date:20151104

Re: [Freesurfer] preproc-sess and stc question

2015-11-04 Thread Douglas N Greve

Hi Chaz, unfortunately version 5 does not support arbitrary slice 
orders. It will be available in version 6.
doug

On 11/03/2015 06:27 PM, Gay,Charles Wysaw wrote:
> Hi -
>
> 1) I am trying to perform preprocessing steps on functional task data 
> that was acquired on a Phillips scanner using an interleaved 
> acquisition. There are 42 slices and the order is 
> [0,6,12,18,24,30,36,1,7,13,19,25,31,37,2,8,14,20,26,32,38,3,9,15,21,27,33,39,4,10,16,22,28,34,40,5,11,17,23,29,35,41].
>  I’ve 
> tried
>  –slice order followed by the sequence but that didn’t seem to work. 
> And I wasn’t able to find anything in stc-sess –help that explained 
> how to enter the exact sequence order.
> If you could show me how to add/change the tutorial code below, that 
> would be great. Thanks.
> 2) Do I need to modify the onsets in the paradigmfile?
>
> Thanks,
> Chaz
>
>
> preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 
> -fwhm 5 -per-run
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Extracing values from ces.nii

2015-11-04 Thread Douglas N Greve

It is done to fit inside the nifti format. You can just put 163842 
columns because nifti only supports max 32k

On 11/04/2015 10:11 AM, Afzal, Afsana wrote:
> Ah, I see. But what do the 27307 rows represent and why are there 6 values 
> per row?
>
> Thanks,
>
> Afsana
> __
> Afsana Afzal
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, November 03, 2015 1:31 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Extracing values from ces.nii
>
> It should be interpreted as a 2D structure of size 27307*6= 163842
> which are the number of vertices in fsaverage
>
>
> On 10/29/2015 11:41 AM, Afzal, Afsana wrote:
>> Hi,
>>
>> I'm trying to extract the contrast values from ces.nii.gz after
>> first-level analysis. My goal is to average the contrast values for
>> each voxel across subjects for a given condition and see where an
>> individual from a separate population falls within the distribution of
>> contrast values.
>>
>> The ces.nii file I'm working with has the following dimension: (27307,
>> 1, 6, 1), which I interpreted as containing information about 27307
>> voxels in a 3D matrix. What does the information in the 6 rows for
>> each voxel represent? I was expecting to get a single raw b-value for
>> each voxel. The structure is consistent with sig.nii and t.nii files
>> as well.
>>
>> Thanks for any 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
>>
>>
>> ___
>> 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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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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>
> ___
> 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] how to obtain individual's pial_lgi value

2015-11-04 Thread Yang, Daniel

Hi all,

Found an answer here: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-March/036542.html

It works for me!

Best,
Daniel

From: 
>
 on behalf of Daniel Yang 
>
Reply-To: Freesurfer support list 
>
Date: Wednesday, November 4, 2015 at 3:30 PM
To: Freesurfer support list 
>
Subject: [Freesurfer] how to obtain individual's pial_lgi value

Dear FreeSurfer Experts,

When I specify --measure pial_lgi, aparcstats2table says it’s an invalid option.

Could you please advise how I can obtain an individual’s pial_lgi value, give a 
label?

Many thanks!
Daniel
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[Freesurfer] Jobs: Postdoctoral Fellow - Neuropsychology/Clinical Neuroscience/Imaging

2015-11-04 Thread Emily Rogalski

http://www.alzforum.org/jobs/postdoctoral-fellow-neuropsychologyclinical-neuroscienceimaging

Employer

Cleveland Clinic-Lou Ruvo Center for Brain Health
Location

Las Vegas, Nevada
Principal Investigator

Please send your CV to Sarah Banks, bank...@ccf.org and Ryan Walsh,
wal...@ccf.org.
Description

The Cleveland Clinic Lou Ruvo Center for Brain Health in Las Vegas, Nevada
is looking for an outstanding postdoctoral researcher to join the team as
soon as possible. The researcher will work with two clinical and
translational researchers, Ryan R. Walsh and Sarah Banks, on a recently
awarded NIH grant (duration of funds: five years) assessing the
neuropsychological and neuroimaging correlates of Alzheimer’s and
Parkinson’s diseases. The study utilizes cutting-edge neuroimaging and
analytic techniques involving both MRI and PET to assess cross-sectional
and longitudinal patterns of cognitive disruption and neuroimaging changes
in these patients. As part of the funding mechanism, the researcher will
also collaborate with Jeff Cummings, and there is potential for
collaboration with another five-year, fully funded project involving
multi-modal MRI imaging in Parkinson’s disease, as well as experts in fMRI
and PET both at the Cleveland Clinic and other institutions.

The Cleveland Clinic Lou Ruvo Center for Brain Health is developing an
excellent research team, featuring accessible, affable clinician-scientists
in neurology and neuropsychology—a multidisciplinary team, in a small and
specialized environment. It has state-of-the-art scanning technology, and a
robust neuroimaging core led by Dietmar Cordes, a dedicated MR physicist
and his team of research engineers, physicists, and mathematicians. This
position will be excellent for anyone who has recently graduated and is
looking to rapidly build his or her academic career in a position with no
immediate need to obtain external funding.
Requirements

The ideal candidate will hold a Ph.D. in neuroscience, psychology, or
similar field and have an interest in and experience with neurodegenerative
disease, cognition, and neuroimaging. He or she will enjoy working in a
multidisciplinary team, be productive, and enjoy contributing to every
stage of data collection, analysis, and presentation. He or she will hit
the ground running, working on existing data sets to answer research
questions related to those posed in the grant, and also develop their own
projects. Once sufficient data has been accrued from the grant projects,
prospective data analysis and manuscript preparation will account for much
of the researcher’s time. As such, great communication and writing skills,
in addition to statistical knowledge and ability, will be important.

--
Emily J Rogalski, PhD
Associate Professor
Northwestern University
Cognitive Neurology and Alzheimer's Disease Center (CNADC)
320 E Superior Street
Searle Building 11th Floor
Chicago, IL 60611
312-503-1155 phone
312-908-8789 fax
erogal...@gmail.com
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Re: [Freesurfer] Surface-based registration

2015-11-04 Thread Bruce Fischl


Hi Ray

that sounds right. The way I visualize these is using nmovie (which I 
think we include in our distribution) and flipping back and forth between 
the different images showing the different surfaces/curv maps.


Which inaccuracy are you referring to?

cheers
Bruce

On Wed, 4 Nov 2015, Razlighi, 
Qolamreza R. wrote:



Dear Bruce,
I did run it again with option (-dist 0.25); however the result did not
change much (See the attachment). These results do not seem right to me and
I think I’m running the command correctly (see the first email). However,
I’m not sure I’m visualizing the curvature maps correctly. I assume the
lh.sphere.reg has the same vertices and facets as lh.sphere but slightly
displaced in space to match the curvature and sulci map of the source
surface to target surface. Therefore, I visualize the lh.sphere.reg by
pulling the same lh.curv file from the source image. If this is wrong,
please let me know how can I correctly visualize the lh.sphere.reg,
otherwise I have no idea why this surface based registration produce such
inaccurate results. Any comments or suggestion is greatly appreciated.

