Re: [Freesurfer] How to convert a surface label to .nii

2016-02-11 Thread Marc Ramos 
My guess is to use mri_label2vol
 instead, and a
mri_convert to convert to nii.gz

I hope this helps.
Marc.




On Thu, Feb 11, 2016 at 3:17 PM, Afzal, Afsana 
wrote:

> Hi,
>
> How can I convert a surface .label file to a .nii format? I'm using
> mri_label2label in the following way but the output is always in .label not
> .nii:
>
> mri_label2label
> --srclabel dlpfc-lh.label
> --outmask dlpfc-lh_mask.nii
> --s fsaverage
> --trglabel dlpfc-lh_mask.nii
> --regmethod surface
> --hemi lh
>
> Thanks for your help,
>
> Afsana
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
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Re: [Freesurfer] FreeSurfer MRI segmentation

2016-02-11 Thread Bruce Fischl 

Hi Maheen

you can look at the aseg.mgz or use the surfaces to create various 
compartments with mris_fill, but sulcal CSF is pretty hard to accurately 
detect with only a T1


cheers
Bruce
On Thu, 11 Feb 2016, Maheen Siddiqui wrote:


Dear FreeSurfer Users, 
I have a T1 weighted MRI scan and have run the recon-all command on it. For
my steps moving forward I need to have 4 layers of tissue i.e. 4
segmentation files - GM, WM, CSF and extra cerebral tissue. Which of the
outputs from recon-all will give me the segmentation? I thought at first
that brain.mgz was what I needed but having viewed brain.mgz in Freeview, it
is just the skull stripped version of the T1 scan. 

Is there any document that details all the outputs of recon-all? 

Many thanks for any advice I can get!

Maheen

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Re: [Freesurfer] Basal Ganglia Segmentation

2016-02-11 Thread Syeda Wajiha Maryam 
I definitely meant to type *Dear in my email.

Cheers,
Maryam

On Thu, Feb 11, 2016 at 2:57 PM, Syeda Wajiha Maryam 
wrote:

> Fear Freesurfer Experts,
>
> I have a feeling this question has been asked already but I'm still
> confused about it. Is there a way to extract the basal ganglia structure
> using freesurfer?
>
> Thanks in advance for your help!
>
> Regards,
> Maryam
>
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Re: [Freesurfer] Basal Ganglia Segmentation

2016-02-11 Thread Bruce Fischl 
sure, we segment putamen, pallidum and caudate as part of the aseg.mgz 
(and nucleus accumbens, although that is less well-defined)
On Thu, 11 Feb 
2016, Syeda Wajiha Maryam wrote:

> Fear Freesurfer Experts,
> 
> I have a feeling this question has been asked already but I'm still confused
> about it. Is there a way to extract the basal ganglia structure using
> freesurfer?
> 
> Thanks in advance for your help!
> 
> Regards,
> Maryam
> 
>
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[Freesurfer] Basal Ganglia Segmentation

2016-02-11 Thread Syeda Wajiha Maryam 
Fear Freesurfer Experts,

I have a feeling this question has been asked already but I'm still
confused about it. Is there a way to extract the basal ganglia structure
using freesurfer?

Thanks in advance for your help!

Regards,
Maryam
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Re: [Freesurfer] Processing of young children using Freesurfer

2016-02-11 Thread Bruce Fischl 
yes, something wrong with the installation but it's outside of my 
expertise. Zeke: can you take a look?


thanks
Bruce
On Thu, 11 Feb 2016, Zoellner, Frank 
wrote:



Hi,

did you find a hint why my installation of freesurfer is not processing the 
data at that stage ?
It seems to be a general problem, we tried also with other data sets of elder 
people etc ..

Any help appreciated.

Yours
Frank


PD Dr. Frank Zoellner
Group Leader "MRI and Medical Image Analysis"
Computer Assisted Clinical Medicine
Medical Faculty Mannheim
Heidelberg University
Theodor-Kutzer-Ufer 1-3
D-68167 Mannheim

Phone: +49 (0)621 3835117
Fax:   +49 (0)621 3835123
Email: frank.zoell...@medma.uni-heidelberg.de
Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/


-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Zoellner, Frank
Gesendet: Dienstag, 9. Februar 2016 15:49
An: Freesurfer support list
Betreff: Re: [Freesurfer] Processing of young children using Freesurfer

Hi Bruce,

thanks for the reply.
Here comes the output (see attached).

I just downloaded the VM with freesurfer from your website, fyi.

Yours
Frank

PD Dr. Frank Zoellner
Group Leader "MRI and Medical Image Analysis"
Computer Assisted Clinical Medicine
Medical Faculty Mannheim
Heidelberg University
Theodor-Kutzer-Ufer 1-3
D-68167 Mannheim

Phone: +49 (0)621 3835117
Fax:   +49 (0)621 3835123
Email: frank.zoell...@medma.uni-heidelberg.de
Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/


-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 9. Februar 2016 14:12
An: Freesurfer support list
Betreff: Re: [Freesurfer] Processing of young children using Freesurfer

hmmm, this doesn't seem to have to do with your data but maybe is an 
installation problem? It says it failed but doesn't give an error message, 
which is unusual. Can you try just typing in directly:

cd /media/sf_cdh_ventrikel/test_002/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz

and send us the output?

cheers
Bruce

On Tue, 9
Feb 2016, Zoellner, Frank wrote:


Hi,
 
I am currently working on a project involving brain morphometry of 2
year old children.
We are interested in segmenting the ventricle and I tried to run
freesurfer using the standard recon-all  -all for a first test.
 
Unfortunately, freesurfer reports an error (see attached log file).
 
I also read about that it is advised to run freesurfer with patient
age >5 but maybe someone has an idea how to solve this.
As far as I get from the step it crashes at the intensity correction step?
Do I need to calculate some sort of template maybe ?
 
Any comments welcome
 
Yours
Frank
 

PD Dr. Frank Zoellner
Group Leader "MRI and Medical Image Analysis"
Computer Assisted Clinical Medicine
Medical Faculty Mannheim
Heidelberg University
Theodor-Kutzer-Ufer 1-3
D-68167 Mannheim
 
Phone: +49 (0)621 3835117
Fax:   +49 (0)621 3835123
Email: frank.zoell...@medma.uni-heidelberg.de
Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/
 
 
 




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[Freesurfer] How to convert a surface label to .nii

2016-02-11 Thread Afzal, Afsana 
Hi,

How can I convert a surface .label file to a .nii format? I'm using 
mri_label2label in the following way but the output is always in .label not 
.nii:

mri_label2label
--srclabel dlpfc-lh.label
--outmask dlpfc-lh_mask.nii
--s fsaverage
--trglabel dlpfc-lh_mask.nii
--regmethod surface
--hemi lh

Thanks for your help,

Afsana

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078
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[Freesurfer] comparison between two hemisphere in single subject

2016-02-11 Thread Ashkan Faghiri 
Hello,

I want to compare the two hemisphere in  one subject (thickness for
example). should I use?

surfreg --s $subject --t fsaverage_sym --lh
surfreg --s $subject --t fsaverage_sym --lh --xhemi

then what? how can I compare the two hemisphere of one subject?

