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Today's Topics:

  1. Fwd: question about volume of mask (Dorsa Haji Ghaffari)
  2. brain mask and T1 are not the same size (Isabelle Deschamps)
  3. Re: error during longitudinal -long stream (Jinsong Tang)
  4. Research Assistants needed for longitudinal brain development
     study at Boston Children's Hospital (Gaab, Nadine)
  5. Re: error during longitudinal -long stream (Martin Reuter)
  6. MNI coordinates of all the vertices of fsaverage (Sabin Khadka)
  7. Running Retinotopy in FSFAST, Design Matrix has Empty
     Regressors (Taylor, Johnmark)
  8. mri_normalize, 110 is too dark (tvg[fs])
  9. Re: brain mask and T1 are not the same size (Douglas Greve)
10. Re: mri_normalize, 110 is too dark (Bruce Fischl)
11. Where are time series from adjusted (post selxavg3) ROIs
     (ERIK JAHNER)
12. Re: significance overlay in freeview (Caroline Beelen)
13. Running recon-all with T1 and FLAIR (Silas)
14. Re: error during longitudinal -long stream (Jinsong Tang)

----------------------------------------------------------------------

Message: 1
Date: Fri, 29 Jul 2016 12:08:43 -0400
From: Dorsa Haji Ghaffari <ghdor@umich.edu>
Subject: [Freesurfer] Fwd: question about volume of mask
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAAe2pvAtEfwUj6=7G+qe8JkNXm23SJ8PYF4zncfkBsHxOtNpPA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Bruce,

I was able to reslice the thalamus mask correctly, but when I measure the
volume of the resliced thalamus, is not the same as the original thalamus.
I was wondering why that is happening and which volume is more accurate. I
appreciate any suggestions. I have attached both masks. Also can you tell
me how to measure the volume of the resliced thalamus in Freesurfer?

Thank you

Dorsa
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Message: 2
Date: Fri, 29 Jul 2016 16:09:31 +0000
From: Isabelle Deschamps <isabelle.deschamps.1@ulaval.ca>
Subject: [Freesurfer] brain mask and T1 are not the same size
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <23B16DC7-F62A-4B8B-99DA-EDDAD20A115F@ulaval.ca>
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Message: 3
Date: Fri, 29 Jul 2016 09:26:58 -0700
From: Jinsong Tang <tangjinsonghn@gmail.com>
Subject: Re: [Freesurfer] error during longitudinal -long stream
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CADf-At00N-cyZYTLt0z7EvK1Hk4b=cYasjvMDE3rG7zsm_rETA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Martin,

I checked all data are completed except the link to fsaverage,
lh.EC_average and rh.EC_average.   I run one analysis from the terminal. it
works. if I run multiple analysis at the same time, it failed.
When I manually linked the 3 files, then run multiple analysis at the same
time, it works good.

Best,

Jinsong

On Wed, Jul 27, 2016 at 8:11 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu>
wrote:

Hi Jinsong,

maybe not everything was copied? The link to fsaverage should be

automatically created if it is missing. I often process cross in a

different directory from base and long (and create symlinks to the cross

subject dirs). It automatically creates fsaverage then.

Try to replicate your problem with a single subject that failed. First try

to do everything on the same computer, then try to do what you did before

(copying parts of it).

Best, Martin

On 07/20/2016 12:56 PM, Jinsong Tang wrote:

Hi Martin,

We run all cross, base and long with 5.3. I guess the problem maybe we run

cross on a computer and then copy the results to another computer to run

the cross and long. the "*fsaverage" is not copied. Does this matter?*

Best?

Jinsong

On Wed, Jul 20, 2016 at 12:21 AM, Martin Reuter <

mreuter@nmr.mgh.harvard.edu> wrote:

Hi Jinsong,

I have never seen this. Stable 5.3 is very stable and I doubt it is a

bug. How did you process base and cross sectionals? Also with 5.3 ?

I would recommend to process cross and base with 5.3, then re-run the

long and see if you can replicate this problem. Let me know what happens.