Best
[IMAGE]
-- 
Ray Razlighi, Ph.D.
Assistant Professor
Quantitative Neuroimaging Laboratory
Division of Cognitive Neuroscience
Department of Neurology
Columbia University

Alt: razli...@gmail.com
Office Phone: 212-342-1352
Office Fax: 212-342-1838
Website: http://www.columbia.edu/cu/qnl/

On Nov 3, 2015, at 3:47 PM, Bruce Fischl  wrote:

  Hi Ray

  the -1 means that the target is a single surface and not an
  atlas, but the registration is still nonlinear. The variances
  will all be 1 so you may have to play with the weights in the
  energy functional. We don't do this very much and it probably
  defaults to quite rigid. Try reducing the weight on the metric
  preservation term (e.g. -dist .25) if you want it to be more
  nonlinear

  cheers
  Bruce

  On Tue, 3 Nov 2015, Razlighi, Qolamreza R. wrote:

Hi Guys,
I read in the sidenote here
(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates)
that
inter-subject surface base registration using
mris_register and -1 flag
performs a sort of rigid registration. So I tried it
between two of my
subjects with the command below
mris_register -1 -curv
P1639/FreeSurferClean/surf/lh.sphere
P1639/FreeSurferClean/surf/lh.sphere
lh.sphere3.reg 
and got the results (see the attachment). It is
clear that the registration
output is just a shifted version of the source.
Having this confirmed I want
to know if there is any way to force the
mris_register to perform a complete
non-linear surface based registration for
inter-subjects registration the
same way it does for template.
I have to mention that I visualize the
lh.sphere3.reg using freeview and
loaded the sane lh.curv on that surface. I hope I’m
not doing anything
stupid.
  
[IMAGE]
Best
-- 
Ray Razlighi, Ph.D.
Assistant Professor
Quantitative Neuroimaging Laboratory
Division of Cognitive Neuroscience
Department of Neurology
Columbia University
Alt: razli...@gmail.com
Office Phone: 212-342-1352
Office Fax: 212-342-1838
Website: http://www.columbia.edu/cu/qnl/

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[Freesurfer] how to obtain individual's pial_lgi value

2015-11-04 Thread Yang, Daniel

Dear FreeSurfer Experts,

When I specify --measure pial_lgi, aparcstats2table says it’s an invalid option.

Could you please advise how I can obtain an individual’s pial_lgi value, give a 
label?

Many thanks!
Daniel
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Re: [Freesurfer] recon-all

2015-11-04 Thread Douglas N Greve



On 11/04/2015 10:22 AM, John Anderson wrote:
> Hi freesurfers,
> Following recon-all I have a collection of folders inside the subject 
> folder.
> Inside the folder "mri" I have collection of files:
> 1. What is the differnce between the file "orig.mgz" and the file 
> "norm.mgz" ?
norm has been skull stripped and intensity normalized
> 2. Why the voxel dimentions are differnt? (i.e In norm.mgz the voxel 
> dimentions are equal while in orig.mgz it is not)?
They should be the same. It might be differnt than rawavg.mgz or your 
input data because we "conform" all inputs to 256^3 1mm3
> 3. Is it correct if I convert norm.mgz to "nii" file and use it as a 
> "T1" for further processing?
I don't know without knowing more about the "further processing". It is 
not a T1 image itself (ie, the voxel intensities are not T1 in msec).
> bests,
> John Anderson
>
>
>
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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] Surface-based registration

2015-11-04 Thread Razlighi, Qolamreza R.

Hi Bruce,
Thanks for reply. I thought after registering, the source surface's curvature 
map should be very similar to the target one. I don't see that here. The 
registered surface has pretty much the same curvature map only slightly shifted.
Am I missing something here?

Best

On Nov 4, 2015, at 5:56 PM, Bruce Fischl 
 wrote:

> Hi Ray
> 
> that sounds right. The way I visualize these is using nmovie (which I think 
> we include in our distribution) and flipping back and forth between the 
> different images showing the different surfaces/curv maps.
> 
> Which inaccuracy are you referring to?
> 
> cheers
> Bruce
> 
> On Wed, 4 Nov 2015, Razlighi, Qolamreza R. wrote:
> 
>> Dear Bruce,
>> I did run it again with option (-dist 0.25); however the result did not
>> change much (See the attachment). These results do not seem right to me and
>> I think I’m running the command correctly (see the first email). However,
>> I’m not sure I’m visualizing the curvature maps correctly. I assume the
>> lh.sphere.reg has the same vertices and facets as lh.sphere but slightly
>> displaced in space to match the curvature and sulci map of the source
>> surface to target surface. Therefore, I visualize the lh.sphere.reg by
>> pulling the same lh.curv file from the source image. If this is wrong,
>> please let me know how can I correctly visualize the lh.sphere.reg,
>> otherwise I have no idea why this surface based registration produce such
>> inaccurate results. Any comments or suggestion is greatly appreciated.
>> Best
>> [IMAGE]
>> -- 
>> Ray Razlighi, Ph.D.
>> Assistant Professor
>> Quantitative Neuroimaging Laboratory
>> Division of Cognitive Neuroscience
>> Department of Neurology
>> Columbia University
>> Alt: razli...@gmail.com
>> Office Phone: 212-342-1352
>> Office Fax: 212-342-1838
>> Website: http://www.columbia.edu/cu/qnl/
>> On Nov 3, 2015, at 3:47 PM, Bruce Fischl  wrote:
>> 
>>  Hi Ray
>> 
>>  the -1 means that the target is a single surface and not an
>>  atlas, but the registration is still nonlinear. The variances
>>  will all be 1 so you may have to play with the weights in the
>>  energy functional. We don't do this very much and it probably
>>  defaults to quite rigid. Try reducing the weight on the metric
>>  preservation term (e.g. -dist .25) if you want it to be more
>>  nonlinear
>> 
>>  cheers
>>  Bruce
>> 
>>  On Tue, 3 Nov 2015, Razlighi, Qolamreza R. wrote:
>> 
>>Hi Guys,
>>I read in the sidenote here
>>(https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates)
>>that
>>inter-subject surface base registration using
>>mris_register and -1 flag
>>performs a sort of rigid registration. So I tried it
>>between two of my
>>subjects with the command below
>>mris_register -1 -curv
>>P1639/FreeSurferClean/surf/lh.sphere
>>P1639/FreeSurferClean/surf/lh.sphere
>>lh.sphere3.reg 
>>and got the results (see the attachment). It is
>>clear that the registration
>>output is just a shifted version of the source.
>>Having this confirmed I want
>>to know if there is any way to force the
>>mris_register to perform a complete
>>non-linear surface based registration for
>>inter-subjects registration the
>>same way it does for template.
>>I have to mention that I visualize the
>>lh.sphere3.reg using freeview and
>>loaded the sane lh.curv on that surface. I hope I’m
>>not doing anything
>>stupid.
>>  
>>[IMAGE]
>>Best
>>-- 
>>Ray Razlighi, Ph.D.
>>Assistant Professor
>>Quantitative Neuroimaging Laboratory
>>Division of Cognitive Neuroscience
>>Department of Neurology
>>Columbia University
>>Alt: razli...@gmail.com
>>Office Phone: 212-342-1352
>>Office Fax: 212-342-1838
>>Website: http://www.columbia.edu/cu/qnl/
>> 
>>  ___
>>  Freesurfer mailing list
>>  Freesurfer@nmr.mgh.harvard.edu
>>  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>>  The information in this e-mail is intended only for the person
>>  to whom it is
>>  addressed. If you believe this e-mail was sent to you in error
>>  and the e-mail
>>  contains patient information, please contact the Partners
>>  Compliance HelpLine at
>>  http://www.partners.org/complianceline . If the e-mail was sent
>>  to you in error
>>  but does not contain patient information, please contact the
>>  sender and properly
>>  dispose of the e-mail.
>