Regards,
Ashkan

-- 
-- 
Ashkan Faghiri
MSc student of Bioelectrical Engineering
Department of Electrical Engineering
Sharif University of Technology
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[Freesurfer] FreeSurfer MRI segmentation

2016-02-11 Thread Maheen Siddiqui 
Dear FreeSurfer Users,

I have a T1 weighted MRI scan and have run the recon-all command on it. For
my steps moving forward I need to have 4 layers of tissue i.e. 4
segmentation files - GM, WM, CSF and extra cerebral tissue. Which of the
outputs from recon-all will give me the segmentation? I thought at first
that brain.mgz was what I needed but having viewed brain.mgz in Freeview,
it is just the skull stripped version of the T1 scan.

Is there any document that details all the outputs of recon-all?

Many thanks for any advice I can get!

Maheen
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Re: [Freesurfer] epidewarp.fsl for FSL 5.x

2016-02-11 Thread Joseph Dien 
MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag 
/Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-1-01-01.nii
 --dph 
/Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii
 --tediff 2.46 --esp 0.51 --epi fMRI/RPA003/bold/001/f.nii.gz --vsm 
fMRI/RPA003/bold/b0dcmap.nii.gz



> On Feb 10, 2016, at 22:58, Douglas Greve  wrote:
> 
> what is your command line? I think there is a rescaling in which it expcts 
> the phase to be 0-2048 (or 4096) as this is how it comes of the (siemens) 
> scanner. Could that be the problem?
> 
> 
> On 2/10/16 10:40 PM, Joseph Dien wrote:
>> I ran into the same issue:
>> 
>> FSLVersion 5.0.4
>> FSLVerMaj 5
>> FSL Version is 5.0.4, must be 3.X or 4.X
>> 
>> I downloaded the epidewarp.fsl script from the suggested ftp site and 
>> replaced the existing script.  It did indeed fix the version incompatibility 
>> with FSL 5.x.
>> 
>> I ran into a new problem where it was aborting.  After some trouble shooting 
>> and looking over the documentation, I realized that —-epi is a required 
>> input without which the script crashes (or is it supposed to be optional but 
>> there is a bug in the script?).
>> 
>> After including it, it ran much further but then aborted with the following 
>> error:
>> 
>> ERROR: input phase image exceeds allowable phase range.
>> Allowable range is 6.283 radians.  Image range is: 12.5633 radians.
>> 
>> This is consistent with the documentation.  I’m not sure why the phase image 
>> exceeds the range though.
>> 
>> It ran without problems with SPM’s FieldMap Toolbox and it is from a 
>> standard Siemen’s scanner sequence (two magnitude files and one phase 
>> difference file).
>> 
>> Do I just divide the values by two with something like fslmaths since it 
>> seems to have exactly double the required range?
>> 
>> Joe
>> 
>>> On Nov 26, 2014, at 21:36, Douglas Greve < 
>>> gr...@nmr.mgh.harvard.edu 
>>> > wrote:
>>> 
>>> 
>>> It is there again. I don't know what the status if it  is in terms of the 
>>> version. Try it and let me know
>>> doug
>>> 
>>> On 11/25/14 4:34 PM, Morgan Hough wrote:
 Hi Doug,
 
 Could you put the epidewarp.fsl script back on your ftp site? I don’t see 
 it at the link in the archives:
 
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
  
 
 
 BTW, is the script updated in some way for 5.x or can I can the old script 
 just be changed to accept 5.x version numbers. 
 
 Cheers,
 
 -Morgan
>>> 
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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
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>>>  . 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.
>> 
>> 
>> 
>> Joseph Dien, PhD
>> Senior Research Scientist
>> Maryland Neuroimaging Center
>> University of Maryland, College Park
>> E-mail: jdie...@mac.com 
>> Cell Phone: 202-297-8117
>> http://joedien.com 
>> 
>> 
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Senior Research Scientist
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University of Maryland, College Park
E-mail: jdie...@mac.com

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-11 Thread Jennifer Legault 
Thank you for your response.  Do I need to run the glm_fit-sim command to
make the csd file?  I feel this would be inappropriate for my data since I
already ran the LME model.

Second, is there an argument to make an output file that can be visualized
via freeview?  In other words, how can I view my cluster thresholded data?

Your help is greatly appreciated,

Jen



On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve 
wrote:

> There is a (very long) command line on that page. Mainly you need a csd
> file. To get that you need the FWHM of your analysis, the voxel-wise
> threshold, and the sign of the contrast (or abs). Then the relevant output
> will be the --sum. You can run it with --help to get more info.
>
>
> On 2/10/16 5:11 PM, Jennifer Legault wrote:
>
> Thank you very much for your help!  I still received a "cannot read file
> type" error when I only added the path to the output --o part, however when
> I also added the path to the input file, it worked!
>
> I do have one more question: Which argument can I add so that in my output
> file I see the clusterwise P value, like it is shown here
> 
> ?
>
> Best,
>
> Jen
>
> On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> I meant for the output files, so the --o in particular
>>
>> On 02/10/2016 01:47 PM, Jennifer Legault wrote:
>> > Douglas,
>> >
>> > Thank you for your quick response.  When I add --sd [path_location], I
>> > get the following error:
>> > Loading source values
>> > mri_read(): couldn't determine type of file
>> [path_location]/rh_time_spval
>> > ERROR: could not read rh_time_spval as type
>> >
>> > Should I use another argument?
>> >
>> > Best,
>> >
>> > Jen
>> >
>> >
>> >
>> > On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve
>> > > wrote:
>> >
>> > Try specifying the full path to the output
>> >
>> > On 02/10/2016 12:59 PM, Jennifer Legault wrote:
>> > > Dear experts,
>> > >
>> > > I am trying to use the cluster thresholding command for my
>> > freesurfer
>> > > LME outputs as referred to here
>> > >
>> > > >.
>> > > Any feedback or comments would be greatly appreciated.
>> > >
>> > > I am aware that there have been permission denied errors when
>> using
>> > > mri_surfcluster and that applying this patch
>> > >
>> > <
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mni152reg
>> >
>> > > should solve the problem (which I tried), however I am still
>> either
>> > > receiving errors stating the permission is denied.
>> > >
>> > > This is the command I am trying to run:
>> > >
>> > >  mri_surfcluster --subject fsaverage --hemi rh --in
>> > rh_time_spval.mgh
>> > > --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster
>> --sum
>> > > rh_time_cluster_sum
>> > >
>> > >
>> > > Here is the error log:
>> > >
>> > > mri_surfcluster --subject fsaverage --hemi rh --in
>> rh_time_spval.mgh
>> > > --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster
>> --sum
>> > > rh_time_cluster_sum thsign = pos, id = 1
>> > > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05
>> > greve Exp $
>> > > hemi   = rh
>> > > srcid  = rh_time_spval.mgh
>> > > srcsubjid  = fsaverage
>> > > srcsurf= white
>> > > srcframe   = 0
>> > > thsign = pos
>> > > thmin  = -1
>> > > thmax  = -1
>> > > fdr= 0.05
>> > > minarea= 0
>> > > xfmfile= talairach.xfm
>> > > nth = -1
>> > > outid= rh_time_cluster paint
>> > > sumfile  = rh_time_cluster_sum
>> > > subjectsdir= /gpfs/home/jtl190/work/structurals
>> > > FixMNI = 1
>> > > - XFM matrix (RAS2RAS) ---
>> > >
>> >
>>  /gpfs/home/jtl190/work/structurals/fsaverage/mri/transforms/talairach.xfm
>> > >  1.000   0.000   0.000   0.000;
>> > >  0.000   1.000   0.000   0.000;
>> > >  0.000   0.000   1.000   0.000;
>> > >  0.000   0.000   0.000   1.000;
>> > > 
>> > > Reading source surface
>> > > /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.white
>> > > Done reading source surface
>> > > Computing metric properties
>> > > Loading source values
>> > > number of voxels in search space = 163842
>> > > Done loading source values (nvtxs = 163842)
>> > > overall max = 1 at vertex 27
>> > > overall min = 1.52021e-05 at vertex 125620
>> > > surface nvertices 163842
>> > > surface area 65020.929688
>> > > surface area 65020.765625
>> > > Setting voxel-wise threshold with FDR =

