recon-all -s bert -autorecon1
and got this output:
FREESURFER_HOME: Undefined variable.
I did echo $FREESURFER_HOME to check the export/source worked and it returned 
/Applications/freesurfer which is correct!

I'm not sure what is going wrong! Thanks for any help!


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Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."

[Douglas Greve]

sorry, I wanted the mkanalysis-sess cmd, not the mkcontrast-sess

On 1/30/15 1:50 PM, Karahanoglu, Fikret Isik wrote:

So we ran

mkcontrast-sess -an RM_hard_easy_fake_error -co hard_v_fake+easy -a 1 -c 2 -c 3

from the terminal. I attach the mkcontrast-sess.log and anlaysis.info.
isik

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, January 30, 2015 1:39 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."

sorry, can you send me your mkanalysis-sess command line as well? You
can find it in the analysis.info file in the analysis folder

On 1/30/15 12:15 PM, Karahanoglu, Fikret Isik wrote:

Dear all,

We are trying to make a new contrast for our GLM analysis, however we have the 
following flag error.

Is there any solution for this?

Thank you
isik

[schnook:subjects] (nmr-stable53-env) mkcontrast-sess -an 
RM_hard_easy_fake_error -co hard_v_fake+easy -a 1 -c 2 -c 3
(standard_in) 1: syntax error
INFO: Found 4 Non-Null Conditions
INFO: Found  Delays
Condition Weights: 1. -.5000 
-.5000 0
mkcontrast -anadir RM_hard_easy_fake_error -wcond 1. 
-.5000 -.5000 0 -sumconds -o 
RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
$Id: mkcontrast,v 1.10.2.1 2011/09/27 15:56:27 greve Exp $
(standard_in) 1: syntax error
ERROR: Flag 1 unrecognized.
-anadir RM_hard_easy_fake_error -wcond 1. 
-.5000 -.5000 0 -sumconds -o 
RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
ERROR running mkcontrast
mkcontrast -anadir RM_hard_easy_fake_error -wcond 1. 
-.5000 -.5000 0 -sumconds -o 
RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
Fri Jan 30 12:07:42 EST 2015



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Re: [Freesurfer] missing raw.fsnr files

[Douglas Greve]

There is an error msg in the log file:

cat: 
/autofs/cluster/manoach/AS/RespMon12C/subjects/RMSCH012/subjectname: No 
such file or directory


Can you check whether this file exists? I don't have permission to view it.

doug


On 1/30/15 1:43 PM, Karahanoglu, Fikret Isik wrote:

OK, we will try with -no-anamaps flag.

the subjects_dir: /cluster/manoach/AS/RespMon12C/subjects

I attach our simple code and the log output.

Thank you,
bengi and isik



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, January 30, 2015 11:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] missing raw.fsnr files

I have no idea what the problem is. You can have it exclude the fsnr maps by 
adding -no-anamaps, though there might be something else going on with the 
data. Can you give me the location of your data and SUBJECTS_DIR as well as the 
command line you ran and the full terminal  output of the command line?

doug

On 1/29/15 2:33 PM, Baran, Bengi wrote:
Hi,

We're trying to run isxconcat -sess and ran into the following error:

ERROR: cannot determine format for stem /raw.fsnr

Apparently our individual subject analysis files do not include a raw.fsnr file 
instead we have fsnr.nii in all the contrast folders.

This error terminates isxconcat so we're unable to get the surface based 
ces.nii etc files

Any idea why that may be the case or is there any flag to remove this step?

Best,



Bengi Baran, Ph.D.
Post-Doctoral Fellow
Martinos Center for Biomedical Imaging
Harvard Medical School
Massachusetts General Hospital
149 13th Street
Charlestown Navy Yard
Charlestown, MA 02129
email: bba...@partners.org<mailto:bba...@partners.org>
phone: 617-643-7964
fax: 617-726-4078
https://sleep.med.harvard.edu/people/trainees/1598/Bengi+Baran+MA+PhD




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Re: [Freesurfer] average values per cluster

[Douglas Greve]

Actually, that looks correct. Is this what you fed to SPSS?

On 1/30/15 2:07 PM, maaike rive wrote:
Ok, I'm so sorry, I'm afraid I mixed things up. I indeed used DODS, 
and assumed these were may regressors:


diagn1*state1*gender1

diagn1*state1*gender2

diagn1*state2*gender1

diagn1*state2*gender2

diagn2*state1*gender1

diagn2*state1*gender2

diagn2*state2*gender1

diagn2*state2*gender2

diagn1*state1*gender1*age

diagn1*state1*gender2*age

diagn1*state2*gender1*age

diagn1*state2*gender2*age

diagn2*state1*gender1*age

diagn2*state1*gender2*age

diagn2*state2*gender1*age

diagn2*state2*gender2*age


However what I actually meant to do was testing for the effects of 
diagnosis and interactions (e.g. diagnosis*age) by using the 
appropriate contrasts, so I thought that if I used the contrast for 
the diagnosis*age interaction, I was testing whether or not this 
interaction was significant regressing out the effects of state and 
gender. Another example, I thought that if I used the contrast for 
diagnosis1 versus diagnosis2, I was testing wether or not there was a 
significant effect of diagnosis regressing out the effects of state, 
gender and age.



 But that is not the case than? How should I build the model to answer 
these questions?



Maaike




Date: Fri, 30 Jan 2015 13:33:40 -0500
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] average values per cluster


It depends on the actual covariates and whether you used DOSS or DODS. 
The default is DODS, which is a full interaction model. Assuming that 
state is a categorical variable with 2 levels, you'd have 4 regressors 
(gender by state) + 4 more regressors (gender by state by age). If the 
SPSS model did not have 8 regressors, then it is not the same.


doug

On 1/30/15 1:26 PM, maaike rive wrote:

How should I have described the model?


Date: Fri, 30 Jan 2015 13:09:40 -0500
From: gr...@nmr.mgh.harvard.edu 
To: freesurfer@nmr.mgh.harvard.edu

Subject: Re: [Freesurfer] average values per cluster

>>>I told him it the model is a GLM with age, gender and state as
covariates

This is not a sufficient description. Several design matrices
could be derived from this description.

On 1/30/15 11:58 AM, maaike rive wrote:

The p value from SPSS is 0.156. I checked with a statistician,
just to be sure, but he says the SPSS model is correct... (he
doesn't know anything about freesurfer and FSGD files, but I
told him it the model is a GLM with age, gender and state as
covariates).

Date: Fri, 30 Jan 2015 11:46:37 -0500
From: gr...@nmr.mgh.harvard.edu 
To: freesurfer@nmr.mgh.harvard.edu

Subject: Re: [Freesurfer] average values per cluster


You should report the clusterwise p-value. The p-value that
you have computed is not interpretable. If it did not come out
significant, then it would be worrisome, but it is only a
check and cannot be used for anything. What p-value did you
get from SPSS? I'd be curious to know what the source of the
descrpancy is since this has happened several times now.

doug

On 1/30/15 3:25 AM, maaike rive wrote:

Hi Douglas,

I used the matlab code and the p value is signifiant,
although less so than the p-value I get from the
clusterwise statistics (0.0027 vs 0.00010). (Indeed I used
an abs threshold for the clusterwise statistics).

Which p-value should I report?

Thanks,

Maaike



From: r_maa...@hotmail.com 
To: freesurfer@nmr.mgh.harvard.edu

Date: Thu, 29 Jan 2015 19:48:44 +0100
Subject: Re: [Freesurfer] average values per cluster

No not yet; I will do so!

> Date: Thu, 29 Jan 2015 13:44:33 -0500
> From: gr...@nmr.mgh.harvard.edu

> To: freesurfer@nmr.mgh.harvard.edu

> Subject: Re: [Freesurfer] average values per cluster
>
>
> The t is correct. When the contrast matrix only has one
row, then the F
> is just an unsigned t. I don't know anything about SPSS
so I can't tell
> from what you have sent whether it is the same model or
not. Try to get
 

Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."

[Douglas Greve]

This is analysis.info comes from an old version of FS and will not work 
with 5.3. When you made new contrasts before, are you sure you used 5.3?

doug

On 1/30/15 2:26 PM, Karahanoglu, Fikret Isik wrote:

We are just adding new analyses to a previous study, apparently, they didn't 
run mkanalysis-sess. But, instead, they modified
analysis.info and analysis.cfg (attached) from another study with the same 
design. But we had no problem before with other contrasts...
isik


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, January 30, 2015 1:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."

sorry, I wanted the mkanalysis-sess cmd, not the mkcontrast-sess

On 1/30/15 1:50 PM, Karahanoglu, Fikret Isik wrote:


So we ran

mkcontrast-sess -an RM_hard_easy_fake_error -co hard_v_fake+easy -a 1 -c 2 -c 3

from the terminal. I attach the mkcontrast-sess.log and anlaysis.info.
isik

From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on 
behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>]
Sent: Friday, January 30, 2015 1:39 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."

sorry, can you send me your mkanalysis-sess command line as well? You
can find it in the analysis.info file in the analysis folder

On 1/30/15 12:15 PM, Karahanoglu, Fikret Isik wrote:



Dear all,

We are trying to make a new contrast for our GLM analysis, however we have the 
following flag error.

Is there any solution for this?

Thank you
isik

[schnook:subjects] (nmr-stable53-env) mkcontrast-sess -an 
RM_hard_easy_fake_error -co hard_v_fake+easy -a 1 -c 2 -c 3
(standard_in) 1: syntax error
INFO: Found 4 Non-Null Conditions
INFO: Found  Delays
Condition Weights: 1. -.5000 
-.5000 0
mkcontrast -anadir RM_hard_easy_fake_error -wcond 1. 
-.5000 -.5000 0 -sumconds -o 
RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
$Id: mkcontrast,v 1.10.2.1 2011/09/27 15:56:27 greve Exp $
(standard_in) 1: syntax error
ERROR: Flag 1 unrecognized.
-anadir RM_hard_easy_fake_error -wcond 1. 
-.5000 -.5000 0 -sumconds -o 
RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
ERROR running mkcontrast
mkcontrast -anadir RM_hard_easy_fake_error -wcond 1. 
-.5000 -.5000 0 -sumconds -o 
RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
Fri Jan 30 12:07:42 EST 2015



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Re: [Freesurfer] FREESURFER_HOME: Undefined variable. - path issue?

[Douglas Greve]

Do you have write perms to this file and the folder it is in?
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env to 
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env.bak


On 1/30/15 3:09 PM, Tyler Good wrote:

Thanks so much for the fast reply Doug!

I changed the directory for freesurfer home...so now if I source, it 
returns:


source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-Darwin-lion-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Users/Tyler/Documents/freesurfer
FSFAST_HOME   /Users/Tyler/Documents/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Users/Tyler/Documents/freesurfer/subjects
MNI_DIR   /Users/Tyler/Documents/freesurfer/mni
FSL_DIR   /Users/Tyler/fsl

if I run a recon-all:
tyler's-macbook-pro:~ Tyler$ recon-all -s bert -autorecon1
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /Users/Tyler/Documents/freesurfer/subjects
Actual FREESURFER_HOME /Users/Tyler/Documents/freesurfer
rm: 
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.cmd: 
Permission denied
mv: rename 
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env 
to 
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env.bak: 
Permission denied
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env: 
Permission denied.
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env: 
Permission denied.


 I had free surfer on a virtual linux box on this machine previously. 
I changed the permissions to the bert folder so I would have write 
access and be able to avoid using sudo, before getting this message.



Any help would be greatly appreciated!

On Fri, Jan 30, 2015 at 1:50 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:



The sudo is causing it to run under a different user (root) which
means that it opens a new shell that does not have the proper
environment set. Why are you running it as root? If you set
SUBJECTS_DIR to something other than

  /Applications/freesurfer/subjects you won't have to run as root

doug


On 1/30/15 1:43 PM, Tyler Good wrote:

Hi all,

I've seen very similar questions posted, but I haven't seen one
with a response.

I just installed freesurfer onto a mac os x.  I did the following steps:

export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
and got this output:
 freesurfer-Darwin-lion-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/subjects
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /Users/Tyler/fsl
after working through the installation testing commands with no issue 
(qdec, recon-all --help, tkmedit, tksurfer), I tried to perform the following 
command:

sudo recon-all -s bert -autorecon1
and got this output:
FREESURFER_HOME: Undefined variable.
I did echo $FREESURFER_HOME to check the export/source worked and it 
returned /Applications/freesurfer which is correct!

I'm not sure what is going wrong! Thanks for any help!


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The information in this e-mail is intended only for the person to
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the e-mail
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Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."

[Douglas Greve]

I would redo everything with the new version. If you're mixing versions, 
I can't give you recommendations on what would work or not.

On 1/30/15 2:53 PM, Karahanoglu, Fikret Isik wrote:
> We ran individual level analysis with the existing contrasts, which didn't 
> yield any incompatibility issues.
>   So all other contrasts must have been created with old version.
> At that point what do you recommend? We continue with old version or redo 
> everything with new version?
> isik
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, January 30, 2015 2:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."
>
> This is analysis.info comes from an old version of FS and will not work with 
> 5.3. When you made new contrasts before, are you sure you used 5.3?
> doug
>
> On 1/30/15 2:26 PM, Karahanoglu, Fikret Isik wrote:
>
>
> We are just adding new analyses to a previous study, apparently, they didn't 
> run mkanalysis-sess. But, instead, they modified
> analysis.info and analysis.cfg (attached) from another study with the same 
> design. But we had no problem before with other contrasts...
> isik
>
> 
> From: 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>  
> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
>  on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>]
> Sent: Friday, January 30, 2015 1:59 PM
> To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."
>
> sorry, I wanted the mkanalysis-sess cmd, not the mkcontrast-sess
>
> On 1/30/15 1:50 PM, Karahanoglu, Fikret Isik wrote:
>
>
> So we ran
>
> mkcontrast-sess -an RM_hard_easy_fake_error -co hard_v_fake+easy -a 1 -c 2 -c 
> 3
>
> from the terminal. I attach the mkcontrast-sess.log and anlaysis.info.
> isik
> 
> From: 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>  
> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
>  on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>]
> Sent: Friday, January 30, 2015 1:39 PM
> To: 
> freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] mkcontrast-sess "ERROR: Flag 1 unrecognized."
>
> sorry, can you send me your mkanalysis-sess command line as well? You
> can find it in the analysis.info file in the analysis folder
>
> On 1/30/15 12:15 PM, Karahanoglu, Fikret Isik wrote:
>
>
>
> Dear all,
>
> We are trying to make a new contrast for our GLM analysis, however we have 
> the following flag error.
>
> Is there any solution for this?
>
> Thank you
> isik
>
> [schnook:subjects] (nmr-stable53-env) mkcontrast-sess -an 
> RM_hard_easy_fake_error -co hard_v_fake+easy -a 1 -c 2 -c 3
> (standard_in) 1: syntax error
> INFO: Found 4 Non-Null Conditions
> INFO: Found  Delays
> Condition Weights: 1. -.5000 
> -.5000 0
> mkcontrast -anadir RM_hard_easy_fake_error -wcond 1. 
> -.5000 -.5000 0 -sumconds -o 
> RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
> $Id: mkcontrast,v 1.10.2.1 2011/09/27 15:56:27 greve Exp $
> (standard_in) 1: syntax error
> ERROR: Flag 1 unrecognized.
> -anadir RM_hard_easy_fake_error -wcond 1. 
> -.5000 -.5000 0 -sumconds -o 
> RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
> ERROR running mkcontrast
> mkcontrast -anadir RM_hard_easy_fake_error -wcond 1. 
> -.5000 -.5000 0 -sumconds -o 
> RM_hard_easy_fake_error/hard_v_fake+easy.mat -wdelay 1 -no-octave
> Fri Jan 30 12:07:42 EST 2015
>
>
>
> 

Re: [Freesurfer] FREESURFER_HOME: Undefined variable. - path issue?

[Douglas Greve]

Some where in there you don't have perms, it might be one of the higher 
folders, try


chmod -R u+rwX /Users/Tyler/Documents/freesurfer/subjects



On 1/30/15 3:50 PM, Tyler Good wrote:

Hi Doug,
It looks I have rw perms for the both of those files and the folders 
they are in.

?
Thanks!


On Fri, Jan 30, 2015 at 3:11 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:



Do you have write perms to this file and the folder it is in?
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env
to
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env.bak



On 1/30/15 3:09 PM, Tyler Good wrote:

Thanks so much for the fast reply Doug!