Best, Martin

On Jul 20, 2016, at 12:48 AM, Jinsong Tang < <tangjinsonghn@gmail.com>

tangjinsonghn@gmail.com> wrote:

Hi all,

I found an error during the longitudinal -long stream:

recon-all -long P1001-2 P1001 -all

......

FREESURFER_HOME /space/raid/fmri/freesurfer

Actual FREESURFER_HOME /space/raid/fmri/freesurfer

build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21 UTC

2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux

......

mris_spherical_average -erode 1 -orig white -t 0.4 -o

P1001-2.long.P1001 label lh.entorhinal lh sphere.reg lh.EC_average

lh.entorhinal_exvivo.label

painting output onto subject P1001-2.long.P1001.

processing subject lh.EC_average...

MRISread(/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg):

could not open file

eroding label 1 times before writing

thresholding label stat at 0.400 before writing

Not a directory

mris_spherical_average: could not read surface file

/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg

Not a directory

Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21 UTC

2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux

recon-all -s P1001-2.long.P1001 exited with ERRORS at Fri Jul 8

21:33:02 PDT 2016

Please help me fix this error!

Thanks and best regards,

Jinsong

<recon-all.log>_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________

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The information in this e-mail is intended only for the person to whom it

is

addressed. If you believe this e-mail was sent to you in error and the

e-mail

contains patient information, please contact the Partners Compliance

HelpLine at

http://www.partners.org/complianceline . If the e-mail was sent to you

in error

but does not contain patient information, please contact the sender and

properly

dispose of the e-mail.

_______________________________________________

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--

Martin Reuter, PhD

Assistant Professor of Radiology, Harvard Medical School

Assistant Professor of Neurology, Harvard Medical School

A.A.Martinos Center for Biomedical Imaging

Massachusetts General Hospital

Research Affiliate, CSAIL, MIT

Phone: +1-617-724-5652

Web : http://reuter.mit.edu

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it

is

addressed. If you believe this e-mail was sent to you in error and the

e-mail

contains patient information, please contact the Partners Compliance

HelpLine at

http://www.partners.org/complianceline . If the e-mail was sent to you in

error

but does not contain patient information, please contact the sender and

properly

dispose of the e-mail.

--
Jinsong Tang, MD
Institute of Mental Health
The Second Xiangya Hospital , Central South University
139 Renmin Road, Changsha Hunan 410011, P.R. China
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Message: 4
Date: Fri, 29 Jul 2016 16:52:42 +0000
From: "Gaab, Nadine" <Nadine.Gaab@childrens.harvard.edu>
Subject: [Freesurfer] Research Assistants needed for longitudinal
brain development study at Boston Children's Hospital
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <c7db350bece449d8a1e59c2b474de1c7@CHEXMAIL3A.CHBOSTON.ORG>
Content-Type: text/plain; charset="us-ascii"

The Gaab Lab<http://www.thegaablab.com/> in collaboration with the Fetal-Neonatal Neuroimaging and Developmental Science Center<https://fnndsc.babymri.org/> at Boston Children's Hospital is looking for two Research Assistants to assist with all study phases of a new NICHD funded longitudinal project which assesses functional and structural brain development from infancy to early elementary school age. This includes subject recruitment for pediatric research studies which will include close interaction with nurseries, child care centers and elementary schools in the Boston area, scheduling of pediatric research subjects, database maintenance, implementation and maintenance of analysis software; pediatric testing (including MRI/fMRI scanning of young children and infants<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.babymri.org_&d=BQMFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=BlXs1rlsOtuypw3ge9ZEUMlqUZgMh3zgL8uTUz0qnkuKuzwG5BoVaJit39AGl4zC&m=xEiRF5dDCnCPanU058TnB7U0Kr9d-ND9H6Y75csBvfw&s=lq_80T8u8dYsjAtC00C5qgU_1CaP1v2-KJi0Tvx0sR4&e=>) and data analyses (psychometrics, psychophysics and structural/functional magnetic imaging), stimuli design and administrative work (e.g., preparation of internal review board proposals). These positions are ideal for anyone considering future graduate study in cognitive (developmental) neuroscience, developmental psychology, computer science, cognitive science or neuroscience. Bachelor's Degree in computer science, psychology, cognitive science, neuroscience, math, or related field required. Comfort with a heterogeneous computing environment (Linux/Unix, Mac, and Windows) as well as some programming experience preferred; knowledge of psychological experiment software (E Prime, Presentation, etc.) and/or fMRI analyses software helpful. Prior experience with infants and children would be very helpful. Demonstrable pre-existing interest in developmental psychology/ cognitive neuroscience desired; knowledge of neuroanatomy, statistics or machine learning helpf!
ul. Must
be self-motivated and able to work in a fast-paced, changing environment and must like working with infants, children and families. Start date September or October 2016. Please first apply to Nadine.gaab@childrens.harvard.edu<mailto:Nadine.gaab@childrens.harvard.edu> with a cover letter and CV.