Re: [Freesurfer] Processing of young children using Freesurfer

2016-02-11 Thread Z K 
This is a known issue with the VirtualBox installation of freesurfer and 
is related to the mni tools. The mri_nu_correct stage will fail when 
subjects directory is in a shared folder between the host machine and 
the VirtualBox environment. Only known solution is to import the entire 
subject data into the virtual machine.

-Zeke

On 02/11/2016 08:48 AM, Bruce Fischl wrote:
> yes, something wrong with the installation but it's outside of my
> expertise. Zeke: can you take a look?
>
> thanks
> Bruce
> On Thu, 11 Feb 2016, Zoellner, Frank wrote:
>
>> Hi,
>>
>> did you find a hint why my installation of freesurfer is not
>> processing the data at that stage ?
>> It seems to be a general problem, we tried also with other data sets
>> of elder people etc ..
>>
>> Any help appreciated.
>>
>> Yours
>> Frank
>>
>> 
>> PD Dr. Frank Zoellner
>> Group Leader "MRI and Medical Image Analysis"
>> Computer Assisted Clinical Medicine
>> Medical Faculty Mannheim
>> Heidelberg University
>> Theodor-Kutzer-Ufer 1-3
>> D-68167 Mannheim
>>
>> Phone: +49 (0)621 3835117
>> Fax:   +49 (0)621 3835123
>> Email: frank.zoell...@medma.uni-heidelberg.de
>> Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/
>>
>>
>> -Ursprüngliche Nachricht-
>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von
>> Zoellner, Frank
>> Gesendet: Dienstag, 9. Februar 2016 15:49
>> An: Freesurfer support list
>> Betreff: Re: [Freesurfer] Processing of young children using Freesurfer
>>
>> Hi Bruce,
>>
>> thanks for the reply.
>> Here comes the output (see attached).
>>
>> I just downloaded the VM with freesurfer from your website, fyi.
>>
>> Yours
>> Frank
>> 
>> PD Dr. Frank Zoellner
>> Group Leader "MRI and Medical Image Analysis"
>> Computer Assisted Clinical Medicine
>> Medical Faculty Mannheim
>> Heidelberg University
>> Theodor-Kutzer-Ufer 1-3
>> D-68167 Mannheim
>>
>> Phone: +49 (0)621 3835117
>> Fax:   +49 (0)621 3835123
>> Email: frank.zoell...@medma.uni-heidelberg.de
>> Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/
>>
>>
>> -Ursprüngliche Nachricht-
>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce
>> Fischl
>> Gesendet: Dienstag, 9. Februar 2016 14:12
>> An: Freesurfer support list
>> Betreff: Re: [Freesurfer] Processing of young children using Freesurfer
>>
>> hmmm, this doesn't seem to have to do with your data but maybe is an
>> installation problem? It says it failed but doesn't give an error
>> message, which is unusual. Can you try just typing in directly:
>>
>> cd /media/sf_cdh_ventrikel/test_002/mri
>> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
>> --i orig.mgz --o orig_nu.mgz
>>
>> and send us the output?
>>
>> cheers
>> Bruce
>>
>> On Tue, 9
>> Feb 2016, Zoellner, Frank wrote:
>>
>>> Hi,
>>>
>>> I am currently working on a project involving brain morphometry of 2
>>> year old children.
>>> We are interested in segmenting the ventricle and I tried to run
>>> freesurfer using the standard recon-all  -all for a first test.
>>>
>>> Unfortunately, freesurfer reports an error (see attached log file).
>>>
>>> I also read about that it is advised to run freesurfer with patient
>>> age >5 but maybe someone has an idea how to solve this.
>>> As far as I get from the step it crashes at the intensity correction
>>> step?
>>> Do I need to calculate some sort of template maybe ?
>>>
>>> Any comments welcome
>>>
>>> Yours
>>> Frank
>>>
>>> 
>>> PD Dr. Frank Zoellner
>>> Group Leader "MRI and Medical Image Analysis"
>>> Computer Assisted Clinical Medicine
>>> Medical Faculty Mannheim
>>> Heidelberg University
>>> Theodor-Kutzer-Ufer 1-3
>>> D-68167 Mannheim
>>>
>>> Phone: +49 (0)621 3835117
>>> Fax:   +49 (0)621 3835123
>>> Email: frank.zoell...@medma.uni-heidelberg.de
>>> Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/
>>>
>>>
>>>
>>>
>>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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[Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST

2016-02-11 Thread stdp82 
I have used:mri_label2vol --label RIGHT_ROI.label --temp subj/rest/001/f.nii 
--reg subj/rest/001/register.dof6.dat --fillthresh .5 --o RIGHT_ROI.nii.gz


When I open using freeview the f.nii.gz and the RIGHT_ROI they are fine 
overlapped.But, after FS-FAST the sig.ii.gz seem to be wrong, probably bad 
reoriented, especially I have noted this on subcortical connectivity (MNI2mm).
Stefano



Messaggio originale

Da: Douglas Greve 

Data: 11-feb-2016 4.48

A: 

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




  
  
 I may have gotten the exact form of the flag wrong. When it says an
option is not known, you should try running the command with --help
to see if something similar is there. In this way,  you might be
able to figure it out for yourself rather than have to wait a day or
so for us to respond.

doug







On 2/10/16 4:20 PM, std...@virgilio.it
  wrote:



  



If I use:




  mri_label2vol --label
ramgseed_rhsurf.label --temp $SUBJECTS_DIR/subj/mri/orig.mgz
--identity --subject fsaverage --hemi rh --o
RIGHT_ROI.nii.gz --fill-ribbon
  ERROR: Option --fill-ribbon unknown
  

  
Messaggio originale

Da: std...@virgilio.it

Data: 8-feb-2016 20.35

A: "Freesurfer support
list"

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



Thanks.
I have down a right ad left ROI on the surface.
Next, I have run:

  

  
  mri_label2vol --label ramgseed_rhsurf.label --temp
$SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity
--subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz

mri_label2vol --label ramgseed_lhsurf.label --temp
  $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject
  fsaverage --hemi rh --o LEFT_ROI.nii.gz






  mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgz
  mri_convert LEFT_ROI.nii.gz LEFT_ROI.mgz

  
  

  
  fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest
-mean -cfg RIGHT_ROI.config
  fcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest
-mean -cfg LEFT_ROI.config