I changed the directory for freesurfer home...so now if I source,
it returns:

source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-Darwin-lion-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Users/Tyler/Documents/freesurfer
FSFAST_HOME /Users/Tyler/Documents/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Users/Tyler/Documents/freesurfer/subjects
MNI_DIR /Users/Tyler/Documents/freesurfer/mni
FSL_DIR   /Users/Tyler/fsl

if I run a recon-all:
tyler's-macbook-pro:~ Tyler$ recon-all -s bert -autorecon1
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /Users/Tyler/Documents/freesurfer/subjects
Actual FREESURFER_HOME /Users/Tyler/Documents/freesurfer
rm:
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.cmd:
Permission denied
mv: rename
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env
to
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env.bak:
Permission denied
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env:
Permission denied.
/Users/Tyler/Documents/freesurfer/subjects/bert/scripts/recon-all.env:
Permission denied.

 I had free surfer on a virtual linux box on this machine
previously. I changed the permissions to the bert folder so I
would have write access and be able to avoid using sudo, before
getting this message.


Any help would be greatly appreciated!

On Fri, Jan 30, 2015 at 1:50 PM, Douglas Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


The sudo is causing it to run under a different user (root)
which means that it opens a new shell that does not have the
proper environment set. Why are you running it as root? If
you set SUBJECTS_DIR to something other than

  /Applications/freesurfer/subjects you won't have to run as root

doug


On 1/30/15 1:43 PM, Tyler Good wrote:

Hi all,

I've seen very similar questions posted, but I haven't seen
one with a response.

I just installed freesurfer onto a mac os x.  I did the following steps:

export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
and got this output:
 freesurfer-Darwin-lion-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/subjects
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /Users/Tyler/fsl
after working through the installation testing commands with no issue 
(qdec, recon-all --help, tkmedit, tksurfer), I tried to perform the following 
command:

sudo recon-all -s bert -autorecon1
and got this output:
FREESURFER_HOME: Undefined variable.
I did echo $FREESURFER_HOME to check the export/source worked and it 
returned /Applications/freesurfer which is correct!

I'm not sure what is going wrong! Thanks for any help!


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Re: [Freesurfer] fscalc.fsl bad dim error

[Douglas Greve]

what is your command line? Can you reduce it down to a file that seems 
to be giving you problems?


On 2/1/15 1:48 PM, Jonathan DuBois wrote:

Hi Freesurfers,

I am trying to use fscalc.fsl to do calculations on an fsaverage 
vertex map of values (mgh files). In some of these files, but not all, 
I get the following error:


** ERROR: nifti_convert_nhdr2nim: bad dim[1]
** ERROR (nifti_image_read): cannot create nifti image from header 
'./tmp.fscalc.fsl.57121/s1.nii.gz'

** ERROR: nifti_image_open(./tmp.fscalc.fsl.57121/s1): bad header info
ERROR: failed to open file ./tmp.fscalc.fsl.57121/s1
Cannot open volume ./tmp.fscalc.fsl.57121/s1 for reading!

I saw a similar list serve question in 2008 where Doug responded: "How 
many vertices does that subject have and is there a prime factor less 
than 2^15?" However, these surface maps have around 300k vertices, not 
less than 2^15.


I would really appreciate any advice with this. Thanks!

Jon


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Re: [Freesurfer] vertexwise statistical modeling

[Douglas Greve]

On 2/2/15 3:56 AM, Schweren, LJS (med) wrote:


Dear freesurfer experts,

I investigate case-control differences in cortical thickness in a 
group of 11 to 30 year olds. I ran vertex-wise analyses with glmfit, 
with covariates age and age-squared, to take into account confounding 
by age as we have a very wide age range. I use monte-carlo simulation 
testing. What results is the following:


-some clusters of between-group difference (which I was looking for, 
no worries here)


-a cluster covering almost the entire cortex being negatively 
correlated to the linear age term (which I understand, overall 
decreasing CT with increasing age)


-2 small clusters correlated to the quadratic age term

Given these results, if I want to model age optimally, I should 
include the quadratic age-term only in some vertices but not in 
others, right? I have two questions:


1.Is there a way to include different covariates in different 
vertices, still doing the vertex-wise analyses of the entire brain?


You can use the per-vertex regressor option (--pvr) to mri_glmfit. So 
you would remove the quadratic term from the FSGD file, then create an 
image of quadradic values for each veretx and pass that with --pvr to 
glmfit.


2.I apply a cluster-size threshold for the initial results, because I 
want to be sure about the case-control clusters. However for the 
covariates, if I can optimize the model per vertex, I would rather not 
use this threshold to be more sensitive. How could I go about this?



Uncorrected results are stored in the sig.mgh file
doug


Thank you, your help is very much appreciated!

Best wishes,
Lizanne


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Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

[Douglas Greve]

First, I would run the ROI analysis in mri_glmfit to see if you get the 
same results as in SPSS. In the handfull of these cases, no one has been 
able to correctly replicate the FS design matrix in SPSS, so I suspect 
that is part of the discrepancy. The other thing is that ROI and 
vertex-wise analyses are simply different. As an extreme example, if 
some of the vertices are pos and some are neg then they would cancel out 
when you average them in an ROI but individually could be significant at 
the vertex level. If you analyze the average over the cluster then that 
should come out as significant.


doug


On 2/1/15 11:36 PM, Bronwyn Overs wrote:

Dear FreeSurfer Mailing List,

I have a sample of schizophrenia and control subjects for whom I have 
run a case-control analysis of cortical thickness using two separate 
methods (GLM vertex-wise analysis in freesurfer, repeated measures 
ANCOVA analysis of parcellated data in SPSS). However, for each 
methods of analysis I am getting extremely different results. For the 
GLM in Freesurfer I have only 1 small cluster in the frontal lobe that 
differs between cases and controls (controlling for all other IVs, 
FWMH = 10mm, cluster-forming threshold= .05, cluster-wise pval=.05), 
while for the ANCOVA method all but 8 of the parcellated regions 
differ significantly between groups (p<.05). For both methods I have 
used the same model of predictors (independent variables = gender, 
group, scanning site; covariate = age) and exactly the same sample of 
participants. I have also replicated the GLM analysis using the QDEC 
GUI to ensure that I had no made any mistakes.


Can you provide any insight into why I would be seeing such different 
results for each method using the same data set? My findings using the 
ANCOVA analysis make much more sense to me, given previous findings of 
reduced cortical thickness in schizophrenia subjects. I was surprised 
not to find the same pattern of effects using the GLM analysis.

--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to 
the NeuRA Magazine 




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Re: [Freesurfer] subsampling procedure for fsaverages

[Douglas Greve]

you can also use mri_surf2surf to do the mapping

On 2/2/15 11:38 AM, Bruce Fischl wrote:

Hi Ernst
The new vertices are added o the end, so all the fsaverage5 vertex 
numbers should be the same in fsaverage6


Cheers
Bruce



On Feb 2, 2015, at 10:33 AM, Ernst Schwartz 
> wrote:



Hi!

I have some data that's on a low-resolution mesh (fsaverage5) that I 
would like to upsample to higher resolutions (fsaverage6 and 
fsaverage), but I can't figure out the correct vertex numbering. Is 
there a function that I could use (in the sense of 
function_on_fsaverage6 = peform_subdivision(function_on_fsaverage5) ) 
or if there isn't, could you briefly describe how new vertices are 
added during upsampling (eg. the ordering of new vertices with 
respect to the old ones)?


thanks a lot!

~

Ernst Schwartz
Computational Image Research (CIR) Lab
Department of Biomedical Imaging and Image-guided Therapy
Medical University Vienna, Austria

--

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Re: [Freesurfer] Calculate the DTI metrics inside a single voxel

[Douglas Greve]

Hi Mohamed, that looks great, very clear. We'll have to engage your 
services to write some of our wiki pages :)

doug


On 2/2/15 1:05 PM, Alshikho, Mohamad J. wrote:


Sorry for the mistake:

I wanted to correlate the DTI metrics inside this single voxel with 
the concentration of the metabolites (the output of LCMODEL) inside 
the voxel.


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of 
*Alshikho, Mohamad J.

*Sent:* Monday, February 2, 2015 1:02 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] Calculate the DTI metrics inside a single voxel

Dear Doug and Bruce,

I have a single voxel spectroscopic data (SVS) and a (DTI) data for 
the same subjects. I wanted to correlate the DTI metrics inside this 
single voxel with the DTI metrics inside the voxel.


In order to do that I used the following steps:

1.I used mri_convert to convert the T1 slice prescription dicom image 
to nii format


*mri_convert  562000-04-01.dcm t1_MRS_svs.nii*

2.I genetrate the SVS voxel using the following command line:

*mri_volsynth --vol svs.nii --pdf const --dim 40 40 40 1 --res 0.5 0.5 
0.5 1 –cdircos   --rdircos   --sdircos normal> --c_ras *


3.I viewed the SVS voxel as an overlay on the T1 image to be sure that 
SVS is in the correct position


*tkmedit -f t1_MRS_svs.nii -ov svs.nii -fthresh 0.9*

4.I co-registered the T1 slice prescription image with the 
corresponding T1.mgz using the following command line:


*bbregister  --t1 --mov t1_MRS_svs.nii --init-fsl --reg t1.reg.dat --s 
subject*


5.I registered the single voxel and the FreeSurfer anatomical space 
(svs.reg.dat):


*tkregister2 --mov svs.nii --int t1_MRS_svs.nii t1.reg.dat --reg 
svs.reg.dat --noedit --subject *


*6.*I mapped the single voxel into the anatomical space*:*

*mri_vol2vol --mov svs.nii --reg svs.reg.dat --fstarg --interp nearest 
--o svs.anat.nii*


7.I mapped the FA map into the anatomical space:

*mri_vol2vol --mov fa.nii --reg svs.reg.dat --fstarg --interp nearest 
--o fa.anat.nii*


8.I computed the dti metrics inside the SVS

*mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/aparc+aseg.mgz  
--ctab-default --i fa.anat.nii --mask 
/autofs/space/marvin_001/users/MRI/WMA/svs/wmvcalc/${subj}/svs.anat.nii --sum 
svs_fa.summary.dat*


Kindly, Is this plan correct? and do you suggest me any other steps?

I am sorry for this long email but as always I am looking forward to 
learn from you.


Many thanks,

Mohamad



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Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

[Douglas Greve]

Even easier. Run aparcstats2table, then run mri_glmfit passing the 
output of aparcstats2table with --table (instead of --y). There's 
something on  the wiki about it, also look for the ROI tutorial.

doug


On 2/2/15 6:20 PM, Bronwyn Overs wrote:

Hi Doug,

I am not sure how to run an ROI analysis using mri_glmfit. Is there a 
wiki page detailing this method (I was unable to find one)? Is the 
first step to map lh.aparc.label and rh.aparc.label from fsaverage to 
each of my individual subjects using mri_label2label? When I do so and 
then view the mapped label for an individual subject in freeview, it 
appears to be a continuous label for all of the parcellated regions 
combined. Is this correct?


Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au <http://neura.edu.au>

Follow @neuraustralia on twitter 
<https://twitter.com/neuraustralia>Follow NeuRA on facebook 
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to 
the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>


On 3/02/2015 3:31 am, Douglas Greve wrote:


First, I would run the ROI analysis in mri_glmfit to see if you get 
the same results as in SPSS. In the handfull of these cases, no one 
has been able to correctly replicate the FS design matrix in SPSS, so 
I suspect that is part of the discrepancy. The other thing is that 
ROI and vertex-wise analyses are simply different. As an extreme 
example, if some of the vertices are pos and some are neg  then they 
would cancel out when you average them in an ROI but individually 
could be significant at the vertex level. If you analyze the average 
over the cluster then that should come out as significant.


doug


On 2/1/15 11:36 PM, Bronwyn Overs wrote:

Dear FreeSurfer Mailing List,

I have a sample of schizophrenia and control subjects for whom I 
have run a case-control analysis of cortical thickness using two 
separate methods (GLM vertex-wise analysis in freesurfer, repeated 
measures ANCOVA analysis of parcellated data in SPSS). However, for 
each methods of analysis I am getting extremely different results. 
For the GLM in Freesurfer I have only 1 small cluster in the frontal 
lobe that differs between cases and controls (controlling for all 
other IVs, FWMH = 10mm, cluster-forming threshold= .05, cluster-wise 
pval=.05), while for the ANCOVA method all but 8 of the parcellated 
regions differ significantly between groups (p<.05). For both 
methods I have used the same model of predictors (independent 
variables = gender, group, scanning site; covariate = age) and 
exactly the same sample of participants. I have also replicated the 
GLM analysis using the QDEC GUI to ensure that I had no made any 
mistakes.


Can you provide any insight into why I would be seeing such 
different results for each method using the same data set? My 
findings using the ANCOVA analysis make much more sense to me, given 
previous findings of reduced cortical thickness in schizophrenia 
subjects. I was surprised not to find the same pattern of effects 
using the GLM analysis.

--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au <http://neura.edu.au>

Follow @neuraustralia on twitter 
<https://twitter.com/neuraustralia>Follow NeuRA on facebook 
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to 
the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>




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Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

[Douglas Greve]

This is not something you would run the MC sim on because there is no 
clustering, it is just a list of ROIs with their p-values. The p-values 
are uncorrected. You can do bonferoni correction across all the ROIs (or 
just the ones you are interested in). You could do FDR too.


doug


On 2/2/15 9:39 PM, Bronwyn Overs wrote:

Thanks Doug, that worked well.

However, is it possible to run a monte-carlo simulation with this GLM 
ROI analysis? I attempted to run it using the following command...
mri_glmfit-sim --glmdir DesikanROIAnal_case-control.thick.lh.glmdir 
--cache 1.3 abs --cwpvalthresh  0.05 --2spaces

and received the following error:
ERROR: could not determine file for 
DesikanROIAnal_case-control.thick.lh.glmdir/mask


Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au <http://neura.edu.au>

Follow @neuraustralia on twitter 
<https://twitter.com/neuraustralia>Follow NeuRA on facebook 
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to 
the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>


On 3/02/2015 11:03 am, Douglas Greve wrote:


Even easier. Run aparcstats2table, then run mri_glmfit passing the 
output of aparcstats2table with --table (instead of --y). There's 
something on  the wiki about it, also look for the ROI tutorial.

doug


On 2/2/15 6:20 PM, Bronwyn Overs wrote:

Hi Doug,

I am not sure how to run an ROI analysis using mri_glmfit. Is there 
a wiki page detailing this method (I was unable to find one)? Is the 
first step to map lh.aparc.label and rh.aparc.label from fsaverage 
to each of my individual subjects using mri_label2label? When I do 
so and then view the mapped label for an individual subject in 
freeview, it appears to be a continuous label for all of the 
parcellated regions combined. Is this correct?


Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au <http://neura.edu.au>

Follow @neuraustralia on twitter 
<https://twitter.com/neuraustralia>Follow NeuRA on facebook 
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to 
the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>


On 3/02/2015 3:31 am, Douglas Greve wrote:


First, I would run the ROI analysis in mri_glmfit to see if you get 
the same results as in SPSS. In the handfull of these cases, no one 
has been able to correctly replicate the FS design matrix in SPSS, 
so I suspect that is part of the discrepancy. The other thing is 
that ROI and vertex-wise analyses are simply different. As an 
extreme example, if some of the vertices are pos and some are neg  
then they would cancel out when you average them in an ROI but 
individually could be significant at the vertex level. If you 
analyze the average over the cluster then that should come out as 
significant.


doug


On 2/1/15 11:36 PM, Bronwyn Overs wrote:

Dear FreeSurfer Mailing List,

I have a sample of schizophrenia and control subjects for whom I 
have run a case-control analysis of cortical thickness using two 
separate methods (GLM vertex-wise analysis in freesurfer, repeated 
measures ANCOVA analysis of parcellated data in SPSS). However, 
for each methods of analysis I am getting extremely different 
results. For the GLM in Freesurfer I have only 1 small cluster in 
the frontal lobe that differs between cases and controls 
(controlling for all other IVs, FWMH = 10mm, cluster-forming 
threshold= .05, cluster-wise pval=.05), while for the ANCOVA 
method all but 8 of the parcellated regions differ significantly 
between groups (p<.05). For both methods I have used the same 
model of predictors (independent variables = gender, group, 
scanning site; covariate = age) and exactly the same sample of 
participants. I have also replicated the GLM analysis using the 
QDEC GUI to ensure that I had no made any mistakes.


Can you provide any insight into why I would be seeing such 
different results for each method using the same data set? My 
findings using the ANCOVA analysis make much more sense to me, 
given previous findings of reduced cortical thickness in 
schizophrenia subjects. I was surprised not to find the same 
pattern of effects using the GLM analysis.

--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au <http://neura.edu.au>

Follow @neuraustralia on twitter 
<https://twitter.com/

Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses

[Douglas Greve]

There is not a way to do it from the command line. You can do it in 
matlab, something like


sig = MRIread('sig.mgh');
sigmat = fast_vol2mat(sig);
p = 10^-abs(sigmat);
fdr = .05;
pthresh = fast_fdrthresh(p,fdr);
ind = find(p < pthresh); % This will be a list of ROI indices that 
survive FDR


doug

On 2/2/15 10:26 PM, Bronwyn Overs wrote:

Hi Doug,

That makes perfect sense. Just one more thing then, how do you conduct 
an FDR via the command line for an ROI mri_glmfit analysis?


Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au <http://neura.edu.au>

Follow @neuraustralia on twitter 
<https://twitter.com/neuraustralia>Follow NeuRA on facebook 
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to 
the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>


On 3/02/2015 2:00 pm, Douglas Greve wrote:


This is not something you would run the MC sim on because there is no 
clustering, it is just a list of ROIs with their p-values. The 
p-values are uncorrected. You can do bonferoni correction across all 
the ROIs (or just the ones you are interested in). You could do FDR too.


doug


On 2/2/15 9:39 PM, Bronwyn Overs wrote:

Thanks Doug, that worked well.

However, is it possible to run a monte-carlo simulation with this 
GLM ROI analysis? I attempted to run it using the following command...
mri_glmfit-sim --glmdir DesikanROIAnal_case-control.thick.lh.glmdir 
--cache 1.3 abs --cwpvalthresh 0.05 --2spaces

and received the following error:
ERROR: could not determine file for 
DesikanROIAnal_case-control.thick.lh.glmdir/mask


Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au <http://neura.edu.au>

Follow @neuraustralia on twitter 
<https://twitter.com/neuraustralia>Follow NeuRA on facebook 
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to 
the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>


On 3/02/2015 11:03 am, Douglas Greve wrote:


Even easier. Run aparcstats2table, then run mri_glmfit passing the 
output of aparcstats2table with --table (instead of --y). There's 
something on  the wiki about it, also look for the ROI tutorial.

doug


On 2/2/15 6:20 PM, Bronwyn Overs wrote:

Hi Doug,

I am not sure how to run an ROI analysis using mri_glmfit. Is 
there a wiki page detailing this method (I was unable to find 
one)? Is the first step to map lh.aparc.label and rh.aparc.label 
from fsaverage to each of my individual subjects using 
mri_label2label? When I do so and then view the mapped label for 
an individual subject in freeview, it appears to be a continuous 
label for all of the parcellated regions combined. Is this correct?


Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au <http://neura.edu.au>

Follow @neuraustralia on twitter 
<https://twitter.com/neuraustralia>Follow NeuRA on facebook 
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe 
to the NeuRA Magazine 
<http://www.neura.edu.au/help-research/subscribe>


On 3/02/2015 3:31 am, Douglas Greve wrote:


First, I would run the ROI analysis in mri_glmfit to see if you 
get the same results as in SPSS. In the handfull of these cases, 
no one has been able to correctly replicate the FS design matrix 
in SPSS, so I suspect that is part of the discrepancy. The other 
thing is that ROI and vertex-wise analyses are simply different. 
As an extreme example, if some of the vertices are pos and some 
are neg  then they would cancel out when you average them in an 
ROI but individually could be significant at the vertex level. If 
you analyze the average over the cluster then that should come 
out as significant.


doug


On 2/1/15 11:36 PM, Bronwyn Overs wrote:

Dear FreeSurfer Mailing List,

I have a sample of schizophrenia and control subjects for whom I 
have run a case-control analysis of cortical thickness using two 
separate methods (GLM vertex-wise analysis in freesurfer, 
repeated measures ANCOVA analysis of parcellated data in SPSS). 
However, for each methods of analysis I am getting extremely 
different results. For the GLM in Freesurfer I have only 1 small 
cluster in the frontal lobe that differs between cases and 
controls (controlling for all other IVs, FWMH = 10mm, 
cluster-forming threshold= .05, cluster-wise pval=.05), while 
for the ANCO

Re: [Freesurfer] vertexwise statistical modeling

[Douglas Greve]

On 2/3/15 4:21 AM, Schweren, LJS (med) wrote:


Thank you Doug!

One more question for clarification:

“You would remove the quadratic term from the FSGD file, then create 
an image of quadradic values for each veretx and pass that with --pvr 
to glmfit”.


My quadratic value (age-squared) is a constant per participant. Do you 
mean I should create an image file per subject, where each vertex has 
the same value, namely age-squared of that subject? Next I should 
concatenate these files in FSGD-order to create a stacked mgz file, right?


Yes. I assumed from your question that you would set some of the 
vertices = 0  in the case where you thought that having a quad term was 
not helpful.


Second question: is there a way to hierarchically order the pvr-s, 
such that pvr 1 can only be included when pvr 2 is also included?



No, it is an all-or-nothing kind of thing.
doug


Thanks again,

Lizanne

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas 
Greve

*Sent:* maandag 2 februari 2015 17:19
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] vertexwise statistical modeling

On 2/2/15 3:56 AM, Schweren, LJS (med) wrote:

Dear freesurfer experts,

I investigate case-control differences in cortical thickness in a
group of 11 to 30 year olds. I ran vertex-wise analyses with
glmfit, with covariates age and age-squared, to take into account
confounding by age as we have a very wide age range. I use
monte-carlo simulation testing. What results is the following:

-some clusters of between-group difference (which I was looking
for, no worries here)

-a cluster covering almost the entire cortex being negatively
correlated to the linear age term (which I understand, overall
decreasing CT with increasing age)

-2 small clusters correlated to the quadratic age term

Given these results, if I want to model age optimally, I should
include the quadratic age-term only in some vertices but not in
others, right? I have two questions:

1.Is there a way to include different covariates in different
vertices, still doing the vertex-wise analyses of the entire brain?

You can use the per-vertex regressor option (--pvr) to mri_glmfit. So 
you would remove the quadratic term from the FSGD file, then create an 
image of quadradic values for each veretx and pass that with --pvr to 
glmfit.


2.I apply a cluster-size threshold for the initial results, because I 
want to be sure about the case-control clusters. However for the 
covariates, if I can optimize the model per vertex, I would rather not 
use this threshold to be more sensitive. How could I go about this?


Uncorrected results are stored in the sig.mgh file
doug


Thank you, your help is very much appreciated!

Best wishes,
Lizanne



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Re: [Freesurfer] defining ROIs/clusters

[Douglas Greve]

Just run mris_preproc on your healthy group, then run mri_segstats using 
the cluster annotation from your first analysis and the HC stack  as the 
input. Does that make sense?

doug

On 2/3/15 9:18 AM, maaike rive wrote:

Hi all,

Does anyone know how to extract average (thickness/area/GI) values of 
a cluster A for subjects in a group which was NOT included in the 
model where this cluster A emerged? For example: in a t-test for 
diagnosis1>dagnosis2 there is an effect in an insulacluster (found 
with mri_glmfit -sim); post hoc I want to test whether diagnosis1 
and/or diagnosis2 differ from healthy controls in exactly the same 
cluster. I understand I can run the analyses in seperate models (one 
for diagnosis1 vs HC and one for diagnosis2 vs HC; if this cluster 
does not emerge in either model, there is no difference) but if I want 
to plot all groups for visualization purposes, I have no values for 
the HC.


Thanks in advance,

Maaike




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Re: [Freesurfer] mri_glmfit-sim mc-z comapred to mc-full

[Douglas Greve]

Hi Corinna,

In each iteration, the mc-full replaces your data (--y) with white 
gaussian noise, smoothes it, then computes the GLM and p-values from the 
t or F-test. The mc-z ignores your data entirely and creates a single 
frame of WGN in each iteration, smoothes it, rescales it back to a z, 
then converts the z to a p. This is much faster because it only has one 
frame vs how many you have in your data. It is less accurate because a 
p-value map from a smoothed z-map is not the same as computing the glm. 
It has been a while, but I remember the mc-z as being more conservative, 
but it is much much faster.


doug

On 2/3/15 10:12 AM, Corinna Bauer wrote:

Hi all,
I am wondering what the specific reasons might be for choosing to run 
the mc-z simulation compared to mc-full? What are the pros and cons 
for each method for looking at group morphometry differences?


Thanks

Corinna


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Re: [Freesurfer] tksurfer

[Douglas Greve]

Is it world readable? You might also change its name to license.txt


On 2/3/15 12:13 PM, André Schmidt wrote:

Dear experts,

I like to see the obtained annotation files using tksurfer. However, I 
already got the following error message if I use tksurfer HC001 lh 
inflated in the terminal:


FreeSurfer license file /Applications/freesurfer/.license not found

But there is a .license file in that folder.

Can you help me to solve this problem?

Thank you very much
Andre


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Re: [Freesurfer] Surface based smoothing

[Douglas Greve]

There are no explicit weights. It just uses an iterative procedure in 
which the value at a vertex is replaced by the average of itself and its 
neighbors. This approximates gaussian smoothing with the number of 
iterations being related to the FWHM.

doug

On 2/4/15 9:01 PM, Simon Vandekar wrote:
> Hello all,
>
> I am trying to determine the neighbors and weights used in the smoothing 
> implemented in the surface based smooth used by freesurfer (e.g. as called by 
> mris_preproc). Can anyone point me to the code that performs the surface 
> based smoothing in freesurfer?
>
> Thanks in advance,
> Simon
> ___
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>

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Re: [Freesurfer] average values per cluster

[Douglas Greve]

On 2/8/15 1:48 PM, maaike rive wrote:
But how can i run the appropriate preprocessing and smoothing? The --X 
flag s not recognised using mris_preproc.
mri_preproc only uses the fsgd file to get the list of subjects to 
assure that they are ordered in the same way as when mri_glmfit builds 
the X matrix.
I used the same matrix as X in an FSGD file to do this now, it seems 
to work, but I do not no if it is correct. Furthermore, If I try to 
run mri_glmfit --sim for the lGI data, I get an error because fwmh66 
is not available. I did not smooth the lGI data and with the DODS/DOSS 
FSGD models there was no problem, so does this mean my new models are 
not correct?
Wow, it is 66 without smoothing? I'm not sure what to tell you. The lGI 
is often very smooth, but that seems excessive. You can look for 
outliers by loading the y files as a "time coures" in tksurfer (-t 
flag). If it says at 66 then I don't think you can do the voxel-wise 
analysis. Was it that way when you used the FSGD file? It could be that 
your design matrix does not remove the mean offset, so check that too.


> From: r_maa...@hotmail.com
> Date: Fri, 6 Feb 2015 21:41:53 +0100
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] average values per cluster
>
> Ok, thanks!
> Maaike
>
> > Op 6 feb. 2015 om 17:49 heeft "Douglas N Greve" 
 het volgende geschreven:

> >
> >
> > There is not a way to build more flexible models in the FSGD 
structure.
> > However, you can create your own design matrix and include 
anything you

> > want in it and pass it to mri_glmfit with --X instead of --fsgd.
> >
> > doug
> >
> >> On 02/05/2015 06:13 AM, maaike rive wrote:
> >>
> >> Hi Doug,
> >>
> >> I hope I'm not driving you crazy, but I have some additional 
questions
> >> regardig the DOSS/DODS models. Also because of the SPSS 
discrepancies.

> >>
> >> First, the model I discussed with you I used to assess diagn x age
> >> interactions, regressing out the effects of state and gender. 
However,

> >> in this model all interaction terms are incorporated. Is there a way
> >> to build the model only incorporating main effects of diagn, state,
> >> gender, age and diagn*age and diagn*state interactions? Since I 
do not

> >> expect any higher order interactions or state* age interactions, for
> >> instance (this is biologically not very plausible, although I did 
not

> >> formally test it).
> >>
> >> Second, for areas where there is no diagn*age interaction I want to
> >> use a model without any interaction term with age, so I was thinking
> >> to use DOSS (I still want to regress out the effects of age, so 
it was

> >> added as a regressor):
> >>
> >> diagn1*state1*gender1
> >>
> >> diagn1*state1*gender2
> >>
> >> diagn1*state2*gender1
> >>
> >> diagn1*state2*gender2
> >>
> >> diagn2*state1*gender1
> >>
> >> diagn2*state1*gender2
> >>
> >> diagn2*state2*gender1
> >>
> >> diagn2*state2*gender2
> >>
> >> age
> >>
> >> However, here there are still interaction terms with gender in the
> >> model. I do want to regress out the effects of gender (since I 
expect
> >> this to be a confounder), without incorporating the interaction 
term.

> >> How should I do this? The only solution I can think of is building a
> >> model with gender as additional regressor (containing 0 en 1) and
> >> using DOSS. So:
> >>
> >> diagn1*state1
> >>
> >> diagn1*state2
> >>
> >> diagn2*state1
> >>
> >> diagn2*state2
> >>
> >> age
> >>
> >> gender
> >>
> >> Does this make sense?
> >>
> >> Third, if so, it implies that for areas where there is no 
diagn*state
> >> interaction, and where I want to test diagn1 vs diagn2 
(regressing out

> >> the effects of state, since I expect this to be a confounder), I
> >> should again build a new model:
> >>
> >> diagn1
> >>
> >> diagn2
> >>
> >> age
> >>
> >> gender
> >>
> >> state
> >>
> >> I realize this is a lot of work, hence I hope you could give me
> >> any advice about this.
> >>
> >> Thanks,
> >>
> >> Maaike
> >>
> >> 


> >> From: r_maa...@hotmail.com
> >> To: freesurfer@nmr.mgh.harvard.edu
> >> Date: Tue, 3 Feb 2015 13:18:55 +0100
> >> Subject: Re: [Freesurfer] average values per cluster
> >>
> >> Hi Doug,
> >>
> >> Sorry, the statistician doesn't understand it yet; we're currently
> >> building freesurfer and SPSS models step by step to find out what's
> >> going on, but it's a litte time consuming... so, to be continued!
> >>
> >> Maaike
> >>
> >> 


> >> From: r_maa...@hotmail.com
> >> To: freesurfer@nmr.mgh.harvard.edu
> >> Date: Fri, 30 Jan 2015 20:55:27 +0100
> >> Subject: Re: [Freesurfer] average values per cluster
> >>
> >> On second thought, I think the reason for the discrepancy is that I
> >> included state as a factor instead of covariate in the SPSS model. I
> >> ran the model again after having adjusted this and included every
> >> possible interaction; now I reach a p 

Re: [Freesurfer] time series data from FSFAST

[Douglas Greve]

Yes, mri_segstats. Run it with --help. See esp example 6

On 2/9/15 12:31 PM, sabin khadka wrote:

Hi FS Users,
I've preprocessed resting state fmri data using preproc-sess as shown 
in FSFAST functional connectivity walk through manual. I know I can 
extract mean time series of a seed region using fcseed-sess. I am 
trying to find a command to extract mean time series from all Desikan 
(or Destriuex) atlas ROIs. Looks like mri_segstats is the command to 
get the time-series of all the ROIs at once in a .txt or .dat files 
but I am not sure how exactly to do it.


Thanks for help.


Cheers,
Sabin Khadka


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Re: [Freesurfer] time series data from FSFAST

[Douglas Greve]

On 2/9/15 3:16 PM, sabin khadka wrote:
Thanks Doug. I am now able to get average time series from cortical 
ROIs. I used
mri_segstats --annot fsaverage lh aparc --i 
sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txt
That's right, but I would use the unsmoothed data since smoothing will 
cause activity to spill-over between regions.
How would I get time series of the sub-cortical ROIs 
(fmcpr.up.sm5.mni305.2mm.nii.gz)?

I tried doing
mri_segstats --seg fsaverage/mri/aseg.mgz --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txt
but it gave me dimension mismatch error. I'd appreciate if you'd 
direct me on how to get average time series values from subcortical 
regions.

Use fsaverage/mri.2mm/aseg.mgz
doug

Cheers,
Sabin Khadka

----
*From:* Douglas Greve 
*To:* freesurfer@nmr.mgh.harvard.edu
*Sent:* Monday, February 9, 2015 1:24 PM
*Subject:* Re: [Freesurfer] time series data from FSFAST


Yes, mri_segstats. Run it with --help. See esp example 6



On 2/9/15 12:31 PM, sabin khadka wrote:

Hi FS Users,
I've preprocessed resting state fmri data using preproc-sess as shown 
in FSFAST functional connectivity walk through manual. I know I can 
extract mean time series of a seed region using fcseed-sess. I am 
trying to find a command to extract mean time series from all Desikan 
(or Destriuex) atlas ROIs. Looks like mri_segstats is the command to 
get the time-series of all the ROIs at once in a .txt or .dat files 
but I am not sure how exactly to do it.


Thanks for help.


