[Freesurfer] Query about Freesurfer's hippocampal subfield segmentation

[Elijah Mak]

Dear Freesurfer Experts,


I am performing the automated segmentation of hippocampal subfield on an
elderly clinical population with a generalized pattern of atrophy. I
understand that the subfields are segmented using a Bayesian inference
approach and a probabilistic atlas based on normal brains. Can you shed
some light on how this method can account for subjects with more severe
hippocampal atrophy (i.e dementia)?


Many thanks!


Best Wishes,

Elijah



-- 

Elijah Mak,

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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[Freesurfer] Freesurfer 6 estimated release date?

[Elijah Mak]

Hello,

I have just read Iglesias et al (2015) hippocampal subfields paper in
Neuroimage with great interest.

Do you have an estimate on the release date of Freesurfer 6 for Mac OSX?
Apologies in advance if this has already been answered elsewhere on this
site.

Many thanks.

Best Wishes,
Elijah

-- 

Elijah Mak, Gates Scholar

PhD Candidate | Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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[Freesurfer] Segmenting the olfactory bulb

[Elijah Mak]

Hello,

Is there a way to segment and extract volumes of the olfactory bulb in
Freesurfer based on T1-MPRAGE?

Cheers.

Best Wishes,
Elijah


-- 

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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[Freesurfer] FS6 Dev: recon-all error

[Elijah Mak]

Hi Freesurfer Experts,

I have installed the dev version to test recon-alls on some subjects, but I
am running into the following error at the transformation stage. See below
for the error message:

/Applications/freesurfer6/bin/talairach_avi

--i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas
3T18yoSchwartzReactN32_as_orig

$Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $

Darwin dhcp-172-17-49-145.wrd.wireless.private.cam.ac.uk 14.0.0 Darwin
Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014;
root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64

Thu May 28 00:01:12 BST 2015

mri_convert orig_nu.mgz talsrcimg.img

$Id: mri_convert.c,v 1.221 2015/04/16 18:56:00 greve Exp $

reading from orig_nu.mgz...

TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to talsrcimg.img...

Analyze Output Matrix

-1.0   0.0   0.0   128.0;

 0.0   0.0   1.0  -128.0;

 0.0  -1.0   0.0   130.0;

 0.0   0.0   0.0   1.0;



INFO: set hdr.hist.orient to -1

mpr2mni305 talsrcimg

Thu May 28 00:01:13 BST 2015

/Applications/freesurfer6/bin/mpr2mni305 talsrcimg

$Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $

target=3T18yoSchwartzReactN32_as_orig


-

analyzeto4dfp talsrcimg -O0 -y

-


$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $

Thu May 28 00:01:13 2015

Writing: talsrcimg.4dfp.hdr

$Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $

Reading: talsrcimg.hdr

header size 348 bytes

hdr.dime.datatype offset=70 value=2

hdr.dime.bitpix offset=72 value=8

hdr.hist.orient offset=252 value=-1

dimensionality 4

dimensions   256   256   256 1

Reading: talsrcimg.img

Writing: talsrcimg.4dfp.img

Writing: talsrcimg.4dfp.ifh

ifh2hdr talsrcimg -r0to255

ori=2


-

gauss_4dfp talsrcimg 1.1

-


dyld: Library not loaded: /usr/local/lib/libgfortran.3.dylib

  Referenced from: /Applications/freesurfer6/bin/gauss_4dfp

  Reason: image not found

Trace/BPT trap

ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=133

ERROR: mpr2mni305 execution aborted


Any idea what is happening? There were no such problems in the recon-all
with the earlier v5.3 build.

Thanks a lot for your help.

Best Wishes,

Elijah

-- 

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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[Freesurfer] FS6 DEV Hippocampal Subfield Error

[Elijah Mak]

Hi  FS Experts,

When I tried to segment the subfields using the Dev version on subjects
that have been previously processed with v5.3, I get the following error:

INFO: FreeSurfer build stamps do not match

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

Current Stamp: freesurfer-Darwin-mavericks-dev-20150522

INFO: SUBJECTS_DIR is /Users/MacPro/Documents/FS6_hipposubfields_long

Actual FREESURFER_HOME /Applications/freesurfer6

-rw-rw-r--  1 MacPro  staff  1702954 May  6 11:11
/Users/MacPro/Documents/FS6_hipposubfields_long/JT_D372A_3D_A/scripts/recon-all.log

Darwin dhcp-172-17-49-145.wrd.wireless.private.cam.ac.uk 14.0.0 Darwin
Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014;
root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64

INFO: current FREESURFER_HOME does not match that of previous processing.

Current: /Applications/freesurfer6

Previous: /Users/fkm24/freesurfer/

#

#@# Hippocampal Subfields processing (T1 only) left Thu May 28 00:34:04 BST
2015

\n /Applications/freesurfer6/bin/segmentSF_T1.sh
/Applications/freesurfer6/MCRv80 /Applications/freesurfer6 JT_D372A_3D_A
/Users/MacPro/Documents/FS6_hipposubfields_long left \n

See log file:
/Users/MacPro/Documents/FS6_hipposubfields_long/JT_D372A_3D_A/scripts/hippocampal-subfields-T1.log

--

Setting up environment variables

---

DYLD_LIBRARY_PATH is
/Applications/freesurfer6/lib/gcc/lib:.:/Applications/freesurfer6/MCRv80/runtime/maci64:/Applications/freesurfer6/MCRv80/bin/maci64:/Applications/freesurfer6/MCRv80/sys/os/maci64

dyld: Library not loaded: @rpath/libmwi18n.dylib

  Referenced from:
/Applications/freesurfer6/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML

  Reason: image not found

/Applications/freesurfer6/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 40: 54963 Trace/BPT trap: 5
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args

#

#@# Hippocampal Subfields processing (T1 only) right Thu May 28 00:34:04
BST 2015

\n /Applications/freesurfer6/bin/segmentSF_T1.sh
/Applications/freesurfer6/MCRv80 /Applications/freesurfer6 JT_D372A_3D_A
/Users/MacPro/Documents/FS6_hipposubfields_long right \n

See log file:
/Users/MacPro/Documents/FS6_hipposubfields_long/JT_D372A_3D_A/scripts/hippocampal-subfields-T1.log

--

Setting up environment variables

---

DYLD_LIBRARY_PATH is
/Applications/freesurfer6/lib/gcc/lib:.:/Applications/freesurfer6/MCRv80/runtime/maci64:/Applications/freesurfer6/MCRv80/bin/maci64:/Applications/freesurfer6/MCRv80/sys/os/maci64

dyld: Library not loaded: @rpath/libmwi18n.dylib

  Referenced from:
/Applications/freesurfer6/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML

  Reason: image not found

/Applications/freesurfer6/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 40: 55000 Trace/BPT trap: 5
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML
$args


#--


Started at Thu May 28 00:34:01 BST 2015

Ended   at Thu May 28 00:34:04 BST 2015

#@#%# recon-all-run-time-hours 0.001

recon-all -s JT_D372A_3D_A finished without error at Thu May 28 00:34:05
BST 2015
Any help is greatly appreciated, many thanks!

Best Wishes,
Elijah

-- 

Elijah Mak,

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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[Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

[Elijah Mak]

Hi Freesurfer Experts,

For the purpose of defining nodes in a graph theory analysis, I would like
to generate a list of X Y Z coordinates in MNI space for all the labels in
the Destrieux atlas. I came across a previous post with the following steps:

Step 1:

mri_annotation2label --subject fsaverage --hemi lh --annotation
aparc.a2009s --outdir /Users/ElijahMak

Step 2:

mri_surfcluster --in
/Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel
lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin
--centroid --thmin 0 --hemi lh --subject fsaverage
Everything went smoothly, but I would like to check my steps with you
before I proceed to generate the coordinates individually for each ROI
per hemisphere.



The output from #2 is sum.lh.G_and_S_frontomargin. When I load it, I see


dhcp-172-17-218-173:~ ElijahMak$ cat sum.lh.G_and_S_frontomargin

# Cluster Growing Summary (mri_surfcluster)

# $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $

# $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $

# CreationTime 2015/08/10-12:29:31-GMT

# cmdline mri_surfcluster --in
/Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel
lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin
--centroid --thmin 0 --hemi lh --subject fsaverage

# cwd /Users/ElijahMak

# sysname  Darwin

# hostname dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk

# machine  x86_64

# FixVertexAreaFlag 1

# FixSurfClusterArea 1

#

# Input  /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness

# Frame Number  0

# srcsubj fsaverage

# hemi lh

# surface white

# SUBJECTS_DIR /Applications/freesurfer/subjects

# SearchSpace_mm2 65416.6

# SearchSpace_vtx 932

# Bonferroni 0

# Minimum Threshold 0

# Maximum Threshold infinity

# Threshold Signabs

# AdjustThreshWhenOneTail 1

# Area Threshold0 mm^2

# clabelfile lh.G_and_S_frontomargin.label

# clabelinv  0

# Overall max 3.33248 at vertex 83949

# Overall min 0 at vertex 0

# NClusters  1

# Total Cortical Surface Area 65416.6 (mm^2)

# FixMNI = 1

#

# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZNVtxs

   13.332   83949  82219.39-29.4  -22.0   17.4  163842


 Are those TalX TalY TalZ the values I'm looking for?



Many thanks for your time.



Best Wishes,

Elijah




-- 

Elijah Mak,

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

[Elijah Mak]

Hi Douglas,

Thanks for the help! However, when I tried the --nofixmni flag, all the
ROIs appeared to have identical MNI coordinates. I have pasted the output
from 3 ROIS in the LH.

# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZNVtxs
   13.332   83949  82219.39-29.4  -22.0   17.4  163842
   13.533  117158  82219.39-29.4  -22.0   17.4  163842
   13.170   83424  82219.39-29.4  -22.0   17.4  163842


The same thing happens to the ROIs on the RH (XYZ: 29.8 29.8 18.0).

Best Wishes,
Elijah

-- 

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

[Elijah Mak]

Hi Douglas,


Sorry about that! I hope this works. I have pasted the earlier
correspondence here with your response below:


Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas:
Checking steps 
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+Extracting+MNI+Coordinates+from+the+Destrieux+Atlas%5C%3A+Checking+steps%22&o=newest>

Douglas N Greve
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22>
Wed, 12 Aug 2015 07:27:49 -0700
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20150812>

Those are more-or-less talairach coords, not MNI. If you add --nofixmni,
the results will be reported in mni305 coords.

Those are more-or-less talairach coords, not MNI. If you add --nofixmni,
the results will be reported in mni305 coords.

On 08/10/2015 08:39 AM, Elijah Mak wrote:
> Hi Freesurfer Experts,
>
> For the purpose of defining nodes in a graph theory analysis, I would
> like to generate a list of X Y Z coordinates in MNI space for all the
> labels in the Destrieux atlas. I came across a previous post with the
> following steps:
>
> Step 1:
>
> mri_annotation2label --subject fsaverage --hemi lh --annotation
> aparc.a2009s --outdir /Users/ElijahMak
>
> Step 2:
>
> mri_surfcluster --in
> /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel
> lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin
> --centroid --thmin 0 --hemi lh --subject fsaverage
>
>
> Everything went smoothly, but I would like to check my steps with you before
> I proceed to generate the coordinates individually for each ROI per
> hemisphere.
>
>
> The output from #2 issum.lh.G_and_S_frontomargin. When I load it, I see
>
> dhcp-172-17-218-173:~ ElijahMak$ cat sum.lh.G_and_S_frontomargin
>
>
> # Cluster Growing Summary (mri_surfcluster)
>
>
> # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
>
>
> # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
>
>
> # CreationTime 2015/08/10-12:29:31-GMT
>
>
> # cmdline mri_surfcluster --in
> /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel
> lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin
> --centroid --thmin 0 --hemi lh --subject fsaverage
>
>
> # cwd /Users/ElijahMak
>
>
> # sysname  Darwin
>
>
> # hostname dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk
> <http://dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk>
>
>
> # machine  x86_64
>
>
> # FixVertexAreaFlag 1
>
>
> # FixSurfClusterArea 1
>
>
> #
>
>
> # Input  /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness
>
>
> # Frame Number  0
>
>
> # srcsubj fsaverage
>
>
> # hemi lh
>
>
> # surface white
>
>
> # SUBJECTS_DIR /Applications/freesurfer/subjects
>
>
> # SearchSpace_mm2 65416.6
>
>
> # SearchSpace_vtx 932
>
>
> # Bonferroni 0
>
>
> # Minimum Threshold 0
>
>
> # Maximum Threshold infinity
>
>
> # Threshold Signabs
>
>
> # AdjustThreshWhenOneTail 1
>
>
> # Area Threshold0 mm^2
>
>
> # clabelfile lh.G_and_S_frontomargin.label
>
>
> # clabelinv  0
>
>
> # Overall max 3.33248 at vertex 83949
>
>
> # Overall min 0 at vertex 0
>
>
> # NClusters  1
>
>
> # Total Cortical Surface Area 65416.6 (mm^2)
>
>
> # FixMNI = 1
>
>
> #
>
>
> # ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZNVtxs
>
>13.332   83949  82219.39-29.4  -22.0   17.4  163842
>
>
>
>
> Are those TalX TalY TalZ the values I'm looking for?
>
>
> Many thanks for your time.
>
>
> Best Wishes,
> Elijah
>
>
> --
>
> Elijah Mak,
>
> PhD Candidate *|* Psychiatry
>
> University of Cambridge
>
> Trinity College, Cambridge, CB2 1TQ
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR centergr...@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/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-ma

[Freesurfer] Assessing local correlations across 2 modalities

[Elijah Mak]

Dear Freesurfer Community,

I am currently trying to investigate the local correlations across 2
modalities (i.e. Tau-PET and cortical thinning). I understand that this
sort of questions has been conventionally addressed using the Biological
Parametric Mapping (BPM) toolbox in MATLAB.