  
  

  
  fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config
  fcseed-sess -s subj1_FS -cfg LEFT_ROI.config



but during fcseed-sess this error occurs:




  $Id: mri_segstats.c,v 1.75.2.9 2013/02/16
00:09:33 greve Exp $
  cwd 
  cmdline mri_segstats --i

/Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz
--seg

/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz
--id 1 --sum

/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum
--avgwfvol
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh
 
  sysname  Darwin
  hostname iMac-di-Stefano.local
  machine  x86_64
  user Stefano
  UseRobust  0
  Loading
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz
  Loading

/Applications/freesurfer/subjects/fMRI/subj1/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/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh
  Segmentation fault 






  
Messaggio originale

Da: Douglas Greve 

Data: 8-feb-2016 4.38

A: 

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



 Use mri_label2vol to convert the label into a volume in the

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

2016-02-11 Thread stdp82 
I have used:mri_label2vol --label RIGHT_ROI.label --temp subj/rest/001/f.nii 
--reg subj/rest/001/register.dof6.dat --fillthresh .5 --o RIGHT_ROI.nii.gz
When I open with freeview the f.nii.gz and the RIGHT_ROI they are fine 
overlapped.But, after FS-FAST the sig.ii.gz seem to be wrong, probably bad 
reoriented, especially I have noted this on subcortical connectivity (MNI2mm).
Thanks

Stefano



Messaggio originale

Da: Douglas Greve 

Data: 11-feb-2016 4.48

A: 

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




  
  
 I may have gotten the exact form of the flag wrong. When it says an
option is not known, you should try running the command with --help
to see if something similar is there. In this way,  you might be
able to figure it out for yourself rather than have to wait a day or
so for us to respond.

doug







On 2/10/16 4:20 PM, std...@virgilio.it
  wrote:



  



If I use:




  mri_label2vol --label
ramgseed_rhsurf.label --temp $SUBJECTS_DIR/subj/mri/orig.mgz
--identity --subject fsaverage --hemi rh --o
RIGHT_ROI.nii.gz --fill-ribbon
  ERROR: Option --fill-ribbon unknown
  

  
Messaggio originale

Da: std...@virgilio.it

Data: 8-feb-2016 20.35

A: "Freesurfer support
list"

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



Thanks.
I have down a right ad left ROI on the surface.
Next, I have run:

  

  
  mri_label2vol --label ramgseed_rhsurf.label --temp
$SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity
--subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz

mri_label2vol --label ramgseed_lhsurf.label --temp
  $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject
  fsaverage --hemi rh --o LEFT_ROI.nii.gz






  mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgz
  mri_convert LEFT_ROI.nii.gz LEFT_ROI.mgz

  
  

  
  fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest
-mean -cfg RIGHT_ROI.config
  fcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest
-mean -cfg LEFT_ROI.config

  
  

  
  fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config
  fcseed-sess -s subj1_FS -cfg LEFT_ROI.config



but during fcseed-sess this error occurs:




  $Id: mri_segstats.c,v 1.75.2.9 2013/02/16
00:09:33 greve Exp $
  cwd 
  cmdline mri_segstats --i

/Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz
--seg

/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz
--id 1 --sum

/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum
--avgwfvol
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh
 
  sysname  Darwin
  hostname iMac-di-Stefano.local
  machine  x86_64
  user Stefano
  UseRobust  0
  Loading
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz
  Loading

/Applications/freesurfer/subjects/fMRI/subj1/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/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh
  Segmentation fault 






  
Messaggio originale

Da: Douglas Greve 

Data: 8-feb-2016 4.38

A: 

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



 Use mri_label2vol to convert the label into a volume in the

[Freesurfer] Freeview to mark only one specific area

2016-02-11 Thread Luis Fernado Silva Castro de Araújo 
 Hello Freesurfer experts,


I want either a 2D or 3D picture of one of my subjects image, but with only
one colored area. For example, I would like to mark
the lh_lateralorbitofrontal_area.

It seems that the tool to visualize images in Freesurfer is freeview,
however I can't find the label for the left hemisphere
lateralorbitofrontal_area in the GUI. It is not listed in the Volumes tab
with the aparc+aseg item ticked.

I did not find information in your website, maybe I missed.

Could you please provide a pointer towards the answer? Maybe I missed where
it is taught at the documentation, a simple link would do.

Thanks,

luis
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] comparison between two hemisphere in single subject

2016-02-11 Thread Douglas N Greve 

Follow the further instructions in
https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
ie, mris_preproc (which will sample into the common space 
(fsaverage_sym) and compute the difference)
and mris_fwhm, if you want to smooth it. The result will be on 
fsaverage_sym. If you want to map it back to the individual, let me know 
and I can give you instructions


On 02/11/2016 08:25 AM, Ashkan Faghiri wrote:
> Hello,
>
> I want to compare the two hemisphere in  one subject (thickness for 
> example). should I use?
>
> surfreg --s $subject --t fsaverage_sym --lh
> surfreg --s $subject --t fsaverage_sym --lh --xhemi
>
> then what? how can I compare the two hemisphere of one subject?
>
> Regards,
> Ashkan
>
> -- 
> -- 
> Ashkan Faghiri
> MSc student of Bioelectrical Engineering
> Department of Electrical Engineering
> Sharif University of Technology
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Processing of young children using Freesurfer

2016-02-11 Thread fz2 
Ok thx for the info.

Yours
Frank


> Am 11.02.2016 um 17:29 schrieb Z K :
> 
> This is a known issue with the VirtualBox installation of freesurfer and is 
> related to the mni tools. The mri_nu_correct stage will fail when subjects 
> directory is in a shared folder between the host machine and the VirtualBox 
> environment. Only known solution is to import the entire subject data into 
> the virtual machine.
> 
> -Zeke
> 
> On 02/11/2016 08:48 AM, Bruce Fischl wrote:
>> yes, something wrong with the installation but it's outside of my
>> expertise. Zeke: can you take a look?
>> 
>> thanks
>> Bruce
>> On Thu, 11 Feb 2016, Zoellner, Frank wrote:
>> 
>>> Hi,
>>> 
>>> did you find a hint why my installation of freesurfer is not
>>> processing the data at that stage ?
>>> It seems to be a general problem, we tried also with other data sets
>>> of elder people etc ..
>>> 
>>> Any help appreciated.
>>> 
>>> Yours
>>> Frank
>>> 
>>> 
>>> PD Dr. Frank Zoellner
>>> Group Leader "MRI and Medical Image Analysis"
>>> Computer Assisted Clinical Medicine
>>> Medical Faculty Mannheim
>>> Heidelberg University
>>> Theodor-Kutzer-Ufer 1-3
>>> D-68167 Mannheim
>>> 
>>> Phone: +49 (0)621 3835117
>>> Fax:   +49 (0)621 3835123
>>> Email: frank.zoell...@medma.uni-heidelberg.de
>>> Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/
>>> 
>>> 
>>> -Ursprüngliche Nachricht-
>>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von
>>> Zoellner, Frank
>>> Gesendet: Dienstag, 9. Februar 2016 15:49
>>> An: Freesurfer support list
>>> Betreff: Re: [Freesurfer] Processing of young children using Freesurfer
>>> 
>>> Hi Bruce,
>>> 
>>> thanks for the reply.
>>> Here comes the output (see attached).
>>> 
>>> I just downloaded the VM with freesurfer from your website, fyi.
>>> 
>>> Yours
>>> Frank
>>> 
>>> PD Dr. Frank Zoellner
>>> Group Leader "MRI and Medical Image Analysis"
>>> Computer Assisted Clinical Medicine
>>> Medical Faculty Mannheim
>>> Heidelberg University
>>> Theodor-Kutzer-Ufer 1-3
>>> D-68167 Mannheim
>>> 
>>> Phone: +49 (0)621 3835117
>>> Fax:   +49 (0)621 3835123
>>> Email: frank.zoell...@medma.uni-heidelberg.de
>>> Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/
>>> 
>>> 
>>> -Ursprüngliche Nachricht-
>>> Von: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce
>>> Fischl
>>> Gesendet: Dienstag, 9. Februar 2016 14:12
>>> An: Freesurfer support list
>>> Betreff: Re: [Freesurfer] Processing of young children using Freesurfer
>>> 
>>> hmmm, this doesn't seem to have to do with your data but maybe is an
>>> installation problem? It says it failed but doesn't give an error
>>> message, which is unusual. Can you try just typing in directly:
>>> 
>>> cd /media/sf_cdh_ventrikel/test_002/mri
>>> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale
>>> --i orig.mgz --o orig_nu.mgz
>>> 
>>> and send us the output?
>>> 
>>> cheers
>>> Bruce
>>> 
>>> On Tue, 9
>>> Feb 2016, Zoellner, Frank wrote:
>>> 
 Hi,
 