Cheers,
Sabin Khadka


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Re: [Freesurfer] time series data from FSFAST

[Douglas Greve]

That is the "cost" of the registration. You can look in Greve & Fischl 
2009 to see how it is computed.

doug

On 2/9/15 3:45 PM, sabin khadka wrote:

Hi Doug- Works fine. I appreciate your help.
Related but different question: Would you help me understand how the 
QA value(0-1)while checking registration using following command is 
calculated.

tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum
Cheers,
Sabin Khadka

----
*From:* Douglas Greve 
*To:* freesurfer@nmr.mgh.harvard.edu
*Sent:* Monday, February 9, 2015 3:32 PM
*Subject:* Re: [Freesurfer] time series data from FSFAST


On 2/9/15 3:16 PM, sabin khadka wrote:
Thanks Doug. I am now able to get average time series from cortical 
ROIs. I used
mri_segstats --annot fsaverage lh aparc --i 
sess01/bold/001/fmcpr.up.sm5.fsaverage.lh.nii.gz --avgwf test1.txt
That's right, but I would use the unsmoothed data since smoothing will 
cause activity to spill-over between regions.
How would I get time series of the sub-cortical ROIs 
(fmcpr.up.sm5.mni305.2mm.nii.gz)?

I tried doing
mri_segstats --seg fsaverage/mri/aseg.mgz --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txt
but it gave me dimension mismatch error. I'd appreciate if you'd 
direct me on how to get average time series values from subcortical 
regions.

Use fsaverage/mri.2mm/aseg.mgz
doug

Cheers,
Sabin Khadka

--------
*From:* Douglas Greve  
<mailto:gr...@nmr.mgh.harvard.edu>
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu>

*Sent:* Monday, February 9, 2015 1:24 PM
*Subject:* Re: [Freesurfer] time series data from FSFAST


Yes, mri_segstats. Run it with --help. See esp example 6



On 2/9/15 12:31 PM, sabin khadka wrote:

Hi FS Users,
I've preprocessed resting state fmri data using preproc-sess as 
shown in FSFAST functional connectivity walk through manual. I know 
I can extract mean time series of a seed region using fcseed-sess. I 
am trying to find a command to extract mean time series from all 
Desikan (or Destriuex) atlas ROIs. Looks like mri_segstats is the 
command to get the time-series of all the ROIs at once in a .txt or 
.dat files but I am not sure how exactly to do it.


Thanks for help.


Cheers,
Sabin Khadka


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Re: [Freesurfer] Map volume label to surface label

[Douglas Greve]

If the labels are a segmentation volume, then you'll need to run 
mri_vol2surf with --interp nearest.

doug


On 2/10/15 6:39 PM, Bruce Fischl wrote:

Hi Razib

yes, I think mri_label2label will do this if you have reconstructed 
the surfaces.


cheers
Bruce
On Tue, 10 Feb 2015, Muhammad Razib wrote:


Hi,
I am wondering is there a way in freesurfer to map manually labeled 
IBSR MRI

.img/.hdr volume files to freesurfer surface file (e.g. lh.pial/rh.pial
etc.) keeping the original labels?

Thanks,

Razib





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Re: [Freesurfer] Help: error on running dt_recon

[Douglas Greve]

Just give it one of the dicoms (ie, don't use the "*" wild card, just 
give it the actual file name of one of the files in the series, it will 
find the rest)

doug

On 2/11/15 4:28 PM, Sampada Sinha wrote:

Dear freesurfer experts,

Sorry for posting such a long message but I am trying to run dt_recon 
command on DTI images acquired in dicom format using 3T_Toshiba 
(Toshiba_MEC_MR3). Image parameters are: Scanning sequence =Spin Echo; 
TR=9 ; TE=082.0 ; Flip angle = 90; Slice thickness= 3.; 
acquisition matrix is 160. Howsoever, I used many tools to get the 
bval and bvect gr



adient from the conversion of dcm files to nifti but couldn't get one 
(dcm2nii, mricron). Even with freesurfer, I am getting following 
error: (My dcm file is in directory: 
/Users/Sampada/Desktop/DTIDCM/Raw/I*.dcm)

I used following command to get the dt_recon work:

Sampada$ export FREESURFER_HOME=/Applications/freesurfer
 Sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/subjects
MNI_DIR /Applications/freesurfer/mni
FSL_DIR /Applications/fsl
Sampada$ tcsh
Sampada% cd /Users/sampada/Desktop/DTIDCM/Raw/
~/Desktop/DTIDCM/Raw] Sampada% setenv SUBJECTS_DIR 
/Users/Sampada/Desktop/DTIDCM/Raw

~/Desktop/DTIDCM/Raw] Sampada% set subj =Diff001
~/Desktop/DTIDCM/Raw] Sampada% dt_recon --i 
/Users/Sampada/Desktop/DTIDCM/Raw/I*.dcm --s $subj --o 
/Users/Sampada/Desktop/DTIDCM/Raw


Error Message: ERROR: Flag 
/Users/Sampada/Desktop/DTIDCM/Raw/I0005130.dcm unrecognized.
--i /Users/Sampada/Desktop/DTIDCM/Raw/I0005129.dcm 
/Users/Sampada/Desktop/DTIDCM/Raw/I0005130.dcm 
/Users/Sampada/Desktop/DTIDCM/Raw/I0005131.dcm 
/Users/Sampada/Desktop/DTIDCM/Raw/I0005132.dcm 
/Users/Sampada/Desktop/DTIDCM/Raw/I0005133.dcm 
/Users/Sampada/Desktop/DTIDCM/Raw/I0005134.dcm

and so on… (dt_recon exited with ERRORS at Wed Feb 11 01:47:01 CST 2015)

Then I used nii converted file instead of the dcm file and it shows 
the following error


Sampada% dt_recon --i /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii 
--s $subj --o /Users/Sampada/Desktop/DTIDCM/Raw

INFO: SUBJECTS_DIR is /Users/Sampada/Desktop/DTIDCM/Raw
dt_recon logfile
Wed Feb 11 15:02:47 CST 2015
VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $
setenv SUBJECTS_DIR /Users/Sampada/Desktop/DTIDCM/Raw
cd /Users/Sampada/Desktop/DTIDCM/Raw
/Applications/freesurfer/bin/dt_recon --i 
/Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii --s Diff001 --o 
/Users/Sampada/Desktop/DTIDCM/Raw

rmbp.home
Sampada
/Applications/fsl/bin/eddy_correct
ECRefTP 0
#@#---
Converting input
Wed Feb 11 15:02:47 CST 2015
cd /Users/Sampada/Desktop/DTIDCM/Raw
mri_convert /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii 
/Users/Sampada/Desktop/DTIDCM/Raw/dwi.nii
mri_convert /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii 
/Users/Sampada/Desktop/DTIDCM/Raw/dwi.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii...
TR=9000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.994743, 0.0323186, 0.097165)
j_ras = (0.0525116, 0.97562, 0.21309)
k_ras = (0.0879093, -0.217072, 0.972189)
writing to /Users/Sampada/Desktop/DTIDCM/Raw/dwi.nii...


cd /Users/Sampada/Desktop/DTIDCM/Raw
mri_probedicom --i /Users/Sampada/Desktop/DTIDCM/Raw/s700a1001.nii
[rmbp:~/Desktop/DTIDCM/Raw] Sampada%

I would be very grateful if I any response and know where I am going 
wrong. I am also attaching the dt_recon.log file with this query.


Much thanks for your time!

Kind regards,

Sampada
Post-Doctoral Associate
University of Minnesota (East Bank)
Molecular and neuroimaging laboratory
Department of Psychiatry
Minneapolis-55415


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Re: [Freesurfer] Interhemispheric registration of .mgh files

[Douglas Greve]

Probably easier to use mris_apply_reg, something like

mris_apply_reg --src lh.w-g.pct.mgh --trg xhemi.lh.w-g.pct.mgh \
   --streg $SUBJECTS_DIR/$subject/surf/lh.fsaverage_sym.sphere.reg \
  $SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg

mris_apply_reg --src rh.w-g.pct.mgh --trg xhemi.rh.w-g.pct.mgh \
   --streg $SUBJECTS_DIR/$subject/xhemi/surf/lh.fsaverage_sym.sphere.reg \
  $SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg

In the 2nd command line (for rh), lh.fsaverage_sym.sphere.reg is used. 
This is intentional; the left hemis in the xhemi folder are actually 
right hemis.

doug


On 2/11/15 4:12 PM, Bruce Fischl wrote:
> Hi Konrad
>
> you should be able to do this with mri_surf2surf, although the syntax
> might be tricky.
>
> cheers
> Bruce
> On Mon, 9 Feb 2015, Konrad Wagstyl wrote:
>
>> Hi all,
>>
>> We're having some trouble using interhemispheric registration. It works fine 
>> for files that are automatically registered eg thickness, volume etc. but 
>> not for mgh files, like ?h.w-g.pct.mgh.
>> Is there a way of adding files to xhemi/surf/ so that other surfaces files 
>> can be compared between hemispheres?
>>
>> Thanks,
>> Konrad
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Re: [Freesurfer] Interhemispheric registration of .mgh files

[Douglas Greve]

btw, to check, you can run this on the thicknesses and compare to what 
you get with mris_preproc

On 2/11/15 6:01 PM, Douglas Greve wrote:
> Probably easier to use mris_apply_reg, something like
>
> mris_apply_reg --src lh.w-g.pct.mgh --trg xhemi.lh.w-g.pct.mgh \
> --streg $SUBJECTS_DIR/$subject/surf/lh.fsaverage_sym.sphere.reg \
>$SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg
>
> mris_apply_reg --src rh.w-g.pct.mgh --trg xhemi.rh.w-g.pct.mgh \
> --streg $SUBJECTS_DIR/$subject/xhemi/surf/lh.fsaverage_sym.sphere.reg \
>$SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg
>
> In the 2nd command line (for rh), lh.fsaverage_sym.sphere.reg is used.
> This is intentional; the left hemis in the xhemi folder are actually
> right hemis.
>
> doug
>
>
> On 2/11/15 4:12 PM, Bruce Fischl wrote:
>> Hi Konrad
>>
>> you should be able to do this with mri_surf2surf, although the syntax
>> might be tricky.
>>
>> cheers
>> Bruce
>> On Mon, 9 Feb 2015, Konrad Wagstyl wrote:
>>
>>> Hi all,
>>>
>>> We're having some trouble using interhemispheric registration. It works 
>>> fine for files that are automatically registered eg thickness, volume etc. 
>>> but not for mgh files, like ?h.w-g.pct.mgh.
>>> Is there a way of adding files to xhemi/surf/ so that other surfaces files 
>>> can be compared between hemispheres?
>>>
>>> Thanks,
>>> Konrad
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>>>
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Re: [Freesurfer] To visualize contribute of each subject in FS-FAST

[Douglas Greve]

I don't understand what you are trying to do. Do you want a "time" 
course at a voxel, i,e a plot where "time" is subject? Or do you want to 
visualize a map of each subject?


On 2/14/15 5:31 AM, std...@virgilio.it wrote:

Hi,
I'm using FS-FAST for seed based connectivity analysis.
I'd like to visualize the results for each subject in a plot as for qdec.
Is it possible? If no, there is an alternative interface to visualize 
the contribute of each subject in each vertex/region?

Thank you very much in advance.

Stefano


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Re: [Freesurfer] Entorhinal Cortex segmentation and volume

[Douglas Greve]

On 2/16/15 9:31 AM, Bruce Fischl wrote:
> Hi Melina
>
> 1. Can you send us a picture? I'm not sure given your description,
> although the surfaces can be arbitrary in the hippocampus/amygdala and
> should be ignored there.
This corresponds to  the "cortex unknown" label in aparc (and is 
probably labeled WM in the aseg). This is normal.
>
> 2. You should be able to use mri_label2vol for this. Note that you can load
> the label itself directly into freeview if you want without needing to run
> label2vol (but it will follow the white surface I believe and not fill the
> ribbon)
>
> cheers
> Bruce
>
> On Mon, 16 Feb 2015, Melina Lehnerer wrote:
>
>> Hi experts,
>> I'm rather unexperienced with freesurfer so please excuse my basic
>> requests.
>> 1. I controlled the segmentation of the entorhinal cortex (EC) in over
>> 50 subjects following the borders described in Fischl 2009 (Predicting
>> the location of EC from MRI) with tkmedit [mri name] brainmask.mgz -seg
>> aparc-aseg.mgz.
>> I noticed (esp. in the coronar slices and in approximately every mri)
>> brain tissue between amygdala/ hippocampus/ temporalpole and the EC
>> labelled as "none" or "ctx-?h-unknown". Has anything gone wrong with the
>> segmentation? Or is a label (e.g. perirhinal cortex) not loaded?
>>
>> 2. Is there a possibility to visualize the EC volume in freeview or
>> tkmedit from the exvivo.stats or exvivo.label file? I would like to
>> compare it to the other EC volume because they have very different
>> volumes. In the mail archive were similar questions about that but you
>> haven't answered them yet.
>>
>> Many thanks in advance,
>> Melina
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Re: [Freesurfer] Entorhinal Cortex segmentation and volume

[Douglas Greve]

Yes, that is normal

On 2/16/15 11:42 AM, Melina Lehnerer wrote:

Thank you both for your respond.
1. I have attached you some pictures. Like douglas wrote it 
corresponds to white matter in aseg, but is more often labelled as 
"none" than "cortex unknown". So is this "normal" and can I trust 
those borders? Or would you rather advise to control aseg and aparc 
segmentation to estimate the entorhinal cortex segmentation?


2. You're right, Bruce, in freeview the exvivo label it just follows 
the surface. So I'll try mri_label2vol.


Cheers Melina

Am 16.02.2015 um 16:33 schrieb Douglas Greve:

On 2/16/15 9:31 AM, Bruce Fischl wrote:

Hi Melina

1. Can you send us a picture? I'm not sure given your description,
although the surfaces can be arbitrary in the hippocampus/amygdala and
should be ignored there.

This corresponds to  the "cortex unknown" label in aparc (and is
probably labeled WM in the aseg). This is normal.
2. You should be able to use mri_label2vol for this. Note that you 
can load
the label itself directly into freeview if you want without needing 
to run
label2vol (but it will follow the white surface I believe and not 
fill the

ribbon)

cheers
Bruce

On Mon, 16 Feb 2015, Melina Lehnerer wrote:


Hi experts,
I'm rather unexperienced with freesurfer so please excuse my basic
requests.
1. I controlled the segmentation of the entorhinal cortex (EC) in over
50 subjects following the borders described in Fischl 2009 (Predicting
the location of EC from MRI) with tkmedit [mri name] brainmask.mgz 
-seg

aparc-aseg.mgz.
I noticed (esp. in the coronar slices and in approximately every mri)
brain tissue between amygdala/ hippocampus/ temporalpole and the EC
labelled as "none" or "ctx-?h-unknown". Has anything gone wrong 
with the

segmentation? Or is a label (e.g. perirhinal cortex) not loaded?

2. Is there a possibility to visualize the EC volume in freeview or
tkmedit from the exvivo.stats or exvivo.label file? I would like to
compare it to the other EC volume because they have very different
volumes. In the mail archive were similar questions about that but you
haven't answered them yet.

Many thanks in advance,
Melina
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Re: [Freesurfer] Map volume label to surface label

[Douglas Greve]

The registration file maps between the FS anatomical in "conformed" 
space and the label volume. If they are the same voxel-for-voxel space, 
then use --regheader, otherwise use bbregister to get the registration 
file and pass that to vol2surf



On 2/16/15 11:18 AM, Muhammad Razib wrote:

Hi Bruce,

Thanks for the reply. I am not sure if I am fundamentally wrong at 
some places. I am new to freesurfer, previously I processed some .nii 
files with recon-all command which created surfaces like 
lh.pial/rh.pial etc. After that I did cortical percellation. But the 
data  that I am using now are IBSR 
(http://www.nitrc.org/projects/ibsr) manually labeled volume data 
(contains img/hdr/mat file). But I want to get labeled surface like 
lh.pial/rh.pial from this labeled volume data. I was looking into 
mri_vol2surf command, but it needs a parameter --srcreg which I am not 
sure about. How can I get this registration file? Do I need to create 
this using freesurfer?


I highly appreciate your time and suggestion.

Thanks

On Tue, Feb 10, 2015 at 9:54 PM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:



If the labels are a segmentation volume, then you'll need to run
mri_vol2surf with --interp nearest.
doug



On 2/10/15 6:39 PM, Bruce Fischl wrote:

Hi Razib

yes, I think mri_label2label will do this if you have
reconstructed the surfaces.

cheers
Bruce
On Tue, 10 Feb 2015, Muhammad Razib wrote:


Hi,
I am wondering is there a way in freesurfer to map manually
labeled IBSR MRI
.img/.hdr volume files to freesurfer surface file (e.g.
lh.pial/rh.pial
etc.) keeping the original labels?