"If we knew what it was we were doing, it would not be called research, would it?" A. Einstein (1879-1955)

Nadine Gaab, PhD
Associate Professor of Pediatrics
Boston Children's Hospital/Harvard Medical School
Department of Medicine/Division of Developmental Medicine
Laboratories of Cognitive Neuroscience
Mail stop code: BCH3178
1 Autumn Street (Office 643); Boston, MA 02115
nadine.gaab@childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu>
phone: 857-218-3021
www.gaablab.com<http://www.gaablab.com>

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Message: 5
Date: Fri, 29 Jul 2016 14:44:45 -0400
From: Martin Reuter <mreuter@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] error during longitudinal -long stream
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <579BA41D.5070408@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Jinsong,

can you give an example of what exactly does not work.

Thanks, Martin

On 07/29/2016 12:26 PM, Jinsong Tang wrote:

Hi Martin,

I checked all data are completed except the link to fsaverage,

lh.EC_average and rh.EC_average. I run one analysis from the

terminal. it works. if I run multiple analysis at the same time, it

failed.

When I manually linked the 3 files, then run multiple analysis at the

same time, it works good.

Best,

Jinsong

On Wed, Jul 27, 2016 at 8:11 AM, Martin Reuter

<mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> wrote:

Hi Jinsong,

maybe not everything was copied? The link to fsaverage should be

automatically created if it is missing. I often process cross in a

different directory from base and long (and create symlinks to the

cross subject dirs). It automatically creates fsaverage then.

Try to replicate your problem with a single subject that failed.

First try to do everything on the same computer, then try to do

what you did before (copying parts of it).

Best, Martin

On 07/20/2016 12:56 PM, Jinsong Tang wrote:

Hi Martin,

We run all cross, base and long with 5.3. I guess the problem

maybe we run cross on a computer and then copy the results to

another computer to run the cross and long. the "/fsaverage" is

not copied. Does this matter?/

Best?

Jinsong

On Wed, Jul 20, 2016 at 12:21 AM, Martin Reuter

<mreuter@nmr.mgh.harvard.edu

<mailto:mreuter@nmr.mgh.harvard.edu>> wrote:

Hi Jinsong,

I have never seen this. Stable 5.3 is very stable and I doubt

it is a bug. How did you process base and cross sectionals?

Also with 5.3 ?

I would recommend to process cross and base with 5.3, then

re-run the long and see if you can replicate this problem.

Let me know what happens.

Best, Martin

On Jul 20, 2016, at 12:48 AM, Jinsong Tang

<tangjinsonghn@gmail.com <mailto:tangjinsonghn@gmail.com>> wrote:

Hi all,

I found an error during the longitudinal -long stream:

recon-all -long P1001-2 P1001 -all

......

FREESURFER_HOME /space/raid/fmri/freesurfer

Actual FREESURFER_HOME /space/raid/fmri/freesurfer

build-stamp.txt:

freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7

17:32:21 UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux

......

mris_spherical_average -erode 1 -orig white -t 0.4 -o

P1001-2.long.P1001 label lh.entorhinal lh sphere.reg

lh.EC_average lh.entorhinal_exvivo.label

painting output onto subject P1001-2.long.P1001.

processing subject lh.EC_average...

