[Freesurfer] Citing bbregister in articles

[Christopher]

Hi,

Just a quick question to the Freesurfer creators : how could I cite the 
bbregister command line in an article ? I didn't find the correct 
article in the Freesurfer Wiki.

Thanks,

-- 
Christopher Coello, Ph.D.
Preclinical PET/CT unit
Institute of Basic Medical Sciences
Faculty of Medicine, University of Oslo, Norway
tel. +4745154516
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[Freesurfer] Binary volume to surface _ mri_vol2surf

[Christopher]

Dear Freesurfer community,

I have processed a subject (name:P061_pre, 3D MPRAGE T1) with Freesurfer 
5.1. A resection area has been defiened on this volume and exists as a 
binary volume (1:voxels of interest, 0:others) lesionMask.mgz. I now 
would like to project this volume on the surface of the subject, e.g. 
lh.white.
I have tried using mri_vol2surf :
mri_vol2surf --src lesionMask.mgz --out lesionMask_surf.mgh --out_type 
mgh --hemi lh --regheader P061_pre

The command seems to work:

srcvol = lesionMask.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
   Using /root/data/FS51/freesurfer/subjects/P061_pre/mri/orig.mgz as 
target reference.
Reading surface /root/data/FS51/freesurfer/subjects/P061_pre/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
  1 0 0 0
using old
Done mapping volume to surface
Number of source voxels hit = 79054
Writing to ./lesionMask_surf.mgh
Dim: 128233 1 1

But when trying to open the surface with freeview, it returns an error 
message :
freeview -f lesionMask_surf.mgh
ERROR: MRISread: cannot read surface data from file 
/home/epilepsy/sorted/P061/preMR/lesionMask_surf.mgh!

Segmentation fault


What did I miss ?

Thanks for your help,

-- 
Christopher Coello, Ph.D.
Preclinical PET/CT unit
Institute of Basic Medical Sciences
Faculty of Medicine, University of Oslo, Norway
tel. +4745154516
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Re: [Freesurfer] Binary volume to surface _ mri_vol2surf

[Christopher]

Thanks Doug. I can know visualize the resected area using freeview.

As the output of mri_vol2surf produces an overlay and not a surface, 
measurements of area or/and intersection with other outputs from 
mri_vol2surf are not possible using mris_* functions.
What is the best strategy to follow to be able to do simple measurments 
on these mri_vol2surf outputs ? Transform to surface, but how ?

Thanks in advance,

Christopher


> The output of mri_vol2surf is not a surface but an overlay on a surface.
> You will need to run something like:
>
> freeview -f
> $SUBJECTS_DIR/$subject/surf/lh.inflated:overlay=lesionMask_surf.mgh
>
> You'll need to set the threshold to 0.5 in order to see the mask.
> doug

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Re: [Freesurfer] Binary volume to surface _ mri_vol2surf

[Christopher]

Hi Doug,

Not really clear, I do agree.
1/ I would like to measure the area of the surface called 
lesionMask_surf.mgh obtained with mri_vol2surf.
2/ In addition, I have two methods (M1 and M2) to measure a resected 
volume. The binary volumes M1_vol and M2_vol are processed with 
mri_vol2surf to obtain M1_surf and M2_surf. I would like to measure the 
area common to M1_surf and M2_surf.

Best,

Christopher

On 11.03.2013 18:12, Douglas Greve wrote:
> Hi Christopher, I'm not sure I understand your question. What do you
> mean by "simple measurements"?
> doug
>
>
> On 3/11/13 10:59 AM, Christopher wrote:
>> Thanks Doug. I can know visualize the resected area using freeview.
>>
>> As the output of mri_vol2surf produces an overlay and not a surface,
>> measurements of area or/and intersection with other outputs from
>> mri_vol2surf are not possible using mris_* functions.
>> What is the best strategy to follow to be able to do simple
>> measurments on these mri_vol2surf outputs ? Transform to surface, but
>> how ?
>>
>> Thanks in advance,
>>
>> Christopher
>>
>>
>>> The output of mri_vol2surf is not a surface but an overlay on a surface.
>>> You will need to run something like:
>>>
>>> freeview -f
>>> $SUBJECTS_DIR/$subject/surf/lh.inflated:overlay=lesionMask_surf.mgh
>>>
>>> You'll need to set the threshold to 0.5 in order to see the mask.
>>> doug
>>
>>
>
>
>
> 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.
>


-- 
Christopher Coello, Ph.D.
Preclinical PET/CT unit
Institute of Basic Medical Sciences
Faculty of Medicine, University of Oslo, Norway
tel. +4745154516
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[Freesurfer] Cognitive neuroscientist wanted for open position in drug discovery (Cambridge, MA)

[Christopher Chatham]

Dear Freesurfers,

We are looking for a cognitive neuroscientist to join our growing team in
the Neurocognition and Functional Imaging group at Pfizer (Cambridge, MA).
Please feel free to forward this listing to interested parties or other
lists.

See the full job posting or apply via
https://www.linkedin.com/jobs2/view/38609110

Excerpts from the full job posting:

*Role Description *
*To provide expertise in clinical cognitive neuroscience, and its
application to neuropsychiatric / neurodegenerative disorders, in
combination with functional neuroimaging techniques (including e.g. fMRI,
ERP, MEG and/or TMS) to support the development of medicines from target
identification through Proof-of-Concept.
*Provide expertise on data analytic methods as applied to functional
imaging and cognitive data
*Responsibility for the delivery of the portfolio by supporiting clinical
neurocognitive and functional neuroimaging projects to support needs of the
Therapeutic Area divisions. Primary responsibility to the Neuroscience
Research unit in preclinical and early phase clinical development.
*Provide support to key projects in the Business Units that require the
knowledge of neurocognitive and functional neuroimaging for late phase
application.
*Member of a team of imaging scientists (both preclinical and clinical) in
support of the needs of neurosciences and aligned with the overall imaging
stategy of the organization.
*Maintain cutting edge knowledge of the clinical neurocognitive and
functional neuroimaging field; be aware of major advances and emerging
trends, and; maintain excellent links with academic groups worldwide.

*Responsibilities *
*Responsible for scientific quality, experimental design and interpretation
of projects involving cognitive asssessments, particularly in combination
with functional neuroimaging.
*Where relevant, provides expertise in neurocognition and functional
neuroimaging to support review committees and major decision points in the
drug development process
*Provides a point of contact for data analysis expertise, to support
cutting edge analytical procedures
*Responsible for establishing and maintaining external collaborations
(academic and industrial) to specified timelines and milestones.
*Contributes to the development of strategies that integrate knowledge of
neurocognitive and functional neuroimaging with other biological data
(proteomics, metabolomics, genetics, imaging etc…) that underpin the
development of systems biology/systems medicine
*Provides prime input to the Imaging group in terms of a particular
technique being fit for purpose and seeks support for all aspects of image
analysis.

*Qualifications *
Qualifications:
Education:
*PhD in a relevant discipline (experimental psychology preferred; strong
background in cognition essential)

Technical Ability:
*Expert in neurocognition in humans; strong and broad theoretical knowledge
across cognitive domains, demonstrated practical application of wide
variety of cognitive techniques
*Expert in the combination of cognitive assessment in conjunction with
functional neuroimaging.
*Direct experience operationalizing studies in clinical neurocognition, in
conjunction with the application of functional neuroimaging techniques
(fMRI, ERP, MET, TMS), ideally with experience in
neuropsychiatric/neurodegenerative disease populations
*Direct experience of clinical imaging study design, including protocol
develop and data analysis
*Knowledge of disease area pathophysiology, and use of cognitive imaging to
explore circuit-based mechanisms
*Knowledge and experience in the application of neurocognition and
functional neuroimaging to drug discovery and development.
*Ability to provide scientific critique on ideas, interpretation of results
and direction on multiple projects.
*Publication record in the field of neurocognition and/or functional
neuroimaging.
*Strong background in data analysis and computational modelling of
behavioural and/or imaging data
Desirable:
*Direct experience in the preclinical to clinical translation of novel
functional neuroimaging techniques.
*Strong background in the technical acquisition of MRI data

Essential Attributes:
*Identifying and championing new initiatives.
*Strong quantitative skills.
*Scientific leadership combined with research project delivery.
*Successful track record of effectively working in multi- disciplinary
teams.
*Ability to problem solve and influence in complex experimental designs.
*Broad impact in scientific community externally through e.g. steering
committee, conference organizing committee or editorial board memberships.
*Track record of publications in neurocognition and/or functional
neuroimaging and invited external presentations of research activities.
*International research reputation via productive research collaborations.

Desirable Attributes:
*Experience in the application of neurocognition and/or functional
neuroimaging to drug disciovery and development.
*Proven track record of l

Re: [Freesurfer] Tracula: missing or incomplete tracts

[Watson, Christopher]

What about:
freeview -v FA.nii.gz -v V1.nii.gz:vector=yes


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu]
Sent: Tuesday, March 17, 2015 11:57 AM
To: Freesurfer support list; Ruopeng Wang
Subject: Re: [Freesurfer] Tracula: missing or incomplete tracts

Hi Amelia - Sorry, not that I know of. Perhaps this can be a feature
request for Ruopeng to add to freeview :)

BTW, freeview in 5.3 had a bug with the vector display for some input
image orientations, but this has been fixed in the dev version (that you
can download on the web site).

a.y

  On Thu, 12 Mar 2015, Versace, Amelia wrote:

> Dear Anastasia,
> I was wondering if there is a way to automatically (in command line) derive 
> the FA/V1 vector image.
> fslview FA.nii.gz V1.nii.gz   allows to load the FA and V1 image, but then 
> manual section of the (lines) is needed.
> freeview -dti V1 FA   does it too (with different xyz convention), 
> but the 'display as vectors' needs to be manually checked.
> Is there any way to produce this image using command line only? Thanks a 
> lot!! Amelia
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
> Sent: Friday, March 06, 2015 6:56 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tracula: missing or incomplete tracts
>
>
> Hi Eileen - It looks like there was a A-P flip introduced to your gradient 
> vectors. (See screenshot of the tensor eigenvectors. Because they look right 
> in the coronal view but wrong in the sagittal and axial views, that's why I'm 
> assuming the flip is in the A-P direction.) To fix this you need to multiply 
> the y coordinate of your gradient vectors with -1 and rerun.
>
> If there are still any cases of missing tracts, please look at the bottom of 
> your dmrirc file for instructions on how to use the reinit parameter (or 
> search for previous emails on that parameter in the archives).
>
> Note that your DWI voxel size is anisotropic (finer resolution in x/y than 
> z), this may cause bias in tractography, so I'd recommend that you switch to 
> isotropic resolution for future acquisitions if you have control over it.
>
> Hope this helps,
> a.y
>
> On Fri, 27 Feb 2015, Eileen Moore wrote:
>
>> Hi Anastasia,
>>
>> Sorry for the delay -- I missed your response.  I did look at the
>> anatomical segmentations and thought they looked OK. I've uploaded the
>> tracula and corresponding freesurfer data for two subjects: one with 
>> complete tracts and one with missing/incomplete tracts. I also uploaded my 
>> dmrirc file. Thanks for taking a look for me.
>>
>> Eileen.
>>
>>
>>
>> Hi Eileen - Have you checked the anatomical segmentations of the
>> subjects? The mask that's used by default is the aparc+aseg_mask,
>> which comes from registering the cortical parcellationg and subcortical 
>> segmentation from T1 to diffusion space, and then dilating it by a couple of 
>> voxels.
>>
>> If you upload an example data set for me here, I can take a look:
>> 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_filedrop2_&d=BQIDaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=bw42CATdUgaQuKlfBniyB_kCJBdQgH3uC9uSwd5UzJ12A5jbDc-vHb9P3-hkq5C4&m=T2p7z8F4umjzf0YkkzlBSH_xnwrFLJ1rKFdoTAMUxbM&s=TVmCtWOX7TmzlQhiVJibKKVtj6CQczyAkyupGnmGZa0&e=
>> Please include all tracula-related directories of the subject (dmri, dlabel, 
>> etc).
>>
>> Thanks!
>> a.y
>>
>> On Thu, 18 Dec 2014, Eileen Moore wrote:
>>
>> Hi - I'm having difficulty with missing or incomplete tracts most of
>> my subjects. I'm hoping for suggestions on where I can look for data
>> problems.  The majority of my subjects have at least one
>> missing/incomplete tract, but the specific problematic tract varies
>> across subjects (e.g., one subject has a missing L.Uncinate; another
>> subject has a missing Forceps Major; another is missing the ILF
>> bilaterally, etc.).  For my problematic tracts, the path.pd.nii.gz is
>> a single line/curve rather than the diffuse volumetric distribution.
>> I'm not sure how to correct this.
>>
>> I have checked my eigenvectors -- the lines appear to be pointing in
>> the correct directions in my dtifit_V1 -- so I believe my gradient
>> table is correct
>>
>> I've checked my images for motion via visual inspection and by
>> excluding any subjects with dwi_motion outliers in AvgTranslation,
>> AvgRotation, PercentBadSlices, and AvgDropoutScore.
>>
>> I inspected the nodif_brain_mask.nii.gz  to look for chunks of missing
>> brain and did not identify any problems here.
>>
>> I've tried increasing the number of control points for each tract.
>>
>> I'd very much appreciate any suggestions on how to troubleshoot next.
>>
>> Thank you,
>> Eileen.
>>
>> ___
>> Freesurfer mail

[Freesurfer] missing files in fsaverage folder

[Milde, Christopher]

Dear Freesurfer Experts,

is there an easy way to update only folders within the Freesurfer folder? 
Accidentally, I deleted the fsaverage folder from the Freesurfer version. I 
copied the fsaverage folder from another Freesurfer installation. But seemingly 
some essential files (e.g. perirhinal label) are missing because of different 
FS versions.
Due to some missing files in fsaverage some commands do not run.

Furthermore, I cannot find some tools like stxgrinder-sess or func2roi-sess 
within the FSFAST package. So, is there an easy way to make an update?

Info: I’m using Freesurfer v5.3.0 for Linux-centos4

I’m thankful for any advice,

Cheers,

Chris


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Re: [Freesurfer] Freesurfer and Tracula installation.

[Watson, Christopher]

Have you tried these steps: http://wiki.centos.org/TipsAndTricks/NTFS

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fatma Zribi 
[zribi.fa...@gmail.com]
Sent: Thursday, April 23, 2015 9:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer and Tracula installation.

Hi everybody,

I installed CentOS 6.6 in a machine without using internet connexion. 
Everything is fine. I would like now to install Freesurfer and Tracula mounting 
a NTFS partition from an external hard disk. also I note that I can not copy 
Freesurfer in a FAT32 partition.

Actually I'm not sure that CentOs recognizes NTFS or FAT32 formats.

Please is there an expert who knows how to mount a NTFS disk using CentOS?

Thanks a lot for your help and your time.

Best regards,
Fatma

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[Freesurfer] computing cluster overlap

[Milde, Christopher]

Dear Freesurfer-Experts,

I'm looking for an elegant way of computing degree of overlap between activated 
clusters within-subject and between sessions (transversal) on the smoothwm.

I thought about running a conjunction analysis between the sessions to detect 
the extents of common activations, but maybe there are much better ways?

I'm thankful for any advice,

Best wishes,

Christopher


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[Freesurfer] Vertex Index to Vertex RAS withouth using surface visualizer (tksurfer or tkmedit)

[Milde, Christopher]

Dear FS experts

I extracted the vertex indices of several subjects. But unfortunately I did not 
extract the corresponding Vertex RAS values. Is there a command to translate 
the Vertex Index into a Vertex RAS so that I do not have to scroll through all 
the subjects again?

I would like to script the translation from Vertex Index to Vertex RAS

Best wishes,

Christopher
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[Freesurfer] mri_vol2surf nii.gz to .mgh conversion

[Milde, Christopher]

Dear Freesurfers,

I have problems converting .nii.gz files into .mgh files needed e.g. for 
performing ROI analysis.

I used mri_vol2surf and mri_vol2vol to produce .mgh files either to visualize 
contrast estimates and significance maps on volumes or surfaces

I think the problem is due to voxel resolution mismatches between source and 
registration files but I don't know how to solve this problem.

I worked with different registration files: the register.dof6.dat (originally 
outpu from the preproc-sess) as well as register.dat and register.lta by 
running bbregister for the template.nii.gz


---
here is an example command:

# resample to surface

mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg 
$sub/bold/register.lta --projfrac 0.5 \
 --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh


mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg 
$sub/bold/register.lta --projfrac 0.5 \
>  --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh
srcvol = PM_04001/bold/EX.sm5.lh/EX/sig.nii.gz
srcreg = PM_04001/bold/register.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
regio_read_register: loading lta
reading extra input line subject PM_04001
reading extra input line fscale 0.15
WARNING: the voxel resolution in the source volume (1,1,1) differs
 from that listed in the registration file (2.29167,2.29167,2.99)
Reading surface /home/christopher/subjects/PM_04001/surf/lh.white
Done reading source surface
Reading thickness /home/christopher/subjects/PM_04001/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 5
Writing to PM_04001/bold/lh.sig.mgh
Dim: 126553 1 1



Thanks,

Christopher
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Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion

[Milde, Christopher]

Dear Doug,

thanks for the  immediate response. Actually I checked  the registration with 
freeview/tkregister2 and print out the quality values which are perfectly fine 

I did the following fMRI-analysis steps

FSFAST
1. Preproc-sess (for smoothwm as well as fsaverage space)  --> 
register.dof6.dat in bold/001 and bold/002 folders
2. Selxavg-sess on created design matrices and contrasts (one of the 1st-level 
stat files is called EX.sm5.lh)

3. And  interrogated the results with mris_surfcluster (EX.sm5.lh/EX/ includes 
the sig.nii ces.nii as well as txt.files with the mris_surfcluster output)


The main problem is the creation of .mgh files as inputs used for ROI-analysis 
in the mri_segstats cmd. So the conversion of the sig.nii ces.nii into sig.mgh 
and ces.mgh (using mri_vol2vol)
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview

How to transfer the surface nii.gz files into .mgh files used in volume space?

Thanks,

Christopher



-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve
Gesendet: Donnerstag, 2. Juli 2015 14:49
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion

How did you create the EX.sm5.lh analysis? It is probably the case that it is 
already on the surface in which case you don't need to run vol2surf.
doug

On 07/02/2015 04:54 AM, Milde, Christopher wrote:
> Dear Freesurfers,
>
> I have problems converting .nii.gz files into .mgh files needed e.g. 
> for performing ROI analysis.
>
> I used mri_vol2surf and mri_vol2vol to produce .mgh files either to 
> visualize contrast estimates and significance maps on volumes or 
> surfaces
>
> I think the problem is due to voxel resolution mismatches between 
> source and registration files but I don't know how to solve this problem.
>
> I worked with different registration files: the register.dof6.dat 
> (originally outpu from the preproc-sess) as well as register.dat and 
> register.lta by running bbregister for the template.nii.gz
>
>
> --
> -
> here is an example command:
>
> # resample to surface
>
> mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg 
> $sub/bold/register.lta --projfrac 0.5 \  --interp nearest --hemi lh 
> --o $sub/bold/lh.sig.mgh
>
>
> mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg 
> $sub/bold/register.lta --projfrac 0.5 \
> >  --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh
> srcvol = PM_04001/bold/EX.sm5.lh/EX/sig.nii.gz
> srcreg = PM_04001/bold/register.lta
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> ProjFrac = 0.5
> thickness = thickness
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> regio_read_register: loading lta
> reading extra input line subject PM_04001 reading extra input line 
> fscale 0.15
> WARNING: the voxel resolution in the source volume (1,1,1) differs
>  from that listed in the registration file 
> (2.29167,2.29167,2.99) Reading surface 
> /home/christopher/subjects/PM_04001/surf/lh.white
> Done reading source surface
> Reading thickness 
> /home/christopher/subjects/PM_04001/surf/lh.thickness
> Done
> Mapping Source Volume onto Source Subject Surface
>  1 0.5 0.5 0.5
> using old
> Done mapping volume to surface
> Number of source voxels hit = 5
> Writing to PM_04001/bold/lh.sig.mgh
> Dim: 126553 1 1
>
> --
> --
>
> Thanks,
>
> Christopher
>
>
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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] mri_vol2surf nii.gz to .mgh conversion

[Milde, Christopher]

Basically, I try to create the .mgh files from sig.nii.gz and ces.nii.gz files 
needed for mri_segstats in ROI-analysis.

I run already preprocessing and selxavg3-sess stats to produce the different 
stats files (sii/ces.nii.gz)

The .mgh files show the correct anatomy-space dimension (mri_info: 1x1x1 mm; 
256^3, beforehand surface dimension 141526 x 1 x 1) but seem to be corrupted. I 
tried to visualize the whole hemisphere sig.nii.gz converted into sig.mgh but 
now activations show up despite of highly significant activations visible in 
the sig.nii.gz


To create .mgh files and run the ROI-analysis, I used the following commands:

### resample ces.nii volume to anatomical space
#1 resample ces.nii.gz to anatomy
mri_vol2vol --mov $sub/bold/EX.sm5.lh/EX/ces.nii.gz --reg 
$sub/bold/001/register.dof6.dat --fstarg --interp nearest -- o 
$sub/bold/EX.sm5.lh/EX/ces.lh.mgh

#2 resample sig.nii.gz to anatomy
mri_vol2vol --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg 
$sub/bold/001/register.dof6.dat  --fstarg --interp nearest  --o 
$sub/bold/EX.sm5.lh/EX/sig.lh.mgh

#3 run ROI with an unsigned functional constraint
mri-segstats --seg $SUBJECTS_DIR/$sub/mri/aparc+aseg.mgz --ctab 
$FREESURFER_HOME/FreeSurferColorLUT.txt --id 410 -id 407 --i 
$sub/bold/EX.sm5.lh/EX/ces.lh.mgh --maskthresh 2 --masksign abs

The ROI analysis always ends up with zero hrf-amplitudes.

I appreciate your support,

Christopher







-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve
Gesendet: Donnerstag, 2. Juli 2015 17:18
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion

Sorry, can you backup and tell me what you are trying to accomplish?
doug

On 07/02/2015 10:05 AM, Milde, Christopher wrote:
> Dear Doug,
>
> thanks for the  immediate response. Actually I checked  the 
> registration with freeview/tkregister2 and print out the quality 
> values which are perfectly fine
>
> I did the following fMRI-analysis steps
>
> FSFAST
> 1. Preproc-sess (for smoothwm as well as fsaverage space)  --> 
> register.dof6.dat in bold/001 and bold/002 folders 2. Selxavg-sess on 
> created design matrices and contrasts (one of the 1st-level stat files 
> is called EX.sm5.lh)
>
> 3. And  interrogated the results with mris_surfcluster (EX.sm5.lh/EX/ 
> includes the sig.nii ces.nii as well as txt.files with the 
> mris_surfcluster output)
>
>
> The main problem is the creation of .mgh files as inputs used for 
> ROI-analysis in the mri_segstats cmd. So the conversion of the sig.nii 
> ces.nii into sig.mgh and ces.mgh (using mri_vol2vol) 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriInd
> ividual_freeview
>
> How to transfer the surface nii.gz files into .mgh files used in volume space?
>
> Thanks,
>
> Christopher
>
>
>
> -Ursprüngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas 
> N Greve
> Gesendet: Donnerstag, 2. Juli 2015 14:49
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] mri_vol2surf nii.gz to .mgh conversion
>
> How did you create the EX.sm5.lh analysis? It is probably the case that it is 
> already on the surface in which case you don't need to run vol2surf.
> doug
>
> On 07/02/2015 04:54 AM, Milde, Christopher wrote:
>> Dear Freesurfers,
>>
>> I have problems converting .nii.gz files into .mgh files needed e.g.
>> for performing ROI analysis.
>>
>> I used mri_vol2surf and mri_vol2vol to produce .mgh files either to 
>> visualize contrast estimates and significance maps on volumes or 
>> surfaces
>>
>> I think the problem is due to voxel resolution mismatches between 
>> source and registration files but I don't know how to solve this problem.
>>
>> I worked with different registration files: the register.dof6.dat 
>> (originally outpu from the preproc-sess) as well as register.dat and 
>> register.lta by running bbregister for the template.nii.gz
>>
>>
>> -
>> -
>> -
>> here is an example command:
>>
>> # resample to surface
>>
>> mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg 
>> $sub/bold/register.lta --projfrac 0.5 \  --interp nearest --hemi lh 
>> --o $sub/bold/lh.sig.mgh
>>
>>
>> mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg 
>> $sub/bold/register.lta --projfrac 0.5 \
>>>   --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh
>> srcvol = PM_04001/bold/EX.sm5.lh/E

[Freesurfer] Supratentorial Volume Versus Sum of Parts

[Christopher Owen]

Hello,

We're trying to make multiple comparisons between FreeSurfer outputs on
severely atrophied brains and controls. Some of the comparisons are regions
of interest, like hippocampal volume or the volumes of regions in the
frontal lobe, but we've also been making comparisons with
supratentorialnotvent or supratentorial. Often, the comparisons are
consistant - if all the ROIs we're looking at are small then the whole
brain volume (supratentorialnotvent) will be significantly smaller as well.