Re: [Freesurfer] Surface-based registration

2015-11-04 Thread Bruce Fischl


Hi Ray

what version of FS are you using? Can you send me the output of the 
command? The distance term will prevent the curvatures from deforming too 
much. You can set it much smaller and see what happens if you want. There 
may also be an area constraint. Trying using -parea 0 also (or something 
small)


cheers
Bruce

On Wed, 4 Nov 2015, Razlighi, Qolamreza R. 
wrote:



Hi Bruce,
Thanks for reply. I thought after registering, the source surface's curvature 
map should be very similar to the target one. I don't see that here. The 
registered surface has pretty much the same curvature map only slightly shifted.
Am I missing something here?

Best

On Nov 4, 2015, at 5:56 PM, Bruce Fischl 
wrote:


Hi Ray

that sounds right. The way I visualize these is using nmovie (which I think we 
include in our distribution) and flipping back and forth between the different 
images showing the different surfaces/curv maps.

Which inaccuracy are you referring to?

cheers
Bruce

On Wed, 4 Nov 2015, Razlighi, Qolamreza R. wrote:


Dear Bruce,
I did run it again with option (-dist 0.25); however the result did not
change much (See the attachment). These results do not seem right to me and
I think I’m running the command correctly (see the first email). However,
I’m not sure I’m visualizing the curvature maps correctly. I assume the
lh.sphere.reg has the same vertices and facets as lh.sphere but slightly
displaced in space to match the curvature and sulci map of the source
surface to target surface. Therefore, I visualize the lh.sphere.reg by
pulling the same lh.curv file from the source image. If this is wrong,
please let me know how can I correctly visualize the lh.sphere.reg,
otherwise I have no idea why this surface based registration produce such
inaccurate results. Any comments or suggestion is greatly appreciated.
Best
[IMAGE]
--
Ray Razlighi, Ph.D.
Assistant Professor
Quantitative Neuroimaging Laboratory
Division of Cognitive Neuroscience
Department of Neurology
Columbia University
Alt: razli...@gmail.com
Office Phone: 212-342-1352
Office Fax: 212-342-1838
Website: http://www.columbia.edu/cu/qnl/
On Nov 3, 2015, at 3:47 PM, Bruce Fischl  wrote:

 Hi Ray

 the -1 means that the target is a single surface and not an
 atlas, but the registration is still nonlinear. The variances
 will all be 1 so you may have to play with the weights in the
 energy functional. We don't do this very much and it probably
 defaults to quite rigid. Try reducing the weight on the metric
 preservation term (e.g. -dist .25) if you want it to be more
 nonlinear

 cheers
 Bruce

 On Tue, 3 Nov 2015, Razlighi, Qolamreza R. wrote:

   Hi Guys,
   I read in the sidenote here
   (https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates)
   that
   inter-subject surface base registration using
   mris_register and -1 flag
   performs a sort of rigid registration. So I tried it
   between two of my
   subjects with the command below
   mris_register -1 -curv
   P1639/FreeSurferClean/surf/lh.sphere
   P1639/FreeSurferClean/surf/lh.sphere
   lh.sphere3.reg
   and got the results (see the attachment). It is
   clear that the registration
   output is just a shifted version of the source.
   Having this confirmed I want
   to know if there is any way to force the
   mris_register to perform a complete
   non-linear surface based registration for
   inter-subjects registration the
   same way it does for template.
   I have to mention that I visualize the
   lh.sphere3.reg using freeview and
   loaded the sane lh.curv on that surface. I hope I’m
   not doing anything
   stupid.

   [IMAGE]
   Best
   --
   Ray Razlighi, Ph.D.
   Assistant Professor
   Quantitative Neuroimaging Laboratory
   Division of Cognitive Neuroscience
   Department of Neurology
   Columbia University
   Alt: razli...@gmail.com
   Office Phone: 212-342-1352
   Office Fax: 212-342-1838
   Website: http://www.columbia.edu/cu/qnl/

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[Freesurfer] R: Re: error MRS voxel as seed in FS-FAST

2015-11-04 Thread stdp82

Hi Dough,
in summary:
I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri
thus, I have copy this file in fMRI directory (fMRI/Control22_FS) the 
MRS_MASK.mgz
and run:
fcseed-config -segid 1 -seg Control22_FS/MRS_MASK.mgz -fsd rest -mean -
cfg MRS_MASK.config
fcseed-sess -s Control22_FS -cfg MRS_MASK.config

...Writing to 
/Applications/freesurfer/subjects/fMRI/Control22_FS/rest/001/tmp.fcseed-
sess.12305/avgwf.mgh
Segmentation fault 

Therefore, according with your suggestion, I have now run:
fcseed-sess -debug -s -cfg MRS_MASK.config | & tee doug.log
ERROR: cound not find session -cfg

The doug.log is attached.