MRISread(/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg):

could not open file

eroding label 1 times before writing

thresholding label stat at 0.400 before writing

Not a directory

mris_spherical_average: could not read surface file

/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg

Not a directory

Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7

17:32:21 UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux

recon-all -s P1001-2.long.P1001 exited with ERRORS at Fri

Jul 8 21:33:02 PDT 2016

Please help me fix this error!

Thanks and best regards,

Jinsong

<recon-all.log>_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

<mailto:Freesurfer@nmr.mgh.harvard.edu>

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________

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

but does not contain patient information, please contact the

sender and properly

dispose of the e-mail.

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

<mailto:Freesurfer@nmr.mgh.harvard.edu>

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--

Martin Reuter, PhD

Assistant Professor of Radiology, Harvard Medical School

Assistant Professor of Neurology, Harvard Medical School

A.A.Martinos Center for Biomedical Imaging

Massachusetts General Hospital

Research Affiliate, CSAIL, MIT

Phone:+1-617-724-5652 <tel:%2B1-617-724-5652>

Web :http://reuter.mit.edu

_______________________________________________

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

but does not contain patient information, please contact the

sender and properly

dispose of the e-mail.

--

Jinsong Tang, MD

Institute of Mental Health

The Second Xiangya Hospital , Central South University

139 Renmin Road, Changsha Hunan 410011, P.R. China

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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Message: 6
Date: Fri, 29 Jul 2016 14:47:30 -0400
From: Sabin Khadka <mr.sabinkhadka@gmail.com>
Subject: [Freesurfer] MNI coordinates of all the vertices of fsaverage
To: freesurfer <Freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAEjWD0P=0U0qePAkOWWVS_D3qq3MKZ=M8c_WgnkB0x=Nfg_d7A@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Doug, I tried to pick up from the thread below to get MNI coordinates of
each destrieux parcellation region.

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html

I created label files from
mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation
aparc.a2009s --outdir label_destrieux # which works fine

And I tried to get the coordinates of each labels using

mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness --clabel
<label file> --sum <output file> --centroid --thmin 0
--hemi lh --subject fsaverage

But, all left labels would produce the same coordinates and so does right
labels. (I've attached few example files here with). Also, it says TalX,
TalY, TalZ are these coordinates in MNI or Talairach?

Thanks for help.
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Message: 7
Date: Fri, 29 Jul 2016 15:04:58 -0400
From: "Taylor, Johnmark" <johnmarktaylor@g.harvard.edu>
Subject: [Freesurfer] Running Retinotopy in FSFAST, Design Matrix has
Empty Regressors
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAOBxrqzxwhNqkfTtesvkgqczW5US00KVeDGXFONW8H9bjChpGA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello,

I am trying to run a retinotopy analysis in fsfast, using only polar angle.
However, when I try to run it, I am getting the error "Input to SVD must
not contain NaN or Inf." I have traced this error and it looks like the
design matrix X has 12 regressors (the first 12) that consist solely of
zeros. I am using the following commands:

mkanalysis-sess -analysis retinotopy -fsd bold -runlistfile runlist.txt

-native -funcstem fmc -nuisreg mcextreg 3

-retinotopy 36.4 -per-session -paradigm retino.par -inorm

-spmhrf 0 -TR .650 -polyfit 2 -nskip 19

selxavg3-sess -analysis retinotopy -sf sublist.txt -df sessdir

Any idea what the first 12 regressors in the design matrix might correspond
to in retinotopy analyses and why they'd be empty? I have looked at the
documentation and there doesn't seem to be a clear labeling of the
retinotopy design matrix anywhere, although perhaps I'm missing something.