However, there are some cases where the individual regions in the brain do
look smaller than the normal cohort, but the supratentorialnotvent looks
about average. This makes sense if only a few regions are atrophied, but
we've had a few cases where the whole brain is definitely atrophied and the
FS assessor definitely looks like it's that way while segmenting the brain,
but the supratentorialnotvent volume still looks average. Statistically,
the ROI's we're interested in for these cases are two standard deviations
below the mean for their age, while the stnv is still about average. When
looking through the regions FS has available for us that aren't specific
regions we're interested in, they still all look low.

How can we explain or understand these situations? It seems like the parts
should be close to or equivalent with the whole.

Thanks,
Washington University in Saint Louis Medical School
Radiology Research Assistant
Christopher Owen
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Re: [Freesurfer] assigning 74 Destrieux parcellations into lobes, networks, sensory-motor modalities

[Watson, Christopher]

I have tools in R that can do #1, and network/graph theory analysis on top of 
that. I plan to work on things like #2-3 but haven't yet (e.g. there is 
possibly less consensus if region X is limbic vs. para-limbic, as opposed to 
temporal vs. parietal).
I can send you something in a few days/a week.

Although, If you read the Destrieux 2010 paper, you will see the regions (in 
the text) separated by lobe, at the least.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Julie Evans 
[julie.evans.st...@gmail.com]
Sent: Thursday, July 23, 2015 11:39 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] assigning 74 Destrieux parcellations into lobes, 
networks, sensory-motor modalities

Dear FreeSurfer community,

I am a statistician who knows shamefully little about brain anatomy and I am 
writing with a request.

I don’t have easy access to Freesurfer and the original data but have the final 
text output i.e., the /stats folder, from a large cohort, which including 
*h.aparc.a2009s.stats.

I have been attempting to assign higher-order labels to the 74 Destrieux 
parcellations.

1) Categorizing uniquely into the 4 lobes: frontal, occipital, parietal, 
temporal;

2) Categorizing uniquely into “types of networks”: limbic, paralimbic, 
unimodal, heteromodal, subcortical, primary;

3) sensory-motor modality: somatosensory, visual, auditory, motor

As far as I understand these higher-order assignments of the 74 parcellations 
are not uncommon although not all cases are clear-cut so some knowledge of 
anatomy is needed (assuming that I am indeed looking at the correct level – 
gyri and sulci in the aparc.a2009s.stats file).

If so, would anyone mind sharing a text file with the correspondence between 
the 74 parcellations and lobes, network types, and/or modality?

I’d be very grateful for any guidance and help.

Thank you kindly,

J Evans
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Re: [Freesurfer] Supratentorial Volume Versus Sum of Parts

[Christopher Owen]

Hello Douglas,

Sorry about the delay. I was focusing on preparations for a conference.

In the most current case, no, the regions that are supposed to make up the
supratentorial volume do not add up to the volume displayed by freesurfer.
The sum of the parts for supratentoral notvent seems to be about half of
the supratentorianotvent reported by FS, and with ventricles the ratio gets
closer to 0.6 rather than half.

Thanks,
Christopher
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Re: [Freesurfer] Huge difference ini area for the same subject {Disarmed}

[Watson, Christopher]

Doesn't that just mean your colleagues are editing the brains differently?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of amirhossein manzouri 
[a.h.manzo...@gmail.com]
Sent: Tuesday, July 28, 2015 7:33 AM
To: Douglas N Greve
Cc: free surfer
Subject: Re: [Freesurfer] Huge difference ini area for the same subject

Hi Doug,
As you can see in the image I attached the average area is different for the 
same set by two different editor. I wonder if there is any reason for this?

Best regards,
Amirhossein Manzouri




On Mon, Jul 27, 2015 at 9:16 PM, amirhossein manzouri 
mailto:a.h.manzo...@gmail.com>> wrote:
Hi Doug,
Yes, one set of subjects by two editors and no difference in thickness but huge 
difference on the area between two sets. Actually I want to see f there is any 
difference between editors for the same set of subjects.

On Monday, July 27, 2015, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
sorry, I'm not sure I understand. Can you elaborate what you did? Same set of 
subjects edited independtly by two editors? Then you look for a difference 
within the subjects and you don't find it with editor 1 but you do find it with 
editor 2?

On 07/27/2015 07:24 AM, amirhossein manzouri wrote:
Hi,
Two people has done recon-all and edits for the same subjects in FS version 5.1 
. In the qdec comparing same group which has been edited by two persons , we 
found no significant change in Cth but there is a pattern of area difference on 
both hemispheres showing significant decrease in middle area and increase on 
frontal and occipital. Do you have any idea what can be the reason for this?The 
first recon-all and edits and qcache have been done in 2012 and the second in 
2015! Attached is the sample screenshot.

Best regards,
Amirhossein Manzouri



--
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
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ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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--
Best regards,
Amirhossein Manzouri





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Re: [Freesurfer] Using FSL commands through Matlab (Linux)

[Watson, Christopher]

Just use either "system" or the exclamation mark and type the FSL commands


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Albrecht, Daniel S. 
[dsalbre...@mgh.harvard.edu]
Sent: Tuesday, August 04, 2015 4:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Using FSL commands through Matlab (Linux)

Hello,

Sorry if this isn’t the right forum for the question, but not sure where to 
direct it.

I’m trying to incorporate some FSL commands into a Matlab script. I’m using a 
Linux machine and running Matlab 7.11.0 (2010b). I tried to access the FSL 
toolbox through Matlab using:

setenv(‘FSLDIR’,’/autofs/cluster/pubsw/2/pubsw/Linux-2-2.3-x86_64/packages/fsl.64bit/5.0.7’)
system(‘${FSLDIR}/etc/fslconf/fsl.sh’)

But received a “permissions denied” error. Is there an easier way to access FSL 
through Matlab?

Thanks,

Daniel S. Albrecht, PhD
Research Fellow in Radiology
Martinos Center for Biomedical Imaging

Massachusetts General Hospital
149 Thirteenth Street, Room 2301
Charlestown, MA 02129
Phone: (617) 643-6748
Fax: (617) 726-7422
dsalbre...@mgh.harvard.edu
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Re: [Freesurfer] Using FSL commands through Matlab (Linux)

[Watson, Christopher]

Ah, that's probably correct. I think it worked on my system because I source 
the FSL conf file in my .bashrc

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, August 04, 2015 4:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Using FSL commands through Matlab (Linux)

I don't think that will work because the shell where FSLDIR gets set is
not the same shell as that of the system command. Try putting those two
in the same string and then running system on that


On 08/04/2015 04:36 PM, Albrecht, Daniel S. wrote:
> Hello,
>
> Sorry if this isn’t the right forum for the question, but not sure
> where to direct it.
>
> I’m trying to incorporate some FSL commands into a Matlab script. I’m
> using a Linux machine and running Matlab 7.11.0 (2010b). I tried to
> access the FSL toolbox through Matlab using:
>
> setenv(‘FSLDIR’,’/autofs/cluster/pubsw/2/pubsw/Linux-2-2.3-x86_64/packages/fsl.64bit/5.0.7’)
> system(‘${FSLDIR}/etc/fslconf/fsl.sh’)
>
> But received a “permissions denied” error. Is there an easier way to
> access FSL through Matlab?
>
> Thanks,
>
> Daniel S. Albrecht, PhD
> Research Fellow in Radiology
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
> 149 Thirteenth Street, Room 2301
> Charlestown, MA 02129
> Phone: (617) 643-6748
> Fax: (617) 726-7422
> dsalbre...@mgh.harvard.edu
>   >
>
>
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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
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Re: [Freesurfer] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s

[Watson, Christopher]

Andre, I haven't done any statistical comparison, but for my data (pediatric) I 
found the DKT labels to be somewhat more accurate. The biggest differences were 
in superior frontal and rostral middle frontal. Other differences I've seen are 
anterior cingulate, cuneus, and fusiform. See Figure 4 in Klein & Tourville 
(2012).

RE your command example: have you tried including the full path for the images?
 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Son, Andre 
[andre@med.nyu.edu]
Sent: Sunday, August 09, 2015 11:41 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s

Thank you Bruce.
You're alway so helpful, even on the weekend!

I'm also trying to convert mgz to nii and have been following various 
instructions online but can't seem to figure it out.

For ease, I  made a separate folder on the desktop with just mgz files in 
separate subject folders and ran the following commands verbatim:

mri_convert --in_type mgz --out_type nii --out_orientation RAS /mnt/ 
.../desktop/mgz/001/t1.mgz /mnt/ .../t1.nii.gz

I've also tried:
mri_convert /desktop/mgz/001/t1.mgz /desktop/mgz/001/t1.nii.gz

However, neither have worked, saying "mghRead(/desktop/mgz/001/t1.mgz, -1) 
could not open file"

Any suggestions?
Thank you.
AS
___
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Sunday, August 09, 2015 11:34 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] .aparc vs. aparc.DKTatlase40 vs. aparc.a2009s

Hi Andre

it's up to you. The aparc and .aparc.DKTatlas40 are probably pretty
similar, although we haven't looked at the .aparc.DKTatlas40 much. The
aparc.a2009s contains more, smaller parcels, and so is probably less
reliable but might correspond more closely to an anatomical hypothesis you
have.

cheers
Bruce

On Sun, 9 Aug 2015, Son, Andre wrote:

>
> Hello,
>
>
>
> What is the difference b/w the data generated in .aparc vs
> .aparc.DKTatlas40. vs. aparc.a2009s?
>
> Which data should I be using for studies on cortical thickness?
>
>
>
> Thank you,
>
> AS
>
>
>
>
>
>
> 
> This email message, including any attachments, is for the sole use of the
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> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email
> and delete the original message. Please note, the recipient should check
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>
>
>


This email message, including any attachments, is for the sole use of the 
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The informati

Re: [Freesurfer] creating a new subject directory using imported data from existing subject directory

[Watson, Christopher]

I think it's a bit unclear what you're asking for. Have you followed the 
tutorials on the wiki? Can you post your directory structure?

What I do on my system is keep studies separate from one another. Each study 
directory has its own FS directory, and I keep the raw images separate. So 
something like the following:

.
|-- Study A
|-- DTI
|-- MPRAGE
|-- raw
|-- subj01
|-- subj01_mprage.nii.gz
|-- subj01_DICOMS
|-- subj02
|-- Freesurfer
|-- subj01
|-- subj02
|-- FMRI

...and so on



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Emma Thompson 
[vonecono...@gmail.com]
Sent: Monday, August 10, 2015 2:16 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] creating a new subject directory using imported data 
from existing subject directory
Hi,
I'm re-posting my query in case it got buried on the listserve:

Dear Freesurfers,
I created a single subject directory and then imported sdata from two separate 
studies, in the end I realized I should have created two subject directories 
and would like to now rectify the situation. My question is, 1) how do I create 
a second subject directory in a different location? and 2) how do I transfer my 
existing subjects' data from my current subject directory to this new subject 
directory without having to redo any of my work (surface reconstruction). Is 
this even possible at this point? Or is it that I should only have one FS 
directory after all and perhaps I should just move the location of this 
directory so it is more accessible for both of my studies? If this is the case, 
could you advise me on how to go about doing this?

BTW I'm using bash shell.
I hope my questions are clear. Thanks!!!
On Sat, Aug 8, 2015 at 1:24 PM, Emma Thompson 
mailto:vonecono...@gmail.com>> wrote:
Dear Freesurfers,
I created a single subject directory and then imported sdata from two separate 
studies, in the end I realized I should have created two subject directories 
and would like to now rectify the situation. My question is, 1) how do I create 
a second subject directory in a different location? and 2) how do I transfer my 
existing subjects' data from my current subject directory to this new subject 
directory without having to redo any of my work (surface reconstruction). Is 
this even possible at this point? Or is it that I should only have one FS 
directory after all and perhaps I should just move the location of this 
directory so it is more accessible for both of my studies? If this is the case, 
could you advise me on how to go about doing this?

BTW I'm using bash shell.
I hope my questions are clear. Thanks!!!
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Re: [Freesurfer] Computing SA from an older FS version

[Watson, Christopher]

1. Yes, I would expect that

2. Because the pial surface is bigger. (Unless I'm misunderstanding the 
question?)



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Gerrits, Niels 

Sent: Thursday, August 27, 2015 10:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Computing SA from an older FS version


Dear Experts,

With your help, I recalculated the surface area, now using the pial surface 
instead of the wm/gm boundary. I am, however, somewhat surprised by the 
discrepancy between my previous and current results, because the cortical 
surface area that is calculated using the pial is surface is consistently (a 
lot) larger than the SA that was calculated using the WM/GM boundary (please 
see below for an example). While computing the new SA measure, FS also 
automatically calculated both volume and thickness. Since these two measures 
are exactly the same as previously when SA was calculated using the wm/gm 
boundary (as was to be expected), I assume that the calculation of SA using the 
pial surface was correctly executed.

Nonetheless, I am wondering: 1) is such a large difference to be expected, and 
2) what could be a physiological explanation for this discrepancy?

All suggestions are much appreciated!

Best wishes,
Niels Gerrits




LH_cuneus_area

LH_entorhinal_area

LH_fusiform_area

LH_inferiorparietal_area

PP_01

1305

349

2563

3699

PP_02

1351

368

2989

4803

PP_03

1324

490

3489

3963

PP_04

1714

518

4107

4473

PP_05

1573

566

3750

5697

PP_06

1419

387

3206

4543

PP_07

1249

364

2636

4518

PP_08

1386

362

3174

5105

PP_09

1322

562

3239

6264

PP_10

1696

517

3926

5989













LH_cuneus_area

LH_entorhinal_area

LH_fusiform_area

LH_inferiorparietal_area

PP_01

1617

575

3231

4446

PP_02

1555

661

3970

5983

PP_03

1769

886

5059

5143

PP_04

1964

809

5402

5662

PP_05

1788

946

4832

6907

PP_06

1752

667

3944

5449

PP_07

1595

674

3631

5783

PP_08

1779

634

4074

6364

PP_09

1648

912

4353

7395

PP_10

1915

816

4758

7358






-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: maandag 13 juli 2015 14:46
To: Freesurfer support list
Subject: Re: [Freesurfer] Computing SA from an older FS version



Hi Niels



the matlab commands should be:



>> [v, M,mr] = load_mgh('wm.mgz') ;

>> save_mgh(v, 'wm.mgz', M,mr);



cheers

Bruce

On Mon, 13 Jul 2015, Gerrits, Niels

wrote:



>

> Dear Bruce,

>

>

>

> Thanks for the quick reply! I think it might be possible that we used an

> unrelased or developmental version of FreeSurfer, because the building-stamp

> said: freesurfer-Linux-centos5_86_64_dev-20110315. I’m not sure how this

> version ended up onto the server I was working on. Do you think this is a

> problem?

>

>

>

> With respect to the error: you were right, it was longer. I copied the

> command line below:

>

>

>

> $ mris_anatomical_stats -mgz -cortex label/lh.cortex.label -f

> stats/lh.aparc.pial.stats -b -a label/lh.aparc.annot -c

> label/aparc.annot.ctab 0007 lh pial

> INFO: assuming MGZ format for volumes.

> INFO: using label/lh.cortex.label as mask to calc cortex NumVert, SurfArea

> and MeanThickness. computing statistics for each annotation in

> label/lh.aparc.annot. reading

> volume/data2/projects/ysbrand-vumc/pddatabase-freesurfer/niels_test//0007/mri/wm.

> mgz... znzTAGskip: tag=825050957, failed to calloc 1969843200 bytes!

>

>

>

> I then loaded wm.mgh into matlab and then saved it as you suggested and ran

> the command again to calculate SA of the pial surface, but it produces the

> exact same error…

>

>

>

> >> load.mgh wm.mgz;

>

> >> save.mgh wm.mgz;

>

>

>

> Am I doing anything wrong?

>

>

>

> Thanks again!

>

>

>

> Cheers,

>

> Niels

>

>

>

> -Original Message-

> From: freesurfer-boun...@nmr.mgh.harvard.edu

> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl

> Sent: zondag 12 juli 2015 16:44

> To: Freesurfer support list

> Subject: Re: [Freesurfer] Computing SA from an older FS version

>

>

>

> Hi Niels

>

>

>

> is that the entire error? Does it not say what volume produces the error?

>

> That was a bug we had briefly some time ago, but I didn't think it made it

>

> into anything we released.  If you can track down which volume is causing

>

> this problem you can just load it into matlab with load_mgh.m then save it

>

> with save_mgh.m and the error will go away (since the matlab code doesn't

>

> try to read or write the tagged information). Make sure to save all the

>

> volumes that you do this to somewhere before overwriting them.

>

>

>

> cheers

>

> Bruce

>

>

>

> On

>

> Sun, 12 Jul 2015, Gerrits, Niels wrote:

>

>

>

> > Dear FreeSurfer-experts,

>

> >

>

> > Unfortunately, nobody replied to my question so this is a repost (see the

>

> > orig

Re: [Freesurfer] Comparing lists of activated regions between task>ctrl contrasts

[Watson, Christopher]

>From your original mail: I agree with Dr. Kanwisher. When you ask if it is 
>appropriate to "(visually) compare" list of regions, I would answer that it is 
>absolutely not. A direct comparison is necessary. See e.g. Nieuwenhuis et al., 
>2011, Nature Neuroscience.


For your second, I would say that it is not correct. Again, you should directly 
compare them. Otherwise, what are you basing the conclusion on? What effect 
size difference would you use as a cut-off between a "real" and "not real" 
difference? I think reading the above-mentioned paper will help with this 
question as well.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Francesco Puccettone 

Sent: Thursday, August 27, 2015 1:20 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Comparing lists of activated regions between 
task>ctrl contrasts

Sorry, forgot to add one additional (related) question:

is it ever correct to say "for region Y, the activations found for taskA were 
smaller than for taskB" just based on the two contrasts taskA>baseline and 
taskB>baseline? Or is it necessary that taskA and taskB be contrasted directly 
to be able to draw any conclusions (if any are sensible) about what 
smaller/larger activations of a certain region might mean?

Thanks!

On 27 August 2015 at 19:13, Francesco Puccettone 
mailto:francesco.puccett...@gmail.com>> wrote:
Hello all,

I have seen several (older) papers that draw conclusions about the implication 
of a brain region in a given task by using the following logic: region X was 
activated in the contrast taskA>baseline, but not in the contrast 
taskB>baseline; therefore, region X is implicated in/essential for the 
cognitive processes underlying taskA, but not also for that underlying taskB; 
in other words, it dissociates between the two tasks.

I believe Nancy Kanwisher addresses this point in a video lecture where she was 
pointing out that the above logic is flawed, and that said conclusion can only 
be drawn if the two tasks are contrasted directly (A>B). Have I understood this 
correctly, and does it ever make any sense to draw inferrences about implicated 
brain regions based on (visually) comparing the list of regions produced by 
contrasts comparing each task to the same baseline (in other words, by noticing 
which brain regions appear in one list, but not in the other)? Or, on the 
contrary, do all statistics and corrections need to be done voxel-wise, which 
is something that is only done when contrasting the two tasks directly?

Many thanks for any opinions.

--Francesco

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Re: [Freesurfer] Questions about the files of lh.aparc.stats and lh.aparc.DKTatlas40.stats

[Watson, Christopher]

Yes, they are 2 separate atlases. The references are on the FS wiki.

The "ctab" files are colortable files, so I believe the "25 100 40 0" are the 
RGB + transparency/opacity


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of chenhf_uestc 
[chenhf_ue...@163.com]
Sent: Tuesday, September 29, 2015 10:59
To: freesurfer
Subject: [Freesurfer] Questions about the files of lh.aparc.stats and   
lh.aparc.DKTatlas40.stats

Dear Freesurfer experts,

In the stats folder of subject in the SUBJECTS_DIR, I found the files of 
lh.aparc.DKTatlas40.stats and lh.aparc.stats. Are there statistical results 
belong to two different atlas? Because the values and brain regions are 
different in these two files.

In these two files, I found the command "mris_anatomical_stats -mgz -cortex 
../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a 
../label/lh.aparc.annot -c ../label/aparc.annot.ctab NC058 lh white" and 
"mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c 
../label/aparc.annot.DKTatlas40.ctab NC058 lh white".

So, the atlases are the lh.aparc.annot and lh.aparc.DKTatlas40.stats, 
respectively. Right?
However, when I open these two atlas (attached aparc.annot.ctab and 
aparc.annot.DKTatlas40.ctab), I found the contents are same. In addition, I 
would really want to know that the value in the aparc.annot.ctab. For ex.   1  
bankssts 25 100  400; what does the values mean? 25 100 40 0

Best,
Feng

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[Freesurfer] epidewarp.fsl radian phase range error

[Milde, Christopher]

Dear FS experts,

I also encountered this problem when trying to apply epidewarp.fsl:

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

I read that there is an updated version of epidewarp.fsl which might solve this 
problem. Can I rescale the phase images?

I appreciated any support.

Best,

Christopher
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[Freesurfer] Segmentation Fault with mri_convert

[Christopher Finuf]

I'm trying to convert the dicom to the original 001.mgz file using the
following command on a Mac OSX Yosemite version 10.10.5. My
SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/
. My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/
. The following is the output and error that I get. I'm running the latest
version v 5.3.0 of freesurfer. Any suggestions on what the problem is? What
is strange that it works with half my data set but the other has this
error. I've run this command in the exact way many times before and have
never had this issue.





bash-3.2$ recon-all -i
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
-subjid Bigler_Repeatability_0005Ad_M1


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

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

INFO: SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects

Actual FREESURFER_HOME /Applications/freesurfer

Darwin NS112201PSY2.byu.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep  1
21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1

\n mri_convert
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz
\n

mri_convert
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz

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

reading from
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm...

Getting Series No

INFO: Found 178 files in
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1

INFO: Scanning for Series Number 2

Scanning Directory

INFO: found 176 files in series

INFO: loading series header info.


RunNo = 1

INFO: sorting.

INFO: (224 256 176), nframes = 1, ismosaic=0

PE Dir ROW ROW

AutoAlign matrix detected

AutoAlign Matrix -

 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;


FileName
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm

Identification

NumarisVersyngo MR B17

ScannerModel  TrioTim

PatientName   Bigler_Repeatability_AD_M

Date and time

StudyDate 20160512

StudyTime 075942.531000

SeriesTime081401.859000

AcqTime   080647.62

Acquisition parameters

PulseSeq  *tfl3d1_ns

Protocol  t1_mpr_sag_iso_ave2_ipat2_(mprage)

PhEncDir  ROW

EchoNo1

FlipAngle 9

EchoTime  2.26

InversionTime 900

RepetitionTime1900

PhEncFOV  218.75

ReadoutFOV250

Image information

RunNo 1

SeriesNo  2

ImageNo   1

NImageRows256

NImageCols224

NFrames   1

SliceArraylSize   1

IsMosaic  0

ImgPos 75.8389 136.8499 125.

VolRes  0.9766   0.9766   1.

VolDim224  256  176

Vc  0.0767  -0.9971   0.

Vr -0.   0.  -1.

Vs -0.9971  -0.0767   0.

VolCenter  -3.5106  21.0460   0.