Thanks,


Stefano




>Messaggio originale
>Da: gr...@nmr.mgh.harvard.edu
>Data: 4-nov-2015 16.58
>A: 
>Ogg: Re: [Freesurfer] error MRS voxel as seed in FS-FAST
>
>First, when running fcseed-config, don't give it the full path, just 
the 
>path relative to subject/mri (in this case only MRS_MASK.mgz)
>
>However, I don't think that is the  problem. Please run
>
>fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug.log
>
>and send  me doug.log
>
>
>
>
>
>On 11/04/2015 04:14 AM, std...@virgilio.it wrote:
>> Hi list, this error is still occurring:
>>
>> mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz
>> $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz
>> fcseed-config -segid 1 -seg $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz -
fsd
>> rest -mean -cfg MRS_MASK.config
>> fcseed-sess -s -cfg MRS_MASK.config
>>
>> During
>>
>> fcseed-sess -s subj -cfg MRS_MASK.config
>>
>> 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/sub/rest/001/tmp.
>> fcseed-sess.97908/avgwf.mgh
>> Segmentation fault
>>
>> I have read your previous message and you can check the MRS voxel
>> features.
>> MRS voxel mask is in subj directory where I have run recon all -
all.
>>
>> data_type  FLOAT32
>> dim1   256
>> dim2   256
>> dim3   256
>> dim4   1
>> datatype   16
>> pixdim11.00
>> pixdim21.00
>> pixdim31.00
>> pixdim40.010747
>> cal_max0.
>> cal_min0.
>> file_type  NIFTI-1+
>>
>>
>> The features are same of other subject that runs fine.
>> data_type  FLOAT32
>> dim1   256
>> dim2   256
>> dim3   256
>> dim4   1
>> datatype   16
>> pixdim11.00
>> pixdim21.00
>> pixdim31.00
>> pixdim40.010747
>> cal_max0.
>> cal_min0.
>> file_type  NIFTI-1+
>>
>> Thank you very much.
>>
>>
>> Stefano
>>
>>
>>> Messaggio originale
>>> Da: std...@virgilio.it
>>> Data: 16-ott-2015 23.15
>>> A: 
>>> Ogg: [Freesurfer] R: Re:  R: import FS-FAST results in FSL
>>>
>>> I'd like to open with FSLview the sig.nii.gz which is produced by
>>> selxavg3-sess.
>>> If I use mri_surf2vol, which is the template to added in --
template?
>>> It should be in Tailairach space? Where can I find the template 
that
>> I
>>> should added?
>>> Thanks,
>>>
>>> Stefano
>>>
>>> subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz
>>> data_type  FLOAT32
>>> dim1   27307
>>> dim2   1
>>> dim3   6
>>> dim4   1
>>> datatype   16
>>> pixdim11.00
>>> pixdim21.00
>>> pixdim31.00
>>> pixdim41100.00
>>> cal_max49.1815
>>> cal_min-12.3855
>>> file_type  NIFTI-1+
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> Thanks,
>>>
>>> Stefano
>>>
>>>
 Messaggio originale
 Da: gr...@nmr.mgh.harvard.edu
 Data: 29-set-2015 22.09
 A: 
 Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL

 Do you mean surface-based analysis? You'd have to put them back
>> into
>>> the
 volume using mri_surf2vol, write them out as nifti and then run
>>> fslview
 on them

 On 09/29/2015 11:17 AM, std...@virgilio.it wrote:
>  Hi list,
>
>  I would like to import FS-FAST results (conjunction maps) 
in
>>> FSL,
>  opening them by fslview.
>  Could you provide me any suggestion?
>
>  Thank you very much
>  Best regards,
>
>
>  Stefano
>
>
>
>
> ___
> 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:

Re: [Freesurfer] excessive topological defect

2015-11-04 Thread Bruce Fischl

Hi Elisabetta

I don't think that's an error, just a warning. That said, a defect with 
38K vertices is awfully big, almost 1/4 of the surface, which usually means 
something big is wrong (e.g. cerebellum or skull attached to the hemi). Can 
you look at the orig.nofix or the inflated.nofix and see what is wrong? If 
you upload one of the subjects I'll take a look

cheers
Bruce

On Wed, 4 Nov 2015, Elisabetta del Re wrote:

> Dear FreeSurfer team,we are running FreeSurfer on 1.5T cases.
> For a few of them we get error messages that I am attaching.
> Mostly the message error relates to excessive topological defect.
> Any suggestions you can give to us?
> Thank you,
> regards,
> Elisabetta
> 
> --
> Elisabetta C. del Re, Ph.D.
> Instructor,
> Department of Psychiatry
> Harvard Medical School
> phone 617 9675569
> mail elisabetta_de...@hms.harvard.edu
> 
>
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Re: [Freesurfer] LongitudinalTwoStageModel QDEC Help

2015-11-04 Thread Martin Reuter


Heidi,

first: you probably need to keep the .nii in the table for now 
(depending on how your cross sectional directories are really named?). 
If they have the .nii extension, you need to do the same in the qdec table.


If down the road the extension creates problems, it will be very 
complicated to solve this as the naming is propagated to many places (in 
the cross runs, base and long). Cleaning that up retrospectively is 
possible but lot's of work and if you miss a place things will fail. So 
it might be easier to re-run from scratch (depending on the size of the 
data and the edits)? Let's first wait and see what happens.


Best, Martin

On 11/04/2015 09:34 AM, Heidi Foo wrote:

Hi Martin,

Thanks so much for your reply, I really appreciate it.

I will change my qdec file for fsid accordingly from 
FS_PD002_1.nii.long.FSBASE_002 to FS_PD002_1. If the file name and 
file extension are causing the problem, do you have any suggestions 
for me overcome this? Would changing the file name help?


Thanks again.

Regards,
Heidi

On Wed, Nov 4, 2015 at 9:51 PM, Martin Reuter 
> wrote:


Dear Heidi,

maybe there is a problem with your long.qdec.table.dat file? It is
used to create the .long. file names and
obviously that filename is wrong (containing two .long. in it).
Make sure that the first column is only the cross sectional id and
the second one is the base id, so in your case:
fsid fsid-base
FS_PD002_1.nii FSBASE_002

Also it is not a good idea to have the ".nii" as part of the
subject id, as that is a file extension. Next time, when running
the cross sectionals, make sure you call the subject "FS_PD002_1"
without extension. Could be that this leads to other problems (or
it could just work, we'll see).

Best, Martin





On 11/04/2015 08:38 AM, Heidi Foo wrote:

Dear FreeSurfer experts,

I was running the first stage of analysis of preparing of data -
qcache - and I encountered some problems.

When using this command, /long_mris_slopes --qdec
./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg
--do-rate --do-pc1 --do-spc --do-stack --do-label --time years
--qcache fsaverage --sd $SUBJECTS_DIR/, an error message saying:"
FS_PD002_1.nii.long.FSBASE_002.long.FSBASE_002/label/lh.cortex.label
does not exist!" appears.

I tried several other ways such as using long_stats_slopes, but I
keep receiving error messages similar to the one above.

Please advice?

Thank you so much for your kind help!

Regards,
Heidi Foo


-- 
Martin Reuter, PhD

Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone:+1-617-724-5652 
Web  :http://reuter.mit.edu  


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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] Extracing values from ces.nii

2015-11-04 Thread Afzal, Afsana

Ah, I see. But what do the 27307 rows represent and why are there 6 values per 
row?