Is there a way in Freesurfer to properly address this?

My PET data have already been registered and projected to the surfaces for
each individual.

Thanks a lot.

Best Wishes,
Elijah

-- 

Elijah Mak

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Elijah Mak]

Dear Anastasia,

I have also uploaded the file with the problem (22995_EM.zip), and this is
how my config file looks like after modifications:

set subjlist = (22995)
set pathlist = (fmajor_PP)
set ncpts = (7)
set reinit = (1)

Thanks again!

Best Wishes,
Elijah


-- 

Elijah Mak

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Elijah Mak]

Hi Anastasia,

Thank you for looking into that subject. I have tried reinitiliasation a
few times and in all cases, it just could not find a satisfactory control
point fit during the -prior stage. Therefore, the -prior stage has been
running for more than 10 hours now. This occurs in other a small number of
other subjects as well.

WARN: Could not find satisfactory control point fit - try 596

How can I resolve this? And what type of problem could be reflected by
 this? Bad aparc+aseg.mgz / registration to template?

If all else fails, I will exclude subjects using the criteria that you set
in the Neuroimage paper: where a subject was excluded if there were
failures of reconstruction in 2 or more WM tracts.

Thank you for your help!

Best Wishes,
Elijah




-- 

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

[Elijah Mak]

Hi Anastasia,

Thanks, it works, but only for MNI reg option. For the CVS stream, there
was an error message during -prior.

ERROR: fio_pushd:
/Users/MacPro/Documents/22995_EM/dmri/xfms/cvs/final_CVSmorph_tocvs_avg35/mri

This error message did not halt the process though. Could this be a clue?

Thanks for your patience :)

Best Wishes,

Elijah




-- 

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PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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[Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat

[Elijah Mak]

Hi Anastasia and others,

I am trying to visualise the *.path.mean.txt on MNI template after running
trac-all -stat. I used this command:

freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w
stats/*.path.mean.txt

However, it looks like something has gone wrong with the labelling and
position of the tracts (note the CST highlighted in green).

https://www.dropbox.com/s/ndpkfgbrfgvt5q1/Screen%20Shot%202016-08-22%20at%2014.41.37.png?dl=0

Everything was fine and correctly labelled when I checked the merged tracks.

Thanks again for your help!


Best Wishes,
Elijah

P.S. On another note, the reinit=1 trick works very well and I was able to
reconstruct the tracts in almost all cases. Thanks!
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Re: [Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat

[Elijah Mak]

Hi Anastasia,

Yes indeed. I am using a dev version of freeview. I could give it another
go with the freeview that came with v5.3. But does this mean that I shoudl
also I re-run the tracula -stat on a v5.3?

Thanks!

Best Wishes,
Elijah
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Re: [Freesurfer] BBR not recommended for PETSurfer?

[Elijah Mak]

Hi Christopher,

We have very positive experiences with mri_coreg too.

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47135.html

Quite a bit of manual tweaking had to be done along with BBR for our AV and
PK BPnd data. It works just fine on the PIB SUVRs though.

Then, we switched to mri_coreg and manual tweaking was hardly necessary
after that. It truly works wonders :)

Best Wishes,
Elijah
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[Freesurfer] latest version of mri_glmfit-sim?

[Elijah Mak]

H 
ello
Freesurfer Team,


Where may I download the latest version of mri_glmfit-sim and QDEC to
run the mri_surfcluster? I am having errors on mri_glmfit-sim and
monte-carlo simulations in QDEC (dev version that was released quite
awhile back).


A snippet of the error below after MC correction in QDEC

Searching for Clusters ...

thmin=2.00 (2.00), thmax=-1.00 (-1), thsignid=0, minarea=0.00

Found 36 clusters

Max cluster size 2817.874756

INFO: fixing MNI talairach coordinates

Pruning by CW P-Value 0.05

ERROR!

Error in Monte Carlo simulation: Error running mri_surfcluster!


Many thanks for your help.


Best Wishes,

Elijah
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Re: [Freesurfer] Assessing local correlations across 2 modalities

[Elijah Mak]

Hello,

Thanks Doug for your help on this previously. I am quite puzzled by the
vertex-wise local correlations that I've found  (i.e more tau thicker
cortex)... and before I go down the rabbit hole of trying to dissect what
could be happening, I'd like to check if one of the steps in my workflow
has gone wrong?

1) My FSGD is a simple one group design with no other covariates.
2) mri_concat --f stacks_cth_rh15 --o concat_cth_rh15_.mgh **stack of
thickness maps after qcache
3) C_pvr_cth.mtx = 0 1
4) mri_glmfit --y concat_tau_lh_sm8.mgh --pvr concat_cth_lh15.mgh --fsgd
FSGD_tau dods --C C_pvr_cth.mtx --surf fsaverage lh --cortex --glmdir
pvr_lh.glmdir

Thanks a lot! :)

Best Wishes,
Elijah




Writing results
C_pvr_cth
maxvox sig=4.6783  F=34.7936  at  index 31050 0 0 seed=1479612145
mri_glmfit done

Thanks a lot for your help.

Best Wishes,
Elijah
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[Freesurfer] Extracting structural measures from trend-level PET clusters

[Elijah Mak]

Hi Freesurfer Team,

1) We've found some subtle differences in tau accumulation between two
groups. Unfortunately, it does not survive mri_glmfit-sim (voxel threshold
0.001, cwp < 0.05). Still, I would like to extract the structural measures
from the uncorrected tau clusters (p<0.001). What is the most convenient
approach for this?

Could the following URL (http://www.mail-archive.com/f
reesur...@nmr.mgh.harvard.edu/msg16268.html
) be a solution? Can mri_label2label work for sig.mgh with multiple
clusters?

2) A slightly unrelated question: how can I go about using this particular
cluster as a seed for functional or tractography analysis in other
softwares (i.e. FSL or MRTRIX) or even within Freesurfer if possible?

Thanks again. Really appreciate your help!

Best Wishes,
Elijah
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[Freesurfer] How to view overlapping voxels across multiple sig.mgh files?

[Elijah Mak]

Hi Freesurfer Team,

I am just wondering if there is a neat way to derive .mgh files containing
cluster information about spatially overlapping voxels across various
sig.mgh?

Thank you.

Best Wishes,
Elijah
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Re: [Freesurfer] Extracting structural measures from trend-level PET clusters

[Elijah Mak]

Thanks, Doug.

It works but I am not sure if the values I'm getting are correct. Is this
supposed to be reporting the mean cortical thickness of each cluster? I
have pasted the output below from the avgwf below.  The names of the
clusters correspond to the regions from the "summary" text, am I right?


Group lh_fusiform lh_precentral lh_insular lh_precuneus lh_parsorbitalis
1 24.29454 29.53935 14.24736 28.97924 31.54577
1 25.68872 28.26156 17.47828 28.20604 30.38902
2 25.46281 30.75879 19.34943 29.59019 32.0404
2 25.55514 27.23871 17.27937 29.14274 29.75657

Another related question: Is it possible to simply take the mean cortical
thickness across the voxels exceeding p<0.001 from the uncorrected sig.mgh?

Thanks again!

Best Wishes,
Elijah
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Re: [Freesurfer] Extracting structural measures from trend-level PET clusters

[Elijah Mak]

Hi,

A bit more info: the stack of thickness maps consists of
lh.thickness.fwhm15.fsaverage.mghs that were created after -qcache. I used
mri_concat --f --o to create the stack of mghs.  I also noticed that the
vertex values are in the range of 20-30, whereas those in the
lh.thickness.fsvaerage mghs are in the expected range.

Should I be using this for the calculation of the thickness in the clusters
instead?

Best Wishes,
Elijah

On Sat, Nov 12, 2016 at 12:15 AM, Elijah Mak 
wrote:

> Thanks, Doug.
>
> It works but I am not sure if the values I'm getting are correct. Is this
> supposed to be reporting the mean cortical thickness of each cluster? I
> have pasted the output below from the avgwf below.  The names of the
> clusters correspond to the regions from the "summary" text, am I right?
>
>
> Group lh_fusiform lh_precentral lh_insular lh_precuneus lh_parsorbitalis
> 1 24.29454 29.53935 14.24736 28.97924 31.54577
> 1 25.68872 28.26156 17.47828 28.20604 30.38902
> 2 25.46281 30.75879 19.34943 29.59019 32.0404
> 2 25.55514 27.23871 17.27937 29.14274 29.75657
>
> Another related question: Is it possible to simply take the mean cortical
> thickness across the voxels exceeding p<0.001 from the uncorrected sig.mgh?
>
> Thanks again!
>
> Best Wishes,
> Elijah
>
>


-- 

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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[Freesurfer] Comparing z score maps between 2 modalities in a group?

[Elijah Mak]

Hi Freesurfer Team,

We would like to compare Z-scored surface maps between different modalities
(MRI and PET) within a single group. 1 subject = 2 measures.

These are my steps so far, using mri_concat and fscalc for the generation
of the Z score maps. Differences between Z-score maps are tested using the
paired t-test approach as outlined here:
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis

I am not sure if my following steps are correct, so confirmation will be
much appreciated, many thanks for your time and help!

// Generate mean/sd of healthy controls

X
mri_concat --f stacks_X_lh_HC_fsaverage --o group_mean_X_hc_lh.mgh  --mean
mri_concat --f stacks_X_lh_HC_fsaverage --o group_std_X_hc_lh.mgh  --std

Y
mri_concat --f stacks__Y_HC_fsaverage --o group_mean_Y_HC_lh.mgh  --mean
mri_concat --f stacks_Y_lh_HC_fsaverage --o group_std_Y_HC_lh.mgh  --std

QN: Should smoothing be applied here or before?

// Derive individual Z-score map for X and Y

X
for i in `cat list`; do  fscalc $i/surf/lh.X.fsaverage.mgh sub
group_mean_X_hc_lh.mgh div group_std_X_hc_lh.mgh --o
$i/surf/lh.Z.thickness.fsaverage.mgh; done
for i in `cat list; do  fscalc $i/surf/rh.X.fsaverage.mgh sub
group_mean_cth_hc_rh.mgh div group_std_X_hc_rh.mgh --o
$i/surf/rh.Z.thickness.fsaverage.mgh; done

Y
for i in `cat list`; do  fscalc $i/surf/lh.Y.fsaverage.mgh sub
group_mean_X_hc_lh.mgh div group_std_cth_hc_lh.mgh --o
$i/surf/lh.Z.fsaverage.mgh; done
for i in `cat list; do  fscalc $i/surf/rh.Y.fsaverage.mgh sub
group_mean_Y_hc_rh.mgh div group_std_Y_hc_rh.mgh --o
$i/surf/rh.Z.fsaverage.mgh; done


// Derive paired-difference of Z scores between X and Y

mri_concat --f stacks_XminusY_lh --paired-diff --o concat_XminusY_lh.mgh
mri_concat --f stacks_XminusY_rh --paired-diff --o concat_XminusY_rh.mgh

// Smooth concatenated maps of paired differences

mri_surf2surf --s fsaverage --hemi lh --fwhm 4 --sval concat_XminusY_lh.mgh
 --tval concat_XminusY_lh_sm4.mgh

// Test significance of paired differences within the group

mri_glmfit --y concat_XminusY_lh_sm4.mgh --fsgd fsgd_pairediff dods --osgm
--surf fsaverage lh --cortex --glmdir

I used the --osgm flag as there are no covariates here.
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Re: [Freesurfer] Extracting structural measures from trend-level PET clusters

[Elijah Mak]

Hi Doug,

I am not sure if this is the correct way to reply to the thread. I thought
that adding a "RE:" in front of the subject would automatically link the
email to its orginal thread.
I hope this works!

I am pasting the previous emails below.

Thanks again, Doug.