TransferSyntaxUID 1.2.840.10008.1.2.1

UseSliceScaleFactor 0 (slice 0: 1)

Segmentation fault

Darwin NS112201PSY2.byu.edu 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep  1
21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64


recon-all -s Bigler_Repeatability_0005Ad_M1 exited with ERRORS at Wed Jun
8 13:39:08 MDT 2016


For more details, see the log file
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/scripts/recon-all.log

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Segmentation fault in mri_convert

[Christopher Finuf]

I'm trying to convert the dicom to the original 001.mgz file using the
following command on a Mac OSX Yosemite version 10.10.5. My
SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/
. My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/
. The following is the output and error that I get. I'm running the latest
version v 5.3.0 of freesurfer. Any suggestions on what the problem is? What
is strange that it works with half my data set but the other has this
error. I've run this command in the exact way many times before and have
never had this issue.





bash-3.2$ recon-all -i
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
-subjid Bigler_Repeatability_0005Ad_M1


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

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

INFO: SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects

Actual FREESURFER_HOME /Applications/freesurfer

Darwin NS112201PSY2.byu.edu  14.5.0 Darwin
Kernel Version 14.5.0: Tue Sep  1 21:23:09 PDT 2015;
root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64

/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1

\n mri_convert
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz
\n

mri_convert
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz

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

reading from
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm...

Getting Series No

INFO: Found 178 files in
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1

INFO: Scanning for Series Number 2

Scanning Directory

INFO: found 176 files in series

INFO: loading series header info.


RunNo = 1

INFO: sorting.

INFO: (224 256 176), nframes = 1, ismosaic=0

PE Dir ROW ROW

AutoAlign matrix detected

AutoAlign Matrix -

 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;


FileName
/Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm

Identification

NumarisVersyngo MR B17

ScannerModel  TrioTim

PatientName   Bigler_Repeatability_AD_M

Date and time

StudyDate 20160512

StudyTime 075942.531000

SeriesTime081401.859000

AcqTime   080647.62

Acquisition parameters

PulseSeq  *tfl3d1_ns

Protocol  t1_mpr_sag_iso_ave2_ipat2_(mprage)

PhEncDir  ROW

EchoNo1

FlipAngle 9

EchoTime  2.26

InversionTime 900

RepetitionTime1900

PhEncFOV  218.75

ReadoutFOV250

Image information

RunNo 1

SeriesNo  2

ImageNo   1

NImageRows256

NImageCols224

NFrames   1

SliceArraylSize   1

IsMosaic  0

ImgPos 75.8389 136.8499 125.

VolRes  0.9766   0.9766   1.

VolDim224  256  176

Vc  0.0767  -0.9971   0.

Vr -0.   0.  -1.

Vs -0.9971  -0.0767   0.

VolCenter  -3.5106  21.0460   0.

TransferSyntaxUID 1.2.840.10008.1.2.1

UseSliceScaleFactor 0 (slice 0: 1)

Segmentation fault

Darwin NS112201PSY2.byu.edu  14.5.0 Darwin
Kernel Version 14.5.0: Tue Sep  1 21:23:09 PDT 2015;
root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64


recon-all -s Bigler_Repeatability_0005Ad_M1 exited with ERRORS at Wed Jun
8 13:39:08 MDT 2016


For more details, see the log file
/Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/scripts/recon-all.log

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Research Position

[Mcnorgan, Christopher]

Hi Freesurfers,

I wanted to bring to the attention of recent graduates a research assistant 
position in my lab. Briefly, the position entails the application and transfer 
of your proficiency with FreeSurfer in the acquisition and analysis of fMRI 
data collected from healthy adults.

More details can be found at the URL below:
https://www.ubjobs.buffalo.edu/applicants/jsp/shared/position/JobDetails_css.jsp?postingId=217420

Thanks,
Chris

/**
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo,
* The State University of New York
* http://ccnlab.buffalo.edu/
* Office: 716.645.0236
* Lab: 716.645.0222
**/

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[Freesurfer] bbregister surfaces

[Christopher Markiewicz]

Hi all,

According to
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25476.html,
bbregister uses the white matter surface and cortical thickness measures to
perform its registrations, though there was some possibility of using the
pial surface in further releases. I just want to verify that this is still
the case, and the pial surface is not currently being used.

Thanks,
Chris Markiewicz
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Re: [Freesurfer] aparc.DKTatlas40

[Watson, Christopher]

You can read about it here: 
http://www.frontiersin.org/Brain_Imaging_Methods/10.3389/fnins.2012.00171/abstract

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of krista kelly 
[krista.kell...@gmail.com]
Sent: Saturday, November 16, 2013 8:01 PM
To: freesurfer
Subject: [Freesurfer] aparc.DKTatlas40

I'm using freesurfer v. 5.3 and I see a new annotation, aparc.DKTatlas40.annot 
in the labels folder. Can anyone tell me what the difference between this and 
the apart.annot is? Does it just have 40 labels versus the 36 found in the 
older version?

Thanks!


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Re: [Freesurfer] Dura/pial reconstruction: FLAIR vs. multiecho

[Watson, Christopher]

I only have anecdotal evidence based on 4 subjects, but I found that using the 
FLAIR results in much better surface reconstruction than the multiecho. In my 
experience (with kids age 12-16), the pial surface was underestimated when I 
used the multiecho.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Saturday, December 14, 2013 1:10 PM
To: roberto.vivi...@uni-ulm.de
Cc: Andre van der Kouwe; Freesurfer@nmr.mgh.harvard.edu; eberhard.pra...@dzne.de
Subject: Re: [Freesurfer] Dura/pial reconstruction: FLAIR vs. multiecho

Hi Roberto

I think a T2-space FLAIR is your best bet. We have very little experience
with other FLAIR and/or/ T2s, but those seem to work well. They are *much*
higher SNR than the T2* maps that one can get from an memprage where the
last echo is only around 7ms.

cheers
Bruce
  On Sat, 14 Dec 2013,
roberto.vivi...@uni-ulm.de wrote:

> Dear all,
>
> starting from the version of March of this year, FreeSurfer supports
> the use of co-acquired FLAIR images to separate the dura from the gray
> matter. Some years ago, the idea about solving the same problem was to
> use multi-echo MPRAGE images. I am starting a new project, in which I
> am planning to acquire structural images, and I would like to know
> something more about these two ways of addressing the dura problem.
>
> -- is there any experience on the superiority of the FLAIR approach,
> or is there any published evaluation of it / comparison with the
> MEMPRAGE approach (such as the van der Kouwer et al. 2008 paper on the
> MEMPRAGE)  (I looked for it in scholar.google but could not find it)
>
> -- are you planning to support the multi echo approach in the future,
> or is it going to be discontinued
>
> I will also be very interested to hear from anyone who has had any
> experience with the FLAIR approach, or both.
>
> Best wishes,
> Roberto
>
> Roberto Viviani
> University of Ulm, Germany
>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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>
>
>
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[Freesurfer] combine FEAT data with inflated ANATOMY to measure distances

[Milde, Christopher]

Dear Surfers,

At moment I'm dealing with a huge dataset, preprocessed (with and without 
smoothing) and statistically analyzed in FSL FEAT.

I used the reg-feat2anat to project functional EPI on inflated MPRAGE 
(recon-all).

Because I'm interested in measuring Euclidian distances between peak voxels, I 
want to project FEAT EPI-data on cortical flat maps (mris_flatten) or spherical 
surfaces.

è Is it possible to project FEAT-data on flat_maps?

è Does mris_pmake* works equally fine on different projections of the EPI to 
ANATOMY (sphere, flat map) to measure peak/vertex distances?



*https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017866.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-April/017866.html>


I'm a quite Surfer-newby. So sorry for that maybe stupid question...

Thank you in advance,

Christopher


Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany

Phone:  +49-621-1703-6313
E-mail:  christopher.mi...@zi-mannheim.de
Homepage:http://www.zi-mannheim.de/
Office:  Forschungs- und Verwaltungsgebäude, Room 230

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Re: [Freesurfer] combine FEAT data with inflated ANATOMY to measure distances

[Milde, Christopher]

Dear Doug,

I'm very thankful for your helpful comments! I will check the feat2surf script 
and apply it to map FSL-data in individual and common space (preconditions: 
existing FEATdir with non-smoothed EPI's and applied reg-feat2anat). I will 
make use of the -projfrac 0.5 to sample in the middle of the cortical ribbon 
(to account for drain vessel effects).

According to the intended distance measures, relative measures between peak 
voxels are also fine. So, maybe mris_pmake is still a good option...

Greets, Chris


Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience 
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany 

Phone:  +49-621-1703-6313
E-mail:  christopher.mi...@zi-mannheim.de
Homepage:http://www.zi-mannheim.de/
Office:  Forschungs- und Verwaltungsgebäude, Room 230



-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve
Gesendet: Donnerstag, 20. März 2014 16:26
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] combine FEAT data with inflated ANATOMY to measure 
distances


1) Use the feat2surf script
2) I have not used mris_pmake myself. I'm guessing it will *work* on the sphere 
in that it will return a path, but the distances between vertices have no 
relationship to anatomy. It might fail on a flat map because it is a patch.

doug



On 03/20/2014 10:43 AM, Milde, Christopher wrote:
>
> Dear Surfers,
>
> At moment I'm dealing with a huge dataset, preprocessed (with and 
> without smoothing) and statistically analyzed in FSL FEAT.
>
> I used the reg-feat2anat to project functional EPI on inflated MPRAGE 
> (recon-all).
>
> Because *I'm interested in measuring Euclidian distances between peak 
> voxels*, I want to project *FEAT EPI-data on cortical flat maps
> (mris_flatten) or spherical surfaces*.
>
> èIs it possible to project FEAT-data on flat_maps?
>
> èDoes mris_pmake* works equally fine on different projections of the 
> EPI to ANATOMY (sphere, flat map) to measure peak/vertex distances?
>
> *https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017
> 866.html 
> <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-April/0178
> 66.html>
>
> I'm a quite Surfer-newby. So sorry for that maybe stupid question.
>
> Thank you in advance,
>
> Christopher
>
> *Christopher Milde, M.Sc. Biol.*
>
> Institute for Cognitive and Clinical Neuroscience
>
> Central Institute of Mental Health Square J 5
>
> 68159 Mannheim, Germany
>
> Phone: +49-621-1703-6313
>
> E-mail: christopher.mi...@zi-mannheim.de
>
> Homepage: http://www.zi-mannheim.de/ <http://www.zi-mannheim.de/>
>
> Office: Forschungs- und Verwaltungsgebäude, Room 230
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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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] glmfit with correlated covariates

[Watson, Christopher]

I don't want to speak for the Freesurfer team, but I am 99% certain that it is 
Direct/Standard as you list them. There isn't any stepwise variable selection 
going on.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of L. Schweren 
[l.j.s.schwe...@umcg.nl]
Sent: Tuesday, March 25, 2014 6:08 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] glmfit with correlated covariates

Dear FreeSurfer experts,

Thank you for your fast reply. We are extracting cortical thickness values for 
statistical sub-analyses in SPSS (due to corrections required with regard to 
family relatedness within the data); therefore we want to be a 100% certain 
that the statistical model we use in SPSS is identical to the model used by 
mri_glmfit. Can you confirm that, out of the multiple linear regression types 
listed below, mri_glmfit makes use of the Direct (or Standard) regression model?

Type

Characteristics

Direct (or Standard)

· All IVs are entered simultaneously

Hierarchical

· IVs are entered in steps, i.e., some before others
· Interpret: R2 change, F change

Forward

· The software enters IVs one by one until there are no more 
significant IVs to be entered

Backward

· The software removes IVs one to one until there are no more 
non-significant IVs to removed

Stepwise

· A combination of Forward and Backward MLR


Thank you again for your help,

Best wishes,
Lizanne






Date: Wed, 12 Mar 2014 11:04:00 -0400

From: Douglas Greve 

Subject: Re: [Freesurfer] glmfit with correlated covariates

To: freesurfer@nmr.mgh.harvard.edu

Message-ID: <53207760.8010...@nmr.mgh.harvard.edu>

Content-Type: text/plain; charset="iso-8859-1"





It is just a standard multiple regression analysis where all regressors

are fit simultaneously. One weight does not include that of another weight.

doug





On 3/12/14 5:16 AM, L. Schweren wrote:

>

> Dear FreeSurfer experts,

>

> I am attempting to disentangle the effects of different features of

> pharmacological treatment on cortical thickness.

>

> I am running glmfit from the commandline, with multiple covariates

> (a.o. Z_Age, Z_TreatmentDuration and Z_StartAge) in the fsgd-file.

> These covariates are correlated up to approximately  0.6 , which to my

> understanding is not ideal yet not inducing collinearity. Running

> glmfit, I do not get any errors such as ill-designed matrix or so.

>

> My question regards the way the different regression weights are

> calculated in each voxel. If I test the variance in CT of voxel A

> explained by for example TreatmentDuration, and part of the variance

> in voxel A is explained by both TreatmentDuration and StartAge, will

> the regression weigth of TreatmentDuration than include the part that

> is also explained by StartAge? Or are all other covariates first

> "regressed out" of the variance, such that the variable I test can

> only explain the variance that was not explained by any of the other

> covariates?

>

> Thank you very much, your help is very much appreciated!

>

> Best wishes,

>

> Lizanne

>

>

>

> ___

> Freesurfer mailing list

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[Freesurfer] native or fsaverage spherical space for distance measures?

[Milde, Christopher]

Dear Freesurfers,

according to my research and 'playing-around' with Freesurfer tools on 
measuring distances between vertices or peak voxels, I'm still unsure about the 
most adequate way of comparing distances between peak voxels corrected for 
folding patterns.

To my current knowledge, I figured out the following procedures:

Goal: comparing cortical distances between peak voxels between subjects of 
different clinical populations


1.)Manual procedure using Freeview spline tool: using orig.mgz + white and 
pial surfaces + thresh_zstat images (FSL)

è Using Measure tool (spline) to create a smoothed line within the cortical 
ribbon

è Output: absolute cortical distances in [mm]

è Problem: topologically remote but geometrically close by peak voxels (maybe 
avoidable by using the RAS to vertex transformation information of the inflated 
brain)



2.)Automated procedure: using mris_pmake  with start vertex stop vertex 
coordinates derived from the population averaged sphere coordinate systems 
(fsaverage sphere) (functional data mapped into common sphere by either 
feat2surf or mris_preproc)



è Output: only relative distance measures, but the comparability between peak 
voxel distances of different  subjects is ensured (due to distance measures 
within a common spherical coordinate system)*.

è Problem: no absolute measure of distances anymore (but this is actually no 
problem because I'm interested in relative differences in cortical 
reorganization)



- Do you have any suggestions which procedure is preferable??

- *Am I right about the comparability of distance measurements between 
subjects, when using mris_pmake within a common spherical coordinate space??



I appreciate any helpful comment



Sincerely yours,



Christopher

Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany

Phone:  +49-621-1703-6313
E-mail:  christopher.mi...@zi-mannheim.de
Homepage:http://www.zi-mannheim.de/
Office:  Forschungs- und Verwaltungsgebäude, Room 230

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[Freesurfer] interhemispheric registration in native space

[Milde, Christopher]

Dear Freesurfer experts,



is there a way to perform an interhemispheric registration with rh, lh surfaces 
in native space?

Preferentially, I would perform the registration with smoothwm surfaces.



I only found the xhemi command which refers to fsaverage as a target



Best wishes,



Christopher


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[Freesurfer] Graph theory analysis in R

[Watson, Christopher]

Dear Freesurfer users, (apologies for cross-post)

I am pleased to announce the release of an R package I created, called 
"brainGraph", for performing graph theory analyses of brain MRI data. You can 
use it for cortical thickness, volume, surface area, or LGI. It can also be 
used for tractography data (I have code that works with the outputs of FSL's 
"probtrackx2"), and it should work for resting-state fMRI as well. It is very 
heavily dependent on the fantastic R package "igraph" (see 
http://igraph.org/redirect.html). I created a GUI for quick and easy data 
exploration, but it isn't quite as polished as others out there (e.g., BrainNet 
Viewer).

For usage, please see the User Guide I put together (direct PDF link: 
https://www.dropbox.com/s/j831n3q9muyz1go/brainGraph_UserGuide.pdf?dl=0 ). You 
will find some code for getting your data into R, and I have documented many 
analysis steps and include multiple figures. I hope this is intuitive for both 
veteran and novice R users. Additionally, there are System Requirements, 
Installation instructions, and links for help learning R.

Some features that should be of interest include:
* bootstrapping & permutation testing
* random graph generation, small-worldness, and global/local/nodal efficiency
* rich-club calculations
* robustness ("targeted attack" or "random failure") & vulnerability: PDF of 
figure (PNG: https://www.dropbox.com/s/k14gdg1lomhh4l2/failPlot-1.pdf?dl=0)
* Plotting GUI - full GUI (PNG): 
https://www.dropbox.com/s/e0hdng7flrxsgd2/brainGraph_GUI.png?dl=0
* Plotting GUI - union of vertex neighborhoods (PNG): 
https://www.dropbox.com/s/aag5cn1p1z9xzxr/brainGraph_GUI_neighborhoods.png?dl=0
* Plotting GUI - community (module) plots (PNG): 
https://www.dropbox.com/s/8zzpd5j268qstmg/brainGraph_GUI_communities.png?dl=0

You can install it directly in R by typing: install.packages('brainGraph')
My Github page for the package (https://github.com/cwatson/brainGraph) contains 
the development version, and you can install that by typing: 
devtools::install_github('cwatson/brainGraph')
Please see the NEWS.md file 
(https://github.com/cwatson/brainGraph/blob/master/NEWS.md) for updates made 
since the CRAN submission.
To work properly on Windows, you may need to install the devel version.

This is still a work-in-progress, so I am very happy to receive bug reports, 
feature requests, general coding help questions, (constructive) criticism, etc.
Please join the Google Group that I set up for those purposes:  
https://groups.google.com/forum/?hl=en#!forum/brainGraph-help


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

[Mcnorgan, Christopher]

Hi,
I'm attempting an inaugural run through the FS pipeline on some event-related 
data collected over 6 runs. I'm not sure if this makes any difference, but the 
experiment is self-paced, and the events are of varying duration (it's a 
lexical decision task, and participants can take up to 4 seconds to respond but 
typically respond between 600 - 800ms, with an exponentially-decreasing 
jittered ITI between trials).

When I run selxavg3-sess on this single participant, the following error is 
generated:

/**
Saving X matrix to /home/kali/fMRI/LDT/1001_001/bold/LDT.sm6.lh/Xtmp.mat
Error using svd
Input to SVD must not contain NaN or Inf.

Error in cond (line 35)
s = svd(A);

Error in fast_selxavg3 (line 279)
  XCond = cond(XtX);
 
>> --
ERROR: fast_selxavg3() failed\n
***/

If I open up the generated .mat file, I see the several rows/columns of the XtX 
matrix are indeed populated with NaN. We tried running the mkanalysis-sess a 
couple different ways, getting the same error, though our different parameter 
selections for mkanalysis-sess lead to different XtX matrices, so I suspect 
that this might be the source of the problem. Unfortunately, I have no insight 
into what the root of the problem might be. The .par files used have the event 
durations set to the reaction times for each trial, and the -refeventdur value 
is set to the mean reaction time

Thanks for any help anyone might be able to give me
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Re: [Freesurfer] Unknown option DKTatlas40

[Watson, Christopher]

The option should be:
--annot aparc.DKTatlas40

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of marmaduke woodman 
[marmaduke.wood...@univ-amu.fr]
Sent: Wednesday, March 2, 2016 08:27
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Unknown option DKTatlas40

hi

I'm using the dev version of FreeSurfer on 64-bit Fedora 23.


Recon-all runs fine but at the end I see

$ recon-all -s tvb -aparc2aseg
...
  mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos --DKTatlas40

ERROR: Option --DKTatlas40 unknown


Running that command

$ mri_aparc2aseg --s tvb --volmask --aseg aseg.presurf.hypos

without the --DKTatlas40 appears to run correctly.


Is this just an issue with the dev version or have I done something silly?


thanks,
Marmaduke


ps bugr output

FREESURFER_HOME: /opt/freesurfer

Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160229

RedHat release: Fedora release 23 (Twenty Three)

Kernel info: Linux 4.3.3-300.fc23.x86_64 x86_64

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[Freesurfer] preproc-sess error opening tmp brain_mask

[Mcnorgan, Christopher]

I was hoping the developers might be able to help with a problem I'm having 
with a sub-step of preproc-sess.


I executed the following:



preproc-sess -s FS_T1_501 -surface self lhrh -fwhm 6 -per-run -fsd bold

In the relevant output, I see mktemplate-sess completed, followed by a call to 
mkbrainmask-sess, which eventually reported:

# -- Using FSL's BET to Extract Brain-- #
/home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold
bet.fsl /tmp/mkbrainmask_2623/in.nii /tmp/mkbrainmask_2623/brain -m -f 0.1
/usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: 
/bin/remove_ext: not found
/usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: 
/bin/remove_ext: not found
/usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: 
/bin/imtest: not found
/usr/local/freesurfer/bin/bet.fsl: 153: [: =: unexpected operator
/usr/local/freesurfer/bin/bet.fsl: 231: /usr/local/freesurfer/bin/bet.fsl: 
/bin/bet2: not found
mri_binarize --i /tmp/mkbrainmask_2623/brain_mask.nii --min .01 --o 
/tmp/mkbrainmask_2623/brain_mask.nii
niiRead(): error opening file /tmp/mkbrainmask_2623/brain_mask
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold
cmdline mri_binarize --i /tmp/mkbrainmask_3238/brain_mask.nii --min .01 --o 
/tmp/mkbrainmask_3238/brain_mask.nii
sysname  Linux
hostname wernickesarea
machine  x86_64
user chris

input  /tmp/mkbrainmask_3238/brain_mask.nii
frame  0
nErode3d   0
nErode2d   0
output /tmp/mkbrainmask_3238/brain_mask.nii
Binarizing based on threshold
min0.01
max+infinity
binval1
binvalnot 0

It's not obvious from the tail end of the output that this didn't work out, but 
this process finished in just a couple of seconds (making it unlikely that any 
smoothing or slice time correction was performed), and there was no 
brain_mask.nii file to be found either in /tmp/ or in the session folder. Those 
"not found" errors seem relevant, but I can't imagine what to do about them.
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Re: [Freesurfer] preproc-sess error opening tmp brain_mask

[Mcnorgan, Christopher]

du -h /tmp/ shows 256GB available, so that doesn’t seem to be it. Is the “not 
found” error telling me that a binary is not found, or that some expected 
output file is not found? I was looking for /bin/imtest and /bin/remove_ext, 
and those binaries indeed do not exist, but we’ve run Freesurfer on another 
dataset (but on another workstation, but neither were those two binaries to be 
found on that workstation).

Is your /tmp space full?

On 04/15/2016 12:54 PM, Mcnorgan, Christopher wrote:
>
> I was hoping the developers might be able to help with a problem I'm
> having with a sub-step of preproc-sess.

> I executed the following:
>
> preproc-sess -s FS_T1_501 -surface self lhrh -fwhm 6 -per-run -fsd bold
>
> In the relevant output, I see mktemplate-sess completed, followed by a
> call to mkbrainmask-sess, which eventually reported:
>
> # -- Using FSL's BET to Extract Brain-- #
> /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold
> bet.fsl /tmp/mkbrainmask_2623/in.nii /tmp/mkbrainmask_2623/brain -m -f 0.1
> /usr/local/freesurfer/bin/bet.fsl: 1:
> /usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found
> /usr/local/freesurfer/bin/bet.fsl: 1:
> /usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found
> /usr/local/freesurfer/bin/bet.fsl: 1:
> /usr/local/freesurfer/bin/bet.fsl: /bin/imtest: not found
> /usr/local/freesurfer/bin/bet.fsl: 153: [: =: unexpected operator
> /usr/local/freesurfer/bin/bet.fsl: 231:
> /usr/local/freesurfer/bin/bet.fsl: /bin/bet2: not found


/**
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo,
* The State University of New York
* http://ccnlab.buffalo.edu/
* Office: 716.645.0236
* Lab: 716.645.0222
**/

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[Freesurfer] ERROR: DOF=0 in call to mri_glmfit by preproc-sess

[Mcnorgan, Christopher]

Hi,

First, thanks to Doug Greve for helping me isolate my previous problem, which 
turns out to have resulted from a conflicting fsl installation. Now that that's 
resolved, I'm having a problem on a first-level analysis.