Thanks, 

Afsana
__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, November 03, 2015 1:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Extracing values from ces.nii

It should be interpreted as a 2D structure of size 27307*6= 163842
which are the number of vertices in fsaverage


On 10/29/2015 11:41 AM, Afzal, Afsana wrote:
> Hi,
>
> I'm trying to extract the contrast values from ces.nii.gz after
> first-level analysis. My goal is to average the contrast values for
> each voxel across subjects for a given condition and see where an
> individual from a separate population falls within the distribution of
> contrast values.
>
> The ces.nii file I'm working with has the following dimension: (27307,
> 1, 6, 1), which I interpreted as containing information about 27307
> voxels in a 3D matrix. What does the information in the 6 rows for
> each voxel represent? I was expecting to get a single raw b-value for
> each voxel. The structure is consistent with sig.nii and t.nii files
> as well.
>
> Thanks for any 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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--
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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[Freesurfer] recon-all

2015-11-04 Thread John Anderson

Hi freesurfers,

Following recon-all I have a collection of folders inside the subject folder.

Inside the folder "mri" I have collection of files:

 

1. What is the differnce between the file "orig.mgz" and the file "norm.mgz" ? 

2. Why the voxel dimentions are differnt? (i.e In norm.mgz the voxel dimentions are equal while in orig.mgz it is not)?

3. Is it correct if I convert norm.mgz to "nii" file and use it as a "T1" for further processing?

 

bests,

John Anderson

 
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Re: [Freesurfer] applying longitudinal processing on twins

2015-11-04 Thread Martin Reuter


Hi Oerjan,

yes, MZ twins are very similar (InfoAd: are you familiar with our 
BrainPrint NeuroImaging paper where we compare MZ and DZ brain shapes: 
http://www.sciencedirect.com/science/article/pii/S1053811915000476
http://reuter.mit.edu/blue/papers/wachinger-brainprint15/wachinger-brainprint15.pdf 
).


Anyway, I doubt the longitudinal stream is going to work for this, as it 
is really designed for longitudinal and not across subject situations 
(even with MZ twins I expect differences to be too large). Even if a few 
cases work, there will be too many that fail.


Best, Martin



On 11/04/2015 05:13 AM, Örjan de Manzano wrote:

Dear FreeSurfers,

I'm about to analyze cortical thickness in monozygotic twins 
discordant for certain expertise. The within-pair similarities in 
brain morphology are striking (e.g. twin1 x twin2 intracranial volume 
correlation r=.99) and you could easily play a memory game with the 
images. Nonetheless, there are notable within-pair differences in 
gyrification etc. I'm trying to figure out if the longitudinal stream, 
or some version of it, might still be a viable option in this 
situation. The sample is fairly small and I want to do what I can to 
maximize sensitivity. Do any of you have experience with a similar 
data set or ideas/opinions/recommendations?


Best regards,

Örjan


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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] SOLVED Re: zcat issue, lGI processing

2015-11-04 Thread Andrews, Derek

Dear FreeSurfer support team,

It appears that ‘zcat’ appears in line 126 of the load.mgh script, I have
changed this to gzcat which appears to have solved the issue.

Again, thank you for your support. It is very appreciated!

Best, Derek  





Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 04/11/2015 11:33, "Andrews, Derek"  wrote:

>Dear Douglas, 
>
>Thank you for response. To clarify, I need to find out where in the lGI
>scripts zcat is being called so that I can change the code to use
>something like gunzip.
>
>Best, Derek 
>
>
>
>Derek Sayre Andrews, MSc
>PhD Candidate
>
>The Sackler Institute for Translational Neurodevelopment
>Department of Forensic and Neurodevelopmental Sciences
>Institute of Psychiatry, Psychology & Neuroscience, King's College London
>
>Telephone: +44 (0)20 7848 5701
>Email: derek.andr...@kcl.ac.uk
>
>
>
>
>
>On 03/11/2015 17:41, "Douglas N Greve"  wrote:
>
>>
>>you can find out where it is with
>>   which zcat
>>
>>On 11/03/2015 07:42 AM, Andrews, Derek wrote:
>>> Hello Freesurfer Support Team,
>>>
>>> I have encountered an issue running recon-all lgi that I believe is
>>> due to a zcat issue on mac OSx where a .Z is added to the end of the
>>> file name the resulting error looks like thisŠ
>>>
>>> >> reading filled volume...
>>>
>>> zcat: can't stat:
>>> 
>>>/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pia
>>>l
>>>.filled.mgz 
>>> 
>>>(/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pi
>>>a
>>>l.filled.mgz.Z):
>>> No such file or directory
>>>
>>>
>>> Upon reading through some message boards it appears replacing zcat
>>> with gzcat can solve this issue, however I am unsure where this
>>> troublesome zcat command is (it does not appear in the mriscomputelgi
>>> script).
>>>
>>>
>>> Any suggestions or work throughs would be appreciated.
>>>
>>>
>>> Best, Derek
>>>
>>>
>>>
>>> 
>>>
>>>
>>> *Derek Sayre Andrews, MSc*
>>> PhD Candidate
>>>
>>> The Sackler Institute for Translational Neurodevelopment
>>>
>>> Department of Forensic and Neurodevelopmental Sciences
>>>
>>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>>London
>>>
>>> Telephone: +44 (0)20 7848 5701
>>> Email: derek.andr...@kcl.ac.uk
>>>
>>>
>>>
>>>
>>> ___
>>> 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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>>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] zcat issue, lGI processing

2015-11-04 Thread Andrews, Derek

Dear Douglas, 

Thank you for response. To clarify, I need to find out where in the lGI
scripts zcat is being called so that I can change the code to use
something like gunzip.

Best, Derek 



Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





On 03/11/2015 17:41, "Douglas N Greve"  wrote:

>
>you can find out where it is with
>   which zcat
>
>On 11/03/2015 07:42 AM, Andrews, Derek wrote:
>> Hello Freesurfer Support Team,
>>
>> I have encountered an issue running recon-all lgi that I believe is
>> due to a zcat issue on mac OSx where a .Z is added to the end of the
>> file name the resulting error looks like thisŠ
>>
>> >> reading filled volume...
>>
>> zcat: can't stat:
>> 
>>/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial
>>.filled.mgz 
>> 
>>(/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pia
>>l.filled.mgz.Z): 
>> No such file or directory
>>
>>
>> Upon reading through some message boards it appears replacing zcat
>> with gzcat can solve this issue, however I am unsure where this
>> troublesome zcat command is (it does not appear in the mriscomputelgi
>> script).
>>
>>
>> Any suggestions or work throughs would be appreciated.
>>
>>
>> Best, Derek
>>
>>
>>
>> 
>>
>> *Derek Sayre Andrews, MSc*
>> PhD Candidate
>>
>> The Sackler Institute for Translational Neurodevelopment
>>
>> Department of Forensic and Neurodevelopmental Sciences
>>
>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>London
>>
>> Telephone: +44 (0)20 7848 5701
>> Email: derek.andr...@kcl.ac.uk
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>-- 
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
>The information in this e-mail is intended only for the person to whom it
>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
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Re: [Freesurfer] LongitudinalTwoStageModel QDEC Help

2015-11-04 Thread Martin Reuter


Dear Heidi,

maybe there is a problem with your long.qdec.table.dat file? It is used 
to create the .long. file names and obviously that 
filename is wrong (containing two .long. in it). Make sure that the 
first column is only the cross sectional id and the second one is the 
base id, so in your case:

fsid fsid-base
FS_PD002_1.nii FSBASE_002

Also it is not a good idea to have the ".nii" as part of the subject id, 
as that is a file extension. Next time, when running the cross 
sectionals, make sure you call the subject "FS_PD002_1" without 
extension. Could be that this leads to other problems (or it could just 
work, we'll see).