 I am currently working on a project involving brain morphometry of 2
 year old children.
 We are interested in segmenting the ventricle and I tried to run
 freesurfer using the standard recon-all  -all for a first test.
 
 Unfortunately, freesurfer reports an error (see attached log file).
 
 I also read about that it is advised to run freesurfer with patient
 age >5 but maybe someone has an idea how to solve this.
 As far as I get from the step it crashes at the intensity correction
 step?
 Do I need to calculate some sort of template maybe ?
 
 Any comments welcome
 
 Yours
 Frank
 
 
 PD Dr. Frank Zoellner
 Group Leader "MRI and Medical Image Analysis"
 Computer Assisted Clinical Medicine
 Medical Faculty Mannheim
 Heidelberg University
 Theodor-Kutzer-Ufer 1-3
 D-68167 Mannheim
 
 Phone: +49 (0)621 3835117
 Fax:   +49 (0)621 3835123
 Email: frank.zoell...@medma.uni-heidelberg.de
 Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/
 
 
 
 
 
>>> 
>>> ___
>>> 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.
> 




PD Dr. Frank Zoellner
Group Leader "MRI and

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

2016-02-11 Thread Douglas N Greve 
How was the phase nii created?

On 02/11/2016 11:12 AM, Joseph Dien wrote:
> MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag 
> /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-1-01-01.nii
>  
> --dph 
> /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii
>  
> --tediff 2.46 --esp 0.51 --epi fMRI/RPA003/bold/001/f.nii.gz --vsm 
> fMRI/RPA003/bold/b0dcmap.nii.gz
>
>
>
>> On Feb 10, 2016, at 22:58, Douglas Greve > > wrote:
>>
>> what is your command line? I think there is a rescaling in which it 
>> expcts the phase to be 0-2048 (or 4096) as this is how it comes of 
>> the (siemens) scanner. Could that be the problem?
>>
>>
>> On 2/10/16 10:40 PM, Joseph Dien wrote:
>>> I ran into the same issue:
>>>
>>> FSLVersion 5.0.4
>>> FSLVerMaj 5
>>> FSL Version is 5.0.4, must be 3.X or 4.X
>>>
>>> I downloaded the epidewarp.fsl script from the suggested ftp site 
>>> and replaced the existing script.  It did indeed fix the version 
>>> incompatibility with FSL 5.x.
>>>
>>> I ran into a new problem where it was aborting.  After some trouble 
>>> shooting and looking over the documentation, I realized that —-epi 
>>> is a required input without which the script crashes (or is it 
>>> supposed to be optional but there is a bug in the script?).
>>>
>>> After including it, it ran much further but then aborted with the 
>>> following error:
>>>
>>> ERROR: input phase image exceeds allowable phase range.
>>> Allowable range is 6.283 radians.  Image range is: 12.5633 radians.
>>>
>>> This is consistent with the documentation.  I’m not sure why the 
>>> phase image exceeds the range though.
>>>
>>> It ran without problems with SPM’s FieldMap Toolbox and it is from a 
>>> standard Siemen’s scanner sequence (two magnitude files and one 
>>> phase difference file).
>>>
>>> Do I just divide the values by two with something like fslmaths 
>>> since it seems to have exactly double the required range?
>>>
>>> Joe
>>>
 On Nov 26, 2014, at 21:36, Douglas Greve 
  wrote:


 It is there again. I don't know what the status if it  is in terms 
 of the version. Try it and let me know
 doug

 On 11/25/14 4:34 PM, Morgan Hough wrote:
> Hi Doug,
>
> Could you put the epidewarp.fsl script back on your ftp site? I 
> don’t see it at the link in the archives:
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
>
> BTW, is the script updated in some way for 5.x or can I can the 
> old script just be changed to accept 5.x version numbers.
>
> Cheers,
>
> -Morgan

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 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.
>>>
>>> 
>>>
>>> Joseph Dien, PhD
>>> Senior Research Scientist
>>> Maryland Neuroimaging Center
>>> University of Maryland, College Park
>>> E-mail: jdie...@mac.com 
>>> Cell Phone: 202-297-8117
>>> http://joedien.com 
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
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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.
>
> 
>
> Joseph Dien, PhD
> Senior Research Scientist
> Maryland Neuroimaging Center
> University of Maryland, College Park
> E-mail: jdie...@mac.com 
> Cell Phone: 202-297-8117
> http://joedien.com
>
>
>
>