In preparation for calling selxavg3-sess, I am running preproc-sess on an 
individual and am running into an error where the reported DOF is 0. The 
peculiar thing is that these steps work fine with another data set -- from the 
same participant at an earlier time point doing the same task with the same 
parameters (though the procedure to convert the DICOM to nii data was not 
necessarily the same at both time points; unfortunately the original DICOM 
files are unavailable to me). I am able to take the time1 data to the 
completion of FS-FAST, but the time2 data halts at this error.

A potentially relevant difference between the two data sets is that, for the 
functional data that worked, I was able to carry out these steps on the 
original f.nii file, whereas problematic data was first converted to a .mgz 
file in Slicer to fix an "unsupported slice timing pattern 5" error (a search 
in the archives suggested that Slicer would solve this problem, which seems to 
be the case). I'm not clear where this dof value comes from and if anything 
about the .nii file header can be manipulated to fix the problem. The fact that 
the slice timing pattern was off in the problematic data might be symptomatic 
of a generally compromised .nii header (SPM doesn't seem to do anything with 
much of this header information, allowing some invalid header information to go 
undetected).


Thanks


Below is the tail end of the preproc-sess output where it reports the error:


$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold
cmdline mri_glmfit --table 
/home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/table.dat
 --glmdir 
/home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/glm
 --osgm --y-out 
/home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/y.out.nii
 --pca
sysname  Linux
hostname accumbens
machine  x86_64
user chris
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 1
y
/home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/table.dat
logyflag 0
usedti  0
glmdir 
/home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/glm
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory 
/home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/glm
Loading y from 
/home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/table.dat
Found 6 data colums
Found 1 data rows
Saving design matrix to 
/home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T2_501/bold/029/tmpdir.mcdat2extreg.26783/glm/Xg.dat
Normalized matrix condition is 1
Matrix condition is 1
search space = 6.00
DOF = 0
ERROR: DOF = 0



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Re: [Freesurfer] ERROR: DOF=0 in call to mri_glmfit by preproc-sess

[Mcnorgan, Christopher]

?That seems to have been the problem: Running the data through Slicer as 
suggested elsewhere fixed the slice time code, but then saved only a single 
frame of the 4D data. I had been poking around the file header looking for a 
corresponding field, not suspecting that it was a calculated value and that my 
data had been truncated, nor noticing that my image dimensionality field had 
changed value.

I wrote a MATLAB script to modify the slice time value (in addition to the TR 
value, which was also incorrectly set in my data) and was going to publicize 
the script, only to discover the FSL program fsledithd already exists and is 
clearly preferable to the Slicer solution for fixing strange NifTI header 
information. The data now run through preproc-sess without error.

So to summarize for search engines:
slice_code errors and other strange header information can be repaired with 
fsledithd, and the DOF=0 error was the result of an unexpected deletion of all 
but one time point by Slicer.

Incidentally, the data were converted from DICOM to NifTI using MRI Convert 
(Windows), so it is possible that this program populates some header fields 
with strange default values -- I mention this because 5 is not a valid slice 
code according to the NifTI header specification, and others have posted 
problems related to this header field.
Thanks,
Chris


Douglas N 
Greve
 Thu, 28 Apr 2016 10:05:59 
-0700

Does that run only have 1 time point?


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[Freesurfer] External Regressor of Interest in FS-FAST

[Mcnorgan, Christopher]

The references to external regressors in mkanalysis-sess are a little sparse on 
how I would go about analyzing a continuous regressor:
I have a mixed design experiment:

TaskBlock1 Rest TaskBlock2 Rest … TaskBlockN Rest
x6 Runs

Within each block are jittered events (5 of condition A, 5 of condition B). A 
colleague of mine agreed that the A vs B contrast should be pretty robust even 
in a single participant (it’s an established paradigm), considering I have over 
150 trials of each, but I am seeing nothing at any reasonable threshold in my 
single participant. My colleague suggested checking whether there were any 
regions with activity that increased/decreased as a function of block over the 
course of the experiment (essentially, a neural practice effect). 
Hypothetically, such a region would show a linear drift in activity across 6*N 
blocks, but only during the block periods (reverting to baseline during the 
rest periods).

>From the mkanalysis-sess.new wiki page, it appears that the -extreg flag can 
>be used to pass an additional regressor file, but it’s unclear from the rest 
>of the description how to construct this file, nor how to view the GLM 
>associated with this analysis.

Thanks for your time; I’ll post the solution on my lab wiki once it’s all 
sorted out
Chris

/**
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo,
* The State University of New York
* http://ccnlab.buffalo.edu/
* Office: 716.645.0236
* Lab: 716.645.0222
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Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

[Christopher Bell]

Looking at the image posted previously.

https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn

I think it is pretty clear the 5.1 picture has better gray/white contrast.
It is a very subtle difference, but you can see it if you look at some
pieces of
wm that were "missed" by 5.2 in this image.




On Thu, Apr 11, 2013 at 12:33 PM, Yang, Daniel wrote:

> Thanks Nick! I have uploaded the relevant files to you.
>
> Thanks,
> Daniel
>
> --
> Yung-Jui "Daniel" Yang, PhD
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> (203) 737-5454
>
>
>
>
>
>
> On 4/10/13 1:19 PM, "Nick Schmansky"  wrote:
>
> >Daniel,
> >
> >We're repeating our paired-analysis of thickness measures between 5.1
> >and 5.2.  In the meantime, to check for correctness, open the
> >brain.finalsurfs.mgz file with the surfaces overlayed, and check the
> >intensity value of the voxels which appear to be non-cortical 'black
> >spaces', relative to neighboring gm voxels.  ignore the aseg.mgz gm
> >voxels, as those are not accurate (ie, dont load aseg.mgz when
> >inspecting surfaces, or at least turn if off when inspecting gm
> >regionsits still handy to see where hippocampus sits).
> >
> >Nick
> >
> >
> >On Wed, 2013-04-10 at 11:11 +, Yang, Daniel wrote:
> >> Dear FreeSurfer Experts and Users,
> >>
> >> Did anyone find similar things using FS 5.2 (please see my previous post
> >> below)? That is, FS 5.2 is including more non-cortical "black spaces"
> >> within pial surfaces, compared to FS 5.1?
> >>
> >> I'm not interested in nitpicking but I feel this is a rather serious
> >> issue, so I would like to raise it again before it's completely
> >>forgotten.
> >>
> >> At the meantime I keep receiving Emails from people asking me this
> >>issue.
> >>
> >> Thanks!
> >> Daniel
> >>
> >
> >
> >
> >
> >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] Very different results between 5.1.0 and 5.2.0

[Christopher Bell]

The 5.2 image has been smoothed, by a small degree, relative to 5.1.
Either prior to FS processing or by FS, it would seem.


On Mon, Apr 15, 2013 at 3:29 AM, Christopher Bell <
christopherbell2...@gmail.com> wrote:

> Looking at the image posted previously.
>
> https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
>
> I think it is pretty clear the 5.1 picture has better gray/white contrast.
> It is a very subtle difference, but you can see it if you look at some
> pieces of
> wm that were "missed" by 5.2 in this image.
>
>
>
>
> On Thu, Apr 11, 2013 at 12:33 PM, Yang, Daniel wrote:
>
>> Thanks Nick! I have uploaded the relevant files to you.
>>
>> Thanks,
>> Daniel
>>
>> --
>> Yung-Jui "Daniel" Yang, PhD
>> Postdoctoral Researcher
>> Yale Child Study Center
>> New Haven, CT
>> (203) 737-5454
>>
>>
>>
>>
>>
>>
>> On 4/10/13 1:19 PM, "Nick Schmansky"  wrote:
>>
>> >Daniel,
>> >
>> >We're repeating our paired-analysis of thickness measures between 5.1
>> >and 5.2.  In the meantime, to check for correctness, open the
>> >brain.finalsurfs.mgz file with the surfaces overlayed, and check the
>> >intensity value of the voxels which appear to be non-cortical 'black
>> >spaces', relative to neighboring gm voxels.  ignore the aseg.mgz gm
>> >voxels, as those are not accurate (ie, dont load aseg.mgz when
>> >inspecting surfaces, or at least turn if off when inspecting gm
>> >regionsits still handy to see where hippocampus sits).
>> >
>> >Nick
>> >
>> >
>> >On Wed, 2013-04-10 at 11:11 +, Yang, Daniel wrote:
>> >> Dear FreeSurfer Experts and Users,
>> >>
>> >> Did anyone find similar things using FS 5.2 (please see my previous
>> post
>> >> below)? That is, FS 5.2 is including more non-cortical "black spaces"
>> >> within pial surfaces, compared to FS 5.1?
>> >>
>> >> I'm not interested in nitpicking but I feel this is a rather serious
>> >> issue, so I would like to raise it again before it's completely
>> >>forgotten.
>> >>
>> >> At the meantime I keep receiving Emails from people asking me this
>> >>issue.
>> >>
>> >> Thanks!
>> >> Daniel
>> >>
>> >
>> >
>> >
>> >
>> >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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>> 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] pial surface with FLAIR

[Watson, Christopher]

Hi Veronica,
Did you try initially doing "recon-all -i $FLAIR -s $SUBJECT"?
And then, when you do the remaining recon-all steps:

recon-all -autorecon3 -s $SUBJECT -FLAIRpial

It has worked for me. (And worked very well! No edits necessary for the pial 
surface!)

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, April 15, 2013 12:31 PM
To: Popescu, Veronica
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] pial surface with FLAIR

Hi Veronica,

we haven't seen that before. Can you upload your subject including the
FLAIR and we'll take a look?

thanks
Bruce

On Mon, 15 Apr 2013, Popescu, Veronica wrote:

>
> Dear all,
>
> I have already run the FreeSurfer 5.2 -all, and I would like to improve the
> pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I
> have also placed the FLAIR file) I use the following syntax:
>
> recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
>
> It starts running but then it hangs, I never get an output. The FLAIR file
> is in nifti format.
>
> I am not sure what I am doing wrong: it is the syntax? Should I first
> convert the FLAIR file to .mgz?
>
> Thank you in advance for the help!
>
> Veronica Popescu, MD, MSc
> Department of Radiology & Nuclear Medicine
> VU University Medical Center
> Amsterdam, The Netherlands
>
>

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Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

[Watson, Christopher]

I've never had any problems with sym links, but what you have is definitely 
confusing! Is there any reason you have it that way? As a rule of thumb, i'd 
keep things as simple as possible.

From: Garikoitz Lerma-Usabiaga [gariko...@gmail.com]
Sent: Saturday, June 01, 2013 4:21 PM
To: Watson, Christopher
Cc: Freesurfer
Subject: Re: [Freesurfer] REPOST: NFS v4 on CentOS 5.4 or Red Hat 6.2

Hello list,
we found the problem, symbolic links:

/home/glerma/ is the home of the app server where fs is installed.
/home/glerma/glerma/freesurfer/subjects was the SUBJECTS_DIR, but it has a sym 
link, since: glerma -> /bcbl/home/home_g-m/glerma
so changing SUBJECTS_DIR to:
/bcbl/home/home_g-m/glerma/freesurfer/subjects
solved the problem.


Do you think this is a problem with fs resolving sym links? We haven't found 
any problem with matlab or fsl.


thanks again!
Gari




On Sat, May 11, 2013 at 12:46 AM, Garikoitz Lerma-Usabiaga 
mailto:gariko...@gmail.com>> wrote:
Yes,
first two lines for example in SUBJECTS_DIR (I had to change SUBJECTS_DIR since 
now I have it in the app server, as said before):
drwxr-xr-x  77 glerma domain users  4096 Dec 20 17:25 BERTSO
drwxr-xr-x  10 glerma domain users  2048 Feb 14 16:27 BERTSO_MRI

and for the parent directory:
drwxr-xr-x  8 glerma domain users 1024 Mar 14 12:37 OSIRIX
drwxr-xr-x  8 glerma domain users 1024 Mar  8 08:59 OsiriX Data
drwxr-xr-x 26 glerma domain users 2048 May  7 17:55 subjects


thanks!
Gari



On Sat, May 11, 2013 at 12:37 AM, Chris Watson 
mailto:christopher.wat...@childrens.harvard.edu>>
 wrote:
Can you paste the output of "ls -l $SUBJECTS_DIR", so we can see what the 
permissions are? You may also want to paste the output of the parent directory 
as well.

On 05/10/2013 06:18 PM, Garikoitz Lerma-Usabiaga wrote:
Thanks Chris,
>  ls -l $SUBJECTS_DIR: it works
> This is the output of the command (I cannot make sense out of it):

[glerma@cajal ~]$ cat /etc/fstab
/dev/VolGroup00/LogVol00 /   ext3defaults1 1
LABEL=/boot /boot   ext3defaults1 2
tmpfs   /dev/shmtmpfs   defaults0 0
devpts  /dev/ptsdevpts  gid=5,mode=620  0 0
sysfs   /syssysfs   defaults0 0
proc/proc   procdefaults0 0
/dev/VolGroup00/LogVol01 swapswapdefaults0 0
/var/lib/swap/swap_cajal.img swap swap defaults 0 0
#hippocampus-nfs:/data /data nfs defaults 0 2
#hippocampus-nfs:/home/BCBL /home/BCBL nfs defaults 0 2
ltm.bcbl.local:/root_vdm_1/home /bcbl/home nfs4 defaults 0 0
ltm.bcbl.local:/root_vdm_1/data /bcbl/data nfs4 defaults 0 0

#hippocampus-nfs:/home/BCBL  /home/BCBL nfs 
rw,bg,intr,hard,timeo=600,wsize=32768,rsize=32768,nfsvers=3,tcp,noacl 0 2


(this is in the old app server, which worked before the migration to the new 
file system)

thanks again!
Gari


On Sat, May 11, 2013 at 12:07 AM, Chris Watson 
mailto:christopher.wat...@childrens.harvard.edu>>
 wrote:
Can you check that the UID and GID both match on the client and server sides? 
Is it the same user that is able to use other programs, yet unable to write via 
Freesurfer? Is your user an NIS account?

Can you output
# ls -l $SUBJECTS_DIR

I assume that since you say other programs can write to the filesystem, it is 
mounted properly, but can you show what is in /etc/fstab? i.e. make sure you 
see "rw" instead of "ro".


On 05/10/2013 05:55 PM, Garikoitz Lerma-Usabiaga wrote:
Thanks for the answers.
I am not the sys admin, but I think I can answer both questions:
> I assume the system is in read-write mode since the rest of the programs 
> (i.e. Matlab) are working.
> The SUBJECT_DIR is in each personal space, I mean:
--- FS is installed in a Linux CentOS 5 machine, I have an account in that 
machine (and I can work normally if my SUBJECTS_DIR is in that machine)
--- I have a personal drive space in the NFS 4, and I used to have my 
SUBJECTS_DIR in that drive, but after they upgraded it to NFS 4, it didn't work 
again.
> We have a new cluster now, they are testing it, it has Red Hat installed, 
> with FS 5.2, and I've been told that it cannot write (same problem).

The strange thing is that other programs work fine with this setup.

Do you think the problem is in the file system config (it seems so) or in FS 
config to be able to work with NFS 4?

I have asked the sys admin for the output of the system-config-nfs, I don't 
have admin privileges to run it.

thanks again!
Gari



On Fri, May 10, 2013 at 11:46 PM, Nick Schmansky 
mailto:ni...@nmr.mgh.harvard.edu>> wrote:
Gari,

At the NMR Center we use NFS v4 without problems with freesurfer.  Is the
SUBJECTS_DIR writable?  Note that in the default freesurfer distribution,
th

Re: [Freesurfer] mris_preproc --qdec-long problem

[Christopher McCarthy]

Dr. Reuter,

Thanks for your help, it got me through the error I was having.  On to the
next one:

When I enter the command:

mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target fsaverage
--hemi lh --meas thickness --out lh.thickness.mgh

it spits out the following two lines before quitting:

nsubjects = 45
ERROR: cannot find /media/freesurfer/.long.

Any idea what I'm missing?

Thanks for your help and patience,

Chris


On Mon, Jun 3, 2013 at 5:08 PM, Martin Reuter
wrote:

> Hi Chris,
>
> this is a good question for the list (cc'ed), others may or will have the
> same problem.
>
> The problem is with your table file, specifically the new line character.
> DOS uses \r\n , Mac \r and Linux \n.
> Your text file uses \r, so it probably was created on a mac.
>
> The problem is that the "cat" command (at least in linux) does not work on
> your file:
> cat long.qdec.table.dat is empty
>
> You can convert the \r to \n (linux format):
>  tr '\r' '\n' < long.qdec.table.dat > long2.qdec.table.dat
>
> and then should be able to run the preproc command.
>
> People with DOS formats should not run the above "tr' command as they will
> end up with 2 newlines instead of 1. Maybe DOS txt files work with 'cat'
> directly (so there is no need)? If anyone on the list knows a good way of
> cat and awk a file independently of the new line (and working on all OS),
> let me know. This is the command I use:
>
> cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#")
> printf("%s.long.%s\n", $1, $2)}'
>
> to generate the subjects id's from the table's first two columns.
>
> Best, Martin
>
>
>
> On 06/03/2013 03:45 PM, Christopher McCarthy wrote:
>
>> Dr. Reuter,
>>
>> We corresponded in the past about QDEC, and you gave me great help.  The
>> lab I work for is now moving towards using the Longitudinal Mixed Effects
>> Model.  When I go to run the command:
>>
>> mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target
>> study_average --hemi lh --meas thickness --out lh.thickness.mgh
>>
>> I get the error: 'ERROR: no subjects specified.'  I am attaching my
>> long.qdec.table.dat, which works fine when loaded by QDEC.  Do you have any
>> idea of why I am getting this error?
>>
>> Thanks,
>>
>> Chris McCarthy
>>
>
> --
> Martin Reuter, Ph.D.
> Assistant in Neuroscience - Massachusetts General Hospital
> Instructor in Neurology   - Harvard Medical School
> MGH / HMS / MIT
>
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
>
> Phone: +1-617-724-5652
> Email:
>mreu...@nmr.mgh.harvard.edu
>reu...@mit.edu
> 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<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] freesurfer registration

[Parker, Christopher]

Hi,

I understand that the recon-all script registers and then averages two 
anatomical images (after bias field correction) if two are provided in the 
"orig" folder, before performing the other parcellation stages. I am writing a 
report and it might be good to mentioned what registration is used. I'm 
guessing this is a rigid registration using sum of squared differences cost 
function?

Best,
Chris
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Re: [Freesurfer] Painting voxels vs. adding control points

[Watson, Christopher]

1) The right panel shows the aseg voxels. The surfaces are the same in L and R 
panels.
2) What do the surrounding slices look like? It may be that the WM surface 
"fills in" more as you go along.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of ye tian 
[tianye...@gmail.com]
Sent: Thursday, July 04, 2013 11:52 AM
To: Freesurfer
Subject: Re: [Freesurfer] Painting voxels vs. adding control points

Dear Freesurfers,

My first attempt of this message somehow didn't make it to the mailing archive. 
In case it didn't go through, I am sending it again. Sorry to bother you if you 
received the first message.

Two things I was wondering
1) Why do the surfaces shown in the left and right panels disagree? (The right 
one has a lot more white matter).
2) Do I need to edit the white matter? It seems unreasonable to have +8mm thick 
of grey matter. If so, I will probably paint more voxels to wm.mgz.

Thank you very much!

Sincerely,
Ye


On Wed, Jul 3, 2013 at 4:33 PM, ye tian 
mailto:tianye...@gmail.com>> wrote:
Dear freesurfers,

I would like a second eye on my decision to edit wm.mgz. I think that the 
boundary between the gray and the white is unrealistic (e.g. Coronal.png). 
Furthermore, there is a discrepancy between -surfs and -surfs -aseg (e.g. 
attached coronal_aseg.png).

If I indeed need to edit these slices, which way is more preferable, adding 
voxels or control points?

Thank you very much!

Sincerely,
Ye


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Re: [Freesurfer] different results between 5.1.0 and 5.2.0

[Watson, Christopher]

I don't know, but I'm pretty sure the Freesurfer team will recommend you use 
v5.3.0. There are emails saying as much.
Chris

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of clarissa yasuda 
[clayas...@gmail.com]
Sent: Thursday, July 25, 2013 12:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] different results between 5.1.0 and 5.2.0

Dear FreeSurfer Experts

As in some other posts, I have also observed some differences between the two 
releases.  The values from cuneus (thickness) are similar to the post from 
Ritobrato Datta, Ph.D. on 18 march.

 But I also observed some differences in volume of right / left thalami. Did 
anybody observe such asymmetry??
I am now running analysis with patients and controls on data from 5.2.0 and got 
surprised with this asymmetry.

Here I am showing the average I obtained:

R PALLIDUM  L PALLIDUM   R THAL L THAL  RH_CUNEUS   
LH_CUNEUS
5.1 (350 SUBJECTS)  15801688 6701   6970.31 1.845   1.857

5.2 (115 SUBJECTS, subgroup of 350) 151913676520
74012.422.40

Is there any approach to correct it on 5.2 ??
Thanks in advance
clarissa

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Re: [Freesurfer] trac-all inquiry

[Watson, Christopher]

I've found that when using the Bash shell, putting multiple subjects in the 
config file doesn't work. Maybe that's the issue here? Although, I simply never 
bothered to look into it any more.

Chris


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of David Soto 
[d.s...@imperial.ac.uk]
Sent: Friday, August 02, 2013 5:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] trac-all inquiry

Hi,

I have successfully run recon-all in my dataset
and now am attempting to use trac-all on my diffusion data
obtained on a Siemens scanner.

Diffusion dicoms were transformed to .nii using MRIConverter
and then to .mnc using

nii2mnc output.nii output_t.mnc.

I am trying to run trac-all on a single subject and for this I
have created the configuration file attached (tracula02ST)

As you can see the SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui
and within each subject the T1 serving as input for recon-all are in
mri/orig

while the diffusion images are in a folder call diffdata (named
output_t.mnc)
which also contains the bvecs and bvals files, which were transposed and
organised
according to the tutorial (named as bvecs_t.txt and bvals_t.txt)

When I run:
trac-all -c tracula02ST.txt

I get:
ERROR: no analysis step (-{prep,bedp,path}) has been selected

THEN I run:
trac-all -prep -bedp -path -c tracula02ST.txt which runs for 5 seconds or so
and then gives the long output text below with an error message.

Segmentation fault (core dumped)
foreach: No match.

The trac-all.log is attached also.

Could you please help?

Cheers

David


--
http://www1.imperial.ac.uk/medicine/people/d.soto/






wmen-dsoto3:~/Documents/fmri/rsdtianawmgui> trac-all -prep -bedp -path
-c tracula02ST.txt
INFO: SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui
INFO: Diffusion root is /home/dsoto/Documents/fmri/rsdtianawmgui
Actual FREESURFER_HOME /usr/local/freesurfer
trac-paths -c
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/dmrirc.local -log
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/trac-all.log -cmd
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/trac-all.cmd
#-
/usr/local/freesurfer/bin/trac-paths
#-
#@# Path reconstruction Fri Aug  2 09:44:20 BST 2013
/usr/local/freesurfer/bin/dmri_paths --outdir
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.cst_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.cst_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.ilf_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.ilf_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.unc_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.unc_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/fmajor_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/fminor_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.atr_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.atr_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.ccg_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.ccg_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.cab_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.cab_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.slfp_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.slfp_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.slft_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.slft_PP_avg33_mni_bbr
--dwi /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi.nii.gz
--grad /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvecs --bval
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvals --mask
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/lowb_brain_mask.nii.gz
--bpdir /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri.bedpostX
--ntr 2 --fmin 0.05 --roi1
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni

Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

[Watson, Christopher]

This is an FSL problem. You can try the FSL list, and check out some links:
https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge
http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html
http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira 
[jbragapere...@gmail.com]
Sent: Monday, September 02, 2013 9:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Dear Anastasia and FreeSurfers,

I was preprocessing some data using tracula and found this error after running  
trac-all -bedp -c dmrirc:

INFO: SUBJECTS_DIR is /data-02/joana/Last
INFO: Diffusion root is /data-02/joana/tracula/
Actual FREESURFER_HOME /usr/local/freesurfer-5.3
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri
subjectdir is /data-02/joana/tracula/XXX/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Unable to run job: Job was rejected because job requests unknown queue 
"short.q".
Exiting.
Queuing parallel processing stage
Unable to run job: Job was rejected because job requests unknown queue "long.q".
Exiting.
Queuing post processing stage
Unable to run job: denied: "60" is not a valid object name (cannot start with a 
digit)
Job was rejected because job requests unknown queue "long.q".
Exiting.

Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress.
Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the 
queued tasks.

You will get an email at the end of the post-processing stage.


So far no slices have been processed. Does anyone know how to solve it?

Thanks!

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Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

[Watson, Christopher]

Indeed. It's actually really easy to set up, too.

From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Monday, September 02, 2013 3:46 PM
To: Watson, Christopher
Cc: Joana Braga Pereira; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Thanks for the pointers, Chris. I'd call it an "opportunity for FSL
customization" rather than an "FSL problem" per se :o)

On Mon, 2 Sep 2013, Watson, Christopher wrote:

> This is an FSL problem. You can try the FSL list, and check out some links:
> https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge
> http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html
> http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joana Braga Pereira 
> [jbragapere...@gmail.com]
> Sent: Monday, September 02, 2013 9:53 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"
>
> Dear Anastasia and FreeSurfers,
>
> I was preprocessing some data using tracula and found this error after 
> running  trac-all -bedp -c dmrirc:
>
> INFO: SUBJECTS_DIR is /data-02/joana/Last
> INFO: Diffusion root is /data-02/joana/tracula/
> Actual FREESURFER_HOME /usr/local/freesurfer-5.3
> WARN: Running FSL's bedbost locally - this might take a while
> WARN: It is recommended to run this step on a cluster
> bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri
> subjectdir is /data-02/joana/tracula/XXX/dmri
> Making bedpostx directory structure
> Queuing preprocessing stages
> Unable to run job: Job was rejected because job requests unknown queue 
> "short.q".
> Exiting.
> Queuing parallel processing stage
> Unable to run job: Job was rejected because job requests unknown queue 
> "long.q".
> Exiting.
> Queuing post processing stage
> Unable to run job: denied: "60" is not a valid object name (cannot start with 
> a digit)
> Job was rejected because job requests unknown queue "long.q".
> Exiting.
>
> Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress.
> Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the 
> queued tasks.
>
> You will get an email at the end of the post-processing stage.
>
>
> So far no slices have been processed. Does anyone know how to solve it?
>
> Thanks!
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>


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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

[Watson, Christopher]

A. You should overlay the tracts on the subject's FA (see example command line 
on wiki)
B. Check the mailing list archives about reinitializing tracts. That should 
improve the results here. You don't need to reinitialize the tracts that are 
already correct (although none of yours look particularly good).

Is this a noisy dataset or something?


From: Joana Braga Pereira [jbragapere...@gmail.com]
Sent: Thursday, September 05, 2013 9:32 AM
To: Watson, Christopher
Cc: Anastasia Yendiki; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Hi,

Thanks for all the replies, I solved the problem I had before.

However, after finishing the Tracula pre-processing steps I tried to visualize 
the tracts by typing:

freeview -tv CTR01/dpath/merged_avg33_mni_bbr.mgz

And, as you can see in the picture I'm attaching to this email, it seems the 
tracts were not properly reconstructed.

Does anyone know why?

Should I make some changes and for example set the control points differently 
from the ones proposed on Tracula website?

Any help will be greatly appreciated!

Thanks,

joana




2013/9/2 Watson, Christopher 
mailto:christopher.wat...@childrens.harvard.edu>>
Indeed. It's actually really easy to set up, too.

From: Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu<mailto:ayend...@nmr.mgh.harvard.edu>]
Sent: Monday, September 02, 2013 3:46 PM
To: Watson, Christopher
Cc: Joana Braga Pereira; 
freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Thanks for the pointers, Chris. I'd call it an "opportunity for FSL
customization" rather than an "FSL problem" per se :o)

On Mon, 2 Sep 2013, Watson, Christopher wrote:

> This is an FSL problem. You can try the FSL list, and check out some links:
> https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge
> http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html
> http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu
>
> 
> From: 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>  
> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
>  on behalf of Joana Braga Pereira 
> [jbragapere...@gmail.com<mailto:jbragapere...@gmail.com>]
> Sent: Monday, September 02, 2013 9:53 AM
> To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"
>
> Dear Anastasia and FreeSurfers,
>
> I was preprocessing some data using tracula and found this error after 
> running  trac-all -bedp -c dmrirc:
>
> INFO: SUBJECTS_DIR is /data-02/joana/Last
> INFO: Diffusion root is /data-02/joana/tracula/
> Actual FREESURFER_HOME /usr/local/freesurfer-5.3
> WARN: Running FSL's bedbost locally - this might take a while
> WARN: It is recommended to run this step on a cluster
> bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri
> subjectdir is /data-02/joana/tracula/XXX/dmri
> Making bedpostx directory structure
> Queuing preprocessing stages
> Unable to run job: Job was rejected because job requests unknown queue 
> "short.q".
> Exiting.
> Queuing parallel processing stage
> Unable to run job: Job was rejected because job requests unknown queue 
> "long.q".
> Exiting.
> Queuing post processing stage
> Unable to run job: denied: "60" is not a valid object name (cannot start with 
> a digit)
> Job was rejected because job requests unknown queue "long.q".
> Exiting.
>
> Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress.
> Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the 
> queued tasks.
>
> You will get an email at the end of the post-processing stage.
>
>
> So far no slices have been processed. Does anyone know how to solve it?
>
> Thanks!
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error 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
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Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

[Watson, Christopher]

Try this: 
http://www.mail-archive.com/search?q=reinit&l=freesurfer%40nmr.mgh.harvard.edu

From: Joana Braga Pereira [jbragapere...@gmail.com]
Sent: Thursday, September 05, 2013 9:51 AM
To: Watson, Christopher
Cc: Anastasia Yendiki; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Hi Christopher,

Thanks a lot for such a prompt reply.

I know I should overlay the tracts of the FA image, but I just wanted to show 
you how small the reconsctrutions were.

I don't think this is particularly noisy data.

I'm trying to find solutions on the mailing list archives by typing 
"reinitializing tracts Tracula" but I haven't found much information.

Would you kindly suggest me a few that provide solutions to this problem or 
make some recommendations yourself?

Thanks again,

joana




2013/9/5 Watson, Christopher 
mailto:christopher.wat...@childrens.harvard.edu>>
A. You should overlay the tracts on the subject's FA (see example command line 
on wiki)
B. Check the mailing list archives about reinitializing tracts. That should 
improve the results here. You don't need to reinitialize the tracts that are 
already correct (although none of yours look particularly good).

Is this a noisy dataset or something?


From: Joana Braga Pereira 
[jbragapere...@gmail.com<mailto:jbragapere...@gmail.com>]
Sent: Thursday, September 05, 2013 9:32 AM
To: Watson, Christopher
Cc: Anastasia Yendiki; 
freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Hi,

Thanks for all the replies, I solved the problem I had before.

However, after finishing the Tracula pre-processing steps I tried to visualize 
the tracts by typing:

freeview -tv CTR01/dpath/merged_avg33_mni_bbr.mgz

And, as you can see in the picture I'm attaching to this email, it seems the 
tracts were not properly reconstructed.

Does anyone know why?

Should I make some changes and for example set the control points differently 
from the ones proposed on Tracula website?

Any help will be greatly appreciated!

Thanks,

joana




2013/9/2 Watson, Christopher 
mailto:christopher.wat...@childrens.harvard.edu><mailto:christopher.wat...@childrens.harvard.edu<mailto:christopher.wat...@childrens.harvard.edu>>>
Indeed. It's actually really easy to set up, too.

From: Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu<mailto:ayend...@nmr.mgh.harvard.edu><mailto:ayend...@nmr.mgh.harvard.edu<mailto:ayend...@nmr.mgh.harvard.edu>>]
Sent: Monday, September 02, 2013 3:46 PM
To: Watson, Christopher
Cc: Joana Braga Pereira; 
freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"

Thanks for the pointers, Chris. I'd call it an "opportunity for FSL
customization" rather than an "FSL problem" per se :o)

On Mon, 2 Sep 2013, Watson, Christopher wrote:

> This is an FSL problem. You can try the FSL list, and check out some links:
> https://www2.fmrib.ox.ac.uk/phpwiki/index/FslSge
> http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html
> http://chrisfilo.tumblr.com/post/579493955/how-to-configure-sun-grid-engine-for-fsl-under-ubuntu
>
> 
> From: 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
>  
> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>]
>  on behalf of Joana Braga Pereira 
> [jbragapere...@gmail.com<mailto:jbragapere...@gmail.com><mailto:jbragapere...@gmail.com<mailto:jbragapere...@gmail.com>>]
> Sent: Monday, September 02, 2013 9:53 AM
> To: 
> freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: [Freesurfer] Tracula error - unknown queue "long.q", "short.q"
>
> Dear Anastasia and FreeSurfers,
>
> I was preprocessing some data using tracula and found this error after 
> running  trac-all -bedp -c dmrirc:
>
> INFO: SUBJECTS_DIR is /data-02/joana/Last
> INFO: Diffusion root is /data-02/joana/tracula/
> Actual FREESURFER_HOME /usr/local/freesurfer-5.3
> WARN: Ru

Re: [Freesurfer] tool to compare surface files (along the lines of diff)?

[Watson, Christopher]

You could probably load them in matlab and compare there.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of David Romano 
[drom...@stanford.edu]
Sent: Thursday, September 05, 2013 8:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] tool to compare surface files (along the lines of diff)?

Hi everyone,

I'm trying to figure out whether two surfaces which appear identical in 
freeview are indeed identical. Using diff shows the files are not, but since 
they're binary, I can't tell whether this difference is simply due to header 
information that might be embedded in the files, or whether the surfaces do 
indeed differ.   Is there a FreeSurfer command that can be used to determine 
this?

Thanks in advance for your help,
David Romano

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Re: [Freesurfer] recon-all for multiple subjects

[Watson, Christopher]

The problem here is that SZ*.nii presumably refers to a list of files due to 
shell expansion. I don't know how recon-all handles that (e.g. if it will take 
only the first file in the list, or all files), but that command probably won't 
do what you want it to.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anupa AV 
[av.an...@yahoo.com]
Sent: Saturday, September 07, 2013 5:56 AM
To: KOOL; Freesurfer
Subject: [Freesurfer] recon-all for multiple subjects

Dear Sir,
I'd like to know the command lines for running recon-all for multiple datasets.
Can you please help me on that?

I've tried using the following command lines

cd /home/john/Anu (where I kept all the .nii files)

for x in *
do
recon-all -i SZ*.nii -s $x -all
done

But this is not working

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[Freesurfer] parcellations to fmri space

[Christopher Bell]

Hello Freesurfers,


I have developed a pipeline that uses mri_label2vol to take freesurfer
parcellations to
native fmri space, and uses dilation (within mri_label2vol) to make the
ROIs larger since our resolution is only
3.5x3.5x4 we would end up with only a few voxels for some ROIs due to large
voxel
size and partial voluming wihout the dilation. However, since the lh and rh
are done
separately by mri_label2vol, I now have overlap on the midline and have to
go through a bunch
of masking steps to eliminate it.

My question is; is there a tool that will take both lh/rh parcellations to
a new coordinate
system, do dilation, and most importantly control for lh/rh overlap? Or any
other
similar suggestions. Thanks!

Basically I am looking to rework my pipeline, and it seems I should be able
to find a more parsimonious solution, than my "Rube Goldberg" approach.

Chris
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Re: [Freesurfer] nu_correct problem

[Christopher Bell]

I believe this post slipped through the cracks. Anyone have any thoughts
on this nu_correct error. Some subjects ran fine, so it seems to be an
intermittent
problem and not an installation problem.

Also, is this possibly related to the avi_talairach/intensity normalization
issues
being discussed in another post?

Chris Bell
University of Minnesota


On Thu, May 31, 2012 at 12:13 PM,  wrote:

> Hello, I am trying to run recon-all using freesurfer 5.1.0. This worked on
> most of my subjects, but for about 10 subjects, I got an error:
>
> nu_correct: Command not found
>
> I can see on the archive that several others have run into this problem,
> but I couldn't figure out from the archives what the solution is. I do have
> perl installed in usr/bin.
>
> Thanks very much, Katie
>
> --
> Kathryn R. Cullen, M.D.
> Assistant Professor
> University of Minnesota Medical School
> Department of Psychiatry
> Division of Child and Adolescent Psychiatry
> (612) 273-9825
>
> ___
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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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Re: [Freesurfer] MPRAGE intensity variations

[Watson, Christopher]

I'll look into it. I doubt it's been used for the previous scans.
Given that, is there anything I can do (any flags/options to declare) that can 
deal with this kind of issue? I don't mind adding control points and whatnot, 
but an easy fix is obviously desirable.

Thanks,
Chris

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Saturday, July 14, 2012 5:29 PM
To: Watson, Christopher
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MPRAGE intensity variations

Hi Chris
Are you using prescan normalize? It helps a lot
Cheers
Bruce



On Jul 13, 2012, at 1:00 PM, Chris Watson 
mailto:christopher.wat...@childrens.harvard.edu>>
 wrote:

Hello,
I ran a subject through recon-all both with and without the "-mprage" flag, and 
naturally got different results. I'm attaching a screenshot of the pial and 
main surfaces, along with the orig.mgz of the same slice. The image tends to be 
brighter in the frontal lobe, and there is an intensity change when going 
through the slices. The scanner is Siemens 3T (Trio, I think), using a 
32-channel head coil. The imaging parameters are: (not sure which are most 
relevant)

TR: 1410
TI: 800
TE: 2.2
Matrix: 256x256
FOV: 256
Flip angle: 9 deg
ImagingFrequency: 123.259181
Pixel bandwidth: 199

Is there anything I can do to improve the results?
Thanks,
Chris

PS When I didn't use the '-mprage' flag, I used the '-nuintensitycor-3T' flag. 
So I changed 2 separate things.



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Re: [Freesurfer] parcellations to fmri space

[Christopher Bell]

I tried using mri_label2vol with --aparc+aseg instead of --aparc. This
works and provides cortical and subcortical with no overlap. It doesn't
allow me to do cortical dilation, but that is probably because it wouldn't
mesh
well with the subcortical ROIs. Thanks.

Chris


On Mon, Jul 16, 2012 at 9:03 AM, Douglas N Greve
wrote:

>
> Hi Chris, I don't think there is such a tool. One thing you can do is to
> use the aparc+aseg.mgz as the source instead of the lh and rh surfaces
> separately. This might solve all of your problems.
> doug
>
>
> On 07/06/2012 12:02 PM, Christopher Bell wrote:
> >
> > Hello Freesurfers,
> >
> >
> > I have developed a pipeline that uses mri_label2vol to take freesurfer
> > parcellations to
> > native fmri space, and uses dilation (within mri_label2vol) to make
> > the ROIs larger since our resolution is only
> > 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to
> > large voxel
> > size and partial voluming wihout the dilation. However, since the lh
> > and rh are done
> > separately by mri_label2vol, I now have overlap on the midline and
> > have to go through a bunch
> > of masking steps to eliminate it.
> >
> > My question is; is there a tool that will take both lh/rh
> > parcellations to a new coordinate
> > system, do dilation, and most importantly control for lh/rh overlap?
> > Or any other
> > similar suggestions. Thanks!
> >
> > Basically I am looking to rework my pipeline, and it seems I should be
> > able
> > to find a more parsimonious solution, than my "Rube Goldberg" approach.
> >
> > Chris
> >
> >
> > ___
> > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> ___
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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
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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Re: [Freesurfer] Questions about correction over 2 hemispheres and MCC

[Watson, Christopher]

Hi Doug et al,

The 2nd question is something I've wondered about. Doesn't a Bonferroni 
correction assume that the measures are independent? 
If so, I think in the case of subcortical structures, it is incorrect to use 
this method, as e.g. the putamen and pallidal volumes are not independent of 
one another.
If not, and it is acceptable to use when there are dependencies between 
measures, how do you calculate the FWE? It wouldn't be equal to alpha/n, unless 
I am misunderstanding something.

Thanks,
Chris

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: Friday, July 20, 2012 2:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Questions about correction over 2 hemispheres and MCC

Hi Reem, it looks like you've done everything correctly (sorry for the
null result). As for your second, question, I don't think there is a way
other than Bonferroni. You can try FDR, but it makes the interpretation
a little messy.
doug

On 07/19/2012 07:59 PM, Reem Jan wrote:
>
> Hi Doug
>
> I hope it’s okay that I double check I’m doing the correction over 2
> hemispheres correctly and ask a question regarding correction for
> multiple comparisons. I will briefly describe what I have done:
>
> I have 2 groups of subjects – Drug addicts (n= 17) and controls (n=20).
>
> 1.I ran a surface thickness study:
>
> ·For the ‘mri_glmfit’ command, I used DOSS and specified a contrast of
> +1 -1 0 (Controls > MA)
>
> ·I ran a pre-cached simulation with the following command:
> mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos
>
> ·This simulation should only have corrected for the left hemisphere as
> I understand it. My cluster summary text file showed me that a cluster
> survived in the insula. I interpreted this as ‘controls had higher
> grey matter thickness in this cluster located in the insula than drug
> addicts’. However, this was only corrected over the left hemisphere
> (when I ran the same simulation in the right hemisphere, nothing
> survived multiple comparison correction).
>
> ·I now wanted to correct the lh results for 2 hemispheres. From the
> help menu of ‘mri_glmfit-sim’, I understood you can do this in 2 ways,
> are both of these correct and give the same result?
>
> a.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos --2 spaces
> --no-sim csdbase
>
> b.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos
> --cwpvalthresh 0.025
>
> ØNo clusters survived the Bonferroni correction over both hemispheres.
> So I assume I can no longer report this result?
>
> 2.I ran a subcortical volume study:
>
> ·I used SPSS to perform the statistical analysis on each of 14
> subcortical structures (left and right). Is there a good way to
> correct for multiple comparisons, apart from Bonferroni, which would
> be very conservative?
>
> Many thanks for your advice.
>
> Kind regards
>
> Reem
>
> *Reem Jan***
>
> BPharm (Hons), RegPharmNZ
>
> PhD Student / Pharmacist
>
> School of Pharmacy, Faculty of Medical & Health Sciences,
> The University of Auckland, Private Bag 92019,
> Auckland, New Zealand.
>
> Ph: +64 9 373 7599 ext 81138. DDI: +64 9 923 1138
>
> F: +64 9 367 7192
>
> *From:*freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas
> Greve
> *Sent:* Friday, 20 July 2012 11:52 a.m.
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] slice-by-slice predictors
>
> Sorry, not possible.
>
> On 7/19/12 6:56 PM, Caspar M. Schwiedrzik wrote:
>
> Hi!
> Is it possible to have slice-by-slice predictors in Freesurfer, and if
> so, how?
> Thanks,
> Caspar
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu  
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Questions about correction over 2 hemispheres and MCC

[Watson, Christopher]

What about, for example, the correlations I've seen in a cohort of subjects.

In 158 subjects aged 10-19 (both controls and patients), the correlation 
between L & R thalamus is 0.91, and the correlations between L & R of caudate, 
putamen, pallidum, hippocampus, and amygdala were all 0.75 or higher.

I would think that a Bonferroni correction would be incredibly conservative 
and, in my opinion, just plain wrong because true significant diff's would be 
missed. Is there any principled way of dealing with multiple tests that are 
correlated?

Thanks,
Chris

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Saturday, July 21, 2012 12:01 PM
To: Watson, Christopher
Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Questions about correction over 2 hemispheres and MCC

Hi Chris,

bonferroni will be overly conservative in that case, but we rarely really
know the true covariance structure of the data, so we would rather err on
the side of being conservative.

cheers
Bruce
On Fri, 20 Jul 2012, Watson, Christopher
wrote:

> Hi Doug et al,
>
> The 2nd question is something I've wondered about. Doesn't a Bonferroni 
> correction assume that the measures are independent?
> If so, I think in the case of subcortical structures, it is incorrect to use 
> this method, as e.g. the putamen and pallidal volumes are not independent of 
> one another.
> If not, and it is acceptable to use when there are dependencies between 
> measures, how do you calculate the FWE? It wouldn't be equal to alpha/n, 
> unless I am misunderstanding something.
>
> Thanks,
> Chris
> 
> 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: Friday, July 20, 2012 2:38 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Questions about correction over 2 hemispheres and 
> MCC
>
> Hi Reem, it looks like you've done everything correctly (sorry for the
> null result). As for your second, question, I don't think there is a way
> other than Bonferroni. You can try FDR, but it makes the interpretation
> a little messy.
> doug
>
> On 07/19/2012 07:59 PM, Reem Jan wrote:
>>
>> Hi Doug
>>
>> I hope it?s okay that I double check I?m doing the correction over 2
>> hemispheres correctly and ask a question regarding correction for
>> multiple comparisons. I will briefly describe what I have done:
>>
>> I have 2 groups of subjects ? Drug addicts (n= 17) and controls (n=20).
>>
>> 1.I ran a surface thickness study:
>>
>> ·For the ?mri_glmfit? command, I used DOSS and specified a contrast of
>> +1 -1 0 (Controls > MA)
>>
>> ·I ran a pre-cached simulation with the following command:
>> mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos
>>
>> ·This simulation should only have corrected for the left hemisphere as
>> I understand it. My cluster summary text file showed me that a cluster
>> survived in the insula. I interpreted this as ?controls had higher
>> grey matter thickness in this cluster located in the insula than drug
>> addicts?. However, this was only corrected over the left hemisphere
>> (when I ran the same simulation in the right hemisphere, nothing
>> survived multiple comparison correction).
>>
>> ·I now wanted to correct the lh results for 2 hemispheres. From the
>> help menu of ?mri_glmfit-sim?, I understood you can do this in 2 ways,
>> are both of these correct and give the same result?
>>
>> a.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos --2 spaces
>> --no-sim csdbase
>>
>> b.mri_glmfit-sim --glmdir lh.group_age.glmdir --cache 4 pos
>> --cwpvalthresh 0.025
>>
>> ØNo clusters survived the Bonferroni correction over both hemispheres.
>> So I assume I can no longer report this result?
>>
>> 2.I ran a subcortical volume study:
>>
>> ·I used SPSS to perform the statistical analysis on each of 14
>> subcortical structures (left and right). Is there a good way to
>> correct for multiple comparisons, apart from Bonferroni, which would
>> be very conservative?
>>
>> Many thanks for your advice.
>>
>> Kind regards
>>
>> Reem
>>
>> *Reem Jan***
>>
>> BPharm (Hons), RegPharmNZ
>>
>> PhD Student / Pharmacist
>>
>> School of Pharmacy, Faculty of Medical & Health Sciences,
>> The University of Auckland, Private Bag 92019,
>> Auckland, New Zealand.
>>
>> Ph: +64 9 373 7599 ext 81138. DDI: +64

[Freesurfer] CSF segmentation and cortical ribbon

[Christopher Coello]

Dear Freesurfer users,


I have been using the function mri_watershed with options -LABEL and 
-atlas to segment into csf, scalp and skull. This option also gives a 
segmentation of the gm and wm. All voxels of the head are assigned to 
one of the labels.

Nevertheless, the segmentation obtained in the file aseg.mgz of the 
cortical ribbon is of much better quality the fast mri_watershed -LABEL 
one. The problem is now if I use the csf obtained with mri_watershed 
-LABEL together with the aseg.mgz gm segmentation, some voxels in the 
border between cortical ribbon and csf are unassigned.

My question is then : how could I generate a csf map like the one 
obtained with mri_watershed -LABEL, but that is complementary of the 
segmentation present in aseg.mgz of the cortical ribbon ?

Thanks a lot in advance,

Best,

-- 

Christopher Coello, Ph.D.
Preclinical PET/CT unit
http://www.med.uio.no/imb/english/research/about/infrastructure/pet/
Institute of Basic Medical Sciences
Faculty of Medicine, University of Oslo
tel. +4745154516

-- 

Christopher Coello, Ph.D.
Preclinical PET/CT unit
http://www.med.uio.no/imb/english/research/about/infrastructure/pet/
Institute of Basic Medical Sciences
Faculty of Medicine, University of Oslo
tel. +4745154516
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Re: [Freesurfer] CSF segmentation and cortical ribbon

[Christopher Coello]

Hi Bruce,

Absolutely, the voxels I'm referring to are defined regarding their 
distance to the cortical ribbon (let's say within 5 mm)  rather than by 
belonging to a specific tissue type.
Using a distance criteria from the ribbon surface and collect only 
voxels within a certain distance (going outwards) could be one solution. 
Is that possible with some functions in Freesurfer ?