Thank you very much,

JohnMark
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Message: 8
Date: Fri, 29 Jul 2016 15:41:28 -0400
From: "tvg[fs]" <tvg214+fs@nyu.edu>
Subject: [Freesurfer] mri_normalize, 110 is too dark
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAMBOMk9B3kq7u_-93+N3oQk+q3epYj42XO_aiwa+MxgrUMUF=Q@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Dear community and developers,

I am experiencing issues during the normalization step, converting
NU.mgz to T1.mgz. Gray matter is falsely recognized as white matter
and high intensity WM is ignored. The resulting T1.mgz collapses the
wrong voxels into the 110 bin.

It seems that what mri_normalize assumes a peak in the WM intensity
distribution that is too low.
In NU.mgz WM seems centered around 140 not 110. Note that this is not
due to RF-field inhomogeneities. It is likely of physiological origin

- Is there a way to explicitly tell mri_normalize to use a different
intensity peak?

I realize that correction can be done with control points, however I
understand that does not compute a new intensity distribution, but
merely adds voxels around CPs. This is undesirable since I have >20
scans to process. Also this will not correct the falsely tagged GM
voxels.

I've tried to trick mri_normalize by adjusting NU.mgz intensity by -30
(140-30 = 110). This did not give me the wished-for effect.
- Is it possible to bypass preprocessing steps of mri_normalize before
collapsing?

- In general it would help if there is some elaboration on the options:
-no1d,
-nosnr,
-gentle,
-f vs -fonly,
-prune,
-g,
-monkey
- is [-monkey] just shorthand for [-no1d -n 1]?

Thanks,
Tom

System:
Mac OS X 10.10.5
freesurfer-Darwin-lion-stable-pub-v5.3.0

mri_normalize --version

stable5

------------------------------

Message: 9
Date: Fri, 29 Jul 2016 15:56:18 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] brain mask and T1 are not the same size
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <e521fbde-d7c2-b350-bb3e-183fe478be5d@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

So you're saying that the dimension changed after you ran freeview and
saved the volume? Can you replicate it? ie, if you make a copy of the
brainmask.mgz, then edit the copy, does it do the same thing every time
you make a copy and edit it?

On 7/29/16 12:09 PM, Isabelle Deschamps wrote:

Dear FreeSurfer experts,

I am trying to fix the skull strip manually for a group of

participants. For all participants except 4, I get an error when

running recon-all -autorecon-pial -subjid S07_FS, after editing

manually in Freeview the brainmask.

In freeview, I followed the instruction for Edits to the brainmask

(https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewEditingaRecon)

I open freeview using this command on my participant's data:

*freeview -v pial_edits_before/mri/brainmask.mgz \*

*-f pial_edits_before/surf/lh.white:edgecolor=yellow \*

*pial_edits_before/surf/lh.pial:edgecolor=red

pial_edits_before/surf/rh.white:edgecolor=yellow \*

*pial_edits_before/surf/rh.pial:edgecolor=red *

Then, I follow these instructions, which are on the website.

*To fix this type of error you can simply edit away the offending

voxels from the brainmask.mgz volume. To do this you will need to

select the edit voxels tool and set the brush to a size and shape

comfortable for you. A circle brush of radius 2 works well for this

edit. Then you can simply use the shift key and your mouse button to

erase the voxels in the brainmask.mgz, or you can set the brush value

to 1 (so that the edits can be detected if you decide to run

"recon-all -show-edits") and simple draw over the voxels you want to

disappear.*

Then I save the brainmask volume using the save volume button.

When running *recon-all -autorecon-pial -subjid S07_FS* to correct the

pial surface, I get the following error:

ERROR: dimension mismatch between source and mask

The source of the problem is the the brainmask, in which one of the

dimensions is no longer 256. It is either 255 or 254. Prior the

modifications, the brainmask and the T1 had the same dimensions 256^3.

Following the brainmask edits, one dimension (it varies for the 4

problematic participants) is no longer 256. I do not understand why

for all participants except 4, the brainmask edits worked. I followed

the exact same procedure for all participants.

Any ideas or suggestions?