Re: [Freesurfer] Extracting structural measures from trend-level PET
clusters
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+Extracting+structural+measures+from+trend%5C-level+PET+clusters%22&o=newest>

Douglas N Greve
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22>
 Mon, 14 Nov 2016 08:07:03 -0800
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20161114>

Hi Elijah, can you repost with previous correspondence included? We get
a lot of emails here and can't keep track of each person's issue. thanks!

doug


On 11/11/2016 08:06 PM, Elijah Mak wrote:
> Hi,
>
> A bit more info: the stack of thickness maps consists of
> lh.thickness.fwhm15.fsaverage.mghs that were created after -qcache. I
> used mri_concat --f --o to create the stack of mghs.  I also noticed
> that the vertex values are in the range of 20-30, whereas those in the
> lh.thickness.fsvaerage mghs are in the expected range.
>
> Should I be using this for the calculation of the thickness in the
> clusters instead?
>
> Best Wishes,
> Elijah
>
> On Sat, Nov 12, 2016 at 12:15 AM, Elijah Mak  <mailto:fk...@medschl.cam.ac.uk >> wrote:
>
> Thanks, Doug.
>
> It works but I am not sure if the values I'm getting are correct.
> Is this supposed to be reporting the mean cortical thickness of
> each cluster? I have pasted the output below from the avgwf
> below.  The names of the clusters correspond to the regions from
> the "summary" text, am I right?
>
>
> Group lh_fusiform lh_precentral   lh_insular  lh_precuneus
> lh_parsorbitalis
> 1 24.2945429.5393514.2473628.97924
> 31.54577
> 1 25.6887228.2615617.4782828.20604
> 30.38902
> 2 25.4628130.7587919.3494329.59019
> 32.0404
> 2 25.5551427.2387117.2793729.14274
> 29.75657
>
>
> Another related question: Is it possible to simply take the mean
> cortical thickness across the voxels exceeding p<0.001 from the
> uncorrected sig.mgh?
>
> Thanks again!
>
> Best Wishes,
> Elijah
>
>
>
>
> --
>
> Elijah Mak, Gates Scholar
>
> PhD Candidate *|* Psychiatry
>
> University of Cambridge
>
> Trinity College, Cambridge, CB2 1TQ
>
>
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR centergr...@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/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

*Re: [Freesurfer] Extracting structural measures from trend-level PET
clusters*
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+Extracting+structural+measures+from+trend%5C-level+PET+clusters%22&o=newest>

Douglas N Greve
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22>
 Wed, 09 Nov 2016 13:22:06 -0800
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20161109>

You can just


mri_segstats --i thickness.stack.mgh --seg cache.th30.pos.sig.ocn.nii.gz

--excludeid 0 --avgwf thickness.stack.cluster.dat

Each row in thickness.stack.cluster.dat will be a subject, and each

column is a cluster




On 11/09/2016 04:16 PM, Elijah Mak wrote:

> Hi Freesurfer Team,

>

> 1) We've found some subtle differences in tau accumulation between two

> groups. Unfortunately, it does not survive mri_glmfit-sim (voxel

> threshold 0.001, cwp < 0.05). Still, I would like to extract the

> structural measures from the uncorrected tau clusters (p<0.001). What

> is the most convenient approach for this?

>

> Could the following URL

> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg16268.html

> <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg16268.html>

> ) be a solution? Can mri_label2label work for sig.mgh with multiple

> clusters?

>

> 2)

Re: [Freesurfer] Comparing z score maps between 2 modalities in a group?

[Elijah Mak]

Hi Doug,

Thanks for taking a look at the commands!  I appreciate it.

I would like to ask a further question about your concern/s regarding this
approach?

My aim was to have an analytical pipeline in Freesurfer that is analogous
to several studies (using VBM-type of analyses in SPM) where they compared
the relative severity of various pathological processes measured from
different modalities. For reference, see: https://www.ncbi.nlm.nih
.gov/pubmed/24951642 In that study, the authors in that study were trying
to examine whether hypometabolism was relatively more severe compared to
atrophy, and both modalities (PET and T1) were Z-scored relative to
controls, and then compared against each other.

Best Wishes,
Elijah


On Fri, Nov 18, 2016 at 5:24 PM, Elijah Mak  wrote:

> Hi Doug,
>
> Thanks for taking a look at the commands!
>
> I would like to ask a further question about your concern/s regarding this 
> approach? My aim was to have an analytical pipeline in Freesurfer that is 
> analogous to several studies (using VBM-type of analyses in SPM) where they 
> compared the relative severity of various pathological processes measured 
> from different modalities.
>
> I have attached a little screenshot for your reference.
>
> For example, the authors in that study were trying to see whether 
> hypometabolism was relatively more severe compared to atrophy, and both 
> modalites (PET and T1) were Z-scored relative to controls, and then compared 
> against each other. Another study that has used a similar technique is here: 
> https://www.ncbi.nlm.nih.gov/pubmed/24951642
>
> Best Wishes,
> Elijah
>
>
>
>
>
>
> Re: [Freesurfer] Comparing z score maps between 2 modalities in a group? 
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+Comparing+z+score+maps+between+2+modalities+in+a+group%5C%3F%22&o=newest>
>
> Douglas N Greve 
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22>
>  Fri, 18 Nov 2016 08:19:47 -0800 
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20161118>
>
> Those commands look right, though I would do the smoothing before
> computing the standard dev. Also, I don't know whether your overall
> method is valid.
>
> On 11/15/2016 05:48 PM, Elijah Mak wrote:
> > Hi Freesurfer Team,
> >
> > We would like to compare Z-scored surface maps between different
> > modalities (MRI and PET) within a single group. 1 subject = 2 measures.
> >
> > These are my steps so far, using mri_concat and fscalc for the
> > generation of the Z score maps. Differences between Z-score maps are
> > tested using the paired t-test approach as outlined here:
> > https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
> >
> > I am not sure if my following steps are correct, so confirmation will
> > be much appreciated, many thanks for your time and help!
> >
> > // Generate mean/sd of healthy controls
> >
> > X
> > mri_concat --f stacks_X_lh_HC_fsaverage --o group_mean_X_hc_lh.mgh  --mean
> > mri_concat --f stacks_X_lh_HC_fsaverage --o group_std_X_hc_lh.mgh  --std
> >
> > Y
> > mri_concat --f stacks__Y_HC_fsaverage --o group_mean_Y_HC_lh.mgh  --mean
> > mri_concat --f stacks_Y_lh_HC_fsaverage --o group_std_Y_HC_lh.mgh  --std
> >
> > QN: Should smoothing be applied here or before?
> >
> > // Derive individual Z-score map for X and Y
> >
> > X
> > for i in `cat list`; do  fscalc $i/surf/lh.X.fsaverage.mgh sub
> > group_mean_X_hc_lh.mgh div group_std_X_hc_lh.mgh --o
> > $i/surf/lh.Z.thickness.fsaverage.mgh; done
> > for i in `cat list; do  fscalc $i/surf/rh.X.fsaverage.mgh sub
> > group_mean_cth_hc_rh.mgh div group_std_X_hc_rh.mgh --o
> > $i/surf/rh.Z.thickness.
> fsaverage.mgh; done
> >
> > Y
> > for i in `cat list`; do  fscalc $i/surf/lh.Y.fsaverage.mgh sub
> > group_mean_X_hc_lh.mgh div group_std_cth_hc_lh.mgh --o
> > $i/surf/lh.Z.fsaverage.mgh; done
> > for i in `cat list; do  fscalc $i/surf/rh.Y.fsaverage.mgh sub
> > group_mean_Y_hc_rh.mgh div group_std_Y_hc_rh.mgh --o
> > $i/surf/rh.Z.fsaverage.mgh; done
> >
> >
> > // Derive paired-difference of Z scores between X and Y
> >
> > mri_concat --f stacks_XminusY_lh --paired-diff --o concat_XminusY_lh.mgh
> > mri_concat --f stacks_XminusY_rh --paired-diff --o concat_XminusY_rh.mgh
> >
> > // Smooth concatenated maps of paired differences
> >
> > mri_surf2surf --s fsaverage --hemi lh --fwhm 4 --sval
> > concat_XminusY_lh.mgh  --tval concat_XminusY_lh_sm4.mgh
> &

Re: [Freesurfer] [Announcement] Freesurfer v6.0 beta release and testing

[Elijah Mak]

Hi ZK,

Thanks. It is great news! I would like to report the following.

asegstats2table seems to be acting strangely.

 File "/Applications/freesurfer_b6/bin/asegstats2table", line 195

print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'

Even typing asegstats2table --help leads to the same error message.  It was
not found in a prev dev built or in 5.3.

Thanks.

Also, not sure if it's placebo, but  freeview seems to be running quicker
now.

Best Wishes,

Elijah
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[Freesurfer] Freesurfer 6 beta testing: mri_glmfit-sim error

[Elijah Mak]

Hi Freesurfer Team,

I came across the following error while running mri_glmfit-sim. What is
vwsigmax?
Thanks for your help again.

The full log is as follows:

$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Sat Nov 19 02:00:45 GMT 2016
Darwin dhcp-10-240-201-24.cp.wireless.private.cam.ac.uk 14.5.0 Darwin
Kernel Version 14.5.0: Thu Jun 16 19:58:21 PDT 2016;
root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64

MacPro

setenv SUBJECTS_DIR /Volumes/TITAN/cth_wmh_study

FREESURFER_HOME //Users/MacPro/Documents/freesurfer_b6


Original mri_glmfit command line:
cmdline mri_glmfit.bin --y y.mgh --fsgd FSGDs/FSGD_Z_cthVsCTH_AD_age dods
--C Contrasts/C --surf fsaverage lh --cortex --glmdir Glmdirs/ProjectAD

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 20.927757
CSD
//Users/MacPro/Documents/freesurfer_b6/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/abs/th30/mc-z.csd
mri_surfcluster --in Glmdirs/ProjectAD/C/sig.mgh --mask
Glmdirs/ProjectAD/mask.mgh --cwsig
Glmdirs/ProjectAD/C/cache.th30.abs.sig.cluster.mgh --sum
Glmdirs/ProjectAD/C/cache.th30.abs.sig.cluster.summary --ocn
Glmdirs/ProjectAD/C/cache.th30.abs.sig.ocn.mgh --annot aparc --cwpvalthresh
0.05 --o Glmdirs/ProjectAD/C/cache.th30.abs.sig.masked.mgh --no-fixmni
--csd
//Users/MacPro/Documents/freesurfer_b6/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/abs/th30/mc-z.csd
--csdpdf Glmdirs/ProjectAD/C/cache.th30.abs.pdf.dat --vwsig
Glmdirs/ProjectAD/C/cache.th30.abs.sig.voxel.mgh --vwsigmax
Glmdirs/ProjectAD/C/cache.th30.abs.sig.voxel.max.dat --oannot
Glmdirs/ProjectAD/C/cache.th30.abs.sig.ocn.annot --bonferroni 2 --surf white

ERROR: Option --vwsigmax unknown

Best Wishes,

Elijah
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Re: [Freesurfer] ASL processing in Freesurfer? (Douglas Greve)

[Elijah Mak]

Many thanks for the information, Doug! I will give it a go.

Actually, I would like to carry out the following analyses:

Get regional estimates of perfusion within a region of interest as defined
by a significant cluster after mri_glmfit-sim. as well as other cortical
regions that are connected to that cluster in terms of WM paths. Is it
possible to do that in Freesurfer environment?

How can I do PVC for perfusion in  ROIs? Will the -pv ppvol flag be crucial
during the mri_segstats stage?

Thanks again for help.

Best Wishes,
Elijah
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Re: [Freesurfer] ASL processing in Freesurfer?

[Elijah Mak]

Apologies, please ignore the other email response. I believe this should be
tagged to the right thread (hopefully!)
-


Many thanks for the information, Doug! I will give it a go.

Actually, I would like to carry out the following analyses:

Get regional estimates of perfusion within a region of interest as defined
by a significant cluster after mri_glmfit-sim. as well as other cortical
regions that are connected to that cluster in terms of WM paths. Is it
possible to do that in Freesurfer environment?

How can I do PVC for perfusion in  ROIs? Will the -pv ppvol flag be crucial
during the mri_segstats stage?

Thanks again for help.

Best Wishes,
Elijah


Re: [Freesurfer] ASL processing in Freesurfer?


Douglas Greve

 Mon, 21 Nov 2016 12:31:41 -0800


No, not really. If you're not doing anything fancy (eg, just computing
mean of tag-control) and mapping to the surface, it is easy enough to do
(mri_concat --paired-diff --sum, then bbregister to register to the
anat, then mri_vol2surf or mris_preproc to map to fsaverage, then
mri_glmfit and mri_glmfti-sim. If you're trying to correct for decay,
intensity gradients, etc, then no.

On 11/21/16 1:40 PM, Foo Keat Mak wrote:
> Hi Freesurfer Team,
>
> Is there an ASL-friendly processing pipeline embedded in Freesurfer?
> Something like an equivalent to that of PetSurfer? Thanks.
>
> Best Wishes,
> Elijah
>
> Sent from my iPad
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>

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[Freesurfer] Cohen's D = gamma.mgh / rstd.mgh?

[Elijah Mak]

Hi there,

What is the correct way to plot, at each vertex, the Cohen's *D* after a
*mri_glmfit* comparison? I've seen a few variations posted on the mailing
list.