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-11 Thread Douglas N Greve 


On 02/11/2016 11:19 AM, Jennifer Legault wrote:
> Thank you for your response.  Do I need to run the glm_fit-sim command 
> to make the csd file?  I feel this would be inappropriate for my data 
> since I already ran the LME model.
No, look in  $FREESURFER_HOME/average/mult-comp-cor/fsaverage. You will 
need the FWHM though
>
> Second, is there an argument to make an output file that can be 
> visualized via freeview?  In other words, how can I view my cluster 
> thresholded data?
You can use freeview, something like
freeview -f lh.inflated:overlay=sig.mgh
There are other options for loading annotations and curvature. See the 
freeview help
>
> Your help is greatly appreciated,
>
> Jen
>
>
>
> On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve 
> > wrote:
>
> There is a (very long) command line on that page. Mainly you need
> a csd file. To get that you need the FWHM of your analysis, the
> voxel-wise threshold, and the sign of the contrast (or abs). Then
> the relevant output will be the --sum. You can run it with --help
> to get more info.
>
>
> On 2/10/16 5:11 PM, Jennifer Legault wrote:
>> Thank you very much for your help!  I still received a "cannot
>> read file type" error when I only added the path to the output
>> --o part, however when I also added the path to the input file,
>> it worked!
>>
>> I do have one more question: Which argument can I add so that in
>> my output file I see the clusterwise P value, like it is shown
>> here
>> 
>> ?
>>
>> Best,
>>
>> Jen
>>
>> On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve
>> > wrote:
>>
>> I meant for the output files, so the --o in particular
>>
>> On 02/10/2016 01:47 PM, Jennifer Legault wrote:
>> > Douglas,
>> >
>> > Thank you for your quick response. When I add --sd
>> [path_location], I
>> > get the following error:
>> > Loading source values
>> > mri_read(): couldn't determine type of file
>> [path_location]/rh_time_spval
>> > ERROR: could not read rh_time_spval as type
>> >
>> > Should I use another argument?
>> >
>> > Best,
>> >
>> > Jen
>> >
>> >
>> >
>> > On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve
>> > > 
>> > >> wrote:
>> >
>> > Try specifying the full path to the output
>> >
>> > On 02/10/2016 12:59 PM, Jennifer Legault wrote:
>> > > Dear experts,
>> > >
>> > > I am trying to use the cluster thresholding command
>> for my
>> > freesurfer
>> > > LME outputs as referred to here
>> > >
>> >   
>>  
>> .
>> > > Any feedback or comments would be greatly appreciated.
>> > >
>> > > I am aware that there have been permission denied
>> errors when using
>> > > mri_surfcluster and that applying this patch
>> > >
>> >   
>>  
>> 
>> > > should solve the problem (which I tried), however I
>> am still either
>> > > receiving errors stating the permission is denied.
>> > >
>> > > This is the command I am trying to run:
>> > >
>> > >  mri_surfcluster --subject fsaverage --hemi rh --in
>> > rh_time_spval.mgh
>> > > --cwpvalthresh 0.05 --fdr .05 --sign pos --o
>> rh_time_cluster  --sum
>> > > rh_time_cluster_sum
>> > >
>> > >
>> > > Here is the error log:
>> > >
>> > > mri_surfcluster --subject fsaverage --hemi rh --in
>> rh_time_spval.mgh
>> > > --cwpvalthresh 0.05 --fdr .05 --sign pos --o
>> rh_time_cluster  --sum
>> > > rh_time_cluster_sum  thsign = pos, id = 1
>> > > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31
>> 22:10:05
>> > greve Exp $
>> > > hemi   = rh
>> > > srcid  = rh_time_spval.mgh
>> > > srcsubjid  = fsaverage
>> > > srcsurf= white
>> > > srcframe   = 0
>> > > thsign = pos
>> > > thmin  = -1
>> > > thmax  = -1
>> > > fdr= 0.05
>> > > minarea

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

2016-02-11 Thread Joseph Dien 
using spm_read_vols I confirmed that the min and max of the phase difference 
file is indeed -4096 and 4092 respectively.

Further troubleshooting epidewarp.fsl indicates that the script is correctly 
branching to "# Input is phase difference and magnitude”

It then executes the following commands:

  # Rescale the delta phase to be between -pi and pi. Starts out
  # at 0 - 4095. Make sure the phase is float precision with _32R
  set cmd = ($FSLToFloat $dph -sub 2047.5 -mul 0.00153435539 $tmpdir/dph 
$FSLToFloatFlag )
  echo $cmd |& tee -a $LF
  $cmd |& tee -a $LF
  if($status) exit 1;

what echoes to the screen is:

fslmaths 
/Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii
 -sub 2047.5 -mul 0.00153435539 fMRI/RPA003/bold/tmp-epidewarp.90814.fsl/dph 
-odt float

it then aborts at the next section:

  cp $tmpdir/dph.$ext $tmpdir/dph.preprelude.$ext
  set dph = $tmpdir/dph
  if($#epimat) cp $epimat `dirname $dph`/`basename $dph .$ext`.mat # Copy 
matfile

  # Do the phase unwrapping (-f for 3D, -v for verbose)
  set cmd = (prelude -p $dph -a $mag -o $dph -f -v -m $head);
  echo $cmd |& tee -a $LF
  $cmd |& tee -a $LF
  if($status) exit 1;

So apparently this rescaling command is not doing so correctly?  The script 
comment says it expects the values to be between 0 and 4095 whereas the file 
goes to -4096 so perhaps that was a bit more negative than it was expecting?

Joe


> On Feb 11, 2016, at 11:12, Joseph Dien  wrote:
> 
> MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag 
> /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-1-01-01.nii
>  --dph 
> /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii
>  --tediff 2.46 --esp 0.51 --epi fMRI/RPA003/bold/001/f.nii.gz --vsm 
> fMRI/RPA003/bold/b0dcmap.nii.gz
> 
> 
> 
>> On Feb 10, 2016, at 22:58, Douglas Greve > > wrote:
>> 
>> what is your command line? I think there is a rescaling in which it expcts 
>> the phase to be 0-2048 (or 4096) as this is how it comes of the (siemens) 
>> scanner. Could that be the problem?
>> 
>> 
>> On 2/10/16 10:40 PM, Joseph Dien wrote:
>>> I ran into the same issue:
>>> 
>>> FSLVersion 5.0.4
>>> FSLVerMaj 5
>>> FSL Version is 5.0.4, must be 3.X or 4.X
>>> 
>>> I downloaded the epidewarp.fsl script from the suggested ftp site and 
>>> replaced the existing script.  It did indeed fix the version 
>>> incompatibility with FSL 5.x.
>>> 
>>> I ran into a new problem where it was aborting.  After some trouble 
>>> shooting and looking over the documentation, I realized that —-epi is a 
>>> required input without which the script crashes (or is it supposed to be 
>>> optional but there is a bug in the script?).
>>> 
>>> After including it, it ran much further but then aborted with the following 
>>> error:
>>> 
>>> ERROR: input phase image exceeds allowable phase range.
>>> Allowable range is 6.283 radians.  Image range is: 12.5633 radians.
>>> 
>>> This is consistent with the documentation.  I’m not sure why the phase 
>>> image exceeds the range though.
>>> 
>>> It ran without problems with SPM’s FieldMap Toolbox and it is from a 
>>> standard Siemen’s scanner sequence (two magnitude files and one phase 
>>> difference file).
>>> 
>>> Do I just divide the values by two with something like fslmaths since it 
>>> seems to have exactly double the required range?
>>> 
>>> Joe
>>> 
 On Nov 26, 2014, at 21:36, Douglas Greve < 
 gr...@nmr.mgh.harvard.edu 
 > wrote:
 
 
 It is there again. I don't know what the status if it  is in terms of the 
 version. Try it and let me know
 doug
 
 On 11/25/14 4:34 PM, Morgan Hough wrote:
> Hi Doug,
> 
> Could you put the epidewarp.fsl script back on your ftp site? I don’t see 
> it at the link in the archives:
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
>  
> 
> 
> BTW, is the script updated in some way for 5.x or can I can the old 
> script just be changed to accept 5.x version numbers. 
> 
> Cheers,
> 
> -Morgan
 
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Re: [Freesurfer] How to convert a surface label to .nii

2016-02-11 Thread Douglas N Greve 
yep, that's right. Thanks Marc!