Thank you in advance for the help,

Isabelle

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Message: 10
Date: Fri, 29 Jul 2016 16:38:53 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_normalize, 110 is too dark
To: tvg214+fs@nyu.edu, Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1607291638150.6008@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed

Hi Tom

it's tough for us to tell without some images or the data. If you upload
the entire subject dir of a subject that failed we will take a look. You
can't just change which peak is the WM - lots of things downstream would
fail

cheers
Bruce

On Fri, 29 Jul 2016, tvg[fs] wrote:

Dear community and developers,

I am experiencing issues during the normalization step, converting

NU.mgz to T1.mgz. Gray matter is falsely recognized as white matter

and high intensity WM is ignored. The resulting T1.mgz collapses the

wrong voxels into the 110 bin.

It seems that what mri_normalize assumes a peak in the WM intensity

distribution that is too low.

In NU.mgz WM seems centered around 140 not 110. Note that this is not

due to RF-field inhomogeneities. It is likely of physiological origin

- Is there a way to explicitly tell mri_normalize to use a different

intensity peak?

I realize that correction can be done with control points, however I

understand that does not compute a new intensity distribution, but

merely adds voxels around CPs. This is undesirable since I have >20

scans to process. Also this will not correct the falsely tagged GM

voxels.

I've tried to trick mri_normalize by adjusting NU.mgz intensity by -30

(140-30 = 110). This did not give me the wished-for effect.

- Is it possible to bypass preprocessing steps of mri_normalize before

collapsing?

- In general it would help if there is some elaboration on the options:

-no1d,

-nosnr,

-gentle,

-f vs -fonly,

-prune,

-g,

-monkey

- is [-monkey] just shorthand for [-no1d -n 1]?

Thanks,

Tom

System:

Mac OS X 10.10.5

freesurfer-Darwin-lion-stable-pub-v5.3.0

mri_normalize --version

stable5

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

------------------------------

Message: 11
Date: Fri, 29 Jul 2016 23:40:49 -0700
From: ERIK JAHNER <erik.jahner@icloud.com>
Subject: [Freesurfer] Where are time series from adjusted (post
selxavg3) ROIs
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <201965DD-AED2-4F84-9A30-72FF9C16DD5A@icloud.com>
Content-Type: text/plain; charset=us-ascii

Dear Freesurfer experts

I have been going through the documentation trying to figure out how to extract the time series for an ROI (Posteriorcingulate) after removing the regressors that I put in my mkanalysis-sess. I have run the selxavg3.
1. Is this time course what is in the meanfunc.nii.gz?
2. If it is, how do I pull this out in matrix format (.mat) out of the where I basically get one mean adjusted value for the ROI at each timepoint? (e.g. For the Posteriorcingulate, I want 210 values representing the mean activation after removing the effect of my covariates wm and css for each of the 210 timepoints).
3. Is this information in the X.mat file? If so, what is its location?

Thanks
Erik Jahner

------------------------------

Message: 12
Date: Sat, 30 Jul 2016 09:34:08 +0000
From: Caroline Beelen <caroline.beelen@kuleuven.be>
Subject: Re: [Freesurfer] significance overlay in freeview
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <1469871088511.73483@kuleuven.be>
Content-Type: text/plain; charset="iso-8859-1"

Dear Ruopeng,

Yes, I'm running FS 5.3. :)

But then how can I see the correct significance overlay? Cause even when leaving out some commands (which may or may not work in 5.3), freeview does load, but seems to only display the DK-atlas on fs average (... and gets stuck sometimes too), as I described below.

I cant find the right command ...

So I guess my actual question is: Which command should i use to view a (correct) significance overlay in FS 5.3?

Thank you very much for your help!

Regards, Caroline

Hi Caroline,

Are you running FS 5.3? The command on the webpage is based on the upcoming 6.0, I believe. So some of the command line options are not available in 5.3.

Best,
Ruopeng

On Jul 29, 2016, at 9:11 AM, Caroline Beelen <caroline.beelen@kuleuven.be> wrote:

Dear FS team,

Apologies in advance for perhaps again a rather basic question. I attempted to load the aparc overlay in freeview by using the written command from the group analysis page, however it failed to load correctly.