Is gamma.mgh / rstd.mgh is the correct formula? Does rstd.mgh represent
pooled SD across both groups (patients and controls)?

Secondly, after plotting the effect size across the whole brain, is it
feasible to test whether there are regional differences in effect size by
using *mri_segstats* and *aparc* to extract the ROI-averaged effect size in
*fsaverage* space, and then perform a paired t-test between say, frontal vs
occipital ROIs?

Thank you.

Best Wishes,
Elijah
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Re: [Freesurfer] Cohen's D = gamma.mgh / rstd.mgh?

[Elijah Mak]

Dear Doug,

Thanks.


Do you mean use ROI averages as the samples and then test across ROIs?

This would be unusual as the interpretation is problematic. I would

probably compute a single number per subject that is a weighted
sum/difference of the ROI values, then test whether this one number is
different across subjects.


Probably a silly question.. but how can I get the data at the
subject-level as the effectsize.mgh is derived at the group-level
after mri_glmft?


On a similar note, if I want to simply report the effect size of a
significant cluster, could I use mri_glmfit to extract the averaged
effect size for the cluster by feeding it as a mask to mri_segstats?


Best Wishes,

Elijah
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Re: [Freesurfer] Cohen's D = gamma.mgh / rstd.mgh?

[Elijah Mak]

Hi Doug,

This is my main objective.

1. PET in Group 1 vs Group 2
2. Thickness in the same sample, Group 1 vs Group 2
3. ASL in the same sample of Group 1 vs Group 2
4. Create a binary mask of the overlapping corrected sig voxels from 1-3.
5. This mask is therefore a site of co-localised atrophy, perfusion and PET
changes in Group wrt Group 2.

Now, I would like to look at how the effect sizes of 1-3 compare against
one another, above and beyond the spatial overlap.  I hope this is clearer,
but let me know if I could provide more information. I thought about
looking at *Z-scores* like some other studies, but I find that it is highly
dependent on the range of the SD, which differed to a large extent (PET
having a range of 1-10 vs 1-3 in atrophy). Hence I thought the Cohen's
*D *might
represent a more plausible workaround by pooling the SD across both groups,

Thanks.

Best Wishes,
Elijah
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Re: [Freesurfer] PCA on PET / Thickness in Freesurfer

[Elijah Mak]

Hi Doug,

Thanks. It works! What does each vertex represent in V.mgh?
http://imgur.com/W1RZdKn

Here are the results from the stats. Then, I would like to extract the 1st
component and convert it into label for mri_segstats. How may I do that?

  1   105131.57 105131.5773.79   73.79

  29130.61 114262.18 6.41   80.20

  38052.58 122314.77 5.65   85.85

  45480.79 127795.56 3.85   89.69

  54398.33 132193.89 3.09   92.78

  63504.02 135697.91 2.46   95.24

  72386.62 138084.53 1.68   96.92

  82055.74 140140.27 1.44   98.36

  91603.79 141744.06 1.13   99.48

 10 734.89 142478.95 0.52  100.00

 11   0.00 142478.95 0.00  100.00


Thanks.

Best Wishes,
Elijah




Re: [Freesurfer] PCA on PET / Thickness in Freesurfer

2016-12-02

 Thread

 Douglas N Greve


You can run it like that or with --osgm (instead of --fsgd and --C),
osgm = one sample group mean.


On 12/01/2016 07:13 PM, Foo Keat Mak wrote:
> Hi Doug,
> I have pasted the correspondences below. My question is, if I want to
> identify the PCs in a group for a single modality (PET), how should I
> run the mri_glmfit? A single group design with A contrast of 1 0 (for
> a nuisance covariate)?
> Thanks !
> Elijah
> Doug:
> For within modality, you can add --pca to mri_glmfit (run it with
> --help to get more info). We do not have ICA tools in FS.
> On 12/01/2016 02:04 PM, Foo Keat Mak wrote: > Hi Freesurfer Team, > >
> For a given group, I want to look at the covariance patterns between >
> thickness and PET. Within Freesurfer, what are some general workflow >
> tips on how I could go about performing PCA (within modality) or joint
> > ICA analyses looking at the covariance patterns across modalities?
> Is > the -pca flag a good starting point? > > Any feedback is
> appreciated! > > Thanks a lot. > > Best Wishes, > Elijah > > >
> ___ > Freesurfer mailing
> list > Freesurfer@nmr.mgh.harvard.edu
>  >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --
> Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu
>  Phone Number: 617-724-2358 Fax:
> 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>  FileDrop:
> https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> ___ Freesurfer mailing
> list Freesurfer@nmr.mgh.harvard.edu
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The
> information in this e-mail is intended only for the person to whom it
> is addressed. If you believe this e-mail was sent to you in error and
> the e-mail contains patient information, please contact the Partners
> Compliance HelpLine at http://www.partners.org/complianceline . If the
> e-mail was sent to you in error but does not contain patient
> information, please contact the sender and properly dispose of the e-mail.
>
>
> Sent from my iPad
>
> On 1 Dec 2016, at 23:30, Foo Keat Mak  > wrote:
>
>> Thanks Doug. Does that mean that a one group design? With a contrast
>> of 1 0 (adjusting for one variable)?
>>
>>
>
>
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MGH-NMR centergr...@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] PCA on PET / Thickness in Freesurfer

2016-12-01

 Thread

 Foo Keat Mak


Hi Doug,


I have pasted the correspondences below. My question is, if I want to identify
the PCs in a group for a single modality (PET), how should I run the
mri_glmfit? A single group design with A contrast of 1 0 (for a nuisance
covariate)?


Thanks !


E

[Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed scans

[Elijah Mak]

Greetings Freesurfer Community,

I am running a longitudinal study using Freesurfer v.5.3 to compare rate of
cortical thinning between 2 groups of subjects. I hope I can seek some
expert advice on the following situation:

All data (both the baseline and follow-up) has been processed independently
using recon-all. This has been done on Freesurfer 5.0.

Since then, I have upgraded to Freesurfer v5.3 to utilize the linear mixed
effect capability.

For the construction of base and longs, I understand that it is important
to add -clean flag to my recon-all strings to overwrite brainmask.mgz etc.
When must this be done?

I am still new to Freesurer, and I'd greatly appreciate any advice
regarding workflow.

Many Thanks,

Elijah


-- 

Elijah Mak, B.A.

Doctoral Candidate *|* Psychiatry

University of Cambridge *| *Department of Psychiatry

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed scans

[Elijah Mak]

Hi Martin,

Thank you for your help.

By re-processing, do you mean running recon-alls all over again?

Could you elaborate on the advantage of creating a new subjectsdir and
copying over the orig dirs for each subject?

On a related note, would it be better to run the full recon-all pipeline
for each subject? I have been running batches of subjects at each stage
(i.e. autorecon1, autorecon2, and finally autorecon3).

Thank you again.

Best Wishes,
Elijah




On Wed, Jan 15, 2014 at 9:02 PM, Martin Reuter
wrote:

>  Hi Elijah,
>
> if you have minimal edits, I'd recommend to reprocess the data from
> scratch with 5.3 (that is supposed to be the same as using the -clean flag
> when rerunning 5.3 on top of the old 5.0 data). But I'd recommend to create
> a new subjectsdir, copy over the subjedid/mri/orig dirs for each subject
> and rerun from scratch with 5.3 the independent, base and long runs.
>
> Best, Martin
>
>
>
> On 01/13/2014 06:18 PM, Elijah Mak wrote:
>
> Greetings Freesurfer Community,
>
>  I am running a longitudinal study using Freesurfer v.5.3 to compare rate
> of cortical thinning between 2 groups of subjects. I hope I can seek some
> expert advice on the following situation:
>
> All data (both the baseline and follow-up) has been processed
> independently using recon-all. This has been done on Freesurfer 5.0.
>
> Since then, I have upgraded to Freesurfer v5.3 to utilize the linear mixed
> effect capability.
>
> For the construction of base and longs, I understand that it is important
> to add -clean flag to my recon-all strings to overwrite brainmask.mgz etc.
> When must this be done?
>
> I am still new to Freesurer, and I'd greatly appreciate any advice
> regarding workflow.
>
> Many Thanks,
>
> Elijah
>
>
>  --
>
> Elijah Mak, B.A.
>
> Doctoral Candidate *|* Psychiatry
>
> University of Cambridge *| *Department of Psychiatry
>
> Trinity College, Cambridge, CB2 1TQ
>
>
>
>
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>
> --
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> 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
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>



-- 

Elijah Mak, B.A.

Doctoral Candidate *|* Psychiatry

University of Cambridge *| *Department of Psychiatry

Trinity College, Cambridge, CB2 1TQ
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[Freesurfer] Advice: Freesurfer Parallel Processing on Large Dataset

[Elijah Mak]

Hi FSL Experts,

I am currently processing a large dataset and would like to seek some
advice regarding parallel processing.

These are the specifications of my iMac:
3.2GHz , Intel Core i5, No. of processor: 1, Total number of cores: 4, L2
Cache per core: 256kb, L3 Cache: 6MB, Memory: 8GB.

Would it be useful to open 4 terminals and run RECON-ALL on 4 subjects
simultaneously? Lastly, is there some sort of -flag I can use to maximize
parallel RECON-ALLs ?

Currently, I am running 2 RECON-ALLs on 2 terminals and each subject take
on average 7-9 hours for completion, which is rather fast I think.

Many Thanks.

Best Wishes,
Elijah



-- 

Elijah Mak, B.A.

Doctoral Candidate *|* Psychiatry

University of Cambridge *| *Department of Psychiatry

Trinity College, Cambridge, CB2 1TQ
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[Freesurfer] General diffusion workflow questions: QC and extracting FA from subcortical structures

[Elijah Mak]

Dear Freesurfer Community,

1) I am just starting out on some diffusion analyses and I'd like to use
the dt_recon for this. Is there any information about a general workflow
for quality control for the outputs from dt_recon? From the tutorials, I
only see information about checking the registration.  In particular, I
would like to know how dt_recon cope with the occasional flipping/swapping
of some components of the diffusion gradient directions?

2) Another aim of mine is to quantify DTI indices in subcortical regions
segmented from the ASEG pipeline. How does Freesurfer handle partial
volumning via seg-erode in "mri_vol2vol"?

I have pasted my workflow below and I'd like to check if this is correct,
thanks!

1) After processing the scans on recon-all and dt_recon , i resample the
structural data to diffusion space

mri_vol2vol --mov subjectname/dtrecon/lowb.nii.gz
--targ subjectname/mri/aparc+aseg.mgz --inv --interp nearest
--o subjectname/mri/aparc+aseg2diff.mgz  --reg
subjectname/dtrecon/register.dat --no-save-reg

Should I use ASEG instead of APARC+ASEG or WMPARC (which also has labels
for the subcortical regions?)

2) Then, I mask the FA/MD maps with

mri_mask subjectname/dtrecon/fa.nii.gz  subjectname/mri/aparc+aseg2diff.mgz
subjectname/dtrecon/fa-masked_aparcaseg.mgz; done

3) Finally, I collect the FA in the regions with

mri_segstats --seg subjectname/mri/aparc+aseg2diff.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt
--i subjectname/dtrecon/fa-masked_aparcaseg.mgz --seg-erode 1
--sum subjectname/stats/fa_aparc+aseg2diff_segerode_1;done

Thanks a lot for your time and help!

Best Wishes,
Elijah

-- 

Elijah Mak

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] Reading values from overlays with PETcoreg

[Elijah Mak]

Dear Doug,

Is it possible to use BP SUVR PET that have been registered to T1 for this
gtmseg workflow? You mentioned that the mean TAC should be used as the
input. 2 quick questions: What's mean TAC and why?

Thanks.

Best Wishes,
Elijah
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[Freesurfer] mri_cvs_register : output

[Elijah Mak]

Hi Freesurfer Community,

I am running mri_cvs_register for the spatial normalization and it seems to
work very nicely on my set of DTI data in subjects with substantial
atrophy.

However, I can't seem to find the file
combined_tocvs_avg35_elreg_afteraseg-norm.m3z,
however, I have final_CVSmorph_tocvs_avg35.m3z. Is this essentially the
same thing?

Thanks for looking into this.

Best Wishes,
Elijah
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[Freesurfer] PET voxelwise

[Elijah Mak]

Hi Freesurfer Community,

I am trying to run a vertex-wise analyses of PET data.

I have already performed bbregister. Next, I did mri_vol2surf for each
subject, left and right hemispheres.

for i in `cat subjects`; do mri_vol2surf --src
FS6_${i}_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out
FS6_${i}_MPRAGE_Neuro.nii/surf/lh.PETSurface.mgh --hemi lh --regheader
FS6_${i}_MPRAGE_Neuro.nii --projfrac 0.5 --interp nearest; done

Is this command correct? Visual inspection on freeview looks OK.

How may I derive the group average from these individual surfaces and
perform the mri_glmfit?

Any help will be greatly appreciated.

Best Wishes,
Eli
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Re: [Freesurfer] PET voxelwise

[Elijah Mak]

Hi Doug,

Thanks!