Thanks,

Razib





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--
Muhammad Razib
PhD Student in Computer Science
Florida International University
Miami, FL, USA


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Re: [Freesurfer] fsaverage surfaces correspondence across hemispheres

[Douglas Greve]

We don't have anything to do this directly. However, we do have this tool:
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
See if that meets your needs.

doug

On 2/17/15 12:49 PM, David Moreno-Dominguez wrote:
> Hello,
> I am performing clustering ofer data sampled to the fsaverage5 surfaces.
> I would now like to be able to do color matchign and other processes that 
> require a vertex correspondence across both surfaces.
>
> I have noticed that the vertices do not correspond directly (vertex 25 of lh 
> is not the homologous of vertex 25 in rh)
> As both hemispheres have the same number of vertices I guess this has 
> probably already been done, but I have not been able to find this information.
>
> Is there any lookup-table or any easy method to calculate vertex 
> correspondence across hamispheres for fsaverage5 surfaces?
>
> Thank you in advance
>
> David Moreno-Dominguez
> Research Group: Neuroanatomy and Connectivity
> Methods & Development Unit: Cortical Networks and Cognitive Functions
> Max Planck Institute for Human Cognitive and Brain Sciences
> Stephanstraße 1A, 04103 Leipzig, Germany
> Phone: +49 341 9940-2580
> Email: mor...@cbs.mpg.de
> http://www.cbs.mpg.de/~moreno
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Re: [Freesurfer] Register.dof

[Douglas Greve]

Yes, if you've run the T1 through recon-all, then you can use bbregister 
to create a registration between the two. It will also resample to the 
T1 space, but you can also use mri_vol2vol to do so too.

doug


On 2/18/15 5:43 PM, Xiaomin Yue wrote:

Hi,

I like to transfer a epi file to a T1 space.  Is it possible?

Thanks,

Xiaomin




On Tue, Feb 17, 2015 at 1:13 PM -0800, "Douglas Greve" 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:



We don't have anything to do this directly. However, we do have this tool:
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
See if that meets your needs.

doug

On 2/17/15 12:49 PM, David Moreno-Dominguez wrote:
> Hello,
> I am performing clustering ofer data sampled to the fsaverage5 surfaces.
> I would now like to be able to do color matchign and other processes 
that require a vertex correspondence across both surfaces.

>
> I have noticed that the vertices do not correspond directly (vertex 
25 of lh is not the homologous of vertex 25 in rh)
> As both hemispheres have the same number of vertices I guess this 
has probably already been done, but I have not been able to find this 
information.

>
> Is there any lookup-table or any easy method to calculate vertex 
correspondence across hamispheres for fsaverage5 surfaces?

>
> Thank you in advance
>
> David Moreno-Dominguez
> Research Group: Neuroanatomy and Connectivity
> Methods & Development Unit: Cortical Networks and Cognitive Functions
> Max Planck Institute for Human Cognitive and Brain Sciences
> Stephanstraße 1A, 04103 Leipzig, Germany
> Phone: +49 341 9940-2580
> Email: mor...@cbs.mpg.de
> http://www.cbs.mpg.de/~moreno <http://www.cbs.mpg.de/%7Emoreno>
>
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Re: [Freesurfer] cluster colors

[Douglas Greve]

I don't think I understand. What files are you visualizing? What is your 
command to visualize?



On 2/18/15 3:42 PM, Hirsch, Gabriella wrote:

Hi FS experts,

I had a quick question I was hoping someone could help me with; I used 
the group analysis tutorial 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis_tktools) 
to analyse two groups of subjects.


I ran the mri_glmfit command, as well as the clusterwise correction 
(mri_glmfit-sim) on the same data; however upon visualization, the two 
outputs present clusters in different colors (before correction all 
clusters are blue and after post-correction all clusters are red - 
this is consistent across conditions). According to the tutorial, I 
should disregard the red color since it is arbitrary (and not, in 
fact, an inversion of what I see from the uncorrected data). Note that 
I have NOT changed the contrast or any other setting.


Am I understanding this correctly?

Thank you.
Gabriella


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Re: [Freesurfer] FSFAST

[Douglas Greve]

On 2/18/15 4:38 PM, sabin khadka wrote:

Hi FS Users-
After using FSFAST's preproc-sess command (I get the output files: 
fmcpr.up.sm5.fsaverage.lh.nii.gz,fmcpr.up.sm5.fsaverage.rh.nii.gz, 
fmcpr.up.sm5.mni305.nii.gz), I was wondering if we could see or tell 
how well the EPIs are mapping onto the common space (I am assuming 
fsaverage in this case)?
It is just based on how good the registration is, to try register-sess 
to check.
Also, is there a way to band pass filter these time series data. I 
want to use band pass filter and then use the mean time series of FS 
parcellation regions and analyze the data outside the FSFAST console.
I don't have a binary to do bandpass filtering. You could use FSL's 
tool. Or you could compute the mean time course then do the BPF in 
matlab (the order of the operations should not matter since both are 
linear operations)

Cheers,
Sabin Khadka


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Re: [Freesurfer] extract individual label from Destrieux Atlas

[Douglas Greve]

Use --annotation a2009s.aparc


On 2/19/15 8:34 PM, Yang, Daniel wrote:

Dear FreeSurfer experts,

The following command works but how do I get the labels from —a2009s ?

mri_annotation2label --a2005s --subject fsaverage --hemi rh --outdir .

What is the difference between a2005s and a2009s?

Thanks!
Daniel


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Re: [Freesurfer] Bad design matrix

[Douglas Greve]

Try demeaning your covariates. By demeaning, I mean to compute the mean 
across all subjects, then subtract the mean from all values (for each 
covariate).

doug


On 3/1/15 2:40 AM, Anders Hougaard wrote:

Dear all,

I'm comparing cortical thickness of a group of patients to a group of controls.
I want to regress out the effects of gender, age, disease severity and
disease duration.
For the controls, the last two parameters equals zero.

When running mri_glmfit, i get ERROR: matrix is ill-conditioned or
badly scaled, condno = 1e+08
See the design matrix attached. My contrasts are set as
1 -1 0 0 0 0 0 0 0 0
and
-1 1 0 0 0 0 0 0 0 0

What should I do to improve this?

All the best,
Anders


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Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

[Douglas Greve]

Basically looks ok. The only things that jump out at me are that you are 
using regheader (I would create a registration file with bbregister 
rather than assuming that there was no motion between the anatomical and 
the ASL). Where did brain.fsaverage.lh.mgh come from?

doug


On 2/27/15 2:16 PM, Matthieu Vanhoutte wrote:

Dear Freesurfer's experts,

I computed some perfusion maps from ASL data. These perfusion maps 
were registered on anatomical T1 and I would like to make a group 
analysis on surfaces. Please find below my actual commands in order to 
project these volumic maps on fsaverage then smooth the data projected 
on fsaverage :


*Project CBF maps on fsaverage* :
/mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject 
fsaverage --interp trilin --projfrac 0.5 --hemi lh --o 
lh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg//
//mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject 
fsaverage --interp trilin --projfrac 0.5 --hemi rh --o 
rh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg/


*Smooth the data projected on fsaverage (native ASL data size voxel of 
3mm)* :
/mris_fwhm --s fsaverage --hemi lh --smooth-only --i 
lh.fsaverage.cbf.mgh --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh --mask 
brain.fsaverage.lh.mgh//
//mris_fwhm --s fsaverage --hemi rh --smooth-only --i 
rh.fsaverage.cbf.mgh --fwhm 3 --o rh.fwhm3.fsaverage.cbf.mgh --mask 
brain.fsaverage.rh.mgh/


Could you advise me on these two steps and tell me first if this is 
the best way to project CBF maps on fsaverage, then to smooth the data 
on surfaces ? Is my process could be improved ?


Best regards,
--
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France


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Re: [Freesurfer] regional surface area differences

[Douglas Greve]

On 2/27/15 3:41 PM, aqure...@nmr.mgh.harvard.edu wrote:
> Hi Freesurfer group,
>
> I wanted to use mris_preproc to calculate regional differences in surface
> area between two groups.
>
> Ideally I would like to use something that is vertex-wise and preserves
> regional area, but I've had trouble with spherical demons (using the
> Winkler methodology). So I am going to first try using mris_preproc (and
> compare the two methods). I found this old thread suggesting that I should
> use the --area flag.
> But I had some questions:
>
> 1) Which surfname should I use with the --area flag? area.mid vs area.pial
> vs any other file
We usually use area (area of the white surface) since mid and pial will 
have confounding thickness effects.

> 2) Should I use --meas flag in addition and if so which one? (similar to
> how --meas thickness is used for calculating cortical thickness)
I would use --meas area without using --area.
> 3) Which --surfreg file should I use? sphere.reg vs sphere. Or do I not
> need the --surfreg?
sphere.reg (which is the default)
doug

>
>
> Thanks,
> Abid
>
>
> -- Forwarded message --
> From: Anderson M. Winkler 
> Date: Tue, May 14, 2013 at 1:19 AM
> Subject: Re: [Freesurfer] Usage of --area option in estimating the
> vertex-wise maps of surface area
> To: free 
>
>
> Hi Xi-Nian,
>
> As Doug said, they don't do the same thing. The method in the paper
> uses a different kind of interpolation to allows the preservation of
> the amount of area, whereas mris_preproc achieves the same globally
> using a Jacobian correction. The results aren't expected to be
> identical at the vertex level or for small regions.
>
> An implementation of the method we proposed in the paper is available
> for Octave and/or Matlab at http://brainder.org/download/areal
> It works fine, but beware that it's quite slow.
>
> All the best,
>
> Anderson
>
>
>
> 2013/5/13 Douglas Greve 
>>
>> Hi Xi-Nian, it does not do the same thing, but it does something
> similar. Anderson found that it gave similar results in a lot of cases,
> but he has found some differences. If he's still following the FS list,
> maybe he can comment.
>> doug
>>
>>
>>
>>
>>
>> On 5/11/13 9:53 PM, Xinian Zuo wrote:
>>
>> Hello Doug,
>>
>> I am doing some association studies between functional measures and
> surface area. In using  mris_preproc, there is an option --area. Does
> this do sth similar to that as Winkler et al. (2012)?
>> Winkler et al., 2012. Measureing and comparing brain cortical
> surfacearea and other areal quantities.
>> Thank you very much.
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Re: [Freesurfer] freeview registration

[Douglas Greve]

I think that freeview does not correctly generate the registration file. 
You can use it to check the regsitration, but us tkregister if  you need 
to edit  it.

doug


On 2/27/15 10:18 AM, Xiaomin Yue wrote:

Hi All,

After using freeview to manually adjust the registration between a 
functional and T1.mgz generated by bbregister, I saved the 
registration file in freeview as lta format, which seems the only 
option.  However, the registration file has same file name for source 
and target volume.  So, when loading it again to freeview, the 
registration is totally wrong.   In order to avoid the problem, I 
converted the register.dof6.dat to lta formation, where the lta file 
has correct source and target volume name.  Then, I loaded the lta 
file generated from register.dof6.dat, did manual adjustment, and then 
saved adjusted registration as a lta file.  the final lta file has 
same problem.   I am using freesurfer 5.3.  Any suggestion is appreciated.


Thanks,
Xiaomin


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Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer

[Douglas Greve]

On 3/3/15 9:41 AM, Sarah Finnegan wrote:
> Hi Doug,
>
> Thanks I had hoped to use mri_mask but was foiled in my attempt to convert 
> the .label files to .mgz using mri_label2bvol. I assumed I must be on the 
> wrong track.
>
> my command was
>
> mri_label2vol --label V2_lh.label --temp f.nii.gz --reg register.dat 
> --fillthresh .3 --proj frac 0 1 .1 --subject V2_subject5 --hemi lh --o 
> V2_lh.mgz
>
> I have previously used this command successfully to convert labels for usage 
> in FSL. The volume will display using tkmedit on the orig surface, but in 
> tksurfer using the inflated surface there is nothing visible when attempting 
> to open as an overlay.
I'm not sure what you mean here by it displays in tkmedit on the orig 
surface. Can you elaborate? What was your tksurfer command. Also, try a 
fillthresh of 0 as there may be few voxels that have more than 30%.
>
> I have played around with different options and attempted to move forward to 
> mri_mask using the V2_lh.mgz file (hoping to later open the data in tksurfer) 
> but the command
>
> mri_mask -transfer 255 -keep_mask_deletion_edits masked_data V2_lh.mgz 
> lh_colour.mgz V2_colour_lh.mgz
>
> gives
>
> transfer mask voxels=255 to dst vol
> Transferring mask edits ('1' voxels) to dst vol
> ERROR: dimension mismatch between source and mask
>
> I assume I must be missing something fundamental in the mri_label2vol command?
Not sure what you are trying to do in that command. Where did 
lh_colour.mgz come from?
doug
>
> Thank you for your help
> Sarah
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sarah Finnegan 
> [sarah.finne...@stcatz.ox.ac.uk]
> Sent: 26 February 2015 15:12
> To: Freesurfer support list
> Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
>
> Hi Bruce
>
> Thanks for your reply,
> I did use mri_vol2surf for the sampling
>
> mri_vol2surf --src {zstat1} --srcreg {anat2exf.register.dat} --hemi 
> {hemi}--projfrac {0.8} --out {out file name} --out_type {mgz}
>
> I don't believe that I want to average within the ROI. I want to take any 
> clusters of activity within V2 and feed this into a script i'm developing in 
> MATLAB to work out the distance between different voxel clusters and the size 
> of each cluster, but only for within my region defined as V2. Hopefully that 
> makes sense, If I average I think I will lose this spatial information?
>
> Thanks
> Sarah
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: 26 February 2015 15:04
> To: Freesurfer support list
> Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
>
> Hi Sarah
>
> have you used mri_vol2surf to sample the data onto the surface? When you
> say "extract specific regions of functional data from a flat " do you
> want to average within the ROI?
>
> cheers
> Bruce
> On Thu, 26 Feb 2015, Sarah Finnegan wrote:
>
>> I have a question about the equivalent of fslmaths -mas option in
>> freesurfer.
>> I have several manually defined labels in .label form that I want to use to
>> extract specific regions of functional data from a flat patch. Ordinarily in
>> fsl I would just use
>>
>> fslmaths -invol {functional_data} -mas {bin_label} -outvol
>> {masked_functional_data}
>>
>> but I'm a little confused about an equivalent for this in free surfer as I
>> don't want to perform any further stats on these ROI yet, extract them from
>> any surrounding data and overlay onto the flattened surface.
>>
>> I have tried using
>> mri_vol2roi --label {V2_rh.label} --srcvol {functional_data.mgz} --srcreg
>> {anat2exf.register.dat} --roiavg {func_V2_mask} --finalmskvol
>> {func_V2_mask_out}
>> but when overlaying the output file there are no data points visible.
>>
>> Any help would be great as several other functions that I have tried seem to
>> be obsolete,
>>
>> Thanks!
>> Sarah
>>
>>
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Re: [Freesurfer] Problems with MonteCarlo analysis

[Douglas Greve]

The first command sets the voxel-wise threshold to p<.0001, which is 
pretty strict by itself. Is that what you wanted? Do voxels survive 
uncorrected at that level? The 2nd sets the voxelwise threshold at about 
.05. In both cases the clusterwise correction is .05 (ie, neither are 
0.9), so I'm not what it is that is going wrong.


doug


On 3/9/15 7:54 AM, Sofia Rodriguez Penuela wrote:


Dear all,

I’m trying to perform vertex-wise surface analysis on some PET data. 
After performing the group contrast, significant differences 
(uncorrected) are observed in a few clusters.These results apparently 
do not survive the Monte Carlo method. In order to ensure that the 
MC-z is working fine, I have repeated the MC-z only with two 
simulations and have set the statistical threshold to either p < 0.05 
or p < 0.9. I found no significant results in any case. So, I assume 
that something must be wrong in the command line. I’m also planning to 
do regression analyses, and perhaps I should do something different 
when correcting for multiple comparisons with Monte Carlo.


Here are the commands used:

Command to create average subject:

make_average_subject --out avgsubject --subjects subj1 subj2 subj3 subj4

Commandtocreatetheaveragesurface:

mris_preproc --fsgd fsgd_variables.txt –target s00x_average --hemi 
lh--meas SurfPet.mgh –out /ruta/lh.SurfPETpromedio.mgh


Commandtosmooththeavgsurface:

mri_surf2surf --hemi lh --s s00X_average --sval 
/ruta/lh.SurfPETpromedio.mgh --fwhm 10 --cortex --tval 
/ruta/lh.SurfPETpromedio_10mm.mgh


**

Commandtoperform GLM analysis

mri_glmfit--y $FS_HOME/mySubj_average 
/my_lh_stats_dir/lh.SurfPETpromedio_10mm.mgh --fsgd 
$FS_HOME/mySubj_average/my_lh_stats_dir/ fsgd_variables.txt dods --C 
$FS_HOME/mySubj_average /my_lh_stats_dir/lh_contrast.mat --surf 
mySubj_averagelh --label 
$FS_HOME/mySubj_average/label/lh.cortex.label--no-prune 
--glmdir$FS_HOME/mySubj_average/my_lh_stats_dir


Commandtocorrectformultiplecomparisonswith Monte Carlo as in theFSwiki:

mri_glmfit-sim --glmdir ruta\directorio --sim-sign pos --sim mc-z 
1 4 mcz-sim --cwp  0.05


Modifiedcommandtocorrectformultiplecomparisonswith Monte Carlo:

mri_glmfit-sim --glmdir ruta\directorio --sim-sign pos --sim mc-z 
1 1.3010 mcz-sim --cwpvalthresh 0.05 --seed 1297708255


Anyhelpwill behighlyappreciated.