Best, Martin




On 11/04/2015 08:38 AM, Heidi Foo wrote:

Dear FreeSurfer experts,

I was running the first stage of analysis of preparing of data - 
qcache - and I encountered some problems.


When using this command, /long_mris_slopes --qdec 
./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg 
--do-rate --do-pc1 --do-spc --do-stack --do-label --time years 
--qcache fsaverage --sd $SUBJECTS_DIR/, an error message saying:" 
FS_PD002_1.nii.long.FSBASE_002.long.FSBASE_002/label/lh.cortex.label 
does not exist!" appears.


I tried several other ways such as using long_stats_slopes, but I keep 
receiving error messages similar to the one above.


Please advice?

Thank you so much for your kind help!

Regards,
Heidi Foo


--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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Re: [Freesurfer] zcat issue, lGI processing

2015-11-04 Thread Douglas N Greve

load_mgh.m and load_nifti.m in $FREESURFER_HOME/matlab

On 11/04/2015 06:33 AM, Andrews, Derek wrote:
> Dear Douglas,
>
> Thank you for response. To clarify, I need to find out where in the lGI
> scripts zcat is being called so that I can change the code to use
> something like gunzip.
>
> Best, Derek
>
>
> 
> Derek Sayre Andrews, MSc
> PhD Candidate
>
> The Sackler Institute for Translational Neurodevelopment
> Department of Forensic and Neurodevelopmental Sciences
> Institute of Psychiatry, Psychology & Neuroscience, King's College London
>
> Telephone: +44 (0)20 7848 5701
> Email: derek.andr...@kcl.ac.uk
>
>
>
>
>
> On 03/11/2015 17:41, "Douglas N Greve"  wrote:
>
>> you can find out where it is with
>>which zcat
>>
>> On 11/03/2015 07:42 AM, Andrews, Derek wrote:
>>> Hello Freesurfer Support Team,
>>>
>>> I have encountered an issue running recon-all lgi that I believe is
>>> due to a zcat issue on mac OSx where a .Z is added to the end of the
>>> file name the resulting error looks like thisŠ
>>>
> reading filled volume...
>>> zcat: can't stat:
>>>
>>> /Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pial
>>> .filled.mgz
>>>
>>> (/Users/dandrews/data/test/12011/surf/tmp-mris_compute_lgi-lh.pial/lh.pia
>>> l.filled.mgz.Z):
>>> No such file or directory
>>>
>>>
>>> Upon reading through some message boards it appears replacing zcat
>>> with gzcat can solve this issue, however I am unsure where this
>>> troublesome zcat command is (it does not appear in the mriscomputelgi
>>> script).
>>>
>>>
>>> Any suggestions or work throughs would be appreciated.
>>>
>>>
>>> Best, Derek
>>>
>>>
>>>
>>> 
>>>
>>> *Derek Sayre Andrews, MSc*
>>> PhD Candidate
>>>
>>> The Sackler Institute for Translational Neurodevelopment
>>>
>>> Department of Forensic and Neurodevelopmental Sciences
>>>
>>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>> London
>>>
>>> Telephone: +44 (0)20 7848 5701
>>> Email: derek.andr...@kcl.ac.uk
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>
> ___
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>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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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[Freesurfer] Error in processing for local gyrification index

2015-11-04 Thread Dr Meenal Yadav

Hi List,
I am getting the following error when running recon-all lgi for local
gyrification index.
I have changed the script in matlab as we are using matlab 2013b as
mentioned in the previous thread.
I am attaching the script.
Please let me know what else to do.
Thanks Regards
Meenal Budhiraja
PhD student
Karolinska Institute
Stockholm,Sweden.



preparing pial mesh structure ...
...searching for mesh edges...done (349.20 sec).
... creating path file for vertex 1 / 66330
area file for outer ROIs saved at 1
Improper assignment with rectangular empty matrix.

Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);

Error in reorganize_verticeslist (line 28)

[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));

Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
verticeslist, step);

>>
ERROR:  make_roi_paths did not complete successfully!
function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim, step)

% step is typically set between 5 and 10. Default is 7, increasing it will
% limit redundancies in the resulting path file.

verticeslist=[];
si=max(size(perim));
for t=1:step:si
[nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:));
verticeslist= [verticeslist nearestIndexMT];
end
verticeslist=unique(verticeslist);

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Re: [Freesurfer] LongitudinalTwoStageModel QDEC Help

2015-11-04 Thread Martin Reuter

Not sure what is going on. can you find (from the log) the command it 
runs just before that (something with mris_label_calc) and run it in a 
terminal (with the SUBJECT_DIR set etc). It could be that it get's 
confused by the .nii extension, but could also be something else.

Martin

On 11/04/2015 10:09 AM, Heidi Foo wrote:

Hi Martin,

I understand what you mean now. Thanks for your advice!

But I have another error message now: /ERROR 64 : mris_label_calc 
intersect did not work? /Is there something I am doing wrong?

Regards,
Heidi

On Wed, Nov 4, 2015 at 10:39 PM, Martin Reuter 
> wrote:

Heidi,

first: you probably need to keep the .nii in the table for now
(depending on how your cross sectional directories are really
named?). If they have the .nii extension, you need to do the same
in the qdec table.

If down the road the extension creates problems, it will be very
complicated to solve this as the naming is propagated to many
places (in the cross runs, base and long). Cleaning that up
retrospectively is possible but lot's of work and if you miss a
place things will fail. So it might be easier to re-run from
scratch (depending on the size of the data and the edits)? Let's
first wait and see what happens.

Best, Martin

On 11/04/2015 09:34 AM, Heidi Foo wrote:

Hi Martin,

Thanks so much for your reply, I really appreciate it.

I will change my qdec file for fsid accordingly from
FS_PD002_1.nii.long.FSBASE_002 to FS_PD002_1. If the file name
and file extension are causing the problem, do you have any
suggestions for me overcome this? Would changing the file name help?

Thanks again.

Regards,
Heidi

On Wed, Nov 4, 2015 at 9:51 PM, Martin Reuter
> wrote:

Dear Heidi,

maybe there is a problem with your long.qdec.table.dat file?
It is used to create the .long. file names
and obviously that filename is wrong (containing two .long.
in it). Make sure that the first column is only the cross
sectional id and the second one is the base id, so in your case:
fsid fsid-base
FS_PD002_1.nii FSBASE_002

Also it is not a good idea to have the ".nii" as part of the
subject id, as that is a file extension. Next time, when
running the cross sectionals, make sure you call the subject
"FS_PD002_1" without extension. Could be that this leads to
other problems (or it could just work, we'll see).