I manually tweaked the registration of the PET to T1 on a number of
subjects to bring the mincost down to < 0.5.  After saving the pet2free
volume in Freeview, I noticed that a new .lta is produced in the same
directory (i.e. pet2free_fsl.mgz.lta).

Will the option --regheader tell the subsequent commands (i.e.
mri_vol2surf) to use the updated registration .lta instead of the original
.dat that was produced via bbregister?

Best Wishes,
Elijah
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Re: [Freesurfer] PET voxelwise

[Elijah Mak]

mri_concat --f pib_lh_fsaverage (textfile of subjects and their images) --o
concat_lh_pet.mgh

Should I add -mean here for the GLM?

mri_glmfit  --y  concat_lh_pet.mgh  --fsgd  pib_fsgd  --C group1.group2.mtx
 --surf fsaverage lh  --cortex  --glmdir lh.pet.glmdir

My simple 2 group-no-covariates FSGD is as follows. Can I also check that
it is alright to have the Groups interspersed throughout the order?

GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
input FS6_16084_MPRAGE_Neuro.nii Group1
input FS6_22769_MPRAGE_Neuro.nii Group1
input FS6_22863_MPRAGE_Neuro.nii Group1
input FS6_22899_MPRAGE_Neuro.nii Group1
input FS6_22995_MPRAGE_Neuro.nii Group2
input FS6_23008_MPRAGE_Neuro.nii Group1
input FS6_23173_MPRAGE_Neuro.nii Group2
input FS6_23243_MPRAGE_Neuro.nii Group2
input FS6_23244_MPRAGE_Neuro.nii Group1
input FS6_23619_MPRAGE_Neuro.nii Group1
input FS6_23623_MPRAGE_Neuro.nii Group1
input FS6_23755_MPRAGE_Neuro.nii Group2

Thanks again, Doug. Appreciate it so much!

Best Wishes,
Elijah
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[Freesurfer] FA and MD *positively* correlated within same regions ?

[Elijah Mak]

Hi Freesurfer Community,

I recently used mri_segstats to extract FA and MD as suggested here:
http://freesurfer.net/fswiki/FsTutorial/Diffusion

Using the aparc+aseg and wmparc (resampled to diffusion space), I looked at
some of the correlations between FA and MD in the same regions, and came
across a few interesting ones.

wm_lh_entorhinal FA & wm_lh_entorhinal MD: r = 0.6, p <0.001
ctx_lh_entorhinal FA & ctx_lh_entorhinal MD: r = -0.3, p < 0.020

wm_lh_precuneus FA & wm_lh_precuneus MD: r = -0.6, p <0.001

As I understand, a clear-cut interpretation especially with regards to FA
changes is not so easy!  But could someone discuss / speculate as to why FA
and MD could be positively correlated within the entorhinal WM region? That
was found separately within a group of a elderly healthy controls and a
group of dementia subjects.

Thank you for your time!

Best Wishes,
Elijah
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Re: [Freesurfer] Cortical thickness average

[Elijah Mak]

Hi Sahil,

I did something similar recently. I believe you can use mri_concat with the
-mean option to create an average map of the group.

Another option might be make_average_subject?

https://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject

Best Wishes,
Elijah
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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

[Elijah Mak]

Hi Alshikho

,

Yes, I am sure :) Same sequence for everyone.

Just to add. FA and MD were significantly negatively correlated for the
other regions including the fusiform, precuneus, hippocampus, thalamus,
etc.

So I am very curious about what could be going on with the ERC here?

Best Wishes,
Elijah
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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

[Elijah Mak]

Hi Kirstie,

Yes indeed there were 3 subjects at the bottom-left of the plot.

To account for PV, I eroded the boundaries using *-seg-erode 1* during the
*mri_segstats* stage, and this resulted in a few subjects with no data for
the WM entorhinal region (although these were saved as "0" in the .stats
file). Do people generally do this for DTI studies?

All good now.

Many thanks again, Kirstie.

Best Wishes,
Elijah
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[Freesurfer] Viewing eroded structure after -seg-erode 1

[Elijah Mak]

Hi Freesurfer Community,

I have performed -seg-erode 1 during mri_segstats on resampled subcortical
strutures (T1 to FA/MD). Can I view the eroded masks in T1 anatomical space
to visually inspect whether PVE has been adequately accounted for?

Thank you.

Best Wishes,
Elijah
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Re: [Freesurfer] Viewing eroded structure after -seg-erode 1

[Elijah Mak]

Thanks Doug.

Do you mean loading the structure (i.e. LeftHippocampus2diff.mgz) on the
orig.mgz as an overlay? I am able to do that but I can't seem to find an
option for thresholding. Sorry if I misunderstood your original email.

Best Wishes,
Elijah
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[Freesurfer] TRACULA dev version: Error message

[Elijah Mak]

Hi Freesurfer Community,

I am running TRACULA on a single subject in the dev version
(freesurfer-Darwin-OSX-stable-v6-beta-20151015)

#-

/Applications/freesurfer6beta/bin/trac-preproc

#-

#@# Image corrections Mon Apr 11 16:15:19 BST 2016

mri_convert /Users/MacPro/Documents/NIMROD_DTI/16084.nii.gz
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz

mri_convert /Users/MacPro/Documents/NIMROD_DTI/16084.nii.gz
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz

$Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $

reading from /Users/MacPro/Documents/NIMROD_DTI/16084.nii.gz...

TR=11700.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-0.998406, -0.0447105, -0.0344521)

j_ras = (-0.0435914, 0.998518, -0.0325768)

k_ras = (-0.0358576, 0.0310231, 0.998875)

writing to
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz...

cp 16084.bvec
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvecs

cp 16084.bval
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvals

mv -f
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvecs.tmp
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvecs

mv -f
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvals.tmp
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvals

flip4fsl
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.nii.gz

INFO: input image orientation is LAS

INFO: input image determinant is -8

fslswapdim
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz
x y z
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.nii.gz

fslorient -forceradiological
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.nii.gz

mv -f
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.mghdti.bvecs
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvecs

mv: rename
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.mghdti.bvecs
to */Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvecs:
No such file or directory*


*trac-preproc exited with ERRORS at Mon Apr 11 16:16:26 BST 2016*
---

What has gone wrong here?

Thanks!
Elijah
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Re: [Freesurfer] PET voxelwise

[Elijah Mak]

Hi Doug,

One more question about feeding the -reg to mri_vol2surf, please.

I am specifying the registration .lta because I have made edits to it,

mri_vol2surf --src FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out
FS6_24551_MPRAGE_Neuro.nii/surf/lh.PETSurfce.mgh --projfrac 0.5 --hemi lh
--reg FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz.lta --trgsubject
fsaverage

I get the following error:

srcvol = FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz

srcreg = FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz.lta

srcregold = 0

srcwarp unspecified

surf = white

hemi = lh

trgsubject = fsaverage

surfreg = sphere.reg

ProjFrac = 0.5

thickness = thickness

reshape = 0

interp = nearest

float2int = round

GetProjMax = 0

INFO: float2int code = 0

Done loading volume

Input reg is LTA



type  = 0 # LINEAR_VOX_TO_VOX

nxforms   = 1

mean  = 0. 0. 0.

sigma = 1.

1 4 4

9.996573328971863e-01 -2.963314531370997e-03 2.600867860019207e-02
-2.005096435546875e+00

1.517883041479706e-18 9.935718178749084e-01 1.132032126188278e-01
-2.398274230957031e+01

-2.617694810032845e-02 -1.131644248962402e-01 9.932314157485962e-01
1.568508148193359e+01

0.000e+00 0.000e+00 0.000e+00
1.000e+00

src volume info

valid = 1  # volume info valid

filename =
/Users/MacPro/Documents/NIMROD_DTI/FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz

volume = 256 256 256

voxelsize = 1.000e+00 1.000e+00
1.000e+00

xras   = -1.000e+00 -2.328306436538696e-10 0.000e+00

yras   = -1.862645149230957e-09 -2.991509973071516e-08
-1.000e+00

zras   = 0.000e+00 1.000e+00 1.091393642127514e-10

cras   = 1.471549987792969e+00 -1.038517761230469e+01 1.970146179199219e+01

dst volume info

valid = 1  # volume info valid

filename =
/Users/MacPro/Documents/NIMROD_DTI/FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz

volume = 256 256 256

voxelsize = 1.000e+00 1.000e+00
1.000e+00

xras   = -1.000e+00 -2.328306436538696e-10 0.000e+00

yras   = -1.862645149230957e-09 -2.991509973071516e-08
-1.000e+00

zras   = 0.000e+00 1.000e+00 1.091393642127514e-10

cras   = 1.471549987792969e+00 -1.038517761230469e+01 1.970146179199219e+01

fscale 0.15

ERROR: source volume is neither source nor target of the registration

This error does not appear when I use --regheader though?

Best Wishes,

Elijah
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Re: [Freesurfer] Viewing eroded structure after -seg-erode 1

[Elijah Mak]

Hi Doug,

I have pasted the previous emails below. I have computed mri_segstats to
extract the FA and MD from resampled aparc+aseg.mgz in diffusion space.
-seg-erode 1 was performed during mri_segstats. Now, I will like to
visually inspect the results of that erosion for the left and right
hippocampal structures. Is there anyway I can do that and compare that
against the uneroded hippocampus?

 I don't think mri_segstats -seg-erode 1 produce any volumetric outputs so
I am not sure.

Thanks.

Best Wishes,

Elijah


Douglas N Greve
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22>
 Mon, 11 Apr 2016 08:11:06 -0700
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20160411>

You can load it as an overlay in freeview make sure to specify the
registration file as that compted for the DTI. Also make sure to set the
threshold to something like 0.5

On 04/11/2016 09:41 AM, Elijah Mak wrote:
> Hi Freesurfer Community,
>
> I have performed -seg-erode 1 during mri_segstats on resampled
> subcortical strutures (T1 to FA/MD). Can I view the eroded masks in T1
> anatomical space to visually inspect whether PVE has been adequately
> accounted for?
>
> Thank you.
>
> Best Wishes,
> Elijah
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Re: [Freesurfer] PET voxelwise

[Elijah Mak]

Hi Doug,


I edited the registration by hand (after bbregister) in Freeview,
saving the PET_2_T1 volume.


In Freeview (dev FS6) : Tools -> Transform Volume --> Tweaked rotation
and translation --> Save Volume As --> Clicked "Do not resample voxel
data when saving (only update header)"


Using this method, I realise I could simply specify -regheader without
feeding the .lta for mri_vol2surf and it seems to work well.


Best Wishes,

Elijah



How did you edit the registration? Does it work with the unedited version?


On 04/13/2016 10:21 AM, Elijah Mak wrote:
> Hi Doug,
>
> One more question about feeding the -reg to mri_vol2surf, please.
>
> I am specifying the registration .lta because I have made edits to it,
>
> mri_vol2surf --src FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz
> --out FS6_24551_MPRAGE_Neuro.nii/surf/lh.PETSurfce.mgh --projfrac 0.5
> --hemi lh --reg FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz.lta
> --trgsubject fsaverage
>
> I get the following error:
>
> srcvol = FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz
>
> srcreg = FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz.lta
>
> srcregold = 0
>
> srcwarp unspecified
>
> surf = white
>
> hemi = lh
>
> trgsubject = fsaverage
>
> surfreg = sphere.reg
>
> ProjFrac = 0.5
>
> thickness = thickness
>
> reshape = 0
>
> interp = nearest
>
> float2int = round
>
> GetProjMax = 0
>
> INFO: float2int code = 0
>
> Done loading volume
>
> Input reg is LTA
>
>
>
> type  = 0 # LINEAR_VOX_TO_VOX
>
> nxforms   = 1
>
> mean  = 0. 0. 0.
>
> sigma = 1.
>
> 1 4 4
>
> 9.996573328971863e-01 -2.963314531370997e-03 2.600867860019207e-02
> -2.005096435546875e+00
>
> 1.517883041479706e-18 9.935718178749084e-01 1.132032126188278e-01
> -2.398274230957031e+01
>
> -2.617694810032845e-02 -1.131644248962402e-01 9.932314157485962e-01
> 1.568508148193359e+01
>
> 0.000e+00 0.000e+00 0.000e+00
> 1.000e+00
>
> src volume info
>
> valid = 1  # volume info valid
>
> filename =
> /Users/MacPro/Documents/NIMROD_DTI/FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz
>
> volume = 256 256 256
>
> voxelsize = 1.000e+00 1.000e+00
> 1.000e+00
>
> xras   = -1.000e+00 -2.328306436538696e-10
> 0.000e+00
>
> yras   = -1.862645149230957e-09 -2.991509973071516e-08
> -1.000e+00
>
> zras   = 0.000e+00 1.000e+00 1.091393642127514e-10
>
> cras   = 1.471549987792969e+00 -1.038517761230469e+01
> 1.970146179199219e+01
>
> dst volume info
>
> valid = 1  # volume info valid
>
> filename =
> /Users/MacPro/Documents/NIMROD_DTI/FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz
>
> volume = 256 256 256
>
> voxelsize = 1.000e+00 1.000e+00
> 1.000e+00
>
> xras   = -1.000e+00 -2.328306436538696e-10
> 0.000e+00
>
> yras   = -1.862645149230957e-09 -2.991509973071516e-08
> -1.000e+00
>
> zras   = 0.000e+00 1.000e+00 1.091393642127514e-10
>
> cras   = 1.471549987792969e+00 -1.038517761230469e+01
> 1.970146179199219e+01
>
> fscale 0.15
>
> ERROR: source volume is neither source nor target of the registration
>
> This error does not appear when I use --regheader though?
>
> Best Wishes,
>
> Elijah
>
>
>
>
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Re: [Freesurfer] PET voxelwise

[Elijah Mak]

Dear Doug,

One more question:

There are many voxels with negative binding potentials in this dataset,
mostly in the CSF/ventricular regions.  Can I restrict the mri_glmfit to
focus only on the voxels with positive BP?