Manythanks in advance,

Sofía Rodríguez Peñuela, Técnico de Laboratorio.
Laboratorio de Neurociencia Funcional
Departamento de Fisiología, Anatomía y Biología Celular.
Universidad Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Sevilla
- España -
Movil: 627273085
Email: srod...@upo.es
http://www.upo.es/neuroaging/es/


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Re: [Freesurfer] selxavg3-sess error

[Douglas Greve]

It looks like different runs have different number of slices. Is that right?

On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote:

Dear FS experts,

I got an error while running selxavg3-sess for a single subject. The 
log (attached) says the following:


*
** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base 
018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same dimensions!

   Input: nx=64  ny=64  nz=35
   Base:  nx=64  ny=64  nz=37
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
*

I am wondering which 'template.nii' file the script reads to create 
tempvol.nii.gz. We have different functional runs (with different TRs) 
under the subject's bold directory and for the run '/018' the TR 
should be 1900 ms. It looks like the script is reading from a 
'template.nii' located elsewhere for which the TR is 2000 ms.


*
reading from template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998769, -0.00721698, 0.0490727)
j_ras = (-1.73634e-08, -0.989358, -0.145502)
k_ras = (0.0496006, -0.145323, 0.98814)
changing data type from short to float (noscale = 0)...
writing to 018/tmp.mc-afni2.7515/tempvol.nii.gz...
*

Many thanks for your help!
Hamdi


--

Hamdi Eryilmaz, PhD

Massachusetts General Hospital
A.A. Martinos Center for Biomedical Imaging
Psychiatric Neuroimaging Division
149 13th St, Charlestown, MA 02129
Phone: +1 617 643 7462
Email:hamdi.eryil...@mgh.harvard.edu 


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Re: [Freesurfer] Calculating Total Brain Volume using 5.1 outputs

[Douglas Greve]

I think I would download a new version of mri_segstats (call it 
something like mri_segstats-5.3)


ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch

cd $SUBJECTS_DIR/subject
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.53.stats --pv 
mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg 
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz 
--in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol 
--surf-ctx-vol --totalgray --euler --ctab 
/usr/local/freesurfer/stable5_3_0/ASegStatsLUT.txt --subject subjectname


Note the output file is called aseg.53.stats and not aseg.stats

The whole-brain measures are defined here:
http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats

You'll probably want

BrainSegNotVent

doug




On 3/9/15 1:15 PM, Sastry, Nevin (NIH/NIMH) [F] wrote:

Hi,

I was wondering how best to calculate total brain volume when using outputs 
from free surfer 5.1. Could I use aseg SupraTentorial Volume measurements and 
subtract aseg ventricle, csf, and choroid plexus measurements? Is there a way 
to do calculate total brain volume using aparc outputs? I saw online that 
people have formerly calculated brain volume by adding total gray vol to 
cerebellar white matter; is this effective even though it doesn’t include 
subcortical white?

Thanks,

Nevin



Nevin Sastry,


NIMH IRTA Fellow, Child Psychiatry Branch


301-435-5557 | nevin.sas...@nih.gov

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Re: [Freesurfer] selxavg3-sess error

[Douglas Greve]

What is your mris_preproc command? And your mkanalysis-sess command?


On 3/9/15 2:41 PM, Eryilmaz, H. Hamdi wrote:

Hi Doug,

Yes, that's correct. Images in runs 015,016,017 have 37 slices, those 
in run 018 have 35.


Hamdi



*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
[gr...@nmr.mgh.harvard.edu]

*Sent:* Monday, March 09, 2015 2:38 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] selxavg3-sess error


It looks like different runs have different number of slices. Is that 
right?


On 3/9/15 1:13 PM, Eryilmaz, H. Hamdi wrote:

Dear FS experts,

I got an error while running selxavg3-sess for a single subject. The 
log (attached) says the following:


*
** Input 018/tmp.mc-afni2.7515/invol.nii.gz and base 
018/tmp.mc-afni2.7515/tempvol.nii.gz don't have same dimensions!

   Input: nx=64  ny=64  nz=35
   Base:  nx=64  ny=64  nz=37
** FATAL ERROR: perhaps you could make your datasets match?
ERROR: 3dvolreg
*

I am wondering which 'template.nii' file the script reads to create 
tempvol.nii.gz. We have different functional runs (with different 
TRs) under the subject's bold directory and for the run '/018' the TR 
should be 1900 ms. It looks like the script is reading from a 
'template.nii' located elsewhere for which the TR is 2000 ms.


*
reading from template.nii...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998769, -0.00721698, 0.0490727)
j_ras = (-1.73634e-08, -0.989358, -0.145502)
k_ras = (0.0496006, -0.145323, 0.98814)
changing data type from short to float (noscale = 0)...
writing to 018/tmp.mc-afni2.7515/tempvol.nii.gz...
*

Many thanks for your help!
Hamdi


--

Hamdi Eryilmaz, PhD

Massachusetts General Hospital
A.A. Martinos Center for Biomedical Imaging
Psychiatric Neuroimaging Division
149 13th St, Charlestown, MA 02129
Phone: +1 617 643 7462
Email:hamdi.eryil...@mgh.harvard.edu <mailto:heryil...@partners.org>


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Re: [Freesurfer] Monte Carlo Simulation

[Douglas Greve]

Yes, that probably is the reason.
doug

On 3/12/15 4:31 PM, Wolthusen, Rick Peter Fritz wrote:
> To be honest, I checked the between subject alignment and it looked pretty 
> good. None of my subjects was way out of alignment. However, since we cannot 
> fit the whole brain in the slice during scanning, we are always cutting of 
> the top of the brain, sometimes more, sometimes less, depending on the brain 
> size. Could this be the reason why the mask is off? If not, is there anything 
> else I can check?
> 
> 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: Thursday, March 12, 2015 2:47 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Monte Carlo Simulation
>
> I meant which ones are causing the problems when you run mri_glmfit.
> When you run fslview you will see something that looks like a brain. As
> you scroll thru the different time points, you'll see the CBF maps for
> different subjects. They should be more-or-less in alignment. Look for
> ones that are way out of alignment or don't have all of the brain.
>
> On 03/12/2015 02:35 PM, Wolthusen, Rick Peter Fritz wrote:
>> Well, I checked the proper match of ASL and anatomical scans again and one 
>> of the subjects I reported before was indeed wrongly matched. Thanks!
>>
>> What do you mean with "So the next thing I would do is to find which 
>> subjects are the
>> ones that are off."? You mean off when I check for registration? That's what 
>> I did before with tkregister2 and they all looked fine to me. What do I look 
>> for when I open the cbf.talaraich.nii.gz file in fslview?
>> 
>> 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: Thursday, March 12, 2015 12:19 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Monte Carlo Simulation
>>
>> If the registration looks ok, then that is all that counts. However, I'm
>> a bit sceptical that the reg looks ok but the mincost is that much
>> different than the others. You should double check that the ASL is
>> properly matched with the corresponding anatomical (ie, it is not two
>> different subjects). This would also not explain why the masks were so
>> far off. So the next thing I would do is to find which subjects are the
>> ones that are off. You can do this with something like
>>
>> fslview y.nii.gz
>>
>> where y.nii.gz is the stack of cpf maps that you passed to mri_glmfit
>> (you can mri_convert it to nii.gz). You can then step through each frame
>> (or play them as a movie) to see if any look odd.
>>
>> The mincost is from the BBR cost function. It is basically the mean
>> gray/white contrast across cortex passed through a sigmoid function to
>> make its range 0-1, 0 being best. You cannot necessarily generalize the
>> normal range for one modality to that of another.
>>
>>
>> On 03/12/2015 12:11 PM, Wolthusen, Rick Peter Fritz wrote:
>>> Hi Doug et al.,
>>>
>>> I indeed found 3 subjects, whose registration looked ok when I eyeballed 
>>> them with the tkregister 2 command, with values of .9 and higher (all the 
>>> other subjects had values between .44 and .61). Do you recommend to redo 
>>> the analysis without them or to run the first level analysis again with 
>>> --init-spm instead of --init-fsl in bbregister? Also, how is the first 
>>> value in the .mincost file generated and what does it mean? Can you use 
>>> this file for other modalities, too? Let's say if I want to do the first 
>>> level analysis for fct. connectivity instead of PASL for example?
>>>
>>> Thanks,
>>> Rick
>>> 
>>> 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: Wednesday, March 11, 2015 6:34 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Monte Carlo Simulation
>>>
>>> For the range, lower is better, but it impossible to say exactly what is
>>> good enough because it depends on your data. If it is 0.8 or higher,
>>> then that is probably bad. What I'm hoping is that there will be one or
>>> two outliers. The --init-spm was in place of --init-fsl in bbregister.
>>> But you only need that if you find a bad registration.
>>>
>>> On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote:
 I checked registration before and it was fine. However, I'll go back and 
 look at the first value in the aslcal.reg.mincost  file. What is the 
 normal range? Also, I don't understand what you mean with "the FSL 
 initialization fails" and "try --init-spm" - can you please give me some 
 more information? Thanks!
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
>

Re: [Freesurfer] GLM analysis on CBF maps

[Douglas Greve]

For the intercept, you are testing for a difference in the mean CBF 
between the groups regressing out the effects of gender and age.


For the slope, you are testing for an interaction between group and age 
regressing out the effects of gender.


doug

On 3/12/15 1:30 PM, Matthieu Vanhoutte wrote:

Hello,

I have run GLM group analyses with Freesurfer tools according DODS 
model, with six classes ((Male,Female) ; (Control,Left,Right)) and one 
age variable :


/Class MaleControl
Class MaleLeft
Class MaleRight
Class FemaleControl
Class FemaleLeft
Class FemaleRight
Variables Age /

I wanted to test /Control > Left/ and /Control > Right/ on CBF maps. I 
defined with help of the tutorial contrats for that :


/control-left.intercept.mtx : 0.5 -0.5 0 0.5 -0.5 0 0 0 0 0 0 0
control-left.slope.mtx : 0 0 0 0 0 0 0.5 -0.5 0 0.5 -0.5 0
control-right.intercept.mtx : 0.5 0 -0.5 0.5 0 -0.5 0 0 0 0 0 0
control-right.slope.mtx : 0 0 0 0 0 0 0.5 0 -0.5 0.5 0 -0.5/

My problem is that I don't know how to interpret significative results 
in both /Control > Left /contrasts/: //control-left.intercept.mtx 
/and///control-left.slope.mtx. /The same for/Control > Right./ One is 
coding for intercept and the other for slope, but concretely what 
significative results in both contrasts mean ?


Thank you in advance for helping !

Best regards,

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France

2015-03-11 16:51 GMT+01:00 Douglas N Greve >:



the sig value is actually  -log10(p)*sign(gamma) where gamma
is the
contrast (gamma.mgh). The p-value is two-tailed, and the color
indicates
what tail you are on.
doug

On 03/10/2015 01:21 PM, Matthieu Vanhoutte wrote:
> Dear FreeSurfer's experts,
>
> I have launched a GLM analyses following the tutorial :
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>
> Below the command I have used :
>
> /mri_glmfit \
>   --y
>

${FS_DIR}/SurfaceAnalysis_mri_glmfit/lh.all.subjects.fwhm3.fsaverage.cbf_s.mgh
> \
>   --fsgd ${FS_DIR}/SurfaceAnalysis_mri_glmfit/g6v1.fsgd dods \
>   --C
${FS_DIR}/SurfaceAnalysis_mri_glmfit/control-left.intercept.mtx \
>   --surf fsaverage lh \
>   --cortex \
>   --glmdir ${FS_DIR}/SurfaceAnalysis_mri_glmfit/lh.g6v1.glmdir/
>
>
> In order to see the uncorrected results with p<.0001, I ran :
>
> /freeview -f
> 
${SUBJECTS_DIR}/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=${SUBJECTS_DIR}/SurfaceAnalysis_mri_glmfit/lh.g6v1.glmdir/control-left.intercept/sig.mgh:overlay_threshold=4,5
> -viewport 3d/
>
> However, nothing appears with this threshold and when I wanted to
> configure overlay I saw that most of my values in /sig.mgh /were
> negatives between -4 and 0...
>
> How is possible for /-log10(pvalue)/ values ? Could I obtain
> significant uncorrected values from this /sig.mgh/ file ?
>
> Please find attached my needed files : *y.fsgd, mri_glmfit.log,
> **/control-left.intercept.mtx/ and sig.mgh *
>
> Thank you in advance for helping me !!
>
> Best regards,
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
>
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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

FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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__

Re: [Freesurfer] mri_glmfit on Cortical Thickness : variable significant results with cluster threshold

[Douglas Greve]

It does not discredit your results. This is not unexpected behavior. As 
you change cluster forming thresholds, the clusters will change sizes, 
but the null distribution will also change in complicated ways. The end 
result is that it is not easy to predict the effect on the number and 
sig of your clusters.

> Dear Douglas,
>
> I have run GLM group analyses with Freesurfer tools according DODS model, 
> with six classes ((Male,Female) ; (Control,Left,Right)) and one age variable :
>
> Class MaleControl
> Class MaleLeft
> Class MaleRight
> Class FemaleControl
> Class FemaleLeft
> Class FemaleRight
> Variables Age
>
> I wanted to test Control > Left and on CBF maps. I defined with help of the 
> tutorial contrats for that :
>
> control-left.intercept.mtx : 0.5 -0.5 0 0.5 -0.5 0 0 0 0 0 0 0
>
> I have run mri_glmfit-sim to correct for multiple comparisons with three 
> different cluster-forming threshold : 4, 2 and 1.3. What surprising me is 
> that I obtained significant cluster for threshold of 4 and larger significant 
> cluster for threshold of 1.3, but nothing significant with threshold at 2...
>
> How is it possible and does this discredit my significant results ?
>
> Please find attached my results files.
>
> Best regards,
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France   

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Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich

[Douglas Greve]

On 3/13/15 10:10 AM, Krieger, Donald N. wrote:
> Dear List,
>
> Sorry to be unclear in my questions.  I had a fundamental misunderstanding 
> which I hope to rectify.
>
> (1) It appears that what is called the "freesurfer" coordinate system 
> (tkregister) is represented by subject fsaverage.  3D coordinate vectors in 
> label files generated for any subject's scan are in RAS coordinates in the 
> fsaverage coordinate system.  Is this correct?
No, they are in tkregister-coordinates in the individual's conformed 
anatomical space (the coordinate system is defined by the way the col, 
row, and slice are converted into an XYZ)
> (2) Under the assumption that (1) is true, I have plotted the vectors from 
> label files (ROI: lh.postcentral) from fsaverage's and two subjects' scans on 
> axial slices extracted from $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz 
> .  Since all three are in the same coordinate system, no transformation was 
> needed.  The ROI for fsaverage's label file is plotted in black and appears 
> to follow the gray/white boundary well.  The other 2 are plotted in red and 
> green and are in the neighborhood but not the same.  Is this in line with 
> what you would expect?
This is probably not correct since the labels from individuals will need 
to be transformed. Try using mri_label2label

>
> Regards,
>   
> Don
>   
>
> Don Krieger, Ph.D.
> Department of Neurological Surgery
> University of Pittsburgh
>
>> -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 12, 2015 4:25 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] follow up and double check: transform RAS vectors 
>> to
>> talaraich
>>
>> sorry, I don't know what you've done or what you are trying to do or what the
>> mri_info command is related to. Can you fill in the details?
>>
>> On 03/12/2015 04:20 PM, Krieger, Donald N. wrote:
>>> Do the results in the attached images make sense?
>>> Does it make sense that the transformation was obtained: mri_info --vox2ras-
>> fls ?
>>> Regards,
>>>
>>> Don
>>>
>>>
>>> Don Krieger, Ph.D.
>>> Department of Neurological Surgery
>>> University of Pittsburgh
>>>
>>>
 -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 12, 2015 3:44 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] follow up and double check: transform RAS
 vectors to talaraich

 what do you want us to check?