Chris

On 25.07.2012 15:50, Bruce Fischl wrote:
> Hi Chris
>
> that's tough to do with only a T1 image as CSF and bone look the same.
> We don't have any ready-made tools for doing what you want, but you
> could probably get close with some rules. Sounds like the voxels you are
> referring to are CSF or dura given their proximity to brain
> cheers
> Bruce
>
>
> On Wed, 25 Jul 2012, Christopher Coello wrote:
>
>> Dear Freesurfer users,
>>
>>
>> I have been using the function mri_watershed with options -LABEL and
>> -atlas to segment into csf, scalp and skull. This option also gives a
>> segmentation of the gm and wm. All voxels of the head are assigned to
>> one of the labels.
>>
>> Nevertheless, the segmentation obtained in the file aseg.mgz of the
>> cortical ribbon is of much better quality the fast mri_watershed -LABEL
>> one. The problem is now if I use the csf obtained with mri_watershed
>> -LABEL together with the aseg.mgz gm segmentation, some voxels in the
>> border between cortical ribbon and csf are unassigned.
>>
>> My question is then : how could I generate a csf map like the one
>> obtained with mri_watershed -LABEL, but that is complementary of the
>> segmentation present in aseg.mgz of the cortical ribbon ?
>>
>> Thanks a lot in advance,
>>
>> Best,
>>
>>
>
>
> 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.
>

-- 

Christopher Coello, Ph.D.
Preclinical PET/CT unit
http://www.med.uio.no/imb/english/research/about/infrastructure/pet/
Institute of Basic Medical Sciences
Faculty of Medicine, University of Oslo
tel. +4745154516
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Re: [Freesurfer] CSF segmentation and cortical ribbon

[Christopher Coello]

Hi Bruce,

Thanks for the reply.
I'm not really familiar with compiling C functions, I have been working 
all the time with Matlab. Always worth to ask : do you have such set of 
C functions in Matlab also ?

Christopher

On 25.07.2012 16:10, Bruce Fischl wrote:
> Hi Chris,
>
> sure, we can compute distance-to-surface transforms and such, but I
> don't think we have any pre-packaged binaries that will do what you
> want, just a set of C functions
>
>
> Bruce
> On Wed, 25 Jul 2012, Christopher Coello wrote:
>
>> Hi Bruce,
>>
>> Absolutely, the voxels I'm referring to are defined regarding their
>> distance to the cortical ribbon (let's say within 5 mm) rather than by
>> belonging to a specific tissue type.
>> Using a distance criteria from the ribbon surface and collect only
>> voxels within a certain distance (going outwards) could be one
>> solution. Is that possible with some functions in Freesurfer ?
>>
>> Chris
>>
>> On 25.07.2012 15:50, Bruce Fischl wrote:
>>> Hi Chris
>>>
>>> that's tough to do with only a T1 image as CSF and bone look the same.
>>> We don't have any ready-made tools for doing what you want, but you
>>> could probably get close with some rules. Sounds like the voxels you are
>>> referring to are CSF or dura given their proximity to brain
>>> cheers
>>> Bruce
>>>
>>>
>>> On Wed, 25 Jul 2012, Christopher Coello wrote:
>>>
>>>> Dear Freesurfer users,
>>>>
>>>>
>>>> I have been using the function mri_watershed with options -LABEL and
>>>> -atlas to segment into csf, scalp and skull. This option also gives a
>>>> segmentation of the gm and wm. All voxels of the head are assigned to
>>>> one of the labels.
>>>>
>>>> Nevertheless, the segmentation obtained in the file aseg.mgz of the
>>>> cortical ribbon is of much better quality the fast mri_watershed -LABEL
>>>> one. The problem is now if I use the csf obtained with mri_watershed
>>>> -LABEL together with the aseg.mgz gm segmentation, some voxels in the
>>>> border between cortical ribbon and csf are unassigned.
>>>>
>>>> My question is then : how could I generate a csf map like the one
>>>> obtained with mri_watershed -LABEL, but that is complementary of the
>>>> segmentation present in aseg.mgz of the cortical ribbon ?
>>>>
>>>> Thanks a lot in advance,
>>>>
>>>> Best,
>>>>
>>>>
>>>
>>>
>>> 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] TRACULA -prep error

[Watson, Christopher]

I've just taken to making the sym links myself after running trac-prep and 
before running bedpostx. Then everything should run normally.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki 
[ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, August 16, 2012 4:24 PM
To: Richard Binney
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA -prep error

Hi Richard - In the listing you sent below I do see the a
nodif_brain_mask.nii.gz and a control.dat, although I have no idea what
control.dat is. As for data.nii.gz, it should be created as a symbolic
link to dwi.nii.gz, since bedpostx indeed expects it to be called "data".
I have not seen this problem before, but does it occur only when you rerun
and overwrite things in the same directory, or also when you start a fresh
run on a previously non-existent directory?

a.y

On Thu, 16 Aug 2012, Richard Binney wrote:

> Hi Anastasia et al.,
>
> I previously had TRACULA running wonderfully on a test dataset. I was tasked
> with writing an in-house step-by-step manual for dummies. Since then, a
> colleague has followed my manual with a new dataset and had problems. After
> trying to determine whether it was her install or something about her data
> and failing to find anything, I returned to re-run the subject I had already
> successfully processed. Nothing has changed in my install (TRAC-all version
> etc) ODDLY, this re-run is suffering from the same problem as my colleague.
>
> We ran trac-all -prep -dmrirc and it exited without any errors. However,
> there seem to be some files missing from the output:
>
> control.dat
>
> data.nii.gz
>
> nodif_brain_mask.nii.gz
>
>
>
> Bedpostx will not run due to the data file being missing and I'm sure the
> other missing files will cause problems.
>
> What is going on?
>
> I knew to look for these files as at some point I found the following list
> for the \dmri\. I can not re-find a post with this list so I'm sorry if it
> related to a solution to our current problem.
>
> Please help
>
> Richard
>
> brain_anat_mni.nii.gz
>
> dtifit_L2.nii.gz  dwi_orig_flip.nii.gz
>
> brain_anat.nii.gz
>
> dtifit_L3.nii.gz
>
> dwi_orig.mghdti.bvals
>
> brain_anat_orig.nii.gz  dtifit_MD.nii.gz
>
> dwi_orig.mghdti.bvecs
>
> bvals
>
> dtifit_MO.nii.gz  dwi_orig.nii.gz
>
> bvecs
>
> dtifit_S0.nii.gz  dwi_snr.txt
>
> bvecs.norot
>
> dtifit_V1.nii.gz  lowb_brain.nii.gz
>
> control.dat
>
> dtifit_V2.nii.gz
>
> lowb.nii.gz
>
> data.nii.gz
>
> dtifit_V3.nii.gz
>
> mni
>
> dtifit_FA.nii.gz
>
> dwi.ecclog
>
> nodif_brain_mask.nii.gz
>
> dtifit_L1.nii.gz
>
> dwi.nii.gz
>
>  xfms
>
>
>
>

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[Freesurfer] Whole Brain Volume

[Christopher McCarthy]

Hello All,

We are looking into alternative measures for whole brain volume to use for
covarying, and the previous topic mentioned mris_volume as a possibility
but it isn't located on the top of the aseg file.  Has it been moved?

Chris McCarthy
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[Freesurfer] Dynamic PET _ Time frame averaging

[Christopher Coello]

Dear Freesurfer community,

Just a simple question : is there a command-line that allows averaging 
voxel values from different time frames, transforming dynamic 4D volume 
into a static 3D volume ?
mri_convert allows to skip some early frames (--nskip) or drop some at 
the end (--ndrop), but I don't see any option for averaging.

Thanks for your help,

Best,


-- 

Christopher Coello, Ph.D.
Preclinical PET/CT unit
http://www.med.uio.no/imb/english/research/about/infrastructure/pet/
Institute of Basic Medical Sciences
Faculty of Medicine, University of Oslo
tel. +4745154516
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Re: [Freesurfer] Dynamic PET _ Time frame averaging

[Christopher Coello]

Works fine.

Thanks Doug.

On 05.10.2012 18:37, Douglas N Greve wrote:
> Hi Christopher,
> try mri_concat 4dvolume.nii --mean --o 3dvolume.nii
> doug
>
> On 10/05/2012 03:05 AM, Christopher Coello wrote:
>> Dear Freesurfer community,
>>
>> Just a simple question : is there a command-line that allows averaging
>> voxel values from different time frames, transforming dynamic 4D volume
>> into a static 3D volume ?
>> mri_convert allows to skip some early frames (--nskip) or drop some at
>> the end (--ndrop), but I don't see any option for averaging.
>>
>> Thanks for your help,
>>
>> Best,
>>
>>
>

-- 

Christopher Coello, Ph.D.
Preclinical PET/CT unit
http://www.med.uio.no/imb/english/research/about/infrastructure/pet/
Institute of Basic Medical Sciences
Faculty of Medicine, University of Oslo
tel. +4745154516
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[Freesurfer] Error with mris_calc

[Christopher Coello]

Dear Freesurfer community,

Using freeview, I can visualize that two binary volumes are overlaying 
in some parts.
freeview -v binF1.mgz -v binF2.mgz

When using the command
mris_calc -o out.mgz binF1.mgz mul binF2.mgz
to create the intersection of these two volumes, I obtain a file with 
only zeros.
To debug, I added the two volumes
mris_calc -o out.mgz binF1.mgz add binF2.mgz
I was surprise to see that one of the volumes (binF1) is shifted of tens 
of voxels along an axis.
When doing
mris_calc -o out.mgz binF2.mgz add binF1.mgz,
the binF2 is shifted.

Is that a bug ?

mris_calc : v.1.37.2.4 2011/04/04
freeview : v1.0 2011/05/22

Best,

Christopher



-- 

Christopher Coello, Ph.D.
Preclinical PET/CT unit
http://www.med.uio.no/imb/english/research/about/infrastructure/pet/
Institute of Basic Medical Sciences
Faculty of Medicine, University of Oslo
tel. +4745154516
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Re: [Freesurfer] Error with mris_calc

[Christopher Coello]

Hi Bruce,

They have the same geometry, but didn't have the same center (128 128 
128 vs 128 118 72). I guess freeview doesn't not show this difference, 
or handle it in a different way than mris_calc.
Nevertheless, when both volumes have the same center (mri_convert -oc 0 
0 0), the mris_calc -o out.mgz binF2.mgz mul binF1.mgz gives the correct 
and expected result.
Should have checked this earlier, but I have been lured by the overlay 
in freeview.

@ Rudolph : "problem" solved. I didn't express myself correctly, sorry 
about that. The content of binF1 and binF2 were absolutely not modified, 
the input volume was "shifted" (see why below) so that the resulting 
volume was different from what we expected when seeing the overlay in 
freeview.

Best,

Christopher

On 12.10.2012 16:57, Bruce Fischl wrote:
> Hi Christophe
>
> what does mri_info tell you about them? Are they the same geometry?
> Bruce
> On Fri, 12 Oct 2012, Christopher Coello wrote:
>
>> Dear Freesurfer community,
>>
>> Using freeview, I can visualize that two binary volumes are overlaying
>> in some parts.
>> freeview -v binF1.mgz -v binF2.mgz
>>
>> When using the command
>> mris_calc -o out.mgz binF1.mgz mul binF2.mgz
>> to create the intersection of these two volumes, I obtain a file with
>> only zeros.
>> To debug, I added the two volumes
>> mris_calc -o out.mgz binF1.mgz add binF2.mgz
>> I was surprise to see that one of the volumes (binF1) is shifted of tens
>> of voxels along an axis.
>> When doing
>> mris_calc -o out.mgz binF2.mgz add binF1.mgz,
>> the binF2 is shifted.
>>
>> Is that a bug ?
>>
>> mris_calc : v.1.37.2.4 2011/04/04
>> freeview : v1.0 2011/05/22
>>
>> Best,
>>
>> Christopher
>>
>>
>>
>>
>
>
> 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.
>

-- 

Christopher Coello, Ph.D.
Preclinical PET/CT unit
http://www.med.uio.no/imb/english/research/about/infrastructure/pet/
Institute of Basic Medical Sciences
Faculty of Medicine, University of Oslo
tel. +4745154516
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Re: [Freesurfer] TRACULA some fiber volumes being too small

[Watson, Christopher]

There were recently a few messages on the list regarding this.
What you should do is include "set reinit=1" in your config file, and then run
trac-all -priors -c $CONFIG
trac-all -path -c $CONFIG

Make sure you only include the pathway of interest in the config file; 
otherwise, it will re-run the analysis for all 18.
That has worked for me most of the time.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fernando Ventrice 
[fventr...@fleni.org.ar]
Sent: Thursday, October 18, 2012 10:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FW: TRACULA some fiber volumes being too small

Dear Freesurfer/Tracula users,
Finally I could successfully test Tracula and I think it is amazing what it can 
do automatically. These are the commands I used:

export FREESURFER_HOME=${HOME}/Programs/freesurfer_510 && source 
$FREESURFER_HOME/SetUpFreeSurfer.sh
source /etc/fsl/fsl.sh
export FSLPARALLEL=condor
trac-all -prep -c 
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
trac-all -bedp -c 
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
# "trac-all -bedp" gave some errors so I used bedpostx directly:
bedpostx 
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri
trac-all -path -c 
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
freeview -tv 
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dpath/merged_avg33_mni_flt.mgz
 -v 
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri/dtifit_FA.nii.gz
 &

All finished without errors, but there seems to be a problem with CC Forceps 
Mayor volume, which gave very small values. Is this OK or I made some mistake? 
First I tested with some patient and other fiber tracks also gave very small 
volumes. I attached some pictures and the dmrirc and trac-all log files.
Best,
Fernando Ventrice

El contenido del presente mensaje y el de sus adjuntos, es confidencial, 
privado y de uso exclusivo de los destinatarios a los cuales está dirigido, 
pudiendo contener información legalmente protegida. Queda prohibida la 
revisión, divulgación, publicación, modificación, copia, distribución o acción 
en relación con esta información, por personas o entidades distintas al 
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exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
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Re: [Freesurfer] Red Hat Enterprise Linux 6?

[Watson, Christopher]

I've had no problems with it.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Brain Apprentice 
[bapprent...@gmail.com]
Sent: Tuesday, November 20, 2012 11:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Red Hat Enterprise Linux 6?

Hi Surfers,

I was wondering if FreeSurfer v5.1.0 (CentOS 4 x86 (64b)) or V5.X will work on 
Red Hat Enterprise Linux 6?

The reason I ask is that the supercomputer at Brigham Young University is going 
through a major overhaul: changing the OS, adding more nodes, and adding more 
storage.

I am just curious what type of problems I will run into. I know I will need to 
rerun all brains through the new system but more concerning to me is if I can 
run FreeSurfer at all on the new system.

Thanks in advance for any suggestions or insights you can offer.



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Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

[Watson, Christopher]

Hi Bruce,
So would you recommend acquiring a T2 in addition to an (ME)MPRAGE/SPGR? i.e. 
is it worth squeezing another acquisition into a protocol?

Chris

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, November 20, 2012 3:01 PM
To: Winter, Warren
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface 
recons?

Hi Warren

yes, it will be part of the upcoming 5.2 release, hopefully in Dec. It
will use either a FLAIR or T2 (ideally T2-SPACE for either one)

cheers
Bruce
On Tue, 20
Nov 2012, Winter, Warren wrote:

> Hi all,
>
> Back in January and October Bruce mentioned that he had under development 
> some scripts designed to utilize T2-SPACE images for better pial surface 
> reconstruction in the presence of dura -- I was just wondering if any of that 
> is ready for trial?
>
> Thanks!
>
> Warren
>
> --
> Warren Winter
> Research Coordinator
> Boston Children's Hospital
> Sheridan Laboratory of Cognitive Neuroscience
> Division of Developmental Medicine
> 1 Autumn Street, AU 650
> Boston, MA 02215
> 857-218-5224
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] Cortical thickness analysis on data acquired from multiple sites

[Watson, Christopher]

Hi Bruce,
What if she created an FSGD file, and instead of just having "patients" and 
"controls", she would have "patients1.5", "patients3", etc.? With over 400 
subjects this should be feasible, i.e. the loss of d.f. is worth running the 
combined analysis.

Chris

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, February 18, 2013 10:59 AM
To: Jorge Jovicich
Cc: Sinead Kelly; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Cortical thickness analysis on data acquired from 
multiple sites

Hi Sinead

I agree with Jorge - there is bound to be a substantial scanner effect. You
might be better off keeping the data separate and treating the 3T as a
confirmatory study.

cheers
Bruce



On
Mon, 18 Feb 2013, Jorge Jovicich wrote:

> Dear Sinead,
>
> we found global significant differences in thickness between 1.5T and
> 3T, in a group of subjects that was scanned at both scanners
> (http://www.ncbi.nlm.nih.gov/pubmed/16651008). I think that nothing
> stops you from doing the analysis, but maybe model in a field effect to
> asset it in your own data.
>
> Cheers,
>
> jorge
>
>
> On 18/02/2013 16:32, Sinead Kelly wrote:
>> Dear members,
>>
>> I would like to get your opinion on this issue - I have a dataset of
>> over 400 subjects but under half of this data was acquired on a 1.5T
>> scanner and the rest was acquired on a 3T scanner. Would it be
>> acceptable to conduct cortical thickness analysis on the combined
>> dataset? From reading the literature it seems that this is not a major
>> problem but I just wanted to get some more thoughts on this.
>>
>> Thank you for your help,
>>
>> Sinead
>>
>> --
>> Sinead Kelly
>> Neuropsychiatric Genetics Group
>> Trinity Centre
>> St. James's Hospital
>> Dublin 8
>
>
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Re: [Freesurfer] nu_correct: Command not found error

[Christopher Bell]

I have encountered this error in the past, and I think it was because I was
not
sourcing SetUpFreeSurfer.sh correctly. That is the the script
that sets up the MNI_DIR  I think.

echo $MNI_DIR or whatever it is called and it should show you
if it is being setup properly. It may be pointing to the system default
as you say or more likely the variable is not defined at all.





On Mon, Mar 11, 2013 at 7:58 AM, Nick Schmansky
wrote:

> Sinead,
>
> In your freesurfer directory, is there an 'mni' directory?  under that
> directory is a 'bin' directory where nu_correct should be.
>
> Nick
>
> > Hi Nick,
> >
> > I had a look in the bin directory and there is a command called
> > 'mri_nu_correct.mni'. Is this the command the script is trying to call?
> > This is the only nu_correct command I could find. I specify v5.2 in the
> > script as there are other versions installed on the clusters.
> >
> > Thanks again for your help!
> >
> > Sinead
> >
> > On 9 March 2013 23:23, Nick Schmansky  wrote:
> >
> >> Sinead,
> >>
> >> Is 'nu_correct' in your freesurfer/mni/bin directory?  Are you being
> >> careful to run the setup script for just freeview 5.2 and not other
> >> packages or versions which might mess-up the perl paths?
> >>
> >> Nick
> >>
> >>
> >> On Fri, 2013-03-08 at 09:50 +, Sinead Kelly wrote:
> >> > Dear all,
> >> >
> >> >
> >> > I am currently running cortical thickness analysis using Freesurfer
> >> > v5.2 on a high performance computing cluster however, when I run the
> >> > 'recon_all' command I get the following error
> >> >
> >> >
> >> > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0
> >> > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0
> >> > INFO: SUBJECTS_DIR is /home/users/kellys37/CT_TEST/CON3140
> >> > Actual FREESURFER_HOME /home/support/tcin/apps/freesurfer/5.2.0
> >> > Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03
> >> > EST 2012 x86_64 x86_64 x86_64 GNU/Linux
> >> > nu_correct: Command not found.
> >> > #
> >> > #@# MotionCor Thu Mar  7 11:44:10 GMT 2013
> >> > Found 1 runs
> >> > /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz
> >> > Checking for (invalid) multi-frame inputs...
> >> > WARNING: only one run found. This is OK, but motion
> >> > correction cannot be performed on one run, so I'll
> >> > copy the run to rawavg and continue.
> >> >
> >> >
> >> >  cp /home/users/kellys37/CT_TEST/CON3140/001/mri/orig/001.mgz
> >> /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
> >> >
> >> >
> >> > /home/users/kellys37/CT_TEST/CON3140/001
> >> >
> >> >
> >> >  mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
> >> /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform
> >> >
> >> >
> >> > mri_convert /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz
> >> /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz --conform
> >> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> >> > reading
> >> > from /home/users/kellys37/CT_TEST/CON3140/001/mri/rawavg.mgz...
> >> > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> >> > i_ras = (-0.9997, 0.0244327, -0.00148148)
> >> > j_ras = (0.0239203, 0.987991, 0.152651)
> >> > k_ras = (-0.00519336, -0.15257, 0.988279)
> >> > Original Data has (0.898438, 0.898438, 0.9) mm size and (256, 256,
> >> > 180) voxels.
> >> > Data is conformed to 1 mm size and 256 voxels for all directions
> >> > changing data type from float to uchar (noscale = 0)...
> >> > MRIchangeType: Building histogram
> >> > Reslicing using trilinear interpolation
> >> > writing to /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz...
> >> >
> >> >
> >> >  mri_add_xform_to_header
> >> > -c
> >> /home/users/kellys37/CT_TEST/CON3140/001/mri/transforms/talairach.xfm
> >> /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz
> >> /home/users/kellys37/CT_TEST/CON3140/001/mri/orig.mgz
> >> >
> >> >
> >> > INFO: extension is mgz
> >> > #
> >> > #@# Talairach Thu Mar  7 11:44:32 GMT 2013
> >> > /home/users/kellys37/CT_TEST/CON3140/001/mri
> >> >
> >> >
> >> >  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
> >> > --no-rescale --i orig.mgz --o orig_nu.mgz
> >> >
> >> >
> >> > Linux tcin-n02.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03
> >> > EST 2012 x86_64 x86_64 x86_64 GNU/Linux
> >> >
> >> >
> >> > recon-all -s 001 exited with ERRORS at Thu Mar  7 11:44:38 GMT 2013
> >> >
> >> >
> >> > For more details, see the log
> >> > file /home/users/kellys37/CT_TEST/CON3140/001/scripts/recon-all.log
> >> > To report a problem, see
> >> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >> >
> >> >
> >> >
> >> >
> >> > I had did not encounter this error when using an older version of
> >> > Freesurfer on our clusters. Do you know if there is any way to resolve
> >> > this problem? Any advice would be appreciated.
> >> >
> >> >
> >> > Kind regards,
> >> >
> >> >
> >> > Sinead
> >> 

[Freesurfer] long_qdec_table

[Christopher McCarthy]

Hey All,

I am trying to turn my long.qdec.table.dat into a cross.qdec.table.dat
using the following command:

long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out
 ./qdec/cross.qdec.table.dat

However, when I try and load it into QDEC afterwards I get the following
error:

Loading data table /data/freesurfer/qdec/cross.qdec.table.dat...
Number of columns:  103
fsid column:1
Number of factors:  102
Number of subjects: 0
ERROR: QdecDataTable::Load: number of subjects = 0
Error loading the data table.

I attached both the long.qdec and the cross.qdec tables, if someone knows
what I am doing wrong, I would love some help!

Chris


long.qdec.table.dat
Description: Binary data


cross.qdec.table.dat
Description: Binary data
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Re: [Freesurfer] long_qdec_table

[Christopher McCarthy]

Hey Martin,

Thanks for your quick response and all the great work you've done on the
longitudinal pipeline.  Replacing the LongQdecTable.py did the trick.