Best Wishes,
Elijah
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[Freesurfer] REPOST: TRACULA dev version: Error message

[Elijah Mak]

Hi Freesurfer,

Sorry about reposting this email from earlier:

I can't seem to get the TRACULA in the dev version of FS6 to run.

mv -f
/Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/dwi_orig_flip.mghdti.bvecs
/Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/bvecs

mv: rename
/Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/dwi_orig_flip.mghdti.bvecs
to /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/bvecs: No such file or
directory

The contents of that folder are: dwi_orig.mghdti.bvals dwi_orig.mghdti.bvecs
dwi_orig.nii.gz dwi_orig_flip.nii.gz xfms

The full error message is enclosed with this email.
Thanks!

Best Wishes,
Elijah
$Id: trac-preproc,v 1.51.2.1 2015/10/06 02:40:20 zkaufman Exp $
--
dhcp-10-240-197-124:NIMROD_DTI MacPro$ trac-all -prep -c tracula -no-isrunning
INFO: SUBJECTS_DIR is /Users/MacPro/Documents/NIMROD_DTI
INFO: Diffusion root is /Users/MacPro/Documents/NIMROD_DTI
Actual FREESURFER_HOME /Applications/freesurfer6beta
trac-preproc -c 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/scripts/dmrirc.local
 -log 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/scripts/trac-all.log
 -cmd 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/scripts/trac-all.cmd
 -no-isrunning
#-
/Applications/freesurfer6beta/bin/trac-preproc 
#-
#@# Image corrections Fri Apr 15 17:44:30 BST 2016
mri_convert /Users/MacPro/Documents/NIMROD_DTI/16084.nii.gz 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz
mri_convert /Users/MacPro/Documents/NIMROD_DTI/16084.nii.gz 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz
 
$Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $
reading from /Users/MacPro/Documents/NIMROD_DTI/16084.nii.gz...
TR=11700.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998406, -0.0447105, -0.0344521)
j_ras = (-0.0435914, 0.998518, -0.0325768)
k_ras = (-0.0358576, 0.0310231, 0.998875)
writing to 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz...
cp 16084.bvec 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvecs
cp 16084.bval 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvals
mv -f 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvecs.tmp 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvecs
mv -f 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvals.tmp 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvals
flip4fsl 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz
 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -8
fslswapdim 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.nii.gz
 x y z 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.nii.gz
fslorient -forceradiological 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.nii.gz
mv -f 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.mghdti.bvecs
 /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvecs
mv: rename 
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig_flip.mghdti.bvecs
 to /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/bvecs: 
No such file or directory
Darwin dhcp-10-240-197-124.cp.wireless.private.cam.ac.uk 14.0.0 Darwin Kernel 
Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; 
root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64

trac-preproc exited with ERRORS at Fri Apr 15 17:45:37 BST 2016

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Re: [Freesurfer] PET voxelwise & Segmentation Fault during mri_glmfit-sim

[Elijah Mak]

No, more like running the voxelwise comparisons only on voxels that have
positive BP between 2 group.  Is that possible?

On another note, I am running into a puzzling "Segmentation fault" error
with the following command:

mri_glmfit-sim --glmdir  lh_ad_hc.glmdir  --cache 2 neg --cwp  0.05
--2spaces



Reading source surface
/Users/MacPro/Documents/NIMROD_DTI//fsaverage/surf/lh.white

Done reading source surface

Reading annotation
/Users/MacPro/Documents/NIMROD_DTI//fsaverage/label/lh.aparc.annot

reading colortable from annotation file...

colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

Segmentation fault


Strangely, I can't seem to reproduce this error consistently too.
Sometimes, after a pause of few minutes, the exact same command works! This
happens on smoothed and non-smooth PET data.

I have attached the text outputs resulting from both scenarios 1) seg_fault
and 2) no_seg_fault (about 10 minutes between each execution).

The mri_glmfit-sim version is v .53.2.2 2015/08/28 19:00:13
I am running this on a Mac Pro with 64 GB RAM.

Thanks again

Best Wishes,
Elijah
dhcp-10-240-197-124:NIMROD_DTI MacPro$ mri_glmfit-sim --glmdir 
tau_lh_ad_hc.glmdir  --cache 2 neg --cwp  0.05 --2spaces
cmdline mri_glmfit --y concat_ad_hc_lh_tau_sm2.mgh --fsgd tau_ad_control_fsgd 
--C tau_hc_ad.mtx --glmdir tau_lh_ad_hc.glmdir --surf fsaverage lh --cortex
SURFACE: fsaverage lh
log file is tau_lh_ad_hc.glmdir/cache.mri_glmfit-sim.log

cd /Users/MacPro/Documents/NIMROD_DTI
/Applications/freesurfer6beta/bin/mri_glmfit-sim
--glmdir tau_lh_ad_hc.glmdir --cache 2 neg --cwp 0.05 --2spaces

$Id: mri_glmfit-sim,v 1.53.2.2 2015/08/28 19:00:13 greve Exp $
Sat Apr 16 01:20:20 BST 2016
Darwin dhcp-10-240-197-124.cp.wireless.private.cam.ac.uk 14.0.0 Darwin Kernel 
Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; 
root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
MacPro
setenv SUBJECTS_DIR /Users/MacPro/Documents/NIMROD_DTI/
FREESURFER_HOME /Applications/freesurfer6beta

Original mri_glmfit command line:
cmdline mri_glmfit --y concat_ad_hc_lh_tau_sm2.mgh --fsgd tau_ad_control_fsgd 
--C tau_hc_ad.mtx --glmdir tau_lh_ad_hc.glmdir --surf fsaverage lh --cortex

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 12.549009
CSD 
/Applications/freesurfer6beta/average/mult-comp-cor/fsaverage/lh/cortex/fwhm13/neg/th20/mc-z.csd
mri_surfcluster --in tau_lh_ad_hc.glmdir/tau_hc_ad/sig.mgh --csd 
/Applications/freesurfer6beta/average/mult-comp-cor/fsaverage/lh/cortex/fwhm13/neg/th20/mc-z.csd
 --mask tau_lh_ad_hc.glmdir/mask.mgh --cwsig 
tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.cluster.mgh --vwsig 
tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.voxel.mgh --sum 
tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.cluster.summary --ocn 
tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.ocn.mgh --oannot 
tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.ocn.annot --annot aparc 
--csdpdf tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.pdf.dat --cwpvalthresh 
0.05 --o tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.masked.mgh 
--no-fixmni --bonferroni 2 --surf white
Creating CDFs from CSD files
csd->threshsign = -1
thsign = neg, id = -1
version $Id: mri_surfcluster.c,v 1.57 2014/03/06 17:02:46 greve Exp $
hemi   = lh
srcid  = tau_lh_ad_hc.glmdir/tau_hc_ad/sig.mgh 
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = neg
thmin  = 2
thmax  = -1
fdr= -1
minarea= 0
Bonferroni  = 2
xfmfile= talairach.xfm
nth = -1
outid= tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.masked.mgh MGH
ocnid= tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.ocn.mgh MGH
sumfile  = tau_lh_ad_hc.glmdir/tau_hc_ad/cache.th20.neg.sig.cluster.summary
subjectsdir= /Users/MacPro/Documents/NIMROD_DTI/
FixMNI = 0
Found 146238 vertices in mask
Found 146238 vertices in mask
Found 146238 points in clabel.
- XFM matrix (RAS2RAS) ---
/Users/MacPro/Documents/NIMROD_DTI//fsaverage/mri/transforms/talairach.xfm
 1.0   0.0   0.0   0.0;
 0.0   1.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0   0.0   0.0   1.0;

Reading source surface 
/Users/MacPro/Documents/NIMROD_DTI//fsaverage/surf/lh.white
Done reading source surface
Reading annotation 
/Users/MacPro/Documents/NIMROD_DTI//fsaverage/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Segmentation fault dhcp-10-240-197-124:NIMROD_DTI MacPro$ mri_glmfit-sim --glmdir 
tau_lh_ad_hc.glmdir  --cache 2 neg --cwp  0.05 --2spaces
cmdline mr

[Freesurfer] mri_coreg !

[Elijah Mak]

Hi Doug,

I just want to say that mri_coreg worked tremendously well for the
registration of some very blurry PET-PK data. I was not getting any success
with bbregister and init-fsl or mri_robust_register options.

How does this technique differ from the boundary-based registration?

Thanks a lot.

Best Wishes,
Elijah
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[Freesurfer] mri_coreg !

[Elijah Mak]

Hi Doug and Martin,

Thanks both for your responses. I am working with  PK11195, AV-1451,
and PiB. In general, the standard bbregister routine with init-fsl
works well for AV-1451 (adjustments needed in 30% of cases) and PiB
(best performance), but it completely failed with the PK data which
was acquired on the same scanner. I tried running the registration
using the mean image (mri_concat --mean) but it did not help too.

All that being said, mri_coreg works extremely well for the PK11195
(only 3 manual adjustments needed so far for > 50 scans), so I am very
grateful for this tool :)

If I want to run the analyses of the various PET data in the same
study, will it be of concern that I am using a mix of boundary-based
(AV and PIB) and normalised mutual information (PK)?

Best Wishes,
Elijah


Re: [Freesurfer] mri_coreg !
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+mri_coreg+%5C%21%22&o=newest>

Martin Reuter 
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Martin+Reuter%22>
Mon, 16 May 2016 13:23:13 -0700
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20160516>

Hi,

just wanted to mention that the --cost NMI (normalized mutual
information) and MI implementations in mri_robust_register are the same
as spm_coreg and now mri_coreg (if the -nosym flag is specified in
robust register, else it is registering in a symmetric midspace instead
into the target space). If you have cases where robust_register fails,
but the other tools work, let me know, because that could indicate a bug
in my code.

Thanks, Martin


On 05/16/2016 03:19 PM, Douglas N Greve wrote:
> It is my implementation of the spm_coreg program written by John
> Ashburner using normalized mutual information. I liked the spm program
> so much that I put the effort into replicating its behavior in C. My
> guess is that BBR was failing because the initialization was failing.
> Still I like mri_coreg for PET data because the blurriness can throw BBR
> off a bit. What kind of PET data do you have?
>
>
> On 05/16/2016 03:06 PM, Elijah Mak wrote:
>> Hi Doug,
>>
>> I just want to say that mri_coreg worked tremendously well for the
>> registration of some very blurry PET-PK data. I was not getting any
>> success with bbregister and init-fsl or mri_robust_register options.
>>
>> How does this technique differ from the boundary-based registration?
>>
>> Thanks a lot.
>>
>> Best Wishes,
>> Elijah
>>
>>
>>
>>
>>
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>> 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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-- 

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] WM Hyperintensities

[Elijah Mak]

Hi Martin,


I am also following this thread with interest. Is that multi-modal
prototype you mentioned available in the next FS6.0?


Many thanks.


Best Wishes,

Elijah


Navena Rebecca Lingum
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Navena+Rebecca+Lingum%22>
Wed, 18 May 2016 10:25:09 -0700
<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20160518>

Would any member of the FreeSurfer team be able to help with this question?

I would like to use the FreeSurfer software to delineate white matter
hyperintensities. I have processed my T1 images using the recon-all command,
and in the aseg.stat file there is a value for WM hypointensities.

Is there an alternate stream/ FreeSurfer algorithm that exists for the
processing of T2w FLAIR images for WM hyperintensities?

Thanks,
Navena



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

Sent: May 17, 2016 1:32 PM
To: Freesurfer support list
Subject: [Freesurfer] WM Hyperintensities

Hi Navena,

I am the wrong person to answer questions about the WM lesion stream. I think
the one that is available in FreeSurfer is only based on T1 images, but a
prototype of a better stream exists, that can incorporate different modalities.

Best, Martin

P.S. Changed the subject, to reflect that this is not a longitudinal question
any more.

On 05/17/2016 12:37 PM, Navena Rebecca Lingum wrote:
Dear Martin,

Thank you kindly for your prompt response.