On 02/11/2016 09:44 AM, Marc Ramos wrote:
> My guess is to use mri_label2vol 
>  instead, and 
> a mri_convert to convert to nii.gz
>
> I hope this helps.
> Marc.
>
>
>
>
> On Thu, Feb 11, 2016 at 3:17 PM, Afzal, Afsana  > wrote:
>
> Hi,
>
> How can I convert a surface .label file to a .nii format? I'm
> using mri_label2label in the following way but the output is
> always in .label not .nii:
>
> mri_label2label
> --srclabel dlpfc-lh.label
> --outmask dlpfc-lh_mask.nii
> --s fsaverage
> --trglabel dlpfc-lh_mask.nii
> --regmethod surface
> --hemi lh
>
> Thanks for your help,
>
> Afsana
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129 
> Fax: 617-726-4078 
>
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>
>
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> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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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Re: [Freesurfer] epidewarp.fsl for FSL 5.x

2016-02-11 Thread Douglas N Greve 
yes, that is the problem. Where did that phase image come from? You can 
use fslmaths to simply rescale it to 0-4095, then it should work

On 02/11/2016 11:34 AM, Joseph Dien wrote:
> using spm_read_vols I confirmed that the min and max of the phase 
> difference file is indeed -4096 and 4092 respectively.
>
> Further troubleshooting epidewarp.fsl indicates that the script is 
> correctly branching to "# Input is phase difference and magnitude”
>
> It then executes the following commands:
>
>   # Rescale the delta phase to be between -pi and pi. Starts out
>   # at 0 - 4095. Make sure the phase is float precision with _32R
>   set cmd = ($FSLToFloat $dph -sub 2047.5 -mul 0.00153435539 
> $tmpdir/dph $FSLToFloatFlag )
>   echo $cmd |& tee -a $LF
>   $cmd |& tee -a $LF
>   if($status) exit 1;
>
> what echoes to the screen is:
>
> fslmaths 
> /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii
>  
> -sub 2047.5 -mul 0.00153435539 
> fMRI/RPA003/bold/tmp-epidewarp.90814.fsl/dph -odt float
>
> it then aborts at the next section:
>
>   cp $tmpdir/dph.$ext $tmpdir/dph.preprelude.$ext
>   set dph = $tmpdir/dph
>   if($#epimat) cp $epimat `dirname $dph`/`basename $dph .$ext`.mat # 
> Copy matfile
>
>   # Do the phase unwrapping (-f for 3D, -v for verbose)
>   set cmd = (prelude -p $dph -a $mag -o $dph -f -v -m $head);
>   echo $cmd |& tee -a $LF
>   $cmd |& tee -a $LF
>   if($status) exit 1;
>
> So apparently this rescaling command is not doing so correctly?  The 
> script comment says it expects the values to be between 0 and 4095 
> whereas the file goes to -4096 so perhaps that was a bit more negative 
> than it was expecting?
>
> Joe
>
>
>> On Feb 11, 2016, at 11:12, Joseph Dien > > wrote:
>>
>> MegaJoe:fsfastPM jdien$ epidewarp.fsl --mag 
>> /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/4-field_map/sRPA003-0004-1-01-01.nii
>>  
>> --dph 
>> /Volumes/Data2/RP1/fsfastPM/../NIFTI/RPA03/5-field_map/sRPA003-0005-1-01-02.nii
>>  
>> --tediff 2.46 --esp 0.51 --epi fMRI/RPA003/bold/001/f.nii.gz --vsm 
>> fMRI/RPA003/bold/b0dcmap.nii.gz
>>
>>
>>
>>> On Feb 10, 2016, at 22:58, Douglas Greve >> > wrote:
>>>
>>> what is your command line? I think there is a rescaling in which it 
>>> expcts the phase to be 0-2048 (or 4096) as this is how it comes of 
>>> the (siemens) scanner. Could that be the problem?
>>>
>>>
>>> On 2/10/16 10:40 PM, Joseph Dien wrote:
 I ran into the same issue:

 FSLVersion 5.0.4
 FSLVerMaj 5
 FSL Version is 5.0.4, must be 3.X or 4.X

 I downloaded the epidewarp.fsl script from the suggested ftp site 
 and replaced the existing script.  It did indeed fix the version 
 incompatibility with FSL 5.x.

 I ran into a new problem where it was aborting.  After some trouble 
 shooting and looking over the documentation, I realized that —-epi 
 is a required input without which the script crashes (or is it 
 supposed to be optional but there is a bug in the script?).

 After including it, it ran much further but then aborted with the 
 following error:

 ERROR: input phase image exceeds allowable phase range.
 Allowable range is 6.283 radians. Image range is: 12.5633 radians.

 This is consistent with the documentation.  I’m not sure why the 
 phase image exceeds the range though.

 It ran without problems with SPM’s FieldMap Toolbox and it is from 
 a standard Siemen’s scanner sequence (two magnitude files and one 
 phase difference file).

 Do I just divide the values by two with something like fslmaths 
 since it seems to have exactly double the required range?

 Joe

> On Nov 26, 2014, at 21:36, Douglas Greve 
>  wrote:
>
>
> It is there again. I don't know what the status if it  is in terms 
> of the version. Try it and let me know
> doug
>
> On 11/25/14 4:34 PM, Morgan Hough wrote:
>> Hi Doug,
>>
>> Could you put the epidewarp.fsl script back on your ftp site? I 
>> don’t see it at the link in the archives:
>>
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl
>>
>> BTW, is the script updated in some way for 5.x or can I can the 
>> old script just be changed to accept 5.x version numbers.
>>
>> Cheers,
>>
>> -Morgan
>
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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

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-11 Thread Jennifer Legault 
That's very useful, thank you.  In terms of FWHM, I am examining gray
matter volume, not cortical thickness, and was previously instructed by
Martin Reuter not to smooth these data.  Do you think it would make sense
then to just use the fwhm01?  And in terms of the voxel-wise threshold, is
there a commonly used value for GM volume data?  I am still new to
freesurfer and I appreciate any feedback.

For visualization, after I run the mri_surfcluster the only outputs are a
summary file and a .w file, and freeview doesn't accept this format.  Is it
possible to have a cluster-wise corrected map (a sig.cluster.mgh file) as
they do for the Clusterwise Correction for Multiple Comparisons tutorial
here ?


Best,

Jen

On Thu, Feb 11, 2016 at 11:39 AM, Douglas N Greve  wrote:

>
>
> On 02/11/2016 11:19 AM, Jennifer Legault wrote:
> > Thank you for your response.  Do I need to run the glm_fit-sim command
> > to make the csd file?  I feel this would be inappropriate for my data
> > since I already ran the LME model.
> No, look in  $FREESURFER_HOME/average/mult-comp-cor/fsaverage. You will
> need the FWHM though
> >
> > Second, is there an argument to make an output file that can be
> > visualized via freeview?  In other words, how can I view my cluster
> > thresholded data?
> You can use freeview, something like
> freeview -f lh.inflated:overlay=sig.mgh
> There are other options for loading annotations and curvature. See the
> freeview help
> >
> > Your help is greatly appreciated,
> >
> > Jen
> >
> >
> >
> > On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve
> > > wrote:
> >
> > There is a (very long) command line on that page. Mainly you need
> > a csd file. To get that you need the FWHM of your analysis, the
> > voxel-wise threshold, and the sign of the contrast (or abs). Then
> > the relevant output will be the --sum. You can run it with --help
> > to get more info.
> >
> >
> > On 2/10/16 5:11 PM, Jennifer Legault wrote:
> >> Thank you very much for your help!  I still received a "cannot
> >> read file type" error when I only added the path to the output
> >> --o part, however when I also added the path to the input file,
> >> it worked!
> >>
> >> I do have one more question: Which argument can I add so that in
> >> my output file I see the clusterwise P value, like it is shown
> >> here
> >> <
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary
> >?
> >>
> >> Best,
> >>
> >> Jen
> >>
> >> On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve
> >> >
> wrote:
> >>
> >> I meant for the output files, so the --o in particular
> >>
> >> On 02/10/2016 01:47 PM, Jennifer Legault wrote:
> >> > Douglas,
> >> >
> >> > Thank you for your quick response. When I add --sd
> >> [path_location], I
> >> > get the following error:
> >> > Loading source values
> >> > mri_read(): couldn't determine type of file
> >> [path_location]/rh_time_spval
> >> > ERROR: could not read rh_time_spval as type
> >> >
> >> > Should I use another argument?
> >> >
> >> > Best,
> >> >
> >> > Jen
> >> >
> >> >
> >> >
> >> > On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve
> >> >  >> 
> >>  >> >> wrote:
> >> >
> >> > Try specifying the full path to the output
> >> >
> >> > On 02/10/2016 12:59 PM, Jennifer Legault wrote:
> >> > > Dear experts,
> >> > >
> >> > > I am trying to use the cluster thresholding command
> >> for my
> >> > freesurfer
> >> > > LME outputs as referred to here
> >> > >
> >> >
> >>  <
> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels>.
> >> > > Any feedback or comments would be greatly appreciated.
> >> > >
> >> > > I am aware that there have been permission denied
> >> errors when using
> >> > > mri_surfcluster and that applying this patch
> >> > >
> >> >
> >>  <
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mni152reg
> >
> >> > > should solve the problem (which I tried), however I
> >> am still either
> >> > > receiving errors stating the permission is denied.
> >> > >
> >> > > This is the command I am trying to run:
> >> > >
> >> > >  mri_surfcluster --subject

[Freesurfer] wm-hypointensities variables

2016-02-11 Thread Otília 
 

Greetings, 

I am wondering if there is some information regarding
the meaning of "wm-hypointensities" and "non-WM-hypointensities"
variables from the aseg.stats file, ie, what features are included in
these variables and how FS computes them. 

I checked previous posts
that have the same issue I have now. 

I find some non-zero, (some cases
have "quite big") WM-hypointensities values for healthy young brains. I
find it odd. 

I would appreciate some additional information about
these issues. 

Thank you! 

Best regards, 
 



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Re: [Freesurfer] wm-hypointensities variables

2016-02-11 Thread Bruce Fischl 
you can turn this off with the -nowmsa flag I believe in recon-all. The 
labels are for damaged white matter and damaged gray matter, which can be 
tough to distinguish based only a T1. We have some (not-yet-distributed) 
tools that do pretty well on this if you have other contrasts like 
T2/FLAIR/PD.


cheers
Bruce

On Thu, 
11 Feb 2016, Otília wrote:




Greetings,

I am wondering if there is some information regarding the meaning of
“wm-hypointensities” and “non-WM-hypointensities” variables from the
aseg.stats file, ie, what features are included in these variables and how
FS computes them.

I checked previous posts that have the same issue I have now.

I find some non-zero, (some cases have “quite big”) WM-hypointensities
values for healthy young brains. I find it odd.

I would appreciate some additional information about these issues.

Thank you!

Best regards,

 




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Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-11 Thread Douglas N Greve 
by "volume" do you mean a VBM-type analysis or do you mean the volume 
that comes out of FS (thickness*area)? If you are going to use a 
clusterwise correction, then you have to have a FWHM measurement. You 
can try analyzing it in mri_glmfit with --osgm just to get the FWHM out 
of it.

You should be able to output a .mgh file instead of a .w file


On 02/11/2016 01:07 PM, Jennifer Legault wrote:
> That's very useful, thank you.  In terms of FWHM, I am examining gray 
> matter volume, not cortical thickness, and was previously instructed 
> by Martin Reuter not to smooth these data.  Do you think it would make 
> sense then to just use the fwhm01?  And in terms of the voxel-wise 
> threshold, is there a commonly used value for GM volume data?  I am 
> still new to freesurfer and I appreciate any feedback.
>
> For visualization, after I run the mri_surfcluster the only outputs 
> are a summary file and a .w file, and freeview doesn't accept this 
> format.  Is it possible to have a cluster-wise corrected map (a 
> sig.cluster.mgh file) as they do for the Clusterwise Correction for 
> Multiple Comparisons tutorial here 
> ?
>
>
> Best,
>
> Jen
>
> On Thu, Feb 11, 2016 at 11:39 AM, Douglas N Greve 
> > wrote:
>
>
>
> On 02/11/2016 11:19 AM, Jennifer Legault wrote:
> > Thank you for your response.  Do I need to run the glm_fit-sim
> command
> > to make the csd file?  I feel this would be inappropriate for my
> data
> > since I already ran the LME model.
> No, look in $FREESURFER_HOME/average/mult-comp-cor/fsaverage. You will
> need the FWHM though
> >
> > Second, is there an argument to make an output file that can be
> > visualized via freeview?  In other words, how can I view my cluster
> > thresholded data?
> You can use freeview, something like
> freeview -f lh.inflated:overlay=sig.mgh
> There are other options for loading annotations and curvature. See the
> freeview help
> >
> > Your help is greatly appreciated,
> >
> > Jen
> >
> >
> >
> > On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve
> > 
>  >> wrote:
> >
> > There is a (very long) command line on that page. Mainly you
> need
> > a csd file. To get that you need the FWHM of your analysis, the
> > voxel-wise threshold, and the sign of the contrast (or abs).
> Then
> > the relevant output will be the --sum. You can run it with
> --help
> > to get more info.
> >
> >
> > On 2/10/16 5:11 PM, Jennifer Legault wrote:
> >> Thank you very much for your help!  I still received a "cannot
> >> read file type" error when I only added the path to the output
> >> --o part, however when I also added the path to the input file,
> >> it worked!
> >>
> >> I do have one more question: Which argument can I add so
> that in
> >> my output file I see the clusterwise P value, like it is shown
> >> here
> >>   
>  
> ?
> >>
> >> Best,
> >>
> >> Jen
> >>
> >> On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve
> >> 
>  >> wrote:
> >>
> >> I meant for the output files, so the --o in particular
> >>
> >> On 02/10/2016 01:47 PM, Jennifer Legault wrote:
> >> > Douglas,
> >> >
> >> > Thank you for your quick response. When I add --sd
> >> [path_location], I
> >> > get the following error:
> >> > Loading source values
> >> > mri_read(): couldn't determine type of file
> >> [path_location]/rh_time_spval
> >> > ERROR: could not read rh_time_spval as type
> >> >
> >> > Should I use another argument?
> >> >
> >> > Best,
> >> >
> >> > Jen
> >> >
> >> >
> >> >
> >> > On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve
> >> >  
> >>  >
> >>  
> >>   >> >
> >> > Try specifying the full path to the output
> >>