 On 03/12/2015 03:27 PM, Krieger, Donald N. wrote:
> Dear List,
>
> I've done a couple of spot checks which appear to work but want to
> double check with you.
>
> Attached are 5 axial cuts from fsaverage's orig.mgz 5 mm apart.
>
> The "white" surface vectors are shown in black for lh.postcentral.
>
> I also put all of the CC vectors from the aseg; these show on the
> lower 3 cuts.
>
> I've also put in red and green the lh.postcentral "white" surface
> vectors from two of my scans.
>
> What do you think?
>
> Regards,
>
> Don
>
> Signature0001
>
> Don Krieger, Ph.D.
>
> Department of Neurological Surgery
>
> Universityof Pittsburgh
>
> (412)648-9654 Office
>
> (412)521-4431 Cell/Text
>
>
>
> ___
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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
 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
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 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

[Freesurfer] Fwd: Postdoc position in biostatistics in Copenhagen, Denmark, available

[Douglas Greve]

   anyone interested, please contact Gitte directly
doug



 Forwarded Message 
Subject: 	Postdoc position in biostatistics in Copenhagen, Denmark, 
available

Date:   Tue, 17 Mar 2015 14:35:36 +0100
From:   Gitte Moos Knudsen 
To: Douglas N Greve 



Hi Doug
Hope things are well!
Perhaps you would be kind enough to spread this announcement to relevant
places?

http://jobportal.ku.dk/videnskabelige-stillinger/?show=724364

Thanks!
Gitte
--
Gitte M. Knudsen
Professor, MD, DMSc
Chairman of Neurobiology Research Unit and of
Center for Integrated Molecular Brain Imaging
Rigshospitalet and University of Copenhagen
Section 6932
28 Juliane Mariesvej
DK-2100 Copenhagen O
Denmark

Ph: +45 35456720




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Re: [Freesurfer] Multiple and equidistant circular ROIs on the surface

[Douglas Greve]

what do you mean by equidistant distance?

On 3/17/15 12:54 PM, Victor Montal Blancafort wrote:

Hi FS expert,

I was wondering if it is possible to create multiple "circular" ROIs 
on a surface with equidistant distance. Since the distance between 
vertex is not constant, it works if the number of vertices between 
ROIs it is the same.


Any suggestion will be very appreciated!
Thank you in advance,

Victor Montal


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Re: [Freesurfer] R: Re: isxconcat-sess problem

[Douglas Greve]

do you have another double dash (--s) in the command line?

On 4/3/15 1:00 AM, std...@virgilio.it wrote:
Thank you very much. I have resolved Sess49 (--s) error but the 
"ERROR: Flag —s unrecognized" is still remained.



Stefano

Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 31-mar-2015 18.07
A: 
Ogg: Re: [Freesurfer] isxconcat-sess problem

Not sure what is going wrong with the 1st cmd, but the 2nd has a double
dash just before Sess49 (--s) that is causing the problem

doug

On 03/31/2015 07:55 AM, std...@virgilio.it wrote:
> Hi list,
>
> I'm performing the FS-FAST analysis.
>
> Some months ago, I have already preformed this analysis on some
> subjects without problem.
>
> Now, I have added some subjects. When I rerun the analysis i have
> these error:
>
> for isxconcat-sess -sf sessidlist —analysis fc.lthalseed.surf.lh
> -contrast L_Thalamus -o my-group_thal_LH
>
> ERROR: finding sessions
>
> Sess47 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess48
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess49
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess50
>
> [iMac-di-Stefano:freesurfer/subjects/FUNCTIONAL_DATA] Stefano%
>
>
> and for isxconcat-sess -s Sess01 -s Sess02 -s Sess03 -s Sess04 -s
> Sess05 -s Sess06 -s Sess07 -s Sess08 -s Sess09 -s Sess10 -s Sess11 -s
> Sess12 -s Sess13 —s Sess14 -s Sess15 -s Sess16 -s Sess30 -s Sess31 -s
> Sess32 -s Sess33 -s Sess34 -s Sess35 -s Sess36 -s Sess37 -s Sess39 -s
> Sess40 -s Sess41 -s Sess42 -s Sess43 -s Sess44 -s Sess45 -s Sess46 -s
> Sess47 -s Sess48 —s Sess49 -s Sess50 —analysis fc.lthalseed.surf.lh
> -contrast L_Thalamus -o my-group_THAL_LEFT
>
> ERROR: Flag —s unrecognized.
>
>
> FUNCTIONAL_DATA directory contains:
>
>
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lamgseed.surf.lh/
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lthalseed.surf.lh/
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.ramgseed.surf.rh/
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.rthalseed.surf.rh/

> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/file.fsgd
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/g1g2.intercept.mtx

> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group.diff.mtx
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group1.mtx
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group2.mtx
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/GroupDescriptorFile%201

> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/log/
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Amygdala.config
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Thalamus.config
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Amygdala.config
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Thalamus.config

> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess02/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess03/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess04/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess05/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess06/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess07/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess08/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess09/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess10/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess11/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess12/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess13/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess14/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess16/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess30/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess31/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess32/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess33/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess34/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess35/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess36/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess37/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess39/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess40/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess41/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess42/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess43/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess44/
> file:///Applications/free

Re: [Freesurfer] R: Re: R: Re: isxconcat-sess problem

[Douglas Greve]

Does Sess14 have a double dash?

On 4/4/15 3:38 AM, std...@virgilio.it wrote:

No, do you think that a folder is lacking (please see below)?
Thanks

Stefano


Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 3-apr-2015 7.34
A: 
Ogg: Re: [Freesurfer] R: Re: isxconcat-sess problem

do you have another double dash (--s) in the command line?

On 4/3/15 1:00 AM, std...@virgilio.it wrote:
Thank you very much. I have resolved Sess49 (--s) error but the 
"ERROR: Flag —s unrecognized" is still remained.



Stefano

Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 31-mar-2015 18.07
A: 
Ogg: Re: [Freesurfer] isxconcat-sess problem

Not sure what is going wrong with the 1st cmd, but the 2nd has a double
dash just before Sess49 (--s) that is causing the problem

doug

On 03/31/2015 07:55 AM, std...@virgilio.it wrote:
> Hi list,
>
> I'm performing the FS-FAST analysis.
>
> Some months ago, I have already preformed this analysis on some
> subjects without problem.
>
> Now, I have added some subjects. When I rerun the analysis i have
> these error:
>
> for isxconcat-sess -sf sessidlist —analysis fc.lthalseed.surf.lh
> -contrast L_Thalamus -o my-group_thal_LH
>
> ERROR: finding sessions
>
> Sess47 /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess48
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess49
> /Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess50
>
> [iMac-di-Stefano:freesurfer/subjects/FUNCTIONAL_DATA] Stefano%
>
>
> and for isxconcat-sess -s Sess01 -s Sess02 -s Sess03 -s Sess04 -s
> Sess05 -s Sess06 -s Sess07 -s Sess08 -s Sess09 -s Sess10 -s Sess11 -s
> Sess12 -s Sess13 —s Sess14 -s Sess15 -s Sess16 -s Sess30 -s Sess31 -s
> Sess32 -s Sess33 -s Sess34 -s Sess35 -s Sess36 -s Sess37 -s Sess39 -s
> Sess40 -s Sess41 -s Sess42 -s Sess43 -s Sess44 -s Sess45 -s Sess46 -s
> Sess47 -s Sess48 —s Sess49 -s Sess50 —analysis fc.lthalseed.surf.lh
> -contrast L_Thalamus -o my-group_THAL_LEFT
>
> ERROR: Flag —s unrecognized.
>
>
> FUNCTIONAL_DATA directory contains:
>
>
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lamgseed.surf.lh/
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.lthalseed.surf.lh/
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.ramgseed.surf.rh/
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/fc.rthalseed.surf.rh/

> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/file.fsgd
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/g1g2.intercept.mtx

> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group.diff.mtx
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group1.mtx
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/group2.mtx
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/GroupDescriptorFile%201

> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/log/
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Amygdala.config
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.L_Thalamus.config
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Amygdala.config
> 
file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/mean.R_Thalamus.config

> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess01/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess02/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess03/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess04/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess05/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess06/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess07/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess08/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess09/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess10/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess11/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess12/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess13/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess14/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess15/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess16/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess30/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess31/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess32/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess33/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess34/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess35/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess36/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess37/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess39/
> file:///Applications/freesurfer/subjects/FUNCTIONAL_DATA/Sess40/

Re: [Freesurfer] Extreme mean values for significant clusters (using GLM)

[Douglas Greve]

I'm not sure what the problem is, but it occurs to me that computing the 
mean over the cluster is probably not what should be done. Instead, the 
total should be computed. In the header of that file, there should be a 
command line for mri_segstats. Cut and paste that into a shell and add 
--accumulate and see if the numbers get more reasonable.


doug

On 4/6/15 9:48 PM, Bronwyn Overs wrote:

Dear Freesurfer Mailing List,

I have just run a GLM analysis using mri_glmfit with area as the 
measure of interest. For each of my significant contrasts, I extracted 
the mean area for each subjects from the corresponding 
cache.th13.abs.y.ocn.dat file. I then plotted these values to examine 
the nature of the interaction. In doing so I identified three 
individuals who had extreme mean area values (up to 11 sd from the 
average of the mean area) for many of the significant clusters. For 
each of these individuals I cannot see any problems with the 
freesurfer .mgz files or the cortical segmentation.


So my questions are:
1. Are extreme mean values for significant clusters in GLM a problem? 
If so, do you have any idea what could be causing these values if the 
scans appear to be well segmented?
2. If the significant clusters are calculated at a group level, how 
are the individual mean values (in cache.th13.abs.y.ocn.dat) generated?

--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 





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Re: [Freesurfer] fs-fast analysis on a group averaged surface

[Douglas Greve]

Use the (undocumented) -trgsubject flag

On 4/6/15 9:10 AM, Xiaomin Yue wrote:

Hi All,

I generated a group averaged surface using make_average_surface 
successfully.  Currently, I like to process the fMRI data using this 
group surface, instead of fsaverage, using the fs-fast pipeline.   For 
doing so, I need to run rawfunc2surf-sess with a parameter where I can 
input this group averaged surface before running mkanalysis-sess, 
mkcontrast-sess, and selxavg3-sess.  But it seems that 
rawfunc2surf-sess doesn't accept input other than self or fsaverage. 
 Is there a way to do this in the current fs-fast pipeline?


Thanks,
Xiaomin




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Re: [Freesurfer] Content of register.dof6.dat.param

[Douglas Greve]

Those numbers do not have the same interpretation as as the ones in 
fmc.mcdat but they represent the same information. If you construct a 
new file with the same format as fmc.mcdat but with those numbers 
substituted in cols 2-7 then you should get pretty similar results.


On 4/9/15 7:04 AM, pfannmo...@uni-greifswald.de wrote:
> Sorry, I ment the first six numbers in "register.dof6.dat.param".
>
>
>
> On Thu, 9 Apr 2015 12:33:49 +0200
> pfannmo...@uni-greifswald.de wrote:
>
>> Dear Experts,
>>
>> is there a possibility to extract the "motion parameter" from a BBR 
>> registration? Possibly the first three numbers of the
>>   
>> register.dof6.dat.param
>>
>> file are the same parameter as found in column 2 - 7 in:
>>
>> fmcpr.mcdat.
>>
>> If I have a series of "register.dof6.dat.param" can I use "mcdat2mcextreg" 
>> to calculate motion regressors from those transformations?
>>
>> Thanks pfannmoe
>>
>>
>>
>>
>>
>> -- 
>> Joerg Pfannmoeller 
>> ___
>> 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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Re: [Freesurfer] mri_vol2surf for 4D functional images in freesurfer space

[Douglas Greve]

Just use

--regheader subject



On 4/11/15 11:27 AM, Sabine Oligschläger wrote:

Dear FreeSurfer's,

A question regarding mri_vol2surf usage:

I have 4D functional images that are preprocessed and already in 
freesurfer space. I would like to project them to the fsaverage 
surface template using mri_vol2surf.


I assume that I should not include the --srcreg option since this 
transformation in register.dat has already been applied. However on 
the information page 
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf), --srcreg is 
listed as required argument.


How should I be using mri_vol2surf in this scenario?

Many many thanks in advance!

Kind regards,
Sabine


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Re: [Freesurfer] Clusterwise correction for multiple comparisons : volumic Tmap projected on fsaverage surface

[Douglas Greve]

If you did the analysis in the volume, then you have to do the 
clusterwise correction in the volume.


On 4/13/15 6:05 AM, Matthieu Vanhoutte wrote:

Dear experts,

I had to make volumic statistical analysis for the need to use BPM 
toolbox. So, I got in the output of this statistical analysis some 
volumic Tmaps.


As I did before some group analysis according to FStutorial, I would 
like to apply the same method of Clusterwise Correction on my volumic 
Tmaps. I have projected my Tmpas on fsaverage surface, but don't know 
if it is possible to apply multiple comparisons correction on these ? 
And if it is the case, how to do it ?


Thanks in advance for any help you could supply to me !

Best regards,

Matthieu


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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Content of register.dof6.dat.param

[Douglas Greve]

yes

On 4/13/15 10:32 AM, pfannmo...@uni-greifswald.de wrote:
> Just to make that point: Is it valid to apply "mcparams2extreg -mcfile 
> fmc.mcdat -extreg mcextreg" after substitution of the numbers in
> "register.dof6.dat.param" into "fmc.mcdat"? Is the result for the motion 
> regressors valid?
>
>
>
> On Mon, 13 Apr 2015 10:15:08 -0400
> Douglas Greve  wrote:
>
>> Those numbers do not have the same interpretation as as the ones in
>> fmc.mcdat but they represent the same information. If you construct a
>> new file with the same format as fmc.mcdat but with those numbers
>> substituted in cols 2-7 then you should get pretty similar results.
>>
>>
>> On 4/9/15 7:04 AM, pfannmo...@uni-greifswald.de wrote:
>>> Sorry, I ment the first six numbers in "register.dof6.dat.param".
>>>
>>>
>>>
>>> On Thu, 9 Apr 2015 12:33:49 +0200
>>> pfannmo...@uni-greifswald.de wrote:
>>>
>>>> Dear Experts,
>>>>
>>>> is there a possibility to extract the "motion parameter" from a BBR 
>>>> registration? Possibly the first three numbers of the
>>>>
>>>> register.dof6.dat.param
>>>>
>>>> file are the same parameter as found in column 2 - 7 in:
>>>>
>>>> fmcpr.mcdat.
>>>>
>>>> If I have a series of "register.dof6.dat.param" can I use "mcdat2mcextreg" 
>>>> to calculate motion regressors from those transformations?
>>>>
>>>> Thanks pfannmoe
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> -- 
>>>> Joerg Pfannmoeller 
>>>> ___
>>>> Freesurfer mailing list
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Re: [Freesurfer] Clusterwise correction for multiple comparisons : volumic Tmap projected on fsaverage surface

[Douglas Greve]

Does the BPM toolbox (what's that?) not give you cluster correction? You 
can try using mri_volcluster with the --grf option, but you'll need to 
know the FWHM. Afterwards you can map the result to the surface


On 4/13/15 10:46 AM, Matthieu Vanhoutte wrote:

Hello Douglas,

Thanks but even if I do the clusterwise correction in the volume, I 
can't get an clusterwise corrected output volume image. The only 
things I have are the Tmaps that I can threshold if wanted.


And I would like to project on fsaverage surface the results of the 
clusterwise correction in the volume. How could I do ?


Best regards,

Matthieu

2015-04-13 16:27 GMT+02:00 Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>>:


If you did the analysis in the volume, then you have to do the
clusterwise correction in the volume.


On 4/13/15 6:05 AM, Matthieu Vanhoutte wrote:

Dear experts,

I had to make volumic statistical analysis for the need to use
BPM toolbox. So, I got in the output of this statistical analysis
some volumic Tmaps.

As I did before some group analysis according to FStutorial, I
would like to apply the same method of Clusterwise Correction on
my volumic Tmaps. I have projected my Tmpas on fsaverage surface,
but don't know if it is possible to apply multiple comparisons
correction on these ? And if it is the case, how to do it ?

Thanks in advance for any help you could supply to me !

Best regards,

Matthieu


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Re: [Freesurfer] bootstrap/jackknife in qdec?

[Douglas Greve]

No, sorry.
doug

On 4/14/15 7:28 AM, Fred Dick wrote:
> Dear Doug et al.,
>
> is there a hidden option (perchance) to get bootstrapped estimates of the 
> correlation coefficients/regression parameters in qdec?
>
> cheers
> Fred
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Re: [Freesurfer] mri_segstats_flags_more questions

[Douglas Greve]

On 4/14/15 9:59 AM, Alshikho, Mohamad J. wrote:


Hi Doug,

If I check the file "aseg.stats" ( the output of the command line 
recon-all –subjid –all  ) I don't see in the table (in the file 
"aseg.stats" ) any volumes regarding right and left hemispheric white 
matter.