Thanks again,

Chris


On Thu, Mar 14, 2013 at 12:38 PM, Martin Reuter  wrote:

>  Hi Chris,
>
> try to
> rename the LongQdecTable.* files in your FS install and place a new
> LongQdecTable.py file there
>
> from here:
> http://martinos.org/~mreuter/LongQdecTable.py
>
> the new one uses universal newline support. Not sure if the Python on your
> system supports this. Let me know (also what system you are using and what
> OS version, also the version of Python)
>
> Thanks, Martin
>
>
>
> On 03/13/2013 08:20 AM, Christopher McCarthy wrote:
>
> Hey All,
>
>  I am trying to turn my long.qdec.table.dat into a cross.qdec.table.dat
> using the following command:
>
> long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out
>  ./qdec/cross.qdec.table.dat
>
>  However, when I try and load it into QDEC afterwards I get the following
> error:
>
>  Loading data table /data/freesurfer/qdec/cross.qdec.table.dat...
> Number of columns:  103
> fsid column:1
> Number of factors:  102
> Number of subjects: 0
>  ERROR: QdecDataTable::Load: number of subjects = 0
> Error loading the data table.
>
>  I attached both the long.qdec and the cross.qdec tables, if someone
> knows what I am doing wrong, I would love some help!
>
> Chris
>
>
>
>
> ___
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>
>
> --
> Dr. Martin Reuter
> Assistant in Neuroscience - Massachusetts General Hospital
> Instructor in Neurology   - Harvard Medical School
> MGH / HMS / MIT
>
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
>
> Phone: +1-617-724-5652
> Email:
>mreu...@nmr.mgh.harvard.edu
>reu...@mit.edu
> 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
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> but does not contain patient information, please contact the sender and
> properly
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[Freesurfer] Expert file for recon-all -hires

[Christopher Markiewicz]

Hi all,

If I'm reading this <
https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon> correctly,
the current best practice for `-hires` is to include an expert file
containing "mris_inflate -n 15", and that this should work for all voxel
sizes (0.75mm)^3 - (1mm)^3? Or do we need to empirically determine the best
value for a given voxel size, and if so, what should be the criteria for
making this determination?

Thanks,
Chris Markiewicz
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Re: [Freesurfer] Parallelization not working as implemented

[Bird, Christopher]

Hello,

I'd like to suggest an alternative, for anyone interested in going faster than 
4 hours. I can't verify compatibility from a technical standpoint, but GNU 
Parallel (https://www.gnu.org/software/parallel/) has worked fast and run to 
completion reliably when batching multiple recon-all subjects. You'll just need 
to determine your batch size based on your RAM (4GB per subject has worked ok 
for me). It takes about 20 hours on a good computer, which is equivalent to 
running recon-all on a single subject without parallelization. So, for example, 
with 32 subjects run together on 32 cores with 128GB of RAM available, it 
averages out to just over half an hour per subject.

First, you would just need to give parallel a text file of your raw data (your 
nifti files) and their directory. You could make one like so:

freesurferRawData=/path/to/your/raw/data
ls $freesurferRawData | grep .nii > $freesurferRawData/subjects.txt

Next, you could decide a max number of subjects that you want to run 
simultaneously. Note that the number of subjects in your list can be larger 
than this number, or vice versa. You can set your maximum batch size based on 
your available RAM like so:

#max subjects that can be run with >= 4GB RAM available per subject
maxSubjects=$( free -t -m | grep ^Total: | tr -s ' ' | cut -d ' ' -f 4 )
maxSubjects=$(( maxSubjects/4096 ))
#trucated float < 1
[ $maxSubjects != 0 ] || maxSubjects=1

And then run parallel once you've set $maxSubjects, $freesurferRawData, and 
subjects.txt:

parallel -a $freesurferRawData/subjects.txt -j$maxSubjects --joblog 
$freesurferRawData/joblog.txt --progress --group recon-all -all -subjid {1.} -i 
$freesurferRawData/{1}

I've included some useful parallel flags:

a. joblog.txt will list all your completed subjects as they finish.
b. a progress indicator in terminal lets you know how many are currently 
running and how many have completed
c. rather than mixing up the text in real time, the entire recon-all terminal 
output will be display in the correct order once a subject has completed 
(--group)
d. The subject ID in your subjects folder will be the name of the raw file 
without the extension

Regards,
Chris

-Original Message-
From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] 
Sent: Tuesday, February 14, 2017 9:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Parallelization not working as implemented

I will have to inspect our Mac test results for parallel processing, but 
generally speaking we do not see much performance increase in terms of run 
times after using 4 threads.

On 02/13/2017 06:13 PM, Francis Tyson Thomas wrote:
> I did provide the execution times in my first email. I have copied it 
> once more for quick reference,
>
> no parallelization :  7
> hrs and 58 mins
> -parallel   (coarse parallelization):  4 hrs and
> 39 mins
> -parallel -openmp 8 (fine parallelization) :  4 hrs and 34 mins
> -parallel -openmp 14   (fine parallelization ):  4 hrs and 37 mins
>
>
> I have attached the logs to this email. The naming convention is as 
> follows,
>
> serial_recon-all.log   :   serial execution with no parallelization
> parallel_recon-all.log:   parallelization using -parallel
> openmp8_recon-all.log :   parallelization using -parallel -openmp 8
> openmp14_recon-all.log   :   parallelization using -parallel -openmp 14
>
> I'll rerun this with/-time/ later and see what I get. It is gonna take 
> some time to get those logs.
>
> Thanks,
> Tyson
>
> On Mon, Feb 13, 2017 at 3:19 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> What are your execution times? Can you send the recon-all files for your
> parallel and non-parallel runs? If you run it with -time, then lots of
> information will be printed to the log for each command. This can be
> helpful for debugging these types of things.
>
>
> On 02/13/2017 05:13 PM, Francis Tyson Thomas wrote:
> > Hi,
> >
> > I have run recon-all with both -parallel enabled (including different
> > openmp threads) and disabled and I'm not able to get processing times
> > same as the information provided in recon-all help. The CPU used is
> > *Dual Intel **Xeon E5-2623 v3* paired with 32GB DDR4 RAM. Is the
> > configuration presented in recon-all help a dual cpu configuration?
> >
> > Following are the runtimes I have obtained,
> >
> > no parallelization   :  7 hrs and 58 mins
> > -parallel (coarse parallelization)  :  4 hrs and 39 mins
> > -parallel (fine parallelization; -openmp 8):  4 hrs and 34 mins
> > -parallel (fine parallelization; -openmp 14)  :  4 hrs and 37 mins
> >
> > Somehow varying the number of threads is having no effect in the
> > execution time of recon-all as can been seen from the processing
> > times. If you

[Freesurfer] Adjust bbregister affine to target raw T1

[Christopher Markiewicz]

Hi all,

Suppose you have a sub-pipeline:

$ recon-all -s $SUBJ -i $T1 -all
$ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat --fslmat
fsl.mat

Now `bbreg.dat`/`fsl.mat` is registered to
`$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to $T1?

I've tried:

$ tkregister2 --no-edit --mov $EPI --reg bbreg.dat --targ $T1 --fslregout
adjusted.mat

And that's clearly wrong, but I'm kind of stuck on where to go from here.
Anybody see where I'm going wrong?

Thanks,
Chris
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Re: [Freesurfer] Adjust bbregister affine to target raw T1

[Christopher Markiewicz]

Hi Doug,

This is the final line with "cost" in it:

MinCost: 0.862331 7440.183178 7411.264107 -1.819400

We're switching from FLIRT BBR (two-pass) to bbregister when there's a
reconstructed subject available, so I'm using `--init-fsl` to try to
minimize the differences in the pipeline in the two cases, but I can try
`--init-coreg` if there's something wrong with the initialization.

Thanks,
Chris


On Thu, Mar 9, 2017 at 3:29 PM, Douglas N Greve 
wrote:

> that should have worked. what was the bbregister final cost function? It
> could have been that fsl did not provide a good initial registration. If
> you have v6, you can leave off --init-fsl and it will use mri_coreg
> (which is more robust).
>
>
> On 03/09/2017 03:24 PM, Christopher Markiewicz wrote:
> > Hi all,
> >
> > Suppose you have a sub-pipeline:
> >
> > $ recon-all -s $SUBJ -i $T1 -all
> > $ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat
> > --fslmat fsl.mat
> >
> > Now `bbreg.dat`/`fsl.mat` is registered to
> > `$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to
> $T1?
> >
> > I've tried:
> >
> > $ tkregister2 --no-edit --mov $EPI --reg bbreg.dat --targ $T1
> > --fslregout adjusted.mat
> >
> > And that's clearly wrong, but I'm kind of stuck on where to go from
> > here. Anybody see where I'm going wrong?
> >
> > Thanks,
> > Chris
> >
> >
> > ___
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> > 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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>
>
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> is
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> properly
> dispose of the e-mail.
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[Freesurfer] BUG: bbregister --init-best needs to unset InitCoreg

[Christopher Markiewicz]

Hi all,

bbregister --init-best always produces "ERROR: cannot spec an init method
with --init-best", because InitCoreg is defined as 1 by default, and never
set to 0 by --init-best. (Setting something else that unsets InitCoreg will
trigger the same error.)

Example, given SUBJ and EPI:

$ bbregister --init-best --s $SUBJ --mov $EPI --o ${EPI%.nii.gz}_bbr.nii.gz
--reg ${EPI%.nii.gz}_bbr.dat
ERROR: cannot spec an init method with --init-best

Using FreeSurfer 6.0 release installed on an Ubuntu 16.04 machine.

Thanks,
Chris
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Re: [Freesurfer] Adjust bbregister affine to target raw T1

[Christopher Markiewicz]

Hi Doug,

As an update, --init-coreg produced essentially the same result as
--init-fsl; however, that was on EPIs we've discovered were LR flipped
during reconstruction, so I've switched to a different test subject for now.

Now, for --init-fsl and --init-coreg, respectively, we get:

MinCost: 0.552768 531.638763 549.553173 0.397916
MinCost: 0.552773 531.586204 549.501644 0.394639

Again, very little difference between the two cases, so that's good. I'm
not really sure how to judge what a reasonable min cost is. What criteria
do you use, and is there more detailed documentation somewhere?

Thanks,
Chris


On Fri, Mar 10, 2017 at 10:41 AM, Douglas Greve 
wrote:

> That min cost (.86) is too high for sure. My guess is that it is the fsl
> init. In general, bbregister is pretty insensitive to the initialization
> method (as long as the init does not fail), so I would not worry about some
> being done with coreg and some with flirt
>
> On 3/9/17 3:40 PM, Christopher Markiewicz wrote:
>
> Hi Doug,
>
> This is the final line with "cost" in it:
>
> MinCost: 0.862331 7440.183178 7411.264107 -1.819400
>
> We're switching from FLIRT BBR (two-pass) to bbregister when there's a
> reconstructed subject available, so I'm using `--init-fsl` to try to
> minimize the differences in the pipeline in the two cases, but I can try
> `--init-coreg` if there's something wrong with the initialization.
>
> Thanks,
> Chris
>
>
> On Thu, Mar 9, 2017 at 3:29 PM, Douglas N Greve  > wrote:
>
>> that should have worked. what was the bbregister final cost function? It
>> could have been that fsl did not provide a good initial registration. If
>> you have v6, you can leave off --init-fsl and it will use mri_coreg
>> (which is more robust).
>>
>>
>> On 03/09/2017 03:24 PM, Christopher Markiewicz wrote:
>> > Hi all,
>> >
>> > Suppose you have a sub-pipeline:
>> >
>> > $ recon-all -s $SUBJ -i $T1 -all
>> > $ bbregister --s $SUBJ --mov $EPI --init-fsl --t2 --reg bbreg.dat
>> > --fslmat fsl.mat
>> >
>> > Now `bbreg.dat`/`fsl.mat` is registered to
>> > `$SUBJECTS_DIR/$SUBJ/mri/T1.mgz`; what's the best way to register to
>> $T1?
>> >
>> > I've tried:
>> >
>> > $ tkregister2 --no-edit --mov $EPI --reg bbreg.dat --targ $T1
>> > --fslregout adjusted.mat
>> >
>> > And that's clearly wrong, but I'm kind of stuck on where to go from
>> > here. Anybody see where I'm going wrong?
>> >
>> > Thanks,
>> > Chris
>> >
>> >
>> > ___
>> > 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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[Freesurfer] First-level GLM on externally-preprocessed functionals

[Christopher Markiewicz]

Hi list,

We're working on making a preprocessing stream that will be generally
accessible to different analysis streams, including FreeSurfer. One
component of this is sampling functional volumes to FreeSurfer meshes, and
I want to test this component by running a simple first-level GLM in
FreeSurfer.

I've always done this through the FSFAST pipeline, but that may be a bit
much, given that I'm starting from surface time series (the equivalent of
`$FUNCTIONALS_DIR/$SESS_ID/bold/$RUN/fmcpr.sm0.fsaverage.lh.nii.gz`, but as
a GIFTI file).

Supposing I have a paradigm file and the files described above, what's the
best way to do a basic GLM? Would it be to `mri_surf2surf` our GIFTI
surfaces into `fmcpr.sm0.fsaverage.lh.nii.gz` files in a FSFAST directory
structure, and pick up at `mkanalysis-sess`? Or is there a more
straightforward way to just get a simple set of contrasts to compare with a
volumetric analysis?

Thanks in advance,
Chris Markiewicz
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[Freesurfer] Survey on inputs for surface-based analysis pipelines

[Christopher Markiewicz]

Hi list,

We're working on FMRIPREP , a 
pipeline aimed at performing baseline preprocessing, and producing cleaned 
structural and functional data which can be fed into any of a number of 
analysis pipelines.

We've recently begun incorporating surface reconstruction and surface-mapped 
functionals, and we'd like to get feedback on what outputs would be most 
valuable to people, in terms of formats, spaces and sampling strategies.

1) What surfaces do you use for sampling functional data and visualization? If 
you use down-sampled surfaces, do you have a preferred down-sampling strategy 
or target mesh?

2) What statistical analyses and model-fitting tools do you use for 
surface-based analyses? And are there any particular considerations you have 
for preparing your data for use by these tools?

I appreciate your time and any input you may have to help us build a tool that 
fits the needs of the community.

Thanks,
-- 
Chris Markiewicz
Center for Reproducible Neuroscience
Stanford University


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[Freesurfer] mri_glmfit error (mri_reshape number of elements)

[Mcnorgan, Christopher]

Hi,
I’m running a group-level analysis and have encountered an error that results 
in a core dump. The first-level analyses were run using the fsaverage surfaces, 
rather than self surfaces. I’ve already inspected the individual contrasts, 
loading the fsaverage surface in tksurfer and rendering each subject’s contrast 
as an overlay, and would now like to compute the group-level results.

I first ran isxconcat-sess, and saw no errors indicated in the program output.

mri_glmfit was then called as followed, and produced the following output (same 
result for the rh):

$ mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surf fsaverage lh 
--glmdir glm.wls --nii.gz
Reading source surface /home/chris/LDT/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65416.648438
AvgVtxArea   0.399267
AvgVtxDist   0.721953
StdVtxDist   0.195470

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo
cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surf fsaverage 
lh --glmdir glm.wls --nii.gz
sysname  Linux
hostname brocasarea
machine  x86_64
user chris
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 1
y/home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz
logyflag 0
usedti  0
labelmask  /home/chris/LDT/fsaverage/label/lh.cortex.label
maskinv 0
glmdir glm.wls
IllCondOK 0
ReScaleX 1
DoFFx 0
wFile cesvar.nii.gz
weightinv  1
weightsqrt 1
Creating output directory glm.wls
Loading y from /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz
Saving design matrix to glm.wls/Xg.dat
Normalized matrix condition is 1
Matrix condition is 1
Found 149955 points in label.
ERROR: mri_reshape: number of elements cannot change
  nv1 = 163842, nv1 = 537168
Pruning voxels by thr: 0.00
Segmentation fault (core dumped)

This seems to have its root in a mismatch between the vertices in the fsaverage 
lh.cortex label and those in the contrast data. However, I carried out 
subject-level analyses in the fsaverage surface space specifically to 
facilitate a group-level analysis in fsaverage surface space, so I can’t see 
where I went wrong. The only other post I could find that was similar was 
related to an attempt to carry out a group analysis in native surface space, 
which is not the case here.

Thanks for your time

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Re: [Freesurfer] negative header after preproc-sess

[Christopher Markiewicz]

Hi Doug,

I wonder if there's a plan to move to NIfTI-2 as the default encoding for 
.nii(.gz) images that would can't be encoded in a standard-conforming NIfTI-1? 
I believe all of the major packages support NIfTI-2 in their latest releases 
(with the possible exception of ANTs, which I don't believe handles surface 
data in any event).

Chris Markiewwicz

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

Sent: Wednesday, July 5, 2017 7:07:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] negative header after preproc-sess

When the nifti standard was adopted, they used a short int to represent the 
dimensions. Unfortunately, this only allows for a maximum dimension of 32k, 
which is not big enough for surfaces. So I hacked the FS nifti format to put a 
-1 as the first dim at which point the FS code will go to another place in the 
header to get the spatial dimensions. It is possible to reshape the spatial 
dimensions as long as the largest prime factor is less than 32k (see 
mri_surf2surf with --reshape option). Other than that, you might ask the 
nibabel people to program the same hack.

On 6/25/17 6:48 AM, Bai Haohao wrote:
Hello Freesurfer experts,

I am running my data with preproc-sess to project my func data to individual 
anatomy file, and the command shows as below:

preproc-sess -sf ${Sesslist} -fsd "bold" -surface self lhrh -fwhm 0 -per-run 
-force

And the subjectname point to the subject dir that created after recon-all.

After the running completed, I try to load data from fmcpr.sm0.self.lh.nii.gz 
with nibabel, and I get this error info:

>>> f.get_data()
Traceback (most recent call last):
  File "", line 1, in 
  File "/usr/lib/pymodules/python2.7/nibabel/spatialimages.py", line 341, in 
get_data
return np.asanyarray(self._data)
  File "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py", line 512, in 
asanyarray
return array(a, dtype, copy=False, order=order, subok=True)
  File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 55, in 
__array__
self._data = self._read_data()
  File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 60, in 
_read_data
data = self.header.data_from_fileobj(fileobj)
  File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 486, in 
data_from_fileobj
data = self.raw_data_from_fileobj(fileobj)
  File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 458, in 
raw_data_from_fileobj
return array_from_file(shape, dtype, fileobj, offset)
  File "/usr/lib/pymodules/python2.7/nibabel/volumeutils.py", line 493, in 
array_from_file
raise IOError(msg)
IOError: Expected -1804 bytes, got 264809160 bytes from file 
"fmcpr.vol2surf.lh.nii.gz"
 - could the file be damaged?

Then I check the file header by nibabel, and I get this:

>>> print(f.get_header())
 object, endian='<'
sizeof_hdr  : 348
data_type   :
db_name :
extents : 0
session_error   : 0
regular :
dim_info: 0
dim : [  4  -1   1   1 451   1   1   1]
intent_p1   : 0.0
intent_p2   : 0.0
intent_p3   : 0.0
intent_code : none
datatype: float32
bitpix  : 32
slice_start : 0
pixdim  : [-1.  1.  1.  1.  2.0072  
1.  1.
  1.]
vox_offset  : 352.0
scl_slope   : 0.0
scl_inter   : 0.0
slice_end   : 0
slice_code  : unknown
xyzt_units  : 10
cal_max : 0.0
cal_min : 0.0
slice_duration  : 0.0
toffset : 0.0
glmax   : 0
glmin   : 146790
descrip : FreeSurfer May 13 2013
aux_file:
qform_code  : scanner
sform_code  : scanner
quatern_b   : -0.0115927606821
quatern_c   : -0.996071338654
quatern_d   : -0.0864994972944
qoffset_x   : 73344.5546875
qoffset_y   : -1492.14978027
qoffset_z   : -2311.28955078
srow_x  : [ -9.99280393e-01   2.56918129e-02   2.79041883e-02   
7.33445547e+04]
srow_y  : [  2.04970520e-02   9.84766901e-01  -1.72667429e-01  
-1.49214978e+03]
srow_z  : [  3.19152586e-02   1.71971247e-01   9.84584868e-01  
-2.31128955e+03]
intent_name :
magic   : n+1



Note that the dim has value -1, but when I use -surface fsaverage, the dim is 
correct(show as below):

dim : [4 27307 1 6   451 1 1 1]

And I read the source code, the difference between self and fsaverage is 
appeared when running rawfunc2surf-sess, and log files are attached.

I have tried many commands to load data from fmcpr.sm0.self.lh.nii.gz, such as 
fslview, freeview, mri_convert, mri_surf2surf, ...

and only tksurfer could read this file by -timecourse fmcpr.sm0.self.lh.nii.gz.

I want to figure out how could I fix it, and any suggestion would be helpful.

Thanks in advance,

Bai Haohao


Version info:
System: ubuntu-16.04.1-server-amd64
Freesurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-H

[Freesurfer] individual mri_segstats waveforms for vertices or face in label

[Mcnorgan, Christopher]

Though one workaround might be to subdivide a label many, many times using 
mris_divide_parcellation, I was wondering if it is possible to obtain a 
per-vertex (or even per-face) fMRI waveform for a label. In other words, rather 
than compute the average waveform across all vertices, as with mri_segstats 
--label subject semi /path/to/label --avgwf avgwave.txt, which yields a single 
value that averages across, say, 5000 vertices, I would like to obtain each of 
the 5000 waveforms averaged over. I assume this would be more comparable to the 
scale of analysis used by those looking at voxel populations (e.g., as in MVPA).

Thanks, Chris

/**
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo,
* The State University of New York
* http://ccnlab.buffalo.edu/
* Office: 716.645.0236
* Lab: 716.645.0222
**/

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[Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

[Christopher Markiewicz]

Hi,

I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` to 
`T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs). 

The following produces a well-aligned output:

mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii

As does the following:

lta_convert --inlta bold2T1.lta --outfsl bold2T1.mat
c3d_affine_tool -ref T1.nii -src bold.nii bold2T1.mat -fsl2ras -oitk 
bold2T1.txt
antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
bold2T1.txt

However, if one skips the FSL step, the registration is quite far off:

lta_convert --inlta bold2T1.lta --outitk bold2T1.txt
antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
bold2T1.txt

Comparing the ITK transform files:

LTA-FSL-ITK

#Insight Transform File V1.0
#Transform 0
Transform: MatrixOffsetTransformBase_double_3_3
Parameters: 0.9895096215486424 0.011126830936108464 -0.00042204653562094823 
-0.01079971161879626 0.872329255299452 -0.42602926756857834 
-0.004755964529051335 0.42420535065804454 0.8878552541301569 
-1.3066136395454464 -45.60342165876236 -43.10584860730749
FixedParameters: 0 0 0


LTA-ITK

#Insight Transform File V1.0
#Transform 0
Transform: AffineTransform_double_3_3
Parameters: 0.98950976133346558 0.011126830242574215 
-0.00042204943019896746 -0.010799713432788849 0.87232941389083862 
-0.42602935433387756 -0.0047559700906276703 0.42420542240142822 
0.88785547018051147 -2.2848172187805176 -2.9065067768096924 11.744022369384766
FixedParameters: 0 0 0


To 5 significant digits, these are the same, except the last three 
(translation) parameters. And the `AffineTransform_double_3_3` is different 
from `MatrixOffsetTransformBase_double_3_3`, though I'm not sure whether this 
has any effect.

Here is the original LTA:

type  = 1 # LINEAR_RAS_TO_RAS
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
1.010462999343872e+00 -1.063966564834118e-02 4.625014495104551e-03 
-2.332115173339844e+00 
1.228639855980873e-02 9.293417930603027e-01 -4.459420144557953e-01 
2.507942199707031e+00 
4.575361963361502e-04 4.440840482711792e-01 9.132194519042969e-01 
-1.201664733886719e+01 
0.000e+00 0.000e+00 0.000e+00 
9.98807907104e-01 
src volume info
valid = 1  # volume info valid
filename = 
/scratch/fmriprep_wf/single_subject_02_wf/func_preproc_task_short_wf/bold_reg_wf/bbreg_wf/bbregister/uni_masked_xform.nii.gz
volume = 64 64 34
voxelsize = 3.125e+00 3.125e+00 
4.000e+00
xras   = -1.000e+00 0.000e+00 0.000e+00
yras   = 0.000e+00 1.000e+00 0.000e+00
zras   = 0.000e+00 0.000e+00 1.000e+00
cras   = -1.090248107910156e+00 -1.071614074707031e+01 1.619928741455078e+01
dst volume info
valid = 1  # volume info valid
filename = 
/scratch/fmriprep_wf/single_subject_02_wf/anat_preproc_wf/t1_merge/sub-02_T1w_template.nii.gz
volume = 160 192 192
voxelsize = 1.000e+00 1.33015441895e+00 
1.33015441895e+00
xras   = 1.000e+00 0.000e+00 0.000e+00
yras   = 0.000e+00 1.000e+00 0.000e+00
zras   = 0.000e+00 0.000e+00 1.000e+00
cras   = -3.000e+00 2.69482421875e+00 -8.30517578125e+00
subject sub-02
fscale 0.10


If it would be useful, I can provide any relevant images for testing.