I used the following command:

freeview -f fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5 -viewport 3d

? roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis and dyslect is the contrast folder within this file (main effect of dyslexia), containing a sig.mgh file (all seems fine)

Unfortunately, I got an error that it does not recognize ?overlay_treshold=4,5?. I used freeview ?h and tried certain commands alike, but they didn?t work. When leaving out this part, I got another error that it failed to recognize ?annot_outline=1?. Again, leaving this out too, freeview loads itself and the DK-regions become visible. However, nothing else seems to get activated, and even not when putting ?configure overlay? (which is set to sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens.

When looking at the command line it says that it implemented the colortable of DK-atlas (even twice), but it tells me nothing else. Also, after closing and reloading Freeview by using the similar command and then clicking on ?configure overlay? the screen sometimes gets stuck, giving me the impression that something must be wrong with the command.

Could you please help me out and provide me the right command-line for loading the overlay of the significance map of ?roi.lh.area.dyslect_basic.glmdir/dyslect??

Thanks in advance!

Kind regards, Caroline

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Message: 13
Date: Sat, 30 Jul 2016 15:10:38 +0000
From: Silas <silasnielsen@hotmail.com>
Subject: [Freesurfer] Running recon-all with T1 and FLAIR
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<AM3PR03MB0902B913832CF14559DF0D2ADD020@AM3PR03MB0902.eurprd03.prod.outlook.com>

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

Dear FreeSurfer team,

I'm doing a structural analysis with 50 MS patients and 50 healthy controls (T1, T2 and FLAIR). The MS patients have multiple lesions mainly in white matter. My co-worker did manual editing (bullet points) in the FLAIR images, and i would like to use these edits when running recon-all in order to avoid further manual editing.

The data i'm working with is already resliced to 1 mm and co-registered in MNI-space.

1) Can i use this data or would it be preferable to use the original T1's?

My thought was to run the following command:

recon-all -subject subjectname -i /path/to/input_volume -FLAIR /path/to/FLAIR_volume_with_edits -FLAIRpial -all

2) Does this look correct? Is there anything i should be aware of?

3) Does it make a difference running recon-all -all with the FLAIR image - compared to running recon-all -autorecon3 with the FLAIR after running recon-all -all with only the T1?

4) I've also thought about using the lesion segmentation toolbox for SPM and completely avoid manual editing - is this preferable to using the FLAIR with manual editing?

5) How is the general strength of analysing corpus callosum structurally in MS patients using FreeSurfer?

Best, Silas
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Message: 14
Date: Sat, 30 Jul 2016 08:21:10 -0700
From: Jinsong Tang <tangjinsonghn@gmail.com>
Subject: Re: [Freesurfer] error during longitudinal -long stream
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CADf-At3gyEubK4g3yNSGZ5tXMWQKsabqSC2E7_RY3m-h_N-YEg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Martin?

I tried 2 times again (run 4 analysis at the same time). This time, it
works well, The link to fsaverage is automatically created. I did not
replicate the error message.

Thank you so much!

Best,

Jinsong

On Fri, Jul 29, 2016 at 11:44 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu

wrote:

Hi Jinsong,

can you give an example of what exactly does not work.

Thanks, Martin

On 07/29/2016 12:26 PM, Jinsong Tang wrote:

Hi Martin,

I checked all data are completed except the link to fsaverage,

lh.EC_average and rh.EC_average. I run one analysis from the terminal.

it works. if I run multiple analysis at the same time, it failed.

When I manually linked the 3 files, then run multiple analysis at the same

time, it works good.

Best,

Jinsong

On Wed, Jul 27, 2016 at 8:11 AM, Martin Reuter <

mreuter@nmr.mgh.harvard.edu> wrote:

Hi Jinsong,

maybe not everything was copied? The link to fsaverage should be

automatically created if it is missing. I often process cross in a

different directory from base and long (and create symlinks to the cross

subject dirs). It automatically creates fsaverage then.

Try to replicate your problem with a single subject that failed. First

try to do everything on the same computer, then try to do what you did

before (copying parts of it).