I am actually having difficulties with the delineation of White Matter
Hyperintensities at a single time point. I apologize if my question is
redundant and perhaps an answer to it is already mentioned elsewhere.

As it stands, I am finding it difficult to understand the exact "pipeline" of
commands necessary to perform this segmentation and accurate delineation of
WMH. I have ran the recon -all command on my T1w images, but I suspect a proper
segmentation of WMH would require a T2w Flair (which I have). How do I go about
combining the preprocessing data produced by FreeSurfer with my T2w images to
produce a WMH mask/volume/stats?

Any help on the matter is much appreciated!

Kindly,
Navena Lingum


On May 16, 2016, at 4:24 PM, Martin Reuter
mailto:mreu...@nmr.mgh.harvard.edu
>> wrote:

Hi Navena,

There is currently no dedicated stream for longitudinal WM abnormalities (in
the sense of joint estimation and modeling). You can, however, make use of the
longitudinal stream and it's increase reliability - e.g it is working in the
same space across time, which should help get more reliable estimates.

Best, Martin

On 05/16/2016 01:47 PM, Navena Rebecca Lingum wrote:
Dear FreeSurfer experts,

My colleagues and I would like to use FreeSurfer to perform a longitudinal
analysis of white matter hyperintensities. Is there an additional add-on for
the software to perform this analysis or can this analysis be performed using
the recon-all command?

Navena Lingum



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Phone: +1-617-724-5652
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Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

[Elijah Mak]

Hi, 

I've also come across similar situations in my FS 6.0 dataset. 

I have tried tweaking the seg-wlo and seg-ghi values and these steps have led 
to marked improvements in some cases. 

Curious to hear from the FS team too. 

Thanks. 

Best Wishes, 
Elijah


Elijah Mak, Research Associate Department of Psychiatry, Old Age Psychiatry 
Group 
University of Cambridge
Trinity College, CB21TQ, UK 
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 





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[Freesurfer] Extracting fMRI mean time series from Desikan ROIs

[Elijah Mak]

Hello Freesurfer Experts,

I have a question to ask about extracting the mean time series from 
resting-state fMRI (239 volumes).

I have used bbregister to bring the 4D fMRI data into T1 space. My next 
objective is to project the data onto the fsaverage surface, and then extract 
the mean time series for each ROI.

These are my steps so far. Can anyone let me know if I am on the right/wrong 
track?

bbregister --s  $i --mov ${i}_medn.nii (fMRI resting-state) --init-fsl --t2 
--reg ${i}/fmri/fmri_t1.dat --o ${i}/fmri/fmri_t1.mgz

mri_vol2surf --src ${i}/fmri/fmri_t1.mgz --out ${i}/surf/lh.fmri.mgh --hemi lh 
--projfrac 0.5 --interp nearest --regheader ${i} --trgsubject fsaverage

mri_segstats --i ${i}/surf/lh.fmri.mgh  --annot fsaverage lh aparc --sum 
${i}/stats/lh.fmri_aparc.sum

Ultimately, how may I derive a 239 (volumes) x 34 (ROIs per hemisphere) matrix 
of the data?

Appreciate your help. Thanks!

Best Wishes,
Elijah 


Elijah Mak, Research Associate
Department of Psychiatry,  Old Age Psychiatry Group
University of Cambridge
Trinity College, CB21TQ, UK


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[Freesurfer] Thresholding sig.mgh with cluster extent K > 20 voxels

[Elijah Mak]

Hi Everyone,

How may I threshold the sig.mgh (p<0.001) with a cluster extent K > 20 voxels? 
Is it possible to do this in Freesurfer?

Thanks.

Best Wishes,
Elijah

Dr. Elijah Mak, Research Associate
Department of Psychiatry,  Old Age Psychiatry Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 

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Re: [Freesurfer] Thresholding sig.mgh with cluster extent K > 20 voxels

[Elijah Mak]

Thanks Doug. Just to confirm do I get this voxels number from the cluster 
summary text file then?

Best Wishes,
Elijah

Dr. Elijah Mak, Research Associate
Department of Psychiatry,  Old Age Psychiatry Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 


On 22 May 2017 at 15:49:16, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote:

There is not a straight-forward way to do it as mri_glmfit-sim only  
takes a clusterwise p-value threshold. You can change that until you get  
20 voxels.  


On 05/21/2017 09:48 AM, Elijah Mak wrote:  
> Hi Everyone,  
>  
> How may I threshold the sig.mgh (p<0.001) with a cluster extent K > 20  
> voxels? Is it possible to do this in Freesurfer?  
>  
> Thanks.  
>  
> Best Wishes,  
> Elijah  
>  
> *Dr. Elijah Mak, Research Associate*  
> Department of Psychiatry, Old Age Psychiatry Group  
> University of Cambridge  
> Trinity College, CB21TQ, UK  
> http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24  
>  
>  
>  
> ___  
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--  
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MGH-NMR Center  
gr...@nmr.mgh.harvard.edu  
Phone Number: 617-724-2358  
Fax: 617-726-7422  

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting  
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Re: [Freesurfer] Hyperintensities Volume ?

[Elijah Mak]

Hi, 

Not that I'm aware of. You could use the WM Hypointensities label from aseg 
though. Despite its understimation of WMH, we have actually found a high 
correlation with WMH segmented from FLAIRS in over 100 elderly and demented 
subjects (r < 0.8). 

Cheers, 
Elijah 

Dr. Elijah Mak, Research Associate
Department of Psychiatry, Old Age Psychiatry Group 
University of Cambridge
Trinity College, CB21TQ, UK 
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24





From: Yi-Yu Chou (mailto:yiyu.c...@gmail.com)
Reply: list Freesurfer support 
(mailto:freesurfer@nmr.mgh.harvard.edu)
Date: 22 May 2017 at 19:07:01
To: list Freesurfer support 
(mailto:freesurfer@nmr.mgh.harvard.edu)
Subject: [Freesurfer] Hyperintensities Volume ?

> Dear FreeSurfer experts: 
> 
> Does the white matter volume shown in the aseg.stats include the 
> hyperintensities volume ? 
> 
> Thanks 
> Best Regards,
> 
> Yiyu 
> 
> 
> 
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[Freesurfer] Creating age-adjusted z score maps against a control group

[Elijah Mak]

Hi Doug,

I have used fscalc to create subject-level Z score maps of cortical thickness 
against a set of healthy controls. 

fscalc $i/surf/lh.fsaverage.mgh sub
group_mean_control_lh.mgh div group_std_control_lh.mgh --o
$i/surf/lh.Z.thickness.fsaverage.mgh; done

Beyond this, is there a way to adjust the Z score maps for age, and then 
produce an age-adjusted Z score map?

Thanks for your help.

Best Wishes,
Elijah



Dr. Elijah Mak, Research Associate
Department of Psychiatry,  Old Age Psychiatry Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 

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Re: [Freesurfer] Question - multiple comparisons in FS versus SPSS

[Elijah Mak]

Hi Siri,

Are you trying to overlay the p value associated with each region on the 
fsaverage surface? This may help:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50465.html

Best Wishes,
Elijah 

Dr. Elijah Mak, Research Associate
Department of Psychiatry,  Old Age Psychiatry Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 


On 23 May 2017 at 10:46:38, Noordermeer, S.D.S. (sds.noorderm...@vu.nl) wrote:

Dear Freesurfer experts,

 

I haven’t had the pleasure of receiving a response (yet), and was wondering 
whether that is because more information is needed?

 

In addition to the general theoretical question, the second part of the 
question is as important to me: Is there is any way, known to you experts, for 
me to visualize my SPSS results in a statistical-map-way?

 

If anyone could spare some time to help me out I would greatly appreciate it!!

Best,

Siri

 

 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Noordermeer, S.D.S.
Sent: zaterdag 13 mei 2017 22:22
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Question - multiple comparisons in FS versus SPSS

 

Hi there!


I was hoping you could help me with the following 'problem' I am experiencing.

 

Short background: 

I compared volumetric brain characteristics as output from FreeSurfer 
parcellations and segmentations between 3 groups, by extracting the volumes per 
anatomical label from FreeSurfer and analyzing these in SPSS. In SPSS I did a 
mixed-model analysis, and performed subsequent Benjamini-Hochberg FDR 
correction for multiple comparisons.

 

At the moment, I want to make brain maps (because this is a nice way to 
visualize the data and a reviewer suggested it). However... I believe I end up 
with only being able to use the uncorrected maps? 

When I perform an FDR-correction (or MonteCarlo, or clusterwise) in FreeSurfer 
all the group differences disappear. Unfortunately there is nobody that I can 
consult on this matter in my lab, thus I really hope someone here can help me?
Personally, I think that the difference in the presence (SPSS) versus absence 
(FS) of groups effects is due to the correction method. I believe that in 
FreeSurfer I apply a whole brain multiple comparison correction, while in SPSS 
I merely apply a ROI-based FDR-correction I in SPSS (because I look at volume 
per label). 

 

However, I am not sure if this is indeed (theoretically) sound? Could anyone 
advise me? Is there a way I could visualise my own (SPSS) results?

If more info is needed please do say so, and I will provide it!

Thank you very much for your time and reply!

Best,

Siri

 

 

 

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Re: [Freesurfer] Creating age-adjusted z score maps against a control group

[Elijah Mak]

Hi Freesurfer team,

Sorry for reposting. The previous email might have slipped through the cracks.

I was wondering if anyone know how to create subject-level Z score maps of 
thickness (against a set of healthy controls) after regressing out various 
covariates such as age / education ?

Thank you.

Best Wishes,
Elijah

Dr. Elijah Mak, Research Associate
Department of Psychiatry,  Old Age Psychiatry Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24


On 23 May 2017 at 09:21:24, Elijah Mak (fk...@medschl.cam.ac.uk) wrote:

Hi Doug,

I have used fscalc to create subject-level Z score maps of cortical thickness 
against a set of healthy controls. 

fscalc $i/surf/lh.fsaverage.mgh sub
group_mean_control_lh.mgh div group_std_control_lh.mgh --o
$i/surf/lh.Z.thickness.fsaverage.mgh; done

Beyond this, is there a way to adjust the Z score maps for age, and then 
produce an age-adjusted Z score map?

Thanks for your help.

Best Wishes,
Elijah



Dr. Elijah Mak, Research Associate
Department of Psychiatry,  Old Age Psychiatry Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 

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Re: [Freesurfer] Regarding: Group analysis of WMHs

[Elijah Mak]

Hi Doug,

I am referring to a rather old thread where you have provided some interesting 
suggestions to perform group-wise analysis of WMHs. I am trying to do something 
similar in patients and controls. First, mri_binarize was used to extract the 
individual WMH volumes from aseg.mgz. These volumes were subsequently warped 
into MNI305 space and smoothed (using mri_fwhm 8mm). The goal is to compare the 
spatial distributions of WMH between both groups. Finally, mri_concat --mean 
was used to visualise group averaged WMH volumes. The outputs can be found 
here: http://imgur.com/a/curYf

Do these steps look alright? On a conceptual level, is it statistically valid 
to compare stacks of binarised lesion maps between groups (using mri_glmfit and 
then performing MC with FDR/mri_glmfit-sim)? 

On an individual level, I noticed that some WMH voxels show up inside the 
MNI305 ventricles for a few subjects. This happens despite a good-looking 
talairach registration.

Thanks a lot for your time in advance and I’ll appreciate any thoughts you may 
have on this.

Sincerely,
Elijah

Dr. Elijah Mak, Research Associate
Department of Psychiatry,  Old Age Psychiatry Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24

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Re: [Freesurfer] Regarding: Group analysis of WMHs

[Elijah Mak]

Thanks Doug. I will look those tools up!

Regarding the spatial normalisation, would mri_cvs_register be suited for this 
purpose? Specifically, using the —mni option so that I still run the eventual 
comparisons in MNI space?

Best Wishes,
Elijah 


On 9 June 2017 at 21:42:44, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote:


On 06/09/2017 04:32 PM, Elijah Mak wrote:  
> Hi Doug,  
>  
> I am referring to a rather old thread where you have provided some  
> interesting suggestions to perform group-wise analysis of WMHs. I am  
> trying to do something similar in patients and controls. First,  
> mri_binarize was used to extract the individual WMH volumes from  
> aseg.mgz. These volumes were subsequently warped into MNI305 space and  
> smoothed (using mri_fwhm 8mm). The goal is to compare the spatial  
> distributions of WMH between both groups. Finally, mri_concat --mean  
> was used to visualise group averaged WMH volumes. The outputs can be  
> found here: http://imgur.com/a/curYf  
>  
> Do these steps look alright? On a conceptual level, is it  
> statistically valid to compare stacks of binarised lesion maps between  
> groups (using mri_glmfit and then performing MC with FDR/mri_glmfit-sim)?  
I'm sure there is a lot to find wrong with it, the data are not gaussian  
for starters. You might do better to use permutation with cluster or max  
correction (if your design is orthogonal, or use PALM). I don't have  
anything that will do voxel-wise permutation (which you would need to do  
an FDR correction), though you could do it fairly easily in matlab.  
>  
> On an individual level, I noticed that some WMH voxels show up inside  
> the MNI305 ventricles for a few subjects. This happens despite a  
> good-looking talairach registration.  
You are very optimistic about how good the affine registration is. If  
you were to look at the individual subjects, you would see that GM, WM,  
and CSF would be all over the place. Don't take the MNI305 anatomical  
image too seriously. Having said that, you can check the registration in  
the problematic subjects.  