--
Chris Markiewicz
Center for Reproducible Neuroscience
Stanford University


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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

[Christopher Markiewicz]

Doug,

Sorry if I muddied things by going into the significant digits - accurate to 5 
seems reasonable. I was simply meaning to say that the rotation and scaling 
parameters are not the issue, to save the reader time inspecting them.

The translations (final three parameters) are off by anywhere 3 to 54mm, though.

LTA-FSL-ITK: 1.3066136395454464 -45.60342165876236 -43.10584860730749
LTA-ITK: -2.2848172187805176 -2.9065067768096924 11.744022369384766

I'm guessing lta_convert has the wrong model of the origin in ITK style 
affines, at least as applied by antsApplyTransforms.

Chris

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

Sent: Monday, October 16, 2017 12:39:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are 
correctly applied by antsApplyTransforms

Not sure I understand. If the two transforms are only off by less than
the 5th decimal, then why are the registrations off so much. As for why
it would be off at the 5ht dec, it probably has to do with the way we
store the matrix. When a volume is read in, the matrix is decomposed
into translation, scale, and direction cosine, and then the matrix is
thrown away. When a volume with the same geometry is written out, the
matrix is recomputed. Some resolution is lost during the
decomposition/recomposition, and we don't end up with the exact same matrix.


On 10/14/17 1:30 PM, Christopher Markiewicz wrote:
> Hi,
>
> I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` 
> to `T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs).
>
> The following produces a well-aligned output:
>
>  mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii
>
> As does the following:
>
>  lta_convert --inlta bold2T1.lta --outfsl bold2T1.mat
>  c3d_affine_tool -ref T1.nii -src bold.nii bold2T1.mat -fsl2ras -oitk 
> bold2T1.txt
>  antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
> bold2T1.txt
>
> However, if one skips the FSL step, the registration is quite far off:
>
>  lta_convert --inlta bold2T1.lta --outitk bold2T1.txt
>  antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
> bold2T1.txt
>
> Comparing the ITK transform files:
>
> LTA-FSL-ITK
>
>  #Insight Transform File V1.0
>  #Transform 0
>  Transform: MatrixOffsetTransformBase_double_3_3
>  Parameters: 0.9895096215486424 0.011126830936108464 
> -0.00042204653562094823 -0.01079971161879626 0.872329255299452 
> -0.42602926756857834 -0.004755964529051335 0.42420535065804454 
> 0.8878552541301569 -1.3066136395454464 -45.60342165876236 -43.10584860730749
>  FixedParameters: 0 0 0
>
>
> LTA-ITK
>
>  #Insight Transform File V1.0
>  #Transform 0
>  Transform: AffineTransform_double_3_3
>  Parameters: 0.98950976133346558 0.011126830242574215 
> -0.00042204943019896746 -0.010799713432788849 0.87232941389083862 
> -0.42602935433387756 -0.0047559700906276703 0.42420542240142822 
> 0.88785547018051147 -2.2848172187805176 -2.9065067768096924 11.744022369384766
>  FixedParameters: 0 0 0
>
>
> To 5 significant digits, these are the same, except the last three 
> (translation) parameters. And the `AffineTransform_double_3_3` is different 
> from `MatrixOffsetTransformBase_double_3_3`, though I'm not sure whether this 
> has any effect.
>
> Here is the original LTA:
>
>  type  = 1 # LINEAR_RAS_TO_RAS
>  nxforms   = 1
>  mean  = 0. 0. 0.
>  sigma = 1.
>  1 4 4
>  1.010462999343872e+00 -1.063966564834118e-02 4.625014495104551e-03 
> -2.332115173339844e+00
>  1.228639855980873e-02 9.293417930603027e-01 -4.459420144557953e-01 
> 2.507942199707031e+00
>  4.575361963361502e-04 4.440840482711792e-01 9.132194519042969e-01 
> -1.201664733886719e+01
>  0.000e+00 0.000e+00 0.000e+00 
> 9.98807907104e-01
>  src volume info
>  valid = 1  # volume info valid
>  filename = 
> /scratch/fmriprep_wf/single_subject_02_wf/func_preproc_task_short_wf/bold_reg_wf/bbreg_wf/bbregister/uni_masked_xform.nii.gz
>  volume = 64 64 34
>  voxelsize = 3.125e+00 3.125e+00 
> 4.000e+00
>  xras   = -1.000e+00 0.000e+00 
> 0.000e+00
>  yras   = 0.000e+00 1.000e+00 
> 0.000e+00
>  zras   = 0.000e+00 0.000e+00 
> 1.000e+00
>  cras   = -1.090248107910156e+00 -1.071614074707031e+01 
> 1.619928741455078e+01
>  dst volume info
> 

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

[Christopher Markiewicz]

Hi Martin,

I've uploaded a .tgz file with a T1w volume, BOLD volume, and a valid LTA file.

https://gate.nmr.mgh.harvard.edu/filedrop2/?g=7f71pykmv7p

Chris

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Martin Reuter 

Sent: Tuesday, October 17, 2017 9:32:54 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are 
correctly applied by antsApplyTransforms

Hi Chris,

thanks, can you send the images and the exact commands. We have had success in 
the past, could be that you have a special case (e.g. maybe we never tested 
registration across different resolutions or whatever?).

Thanks, Martin

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


On 16. Oct 2017, at 19:37, Christopher Markiewicz 
mailto:markiew...@stanford.edu>> wrote:

Doug,

Sorry if I muddied things by going into the significant digits - accurate to 5 
seems reasonable. I was simply meaning to say that the rotation and scaling 
parameters are not the issue, to save the reader time inspecting them.

The translations (final three parameters) are off by anywhere 3 to 54mm, though.

LTA-FSL-ITK: 1.3066136395454464 -45.60342165876236 -43.10584860730749
LTA-ITK: -2.2848172187805176 -2.9065067768096924 11.744022369384766

I'm guessing lta_convert has the wrong model of the origin in ITK style 
affines, at least as applied by antsApplyTransforms.

Chris

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>>
Sent: Monday, October 16, 2017 12:39:28 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are 
correctly applied by antsApplyTransforms

Not sure I understand. If the two transforms are only off by less than
the 5th decimal, then why are the registrations off so much. As for why
it would be off at the 5ht dec, it probably has to do with the way we
store the matrix. When a volume is read in, the matrix is decomposed
into translation, scale, and direction cosine, and then the matrix is
thrown away. When a volume with the same geometry is written out, the
matrix is recomputed. Some resolution is lost during the
decomposition/recomposition, and we don't end up with the exact same matrix.


On 10/14/17 1:30 PM, Christopher Markiewicz wrote:
Hi,

I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` to 
`T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs).

The following produces a well-aligned output:

mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii

As does the following:

lta_convert --inlta bold2T1.lta --outfsl bold2T1.mat
c3d_affine_tool -ref T1.nii -src bold.nii bold2T1.mat -fsl2ras -oitk 
bold2T1.txt
antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
bold2T1.txt

However, if one skips the FSL step, the registration is quite far off:

lta_convert --inlta bold2T1.lta --outitk bold2T1.txt
antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
bold2T1.txt

Comparing the ITK transform files:

LTA-FSL-ITK

#Insight Transform File V1.0
#Transform 0
Transform: MatrixOffsetTransformBase_double_3_3
Parameters: 0.9895096215486424 0.011126830936108464 -0.00042204653562094823 
-0.01079971161879626 0.872329255299452 -0.42602926756857834 
-0.004755964529051335 0.42420535065804454 0.8878552541301569 
-1.3066136395454464 -45.60342165876236 -43.10584860730749
FixedParameters: 0 0 0


LTA-ITK

#Insight Transform File V1.0
#Transform 0
Transform: AffineTransform_double_3_3
Parameters: 0.98950976133346558 0.011126830242574215 
-0.00042204943019896746 -0.010799713432788849 0.87232941389083862 
-0.42602935433387756 -0.0047559700906276703 0.42420542240142822 
0.88785547018051147 -2.2848172187805176 -2.9065067768096924 11.744022369384766
FixedParameters: 0 0 0


To 5 significant digits, these are the same, except the last three 
(translation) parameters. And the `AffineTransform_double_3_3` is different 
from `MatrixOffsetTransformBase_double_3_3`, though I'm not sure whether this 
has any effect.

Here is the original LTA:

type  = 1 # LINEAR_RAS_TO_RAS
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
1.010462999343872e+00 -1.063966564834118e-02 4.625014495104551e-03 
-2.332115173339844e+00
1.228639855980873e-02 9.293417930603027e-01 -4.459420144557953e-01 
2.507942199707031e+00
4.575361963361502e-04 4.440840482711792e-01 9.132194519042969e-01 
-1.201664733886719e+01
0.000e+00 0.000e+00 0.000e+00 
9.98807907104e-01
src volume info
valid = 1  # volume info valid
  

[Freesurfer] readVolGeom corner case leads to lta_convert failures

[Christopher Markiewicz]

Hi all,

We've run into an issue where lta_convert is failing if the filename line in a 
volume geometry is of a specific length. We've identified the source of the 
problem, and made a pull request on GitHub that at least partially fixes the 
issue (https://github.com/freesurfer/freesurfer/pull/180). Doug's requested 
that all bugs be posted to the mailing list, so I excerpt the pull request 
below.

-

It is currently possible to create a valid VolGeom string that will break 
readVolGeom, by setting the length of the line beginning "filename = " to be 
255 characters (+ `'\n'`).

The filename is defined to be a 1024 byte string, and so up to 1023 characters:

https://github.com/freesurfer/freesurfer/blob/9b79bf0eef76710a70a5b73142a8f6e2bab1a6b6/include/transform.h#L54

So, in writeVolGeom, a line may be written that is up to 1035 characters long 
(`"filename = "` + 1023 + `'\n'`):

https://github.com/freesurfer/freesurfer/blob/9b79bf0eef76710a70a5b73142a8f6e2bab1a6b6/utils/transform.c#L365

If the line is exactly 255 characters long (excluding newline), then the 
`fgets` call will retrieve the entire contents of the line (256 characters - 
terminating `'\NUL'`) without retrieving a newline. The next call to `fgets` 
will then get a line of length 0, resulting in a premature termination of the 
loop.


To observe an effect of this issue, consider the following LTA file:


type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
2.327464342117310e+00 4.245608299970627e-02 3.455499932169914e-02 
-1.319661331176758e+01 
-7.824462652206421e-02 3.904805898666382e+00 2.233271896839142e-01 
-5.291442871093750e-01 
-4.939173907041550e-02 -1.728723645210266e-01 4.818737983703613e+00 
7.657078552246094e+01 
0.000e+00 0.000e+00 0.000e+00 
1.000e+00 
src volume info
valid = 1  # volume info valid
filename = 
/scratch/03763/oesteban/fmriprep-phase1/work/ds000110/fmriprep_wf/single_subject_07_wf/func_preproc_task_IncidentalencodingtaskusingPosnercueingparadigmwithobjectvgreeblejudgment_run_05_wf/bold_reg_wf/bbreg_wf/bbregister/ants_susceptibility_War
volume = 64 64 30
voxelsize = 3.4375000e+00 3.4375000e+00 4.000e+00
xras   = 1.000e+00 0.000e+00 0.000e+00
yras   = 0.000e+00 9.979115724563599e-01 -6.459446996450424e-02
zras   = 0.000e+00 6.459447741508484e-02 9.979115724563599e-01
cras   = 3.4375000e+00 8.357086181640625e-01 4.582891845703125e+01
dst volume info
valid = 1  # volume info valid
filename = 
/scratch/03763/oesteban/fmriprep-phase1/work/ds000110/fmriprep_wf/single_subject_07_wf/anat_preproc_wf/t1_merge/sub-07_T1w_ras_template.nii.gz
volume = 124 256 256
voxelsize = 1.500e+00 8.593999743461609e-01 8.593999743461609e-01
xras   = 9.998608827590942e-01 1.065783575177193e-02 -1.283265277743340e-02
yras   = -9.511843323707581e-03 9.962262511253357e-01 8.627174794673920e-02
zras   = 1.370369549840689e-02 -8.613768219947815e-02 9.961889982223511e-01
cras   = -3.533935546875000e-01 5.862289428710938e+00 -1.128549194335938e+01
subject sub-07
fscale 0.10


If you save this as `test.lta`, the following command fails in an unexpected 
way:


$ lta_convert --inlta truncated.lta --outlta out.lta
$Id: lta_convert.cpp,v 1.9.2.1 2016/08/09 02:33:22 zkaufman Exp $

--inlta: truncated.lta input LTA transform.
--outlta: out.lta output LTA.
LTAchangeType: dst geometry must be valid


The offending line is:


filename = 
/scratch/03763/oesteban/fmriprep-phase1/work/ds000110/fmriprep_wf/single_subject_07_wf/func_preproc_task_IncidentalencodingtaskusingPosnercueingparadigmwithobjectvgreeblejudgment_run_05_wf/bold_reg_wf/bbreg_wf/bbregister/ants_susceptibility_War


Add or remove a character and the command proceeds without error. However, 
supposing you add a character (and, critically, convert between `RAS_TO_RAS` 
and `VOX_TO_VOX`):


$ lta_convert --inlta extended.lta --outlta out1.lta 
$Id: lta_convert.cpp,v 1.9.2.1 2016/08/09 02:33:22 zkaufman Exp $

--inlta: extended.lta input LTA transform.
--outlta: out1.lta output LTA.
 LTA read, type : 1
 1.01550   0.01035   0.02607  -3.12509;
-0.00760   0.97176  -0.10423   6.51772;
-0.02702   0.10772   1.03053  -46.97261;
 0.0   0.0   0.0   1.0;
Writing  LTA to file out1.lta...
lta_convert successful.
$ lta_convert --inlta out1.lta --outlta out2.lta --ltavox2vox
$Id: lta_convert.cpp,v 1.9.2.1 2016/08/09 02:33:22 zkaufman Exp $

--inlta: out1.lta input LTA transform.
--outlta: out2.lta output LTA.
--ltavox2vox: output LTA as VOX_TO_VOX transform.
 LTA read, type : 1
 1.01550   0.01035   0.02607  -3.12509;
-0.00760   0.97176  -0.10423   6.51772;
-0.02702   0.10772   1.03053  -46.97261;
 0.0   0.0   0.0   1.0;
LTAchangeType: dst geometry must be valid


This is a result of the truncation that occurs during the read.

Thanks for your time,

Re: [Freesurfer] lta_convert does not produce ITK transforms that are correctly applied by antsApplyTransforms

[Christopher Markiewicz]

Hi Martin,

I've tracked down the issue. It turns out that the difference is that the 
VolGeoms are determined by the sform, while ANTs uses the qform. Syncing the 
qform to the sform resolves the issue.

Chris

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Christopher Markiewicz 

Sent: Tuesday, October 17, 2017 12:11:52 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are 
correctly applied by antsApplyTransforms

Hi Martin,

I've uploaded a .tgz file with a T1w volume, BOLD volume, and a valid LTA file.

https://gate.nmr.mgh.harvard.edu/filedrop2/?g=7f71pykmv7p

Chris

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Martin Reuter 

Sent: Tuesday, October 17, 2017 9:32:54 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are 
correctly applied by antsApplyTransforms

Hi Chris,

thanks, can you send the images and the exact commands. We have had success in 
the past, could be that you have a special case (e.g. maybe we never tested 
registration across different resolutions or whatever?).

Thanks, Martin

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


On 16. Oct 2017, at 19:37, Christopher Markiewicz 
mailto:markiew...@stanford.edu>> wrote:

Doug,

Sorry if I muddied things by going into the significant digits - accurate to 5 
seems reasonable. I was simply meaning to say that the rotation and scaling 
parameters are not the issue, to save the reader time inspecting them.

The translations (final three parameters) are off by anywhere 3 to 54mm, though.

LTA-FSL-ITK: 1.3066136395454464 -45.60342165876236 -43.10584860730749
LTA-ITK: -2.2848172187805176 -2.9065067768096924 11.744022369384766

I'm guessing lta_convert has the wrong model of the origin in ITK style 
affines, at least as applied by antsApplyTransforms.

Chris

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>>
Sent: Monday, October 16, 2017 12:39:28 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] lta_convert does not produce ITK transforms that are 
correctly applied by antsApplyTransforms

Not sure I understand. If the two transforms are only off by less than
the 5th decimal, then why are the registrations off so much. As for why
it would be off at the 5ht dec, it probably has to do with the way we
store the matrix. When a volume is read in, the matrix is decomposed
into translation, scale, and direction cosine, and then the matrix is
thrown away. When a volume with the same geometry is written out, the
matrix is recomputed. Some resolution is lost during the
decomposition/recomposition, and we don't end up with the exact same matrix.


On 10/14/17 1:30 PM, Christopher Markiewicz wrote:
Hi,

I've used `bbregister` to generate a transform `bold2T1.lta` from `bold.nii` to 
`T1.mgz` (assume we have a `T1.nii` as well for the sake of ANTs).

The following produces a well-aligned output:

mri_convert --apply_transform bold2T1.lta bold.nii bold_space-T1.nii

As does the following:

lta_convert --inlta bold2T1.lta --outfsl bold2T1.mat
c3d_affine_tool -ref T1.nii -src bold.nii bold2T1.mat -fsl2ras -oitk 
bold2T1.txt
antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
bold2T1.txt

However, if one skips the FSL step, the registration is quite far off:

lta_convert --inlta bold2T1.lta --outitk bold2T1.txt
antsApplyTransforms -i bold.nii -r T1.nii -o bold_space-T1.nii -t 
bold2T1.txt

Comparing the ITK transform files:

LTA-FSL-ITK

#Insight Transform File V1.0
#Transform 0
Transform: MatrixOffsetTransformBase_double_3_3
Parameters: 0.9895096215486424 0.011126830936108464 -0.00042204653562094823 
-0.01079971161879626 0.872329255299452 -0.42602926756857834 
-0.004755964529051335 0.42420535065804454 0.8878552541301569 
-1.3066136395454464 -45.60342165876236 -43.10584860730749
FixedParameters: 0 0 0


LTA-ITK

#Insight Transform File V1.0
#Transform 0
Transform: AffineTransform_double_3_3
Parameters: 0.98950976133346558 0.011126830242574215 
-0.00042204943019896746 -0.010799713432788849 0.87232941389083862 
-0.42602935433387756 -0.0047559700906276703 0.42420542240142822 
0.88785547018051147 -2.2848172187805176 -2.9065067768096924 11.744022369384766
FixedParameters: 0 0 0


To 5 significant digits, these are the same, except the last three 
(translation) parameters. And the `AffineTransform_double_3_3` is different 
from `MatrixOffsetTransformBase_double_3_3`, though I'm not sure whether this 
has any effect.

Here is the original LTA:

type  = 1 # LINEA

[Freesurfer] recon-all on previously segmented volumes

[Mcnorgan, Christopher]

Hi, I’m having some issues generating surfaces for an individual and was hoping 
that a combination of tools might help. In this particular individual, the 
skull stripping went fine, but a fairly large proportion of the anterior 
temporal cortex (primarily inferior) volume is excluded from the data. My hunch 
is that it has to do with the fairly low contrast present in the images. 
Nonetheless, I had also worked on the data in SPM which did a fine job 
segmenting the wm/gm/other voxels when I inspect them as overlays in a program 
like MRICron.

I tried an experiment wherein I used the SPM segmented volumes to create a 
composite brainmask.mgz where the wm voxels were set to exactly 110, the gm 
voxels were set to a somewhat lower value (I used element-wise multiplication, 
so the voxels vary in value, but were around 70-100) and all other voxels were 
set to 1. The resulting volume looks like a meticulously cleaned brain mask. 
Unfortunately, recon-all -autorecon-pial didn’t work any better afterwards. So 
that experiment was a dud.

Assuming I can manipulate/combine the images in any manner, is there a way to 
take advantage of the segmented volumes that I was able to obtain from SPM? If 
I am going to be processing the data in SPM anyways, it would seem that having 
this information would make the process of tessellating the white and grey 
matter surfaces trivial.

/**
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo,
* The State University of New York
* http://ccnlab.buffalo.edu/
* Office: 716.645.0236
* Lab: 716.645.0222
**/

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[Freesurfer] RFC: Changes to nibabel API for .mgh/.mgz files

[Christopher Markiewicz]

Hi all,

I'd like to solicit input for the Python interface to .mgh/.mgz files in 
nibabel[0].

I've recently had cause to dig into this interface (MGHImage[1]), and found 
that the naming of header fields[2] (analogous to variable names in C structs) 
is inconsistent with all of my experience with how FreeSurfer refers to these 
fields in the code (MRI_IMAGE[3]) as well as in the outputs of many programs, 
such as mri_info. (In fact, the current names seem to reflect the intermediate 
variables used in load/save_mgh.m and the description of the affine transforms 
in the FS Coordinates powerpoints[4].)

I'm proposing (https://github.com/nipy/nibabel/pull/569) an API change in 
nibabel, with field names[5] that more closely reflect what I deem to be common 
FreeSurfer usage (although it does not adhere precisely to the C structure 
fields). Given that, it was felt that the FreeSurfer community more broadly 
should have some say in the final API. To put a few specific questions: Do you 
depend on the current MGHHeader field names? Would you be averse to updating 
the field names? If not, are there alternatives to my proposal you would find 
preferable?

While I would be willing to discuss in more detail on this list, I don't want 
to needlessly pollute a support list with discussions of a third party API. If 
it's convenient, I would prefer responses on the pull request linked above.

Thanks,
Chris Markiewicz

[0] http://nipy.org/nibabel/
[1] https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/mghformat.py
[2] 
https://github.com/nipy/nibabel/blob/2139ce0d24e65a83295bb6b3eaaf005eaeaebb5f/nibabel/freesurfer/mghformat.py#L28-L35
[3] https://github.com/freesurfer/freesurfer/blob/master/include/mri.h#L157-L252
[4] https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
[5] 
https://github.com/effigies/nibabel/blob/55c9bf905ec8785617755f900635fc31bae43232/nibabel/freesurfer/mghformat.py#L30-L49

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

[Mcnorgan, Christopher]

An epiphany lead me to the solution to the problem, which I shall post here 
since I am apparently due to experience it again in 2019.
The NAN values in the GLM matrices were the result of there being a condition 
that did not appear in any of the .par files across all of the runs. Once these 
files were edited so that all of conditions 1, 2 and 3 appeared somewhere among 
these files, selxavg3-sess was able to run.


/**
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo, 
* The State University of New York
* http://ccnlab.buffalo.edu/ 
* Office: 716.645.0236
* Lab: 716.645.0222
**/
> Hi Doug et al.,
> 
> It appears I've encountered this problem once before:
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-February/043647.html
>  
> 
> 
> Unfortunately there is no record of any resolution (if there was one) in the 
> original thread, and I have no recollection of what the outcome was. Where 
> the thread did leave off was a request for the Xtmp.mat file, so I will 
> include the Xtmp.mat file from the analysis that worked (GoodXtmp.mat) and 
> the one that failed (BadXtmp.mat).
> 
> The error message:
> 
> Creating Design Matrix
>  ... creation time =  0.019 sec
> DoMCFit = 1
> ntptot = 2592, nX = 81, DOF = 2511
> Saving X matrix to /home/chris/SEM/FS_0231/bold/FAM.self.sm4.down.rh/Xtmp.mat
> Error using svd
> Input to SVD must not contain NaN or Inf.
> Error in cond (line 35)
> s = svd(A);
> Error in fast_selxavg3 (line 279)
>   XCond = cond(XtX);
> 
> Curiously, unless something was overlooked, the same analysis was carried out 
> on another dataset that went through the same preprocessing steps without 
> incident.
> 
> The Xn matrix in BadXtmp.mat contains 3 columns of NaN (:,[7,8,9]), but 
> without knowing how those values are calculated, I can't take a principled 
> stab at fixing the problem.
> 
> Thanks for your help,
> Chris
> 
> 
> 
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