Best, Martin

On 07/20/2016 12:56 PM, Jinsong Tang wrote:

Hi Martin,

We run all cross, base and long with 5.3. I guess the problem maybe we

run cross on a computer and then copy the results to another computer to

run the cross and long. the "*fsaverage" is not copied. Does this

matter?*

Best?

Jinsong

On Wed, Jul 20, 2016 at 12:21 AM, Martin Reuter <

<mreuter@nmr.mgh.harvard.edu>mreuter@nmr.mgh.harvard.edu> wrote:

Hi Jinsong,

I have never seen this. Stable 5.3 is very stable and I doubt it is a

bug. How did you process base and cross sectionals? Also with 5.3 ?

I would recommend to process cross and base with 5.3, then re-run the

long and see if you can replicate this problem. Let me know what happens.

Best, Martin

On Jul 20, 2016, at 12:48 AM, Jinsong Tang < <tangjinsonghn@gmail.com>

tangjinsonghn@gmail.com> wrote:

Hi all,

I found an error during the longitudinal -long stream:

recon-all -long P1001-2 P1001 -all

......

FREESURFER_HOME /space/raid/fmri/freesurfer

Actual FREESURFER_HOME /space/raid/fmri/freesurfer

build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21

UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux

......

mris_spherical_average -erode 1 -orig white -t 0.4 -o

P1001-2.long.P1001 label lh.entorhinal lh sphere.reg lh.EC_average

lh.entorhinal_exvivo.label

painting output onto subject P1001-2.long.P1001.

processing subject lh.EC_average...

MRISread(/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg):

could not open file

eroding label 1 times before writing

thresholding label stat at 0.400 before writing

Not a directory

mris_spherical_average: could not read surface file

/space/raid7/data/london/data/mri/other/jinsong/oneil/ChildOCD/output/lh.EC_average/surf/lh.sphere.reg

Not a directory

Linux funcserv1 3.16.7-35-desktop #1 SMP PREEMPT Sun Feb 7 17:32:21

UTC 2016 (832c776) x86_64 x86_64 x86_64 GNU/Linux

recon-all -s P1001-2.long.P1001 exited with ERRORS at Fri Jul 8

21:33:02 PDT 2016

Please help me fix this error!

Thanks and best regards,

Jinsong

<recon-all.log>_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________

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The information in this e-mail is intended only for the person to whom

it is

addressed. If you believe this e-mail was sent to you in error and the

e-mail

contains patient information, please contact the Partners Compliance

HelpLine at

http://www.partners.org/complianceline . If the e-mail was sent to you

in error

but does not contain patient information, please contact the sender and

properly

dispose of the e-mail.

_______________________________________________

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--

Martin Reuter, PhD

Assistant Professor of Radiology, Harvard Medical School

Assistant Professor of Neurology, Harvard Medical School

A.A.Martinos Center for Biomedical Imaging

Massachusetts General Hospital

Research Affiliate, CSAIL, MIT

Phone: +1-617-724-5652

Web : http://reuter.mit.edu

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it

is

addressed. If you believe this e-mail was sent to you in error and the

e-mail

contains patient information, please contact the Partners Compliance

HelpLine at

http://www.partners.org/complianceline . If the e-mail was sent to you

in error

but does not contain patient information, please contact the sender and

properly

dispose of the e-mail.

--

Jinsong Tang, MD

Institute of Mental Health

The Second Xiangya Hospital , Central South University

139 Renmin Road, Changsha Hunan 410011, P.R. China

_______________________________________________

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--

Martin Reuter, PhD

Assistant Professor of Radiology, Harvard Medical School

Assistant Professor of Neurology, Harvard Medical School

A.A.Martinos Center for Biomedical Imaging

Massachusetts General Hospital

Research Affiliate, CSAIL, MIT

Phone: +1-617-724-5652

Web : http://reuter.mit.edu

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it

is

addressed. If you believe this e-mail was sent to you in error and the

e-mail

contains patient information, please contact the Partners Compliance

HelpLine at

http://www.partners.org/complianceline . If the e-mail was sent to you in

error

but does not contain patient information, please contact the sender and

properly

dispose of the e-mail.