Best, Martin

On 11/04/2015 08:38 AM, Heidi Foo wrote:

Dear FreeSurfer experts,

I was running the first stage of analysis of preparing of
data - qcache - and I encountered some problems.

When using this command, /long_mris_slopes --qdec
./qdec/long.qdec.table.dat --meas thickness --hemi lh
--do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label
--time years --qcache fsaverage --sd $SUBJECTS_DIR/, an
error message saying:"
FS_PD002_1.nii.long.FSBASE_002.long.FSBASE_002/label/lh.cortex.label
does not exist!" appears.

I tried several other ways such as using long_stats_slopes,
but I keep receiving error messages similar to the one above.

Please advice?

Thank you so much for your kind help!

Regards,
Heidi Foo

-- 
Martin Reuter, PhD

Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone:+1-617-724-5652 
Web  :http://reuter.mit.edu  

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.

-- 
Martin Reuter, PhD

Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone:+1-617-724-5652 
Web  :http://reuter.mit.edu  

--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts

Re: [Freesurfer] error MRS voxel as seed in FS-FAST

2015-11-04 Thread Douglas N Greve

First, when running fcseed-config, don't give it the full path, just the 
path relative to subject/mri (in this case only MRS_MASK.mgz)

However, I don't think that is the  problem. Please run

fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug.log

and send  me doug.log





On 11/04/2015 04:14 AM, std...@virgilio.it wrote:
> Hi list, this error is still occurring:
>
> mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz
> $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz
> fcseed-config -segid 1 -seg $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz -fsd
> rest -mean -cfg MRS_MASK.config
> fcseed-sess -s -cfg MRS_MASK.config
>
> During
>
> fcseed-sess -s subj -cfg MRS_MASK.config
>
> 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/sub/rest/001/tmp.
> fcseed-sess.97908/avgwf.mgh
> Segmentation fault
>
> I have read your previous message and you can check the MRS voxel
> features.
> MRS voxel mask is in subj directory where I have run recon all -all.
>
> data_type  FLOAT32
> dim1   256
> dim2   256
> dim3   256
> dim4   1
> datatype   16
> pixdim11.00
> pixdim21.00
> pixdim31.00
> pixdim40.010747
> cal_max0.
> cal_min0.
> file_type  NIFTI-1+
>
>
> The features are same of other subject that runs fine.
> data_type  FLOAT32
> dim1   256
> dim2   256
> dim3   256
> dim4   1
> datatype   16
> pixdim11.00
> pixdim21.00
> pixdim31.00
> pixdim40.010747
> cal_max0.
> cal_min0.
> file_type  NIFTI-1+
>
> Thank you very much.
>
>
> Stefano
>
>
>> Messaggio originale
>> Da: std...@virgilio.it
>> Data: 16-ott-2015 23.15
>> A: 
>> Ogg: [Freesurfer] R: Re:  R: import FS-FAST results in FSL
>>
>> I'd like to open with FSLview the sig.nii.gz which is produced by
>> selxavg3-sess.
>> If I use mri_surf2vol, which is the template to added in --template?
>> It should be in Tailairach space? Where can I find the template that
> I
>> should added?
>> Thanks,
>>
>> Stefano
>>
>> subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz
>> data_type  FLOAT32
>> dim1   27307
>> dim2   1
>> dim3   6
>> dim4   1
>> datatype   16
>> pixdim11.00
>> pixdim21.00
>> pixdim31.00
>> pixdim41100.00
>> cal_max49.1815
>> cal_min-12.3855
>> file_type  NIFTI-1+
>>
>>
>>
>>
>>
>>
>>
>> Thanks,
>>
>> Stefano
>>
>>
>>> Messaggio originale
>>> Da: gr...@nmr.mgh.harvard.edu
>>> Data: 29-set-2015 22.09
>>> A: 
>>> Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL
>>>
>>> Do you mean surface-based analysis? You'd have to put them back
> into
>> the
>>> volume using mri_surf2vol, write them out as nifti and then run
>> fslview
>>> on them
>>>
>>> On 09/29/2015 11:17 AM, std...@virgilio.it wrote:
  Hi list,

  I would like to import FS-FAST results (conjunction maps) in
>> FSL,
  opening them by fslview.
  Could you provide me any suggestion?

  Thank you very much
  Best regards,


  Stefano




 ___
 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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>>> Freesurfer mailing list
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>>> 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] changing the index of labels

2015-11-04 Thread Jacobs H (NP)

Works perfectly! Thank you so much!
Heidi

On 11/3/15, 6:54 PM, "Douglas N Greve"  wrote:

>
>In that case you can do something like
>fscalc lhfile.mgz add 1000 -o lhfile1000.mgz
>mri_mask lhfile1000.mgz lhfile.mgz lhfile1000.mgz
>
>This will add 1000 to the lhlabels. This will make the lh labels
>different from the rh. You can add a constant to the rh too if you want.
>
>doug
>
>
>On 10/30/2015 07:12 PM, Jacobs H (NP) wrote:
>> Yes, there are different mgz files for left and right (but they have the
>> same index numbers and colors).
>>
>> On 10/30/15, 11:16 PM, "Douglas N Greve" 
>>wrote:
>>
>>> Are there different files for the lh and rh? Sorry, never done the
>>> subfields analysis.
>>>
>>>
>>> On 10/30/2015 01:25 PM, Bruce Fischl wrote:
 Hi Heidi

 I guess you could do it yourself in matlab using the aseg to figure
 out which hemisphere you are in

 cheers
 Bruce

 On Fri, 30 Oct 2015, Jacobs H (NP) wrote:

> Hi,
>
> Is there a way to change the index of the segmentation of the
> hippocampal
> subfields, so that when I combine left and right, FreeSurfer treats
> them
> as different regions?
>
> Thanks!
> Best
> Heidi
>
>>> I just checked again in freeview and indeed they have the same
>>>index
>>> (e.g.
>>> CA1 has value 206 for left and also for right).
>>>
>>> On 10/27/15, 5:01 PM, "Douglas Greve" 
>>> wrote:
>>>
 The color is not important. The question is whether they have a
 different index. Can you confirm that lh and rh have the same
index?