It is not supposed to be there. That measure is not as accurate as when 
the surface is used. We prevent it from being reported in the aseg.stats 
by running mri_segstats with --ctab ASegStatsLUT.txt which does not have 
white mater in it. There are volumes in the aseg.stats file for lh and 
rh white matter measured with the surface, but they are not in the 
enumerated list, instead they are something like


# Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left 
hemisphere cortical white matter volume, 237875.057850, mm^3
# Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right 
hemisphere cortical white matter volume, 246435.219579, mm^3
# Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical 
white matter volume, 484310.277429, mm^3



The mri_segstats in aseg.stats was reported as the following:

mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent 
--subcortgray --in mri/norm.mgz --in-intensity-name norm 
--in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol 
--totalgray --ctab  /usr/local/freesurfer/stable5_1_0/ASegStatsLUT.txt 
--subject 005101


I can generate the right and left hemispheric white matter in 
"aseg.stats" If I repeat running the following command line (like what 
was mentioned in FS wiki):


mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg 
--brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name 
norm --in-intensity-units MR --etiv --subject 005101


My Questions are:

1.Which flag is responsible for showing/hiding the left and right 
hemispheric white matter statistics from “aseg.stats”.


2.Why we have slight differences in the resultant volumes as an output 
of the previous command lines.


3.Which command line do you recommend to generate the statistics.

4.Can I feed any additional flags to the command recon-all –subjid 
–all   in order to force mri_segstats to run like in the second 
previous command line.


I am sorry for my long list of questions

Thanks in advance,

**Mohamad



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Re: [Freesurfer] dimension mismatch

[Douglas Greve]

Don't use the --inv flag on vol2vol
doug

On 4/14/15 10:03 AM, Thomas Potrusil wrote:

Dear FreeSurfers!
After successful registration using
dt_recon --i $dcmfile_b0 --b $bvals $bvecs --s $subj --o $outdir_dtirecon
I resampled the anatomical into the functional space using (I´m 
interested in ADC-values)
mri_vol2vol --mov $dti_vol --reg $outdir_dtirecon/register.dat 
--fstarg --inv --o $vol2vol

which worked again very well.
for extracting ADC-values I used
mri_segstats --seg $subj/mri/aparc.a2009s+aseg.mgz --ctab $FSCLUT 
--seg-erode 1 --i $outdir_dtirecon/adc.anat.mgh  --mul 1000 --sum 
$outdir_stat/adc_aparc.stats

Running this command delivers the following error:
ERROR: dimension mismatch between input volume and seg
  input 256 256 47
  seg   256 256 256
Do you have any idea avoiding this?!
Thanks a lot, Tom


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Re: [Freesurfer] mri_vol2vol

[Douglas Greve]

sorry, I don't understand. fstal would imply that you want talairach 
space. If you want to map the functional into the anatomical space, then
mri_vol2vol --mov res-001.nii  --o res-001.t1.space.nii --reg 
register.dof6.dat --fstarg




On 4/14/15 11:36 AM, Xiaomin Yue wrote:

Hi Doug,

I like to convert a native functional data into the anatomical space 
using mri_vol2vol with --fstal, so that the resample data has same 
spatial resolution as the original function data.  However, 
mri_vol2vol give a error: --fstal unknown.  I also tried using 
--fstalres as suggested in the help document, with same error.  I am 
using fs5.3.  the command is: mdi_vol2vol --mov res-001.nii --fstarg 
--fstal 1.5 --o res-001.t1.space.nii --reg register.dof6.dat


Thanks,
Xiaomin


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Re: [Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

[Douglas Greve]

So BPM does not do clusterwise correction? You could use mri_volcluster, 
but you'll need to know the FWHM of your BPM analysis

doug

On 4/14/15 12:17 PM, Matthieu Vanhoutte wrote:

Dear FreeSurfer's experts,

For personnal need I use the BPM toolbox (Biological Parametric 
Mapping) to compute GLM analysis. The outputs of this Toolbox gave me 
beta maps and Tmaps.


However, precedently I used the whole FreeSurfer group analysis 
tutorial on other datas, including the Clusterwise Correction for 
multiple comparisons. And now in order to compare results, I'd like to 
use this Clusterwise Correction consequently to my BPM Toolbox GLM 
analysis.


Is it possible to manually adapt some scripts ? In this way, how could 
I upgrade my outputs to these of "mri_glmfit" in order to launch 
Clusterwise Correction after ?


Many thanks in advance for helping !

Best regards,

Matthieu


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Re: [Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

[Douglas Greve]

I guess I don't understand what you are asking for. If BPM outputs a 
cluster-corrected volume, then why can't you just map that to the 
surface and be done with it?


On 4/14/15 6:48 PM, Matthieu Vanhoutte wrote:


Hello Douglas,

Indeed BPM doesn't do Clusterwise correction.

What does the FWHM of the BPM analysis correspond to ? And how to find 
it ?


Manu thanks !

Best regards,

Matthieu

Le 15 avr. 2015 00:23, "Douglas Greve" <mailto:gr...@nmr.mgh.harvard.edu>> a écrit :


So BPM does not do clusterwise correction? You could use
mri_volcluster, but you'll need to know the FWHM of your BPM analysis
doug

On 4/14/15 12:17 PM, Matthieu Vanhoutte wrote:

Dear FreeSurfer's experts,

For personnal need I use the BPM toolbox (Biological Parametric
Mapping) to compute GLM analysis. The outputs of this Toolbox
gave me beta maps and Tmaps.

However, precedently I used the whole FreeSurfer group analysis
tutorial on other datas, including the Clusterwise Correction for
multiple comparisons. And now in order to compare results, I'd
like to use this Clusterwise Correction consequently to my BPM
Toolbox GLM analysis.

Is it possible to manually adapt some scripts ? In this way, how
could I upgrade my outputs to these of "mri_glmfit" in order to
launch Clusterwise Correction after ?

Many thanks in advance for helping !

Best regards,

Matthieu


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Re: [Freesurfer] mri_vol2vol

[Douglas Greve]

So you want it to be in a volume with field of view 256mm in all three 
dimensions, but the voxel size to be that of the functional data? It is 
possible to do, but not easy to set up. Can you say why you would want 
to do that?



On 4/14/15 8:20 PM, Xiaomin Yue wrote:
Thanks for your response.  The command you gave will generate a new 
function data with the spatial resolution of the anatomical data, 
which in my case is much higher than those of functional data.  What i 
want is to generate a new functional data in the anatomical space, 
with spatial resolution of the original function data. Is it possible? 
 I thought that --fstalres would give me a choice to keep the spatial 
resolution of the original function data.


Xiaomin


Date: Tue, 14 Apr 2015 18:22:00 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2vol

sorry, I don't understand. fstal would imply that you want talairach 
space. If you want to map the functional into the anatomical space, then
mri_vol2vol --mov res-001.nii  --o res-001.t1.space.nii --reg 
register.dof6.dat --fstarg




On 4/14/15 11:36 AM, Xiaomin Yue wrote:

Hi Doug,

I like to convert a native functional data into the anatomical
space using mri_vol2vol with --fstal, so that the resample data
has same spatial resolution as the original function data.
 However, mri_vol2vol give a error: --fstal unknown.  I also tried
using --fstalres as suggested in the help document, with same
error.  I am using fs5.3.  the command is: mdi_vol2vol --mov
res-001.nii --fstarg --fstal 1.5 --o res-001.t1.space.nii --reg
register.dof6.dat

Thanks,
Xiaomin


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Re: [Freesurfer] Why weighted least squares?

[Douglas Greve]

In theory, WLS is the optimal estimator in the case where variance 
differs across subject. The FS implementation actually computes 
"psuedo-WLS" in which the weights are just the inverse of the first 
level variance. A true WLS would use the random effect variance plus the 
lower level variance. The first  level variance is determined from the 
variance of the fMRI time series.


doug

On 4/13/15 6:42 PM, ye tian wrote:

Hello Freesurfers,

I would like to be a little more specific about my question. Was 
heteroskedasticity a reason for Weighted Least Square (WLS)? If so, 
how did Freesurfer determine the weights?


Thank you!

Sincerely,
Ye




On Mon, Apr 13, 2015 at 4:59 PM, ye tian > wrote:


Dear Freesurfers,

Can someone please explain to me why WLS was chosen as the method
of regression?

Thank you very much!

Sincerely,
Ye




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Re: [Freesurfer] mri_vol2vol

[Douglas Greve]

But why do you need to have the same resolution as the original functional?

On 4/14/15 10:30 PM, Xiaomin Yue wrote:
yes, that's precisely what I want.  the reason is the following.  A 
subject was scanned multiple times across days with slightly different 
slice position for each time.  What I need is to extract a peak 
response when a stimuli was presented.   In order to make the voxels 
match from one scan to another, I thought that all scans have to be in 
same space, so that the data extracted for a voxel from different 
scans match.   Could there be a better way to do this?


Thanks,
Xiaomin


Date: Tue, 14 Apr 2015 21:08:15 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2vol


So you want it to be in a volume with field of view 256mm in all three 
dimensions, but the voxel size to be that of the functional data? It 
is possible to do, but not easy to set up. Can you say why you would 
want to do that?



On 4/14/15 8:20 PM, Xiaomin Yue wrote:

Thanks for your response.  The command you gave will generate a
new function data with the spatial resolution of the anatomical
data, which in my case is much higher than those of functional
data.  What i want is to generate a new functional data in the
anatomical space, with spatial resolution of the original function
data. Is it possible?  I thought that --fstalres would give me a
choice to keep the spatial resolution of the original function data.

Xiaomin


Date: Tue, 14 Apr 2015 18:22:00 -0400
From: gr...@nmr.mgh.harvard.edu 
To: freesurfer@nmr.mgh.harvard.edu

Subject: Re: [Freesurfer] mri_vol2vol

sorry, I don't understand. fstal would imply that you want
talairach space. If you want to map the functional into the
anatomical space, then
mri_vol2vol --mov res-001.nii  --o res-001.t1.space.nii --reg
register.dof6.dat --fstarg



On 4/14/15 11:36 AM, Xiaomin Yue wrote:

Hi Doug,

I like to convert a native functional data into the anatomical
space using mri_vol2vol with --fstal, so that the resample
data has same spatial resolution as the original function
data.  However, mri_vol2vol give a error: --fstal unknown.  I
also tried using --fstalres as suggested in the help document,
with same error.  I am using fs5.3.  the command is:
mdi_vol2vol --mov res-001.nii --fstarg --fstal 1.5 --o
res-001.t1.space.nii --reg register.dof6.dat

Thanks,
Xiaomin


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Re: [Freesurfer] dimension mismatch

[Douglas Greve]

I would  think that going into the DTI space would make this worse since 
the voxels are bigger (?). But if that is what you want to do, use 
mri_label2vol to map the aparc+aseg.mgz into the DTI space, then spec 
that aparc+aseg in the mri_segstats cmd


doug

On 4/15/15 2:13 AM, Thomas Potrusil wrote:

Hi doug!
you´re right, it´s working without --inv flag. But I have problems 
with partial volume effects within subcortical areas close to the 
ventricle. ADC values are falsified for some regions when using 
mri_segstats (especially caudate and putamen). I want to overcome this 
problem by resampling the anat to funct space... Visual inspection of 
data showed that registration is very good but scrolling through adc 
map with aseg-overlay revealed these PVEs...

Thanks, Tom
*Gesendet:* Mittwoch, 15. April 2015 um 00:19 Uhr
*Von:* "Douglas Greve" 
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] dimension mismatch
Don't use the --inv flag on vol2vol
doug
On 4/14/15 10:03 AM, Thomas Potrusil wrote:

Dear FreeSurfers!
After successful registration using
dt_recon --i $dcmfile_b0 --b $bvals $bvecs --s $subj --o
$outdir_dtirecon
I resampled the anatomical into the functional space using (I´m
interested in ADC-values)
mri_vol2vol --mov $dti_vol --reg $outdir_dtirecon/register.dat
--fstarg --inv --o $vol2vol
which worked again very well.
for extracting ADC-values I used
mri_segstats --seg $subj/mri/aparc.a2009s+aseg.mgz --ctab $FSCLUT
--seg-erode 1 --i $outdir_dtirecon/adc.anat.mgh --mul 1000 --sum
$outdir_stat/adc_aparc.stats
Running this command delivers the following error:
ERROR: dimension mismatch between input volume and seg
  input 256 256 47
  seg   256 256 256
Do you have any idea avoiding this?!
Thanks a lot, Tom

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Re: [Freesurfer] Clusterwise correction : How to use it on second step in Group Analyses ?

[Douglas Greve]

Sorry, I misread your previous email as "Indeed BPM does do Clusterwise 
correction." instead of "Indeed BPM doesn't do Clusterwise correction." 
The FWHM is the full-width-half-max and is a measure of the spatial 
smoothness. This is always needed for cluster-wise correction. This is 
usually obtained during the group analysis by examining the residuals, 
so it should come out of what ever you are using for group analysis. If 
it does not come out of BPM, then that is a problem that I cannot help 
you with (talk to whoever programmed BPM).


doug

On 4/15/15 3:30 AM, Matthieu Vanhoutte wrote:

Hello Douglas,

Sorry if I haven't been clear. I'm trying to explain my needs :

1) I use the BPM toolbox to compute the GLM analysis as mri_glmfit 
would do. However, outputs of this toolbox only give me beta maps and 
uncorrected Tmaps.
2) With only these uncorrected Tmaps outputs, I'd like to apply 
Clusterwise correction as mri_glmfit-sim would do with the same 
arguments if possible (--cache ; --cwp ; --2spaces ; ...).


--> Is there a way to succeed in 2) with some manual scripting ?

--> Is the mri_volcluster adapted as you proposed : in this case you 
said I need to know the FWHM of my BPM analysis, how could I obtain this ?


--> Would I have access in this way to arguments --cache and --cwp as 
used in mri_glmfit-sim ?


I hope I have been clearly.

Thanks in advance for guiding me !

Best regards,

Matthieu

2015-04-15 3:06 GMT+02:00 Douglas Greve <mailto:gr...@nmr.mgh.harvard.edu>>:


I guess I don't understand what you are asking for. If BPM outputs
a cluster-corrected volume, then why can't you just map that to
the surface and be done with it?


On 4/14/15 6:48 PM, Matthieu Vanhoutte wrote:


Hello Douglas,

Indeed BPM doesn't do Clusterwise correction.

What does the FWHM of the BPM analysis correspond to ? And how to
find it ?

Manu thanks !

    Best regards,

Matthieu

Le 15 avr. 2015 00:23, "Douglas Greve" mailto:gr...@nmr.mgh.harvard.edu>> a écrit :

So BPM does not do clusterwise correction? You could use
mri_volcluster, but you'll need to know the FWHM of your BPM
analysis
doug

On 4/14/15 12:17 PM, Matthieu Vanhoutte wrote:

Dear FreeSurfer's experts,

For personnal need I use the BPM toolbox (Biological
Parametric Mapping) to compute GLM analysis. The outputs of
this Toolbox gave me beta maps and Tmaps.

However, precedently I used the whole FreeSurfer group
analysis tutorial on other datas, including the Clusterwise
Correction for multiple comparisons. And now in order to
compare results, I'd like to use this Clusterwise Correction
consequently to my BPM Toolbox GLM analysis.

Is it possible to manually adapt some scripts ? In this way,
how could I upgrade my outputs to these of "mri_glmfit" in
order to launch Clusterwise Correction after ?

Many thanks in advance for helping !

Best regards,

Matthieu


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Re: [Freesurfer] Exporting Qdec Data

[Douglas Greve]

try
mri_segstats --i y.mgh --vox vertexno 33 0 0 --avgwf out.dat



On 4/15/15 6:41 PM, Lindsay Renae Wessel wrote:
> Thanks! I now get the following error:
>
> "ERROR: Option out.dat unknown"
>
> The exact command I have entered (for vertex 33) is:
>
> "mri_segstats --i y.mgh --vox vertexno 33 --avgwf out.dat"
>
>
> Thanks again.
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Wednesday, April 15, 2015 11:13 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Exporting Qdec Data
>
> Try using --vox instead of --crs
>
>
>
> On 04/15/2015 01:44 PM, Lindsay Renae Wessel wrote:
>>
>> Hello all,
>> I am running Qdec on a large number of subjects and trying to  extract the 
>> data from the plots generated by clicking "find clusters and go to max." I 
>> would like to export the data from the corresponding vertices.
>> I found the following line of code from an earlier, similar question on the 
>> listserve:
>> mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf  out.dat
>> However when I run this I simply get an error: "ERROR: Option --crs unknown"
>>
>> I would love some help understanding the components of the command. Let's 
>> say I am looking at thickness at vertex 33. Would this be the right line of 
>> code to use? Where can I enter the vertex number?
>>
>> Thanks so much,
>>
>> Lindzi Wessel
>> UC Davis ​
>>
>>
>>
>>
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> --
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> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
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