 On 10/27/15 11:53 AM, Jacobs H (NP) wrote:
> Hi Doug,
>
> Yes, for the aseg they are. But not for the hippocampal
>subfields:
> left
> and right have the same color coding.
> I am creating one segmentation, including left and right
> hippocampal
> subfields and aparc, for partial volume correction.
> Any idea how I can make the labels for the hippocampal subfields
> different
> (freesurfer version 6)?
>
> Thanks
> Heidi
>
> On 10/27/15, 4:32 PM, "Douglas Greve" 
> wrote:
>
>> The indices should be different. Eg, 17 is left hippo, 53 is
>>right
>> hippo. If you click on them in freeview and different labels
>> appear,
>> then FS knows they are different
>>
>> On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
>>> Hi.
>>>
>>> Just one another related question: now that I was able to
>>>combine
>>> left
>>> and
>>> right hippocampal subfields with the aparc-aseg correctly, I
>>> noticed
>>> that
>>> the left and right hippocampal subfields have the same color
>>> labels
>>> and
>>> codes. What would be the best way to make sure that FreeSurfer
>>> understand
>>> that the left and right subfields (e.g. Left and right CA1) are
>>> different
>>> areas?
>>>
>>> Thanks!
>>> Heidi
>>>
>>> On 10/21/15, 11:01 PM, "Jacobs H (NP)"
>>> 
>>> wrote:
>>>
 Thanks! Works wonderful!
 Heidi

 On 10/21/15, 10:50 PM, "Douglas N Greve"
 
 wrote:

> If you want to remove them, you can use mri_binarize with the
> --replace
> option, replacing them with whatever you want.
>
> On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
>> Hi,
>>
>> I am trying to generate a segmentation file containing the
>> aseg+aparc
>> but replacing the hippocampus with the hippocampal
>>subfields.
>> With mergeseg I was able to merge the segmentations, but
>> unfortunately
>> parts of the ³old² hippocampus (labeled as 17 and 53) are
>> still
>> in
>> there (as the area covered by the subfields is not 100%
>> equal to
>> the
>> hippocampus of the aseg).
>> How can I remove the remains of the old hippocampal labels?
>>
>> Many thanks!
>> Best
>> Heidi
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
>

[Freesurfer] error MRS voxel as seed in FS-FAST

2015-11-04 Thread stdp82

Hi list, this error is still occurring:

mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz 
$SUBJECTS_DIR//subj/mri/MRS_MASK.mgz
fcseed-config -segid 1 -seg $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz -fsd 
rest -mean -cfg MRS_MASK.config
fcseed-sess -s -cfg MRS_MASK.config

During 

fcseed-sess -s subj -cfg MRS_MASK.config

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/sub/rest/001/tmp.
fcseed-sess.97908/avgwf.mgh
Segmentation fault 

I have read your previous message and you can check the MRS voxel 
features.
MRS voxel mask is in subj directory where I have run recon all -all.

data_type  FLOAT32
dim1   256
dim2   256
dim3   256
dim4   1
datatype   16
pixdim11.00
pixdim21.00
pixdim31.00
pixdim40.010747
cal_max0.
cal_min0.
file_type  NIFTI-1+


The features are same of other subject that runs fine.
data_type  FLOAT32
dim1   256
dim2   256
dim3   256
dim4   1
datatype   16
pixdim11.00
pixdim21.00
pixdim31.00
pixdim40.010747
cal_max0.
cal_min0.
file_type  NIFTI-1+

Thank you very much.


Stefano


>Messaggio originale
>Da: std...@virgilio.it
>Data: 16-ott-2015 23.15
>A: 
>Ogg: [Freesurfer] R: Re:  R: import FS-FAST results in FSL
>
>I'd like to open with FSLview the sig.nii.gz which is produced by 
>selxavg3-sess.
>If I use mri_surf2vol, which is the template to added in --template? 
>It should be in Tailairach space? Where can I find the template that 
I 
>should added?
>Thanks,
>
>Stefano
>
>subj/rest/fc.seed.surf.lh/L_seed/sig.nii.gz 
>data_type  FLOAT32
>dim1   27307
>dim2   1
>dim3   6
>dim4   1
>datatype   16
>pixdim11.00
>pixdim21.00
>pixdim31.00
>pixdim41100.00
>cal_max49.1815
>cal_min-12.3855
>file_type  NIFTI-1+
>
>
>
>
>
>
>
>Thanks,
>
>Stefano
>
>
>>Messaggio originale
>>Da: gr...@nmr.mgh.harvard.edu
>>Data: 29-set-2015 22.09
>>A: 
>>Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL
>>
>>Do you mean surface-based analysis? You'd have to put them back 
into 
>the 
>>volume using mri_surf2vol, write them out as nifti and then run 
>fslview 
>>on them
>>
>>On 09/29/2015 11:17 AM, std...@virgilio.it wrote:
>>>
>>> Hi list,
>>>
>>> I would like to import FS-FAST results (conjunction maps) in 
>FSL,
>>> opening them by fslview.
>>> Could you provide me any suggestion?
>>>
>>> Thank you very much
>>> Best regards,
>>>
>>>
>>> Stefano
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>-- 
>>Douglas N. Greve, Ph.D.
>>MGH-NMR Center
>>gr...@nmr.mgh.harvard.edu
>>Phone Number: 617-724-2358
>>Fax: 617-726-7422
>>
>>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>Outgoing: ftp://surfer.nmr.mgh.harvard.
>edu/transfer/outgoing/flat/greve/
>>
>>___
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>>
>>
>>The information in this e-mail is intended only for the person to 
>whom it is
>>addressed. If you believe this e-mail was sent to you in error and 
>the e-mail
>>contains patient information, please contact the Partners 
Compliance 
>HelpLine at
>>http://www.partners.org/complianceline . If the e-mail was sent to 
>you in error
>>but does not contain patient information, please contact the sender 
>and properly
>>dispose of the e-mail.
>>
>>
>
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[Freesurfer] interaction in glm

2015-11-04 Thread Erik Lindberg

Dear Freesurfer experts,

I know this has been an ongoing topic in the mailing list – however I would
like to raise the issue one more time. In the choice between doss and dods
– I usually check if there is a significant interaction and if so my choice
is dods.

As I understand it you do not recommend to use doss if an interaction is
present. Is the reason for this that I would “over-correct” for the
variable in one group while “under-correcting” for the same variable in the
other group?

It is some time tempting to present result both from a dods and a doss – to
tell where the interaction is present, and where difference are present
while controlling for the variable

But if I understand Doug´s previous comments on this – this would not be a
correct approach?



Thanks

Erik
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The information in this e-mail is intended only for the person to whom it is
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[Freesurfer] applying longitudinal processing on twins

2015-11-04 Thread Örjan de Manzano

Dear FreeSurfers,

I'm about to analyze cortical thickness in monozygotic twins discordant for 
certain expertise. The within-pair similarities in brain morphology are 
striking (e.g. twin1 x twin2 intracranial volume correlation r=.99) and you 
could easily play a memory game with the images. Nonetheless, there are notable 
within-pair differences in gyrification etc. I'm trying to figure out if the 
longitudinal stream, or some version of it, might still be a viable option in 
this situation. The sample is fairly small and I want to do what I can to 
maximize sensitivity. Do any of you have experience with a similar data set or 
ideas/opinions/recommendations?

Best regards,

Örjan
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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.

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