>  
> Thanks a lot for your time in advance and I’ll appreciate any thoughts  
> you may have on this.  
>  
> Sincerely,  
> Elijah  
>  
> Dr. Elijah Mak, Research Associate  
> Department of Psychiatry, Old Age Psychiatry Group  
> University of Cambridge  
> Trinity College, CB21TQ, UK  
> http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24  
>  
>  
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[Freesurfer] mri_cvs_register error: Symbol not found: ___emutls_get_address

[Elijah Mak]

Hi Freesurfer Developers,

I am trying use mri_cvs_register but I ran into an error (Mac OS SIERRA 
10.12.2). The log is pasted below.

Logfile for mri_cvs_register
Sat 10 Jun 2017 17:58:48 BST
--mov 16084
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
dhcp-10-240-198-151.cp.wireless.private.cam.ac.uk
Darwin dhcp-10-240-198-151.cp.wireless.private.cam.ac.uk 16.3.0 Darwin Kernel 
Version 16.3.0: Thu Nov 17 20:23:58 PST 2016; 
root:xnu-3789.31.2~1/RELEASE_X86_64 x86_64
asegfname aseg
Using m3z type morph files.
mris_register -1 -dist 1.0 -inflated /Volumes/CITADEL/16084/surf/lh.sphere 
/Applications/freesurfer/subjects//cvs_avg35/surf/lh.sphere 
/Volumes/CITADEL/16084/surf/lh.cvs.tocvs_avg35.sphere.reg
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

I have also tried to update the freesurfer binaries with sudo -E fs_update but 
the problem persists. 

Thanks for looking into this!

Best Wishes,
Elijah 

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[Freesurfer] Merging outputs of mri_label2vol across hemi

[Elijah Mak]

Hi Freesurfer Team,

I am trying to resample the aparc annotation into functional space using 
mri_label2vol. It works fine and the script produced the segmentation for each 
hemisphere. Is there a way to merge both the left and right volumes together? 
Thanks for your help.

Best Wishes,
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Re: [Freesurfer] Merging outputs of mri_label2vol across hemi

[Elijah Mak]

Great! Many thanks, Doug.

Best Wishes,
Elijah 


On 13 June 2017 at 07:05:13, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote:

You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz

This will work if there are no overlapping voxels. If there are, you'll have to 
do something like

mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz

then use the masked in the mri_concat command


On 6/11/17 11:18 AM, Elijah Mak wrote:
Hi Freesurfer Team,

I am trying to resample the aparc annotation into functional space using 
mri_label2vol. It works fine and the script produced the segmentation for each 
hemisphere. Is there a way to merge both the left and right volumes together? 
Thanks for your help.

Best Wishes,
Elijah


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Re: [Freesurfer] Merging outputs of mri_label2vol across hemi

[Elijah Mak]

Hi Doug,

After resampling the aparc annotation into the functional native space, the LUT 
values no longer correspond to the correct regions. A screenshot is attached 
here: http://i.imgur.com/HNIgrKI.png

The values for the labels range from 1 - 35 only.

The command is mri_label2vol --annot $i/label/rh.aparc.annot --temp 
${i}_medn.nii --reg $i/fmri/fmri_t1_mricoreg.dat --fillthresh 0.5 --hemi rh 
--subject $i --proj frac 0 .1 1 --o ${i}.rh.aparc.in.func.nii

The goal is to apply the annotation and extract the regional fMRI data (4D) 
using this 3D volume parcellation. Could we achieve that by using these steps?

Thanks.

Best Wishes,
Elijah



On 13 June 2017 at 07:05:13, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote:

You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz

This will work if there are no overlapping voxels. If there are, you'll have to 
do something like

mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz

then use the masked in the mri_concat command


On 6/11/17 11:18 AM, Elijah Mak wrote:
Hi Freesurfer Team,

I am trying to resample the aparc annotation into functional space using 
mri_label2vol. It works fine and the script produced the segmentation for each 
hemisphere. Is there a way to merge both the left and right volumes together? 
Thanks for your help.

Best Wishes,
Elijah


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[Freesurfer] mri_vol2surf: visualising the edges at projfrac 0.1 - 0.5

[Elijah Mak]

Hi Freesurfer Team,

Is there a way to visualise the sampling edges across a range of projfrac 
values (0.1 (closer to WM) - 0.5) and overlay them onto PET data?

Any suggestions are greatly appreciated. Thanks.

Best Wishes,
Elijah 


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Re: [Freesurfer] mri_vol2surf: visualising the edges at projfrac 0.1 - 0.5

[Elijah Mak]

Hi Freesurfer Team,

No worries, I have found a helpful solution from an old thread using
mris_expand.
<http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40894.html>

http://i.imgur.com/CrF125X.png

Thanks.

Best Wishes,
Elijah

On Tue, Jun 13, 2017 at 8:47 PM, Elijah Mak  wrote:

> Hi Freesurfer Team,
>
> Is there a way to visualise the sampling edges across a range of projfrac
> values (0.1 (closer to WM) - 0.5) and overlay them onto PET data?
>
> Any suggestions are greatly appreciated. Thanks.
>
> Best Wishes,
> Elijah
>
>
>


-- 

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] Merging outputs of mri_label2vol across hemi

[Elijah Mak]

Hi Doug,

The full log for 1 subject is here:

dhcp-10-240-201-16:T1_Bd elijahmak_imac$ for i in `cat bd_list`; do 
mri_label2vol --annot $i/label/lh.aparc.annot --temp ${i}_medn.nii --reg 
$i/fmri/fmri_t1_mricoreg.lta --fillthresh 0.5 --hemi lh --subject $i --proj 
frac 0 .1 1 --o ${i}.lh.aparc.in.func.nii; done
Number of labels: 0
Annot File:      23950/label/lh.aparc.annot
Template Volume: 23950_medn.nii
Outut Volume: 23950.lh.aparc.in.func.nii
Registration File: 23950/fmri/fmri_t1_mricoreg.lta
Fill Threshold: 0.5
Label Vox Vol:  1
ProjType:       frac
ProjTypeId:     2
ProjStart:      0
ProjStop:       0.1
ProjDelta:      1
Subject:  23950
Hemi:     lh
UseNewASeg2Vol:  0
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR 
/Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd
$Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
Template RAS-to-Vox: 
-0.42918  -0.0  -0.0   31.0;
-0.0  -0.0  -0.42918   39.0;
-0.0   0.42918  -0.0   33.5;
-0.0  -0.0  -0.0   1.0;
Template Voxel Volume: 12.6493
nHits Thresh: 6.32467
Loading registration from 23950/fmri/fmri_t1_mricoreg.lta
regio_read_register: loading lta
RegMat: 
-0.99901  -0.04205  -0.01419  -0.53889;
-0.00761  -0.15273   0.98824  -0.11671;
 0.04372  -0.98737  -0.15226  -9.41649;
 0.0   0.0   0.0   1.0;
Label RAS-to-Vox: 
 0.42876   0.01805   0.00609   31.23128;
-0.01877   0.42377   0.06535   43.04141;
-0.00327  -0.06555   0.42414   33.44991;
 0.0   0.0   0.0   1.0;
  INFO: loading surface  
/Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd/23950/surf/lh.white

nvertices = 152772
Reading thickness 
/Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd/23950/surf/lh.thickness
Loading annotations from 23950/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
annotidmax = 36
nlabels = 36
Allocating Hit Volume (11664432) voxels

PVF (null)
Thesholding hit volume.
mri_label2vol done 

Thanks. Appreciate your help.

Best Wishes,
Elijah 



On 14 June 2017 at 16:18:24, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote:

Hmmm, not sure. can you send the full terminal output?

On 6/13/17 7:03 PM, Elijah Mak wrote:
Hi Doug,

After resampling the aparc annotation into the functional native space, the LUT 
values no longer correspond to the correct regions. A screenshot is attached 
here: http://i.imgur.com/HNIgrKI.png

The values for the labels range from 1 - 35 only.

The command is mri_label2vol --annot $i/label/rh.aparc.annot --temp 
${i}_medn.nii --reg $i/fmri/fmri_t1_mricoreg.dat --fillthresh 0.5 --hemi rh 
--subject $i --proj frac 0 .1 1 --o ${i}.rh.aparc.in.func.nii

The goal is to apply the annotation and extract the regional fMRI data (4D) 
using this 3D volume parcellation. Could we achieve that by using these steps?

Thanks.

Best Wishes,
Elijah



On 13 June 2017 at 07:05:13, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote:

You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz

This will work if there are no overlapping voxels. If there are, you'll have to 
do something like

mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz

then use the masked in the mri_concat command


On 6/11/17 11:18 AM, Elijah Mak wrote:
Hi Freesurfer Team,

I am trying to resample the aparc annotation into functional space using 
mri_label2vol. It works fine and the script produced the segmentation for each 
hemisphere. Is there a way to merge both the left and right volumes together? 
Thanks for your help.

Best Wishes,
Elijah

  
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but doe

[Freesurfer] Extracting cortical PET data from T1: aparc+aseg.mgz vs surface

[Elijah Mak]

Hi Freesurfer team, 

I am trying to extract ROI PET data from the cortical regions using the Desikan 
atlas, and I am wondering which is the recommended approach.

1) mri_segstats on resampled aparc+aseg.mgz in PET space
or
2) mri_segstats on lh.PetSurface.mgh in native surface (not fsaverage).

Option (1) always lead to to substantially lower BPND values in some regions 
compared to the measures derived on the surface.  If I would like to take the 
cortical measurements from lh.PetSurface.mgh, should I smooth the data first?

A second question relates to projfrac.  I am working with tau BPND data and 
there is quite a bit of CSF smearing in the outer layers of the cortex, 
resulting in negative BPND voxels. However, even without CSF contamination, 
there is quite a steep drop off in BPND intensity from the WM boundary to the 
pial surface (projfrac 0.5). The registration is OK too. For my data, sampling 
nearer to the WM surface (0.1) seems to result in positive BPND voxels compared 
to projfrac 0.5. As such, is it OK to use projfrac 0.1 for all subjects in my 
study?

Thanks for taking the time to read this!

Best Wishes,
Elijah 


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[Freesurfer] Using asegstats2table for gtm.stats.dat?

[Elijah Mak]

Hi Unix experts,

I am trying to extract the PVC-ed values from gtm.stats.dat for every subject. 
Is there a fast way to do this using a similar workflow with asegstats2table? 
Thanks.

Best Wishes,
Elijah 
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Re: [Freesurfer] Using asegstats2table for gtm.stats.dat?

[Elijah Mak]

Hi Freesurfer Team

Apologies for bumping this thread up again. I am wondering if is there is a way 
to extract the ROI stats in gtm.stats.dat after mri_gtmpvc (using a similar 
approach such as asegstats2table)?

Thanks for your help!

Best Wishes,
Elijah



On 16 June 2017 at 16:53:33, Elijah Mak (fk...@medschl.cam.ac.uk) wrote:

Hi Unix experts,

I am trying to extract the PVC-ed values from gtm.stats.dat for every subject. 
Is there a fast way to do this using a similar workflow with asegstats2table? 
Thanks.

Best Wishes,
Elijah 
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Re: [Freesurfer] Using asegstats2table for gtm.stats.dat?

[Elijah Mak]

Thanks Doug! It works!

Best Wishes,
Elijah 
On 21 June 2017 at 16:09:29, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote:

use this script  

https://gate.nmr.mgh.harvard.edu/safelinks/greve/gtmstats2table  



On 06/21/2017 10:53 AM, Elijah Mak wrote:  
> Hi Freesurfer Team  
>  
> Apologies for bumping this thread up again. I am wondering if is there  
> is a way to extract the ROI stats in gtm.stats.dat after mri_gtmpvc  
> (using a similar approach such as asegstats2table)?  
>  
> Thanks for your help!  
>  
> Best Wishes,  
> Elijah  
>  
>  
>  
> On 16 June 2017 at 16:53:33, Elijah Mak (fk...@medschl.cam.ac.uk  
> <mailto:fk...@medschl.cam.ac.uk>) wrote:  
>  
>> Hi Unix experts,  
>>  
>> I am trying to extract the PVC-ed values from gtm.stats.dat for every  
>> subject. Is there a fast way to do this using a similar workflow with  
>> asegstats2table? Thanks.  
>>  
>> Best Wishes,  
>> Elijah  
>  
>  
> ___  
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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] Using asegstats2table for gtm.stats.dat?

[Elijah Mak]

Hi Paul,

I did the following steps 

1. Save the file into $FREESURFER/bin (you might need to modify permissions)

2. Create a list of GTM directories from the subjects

for i in `cat list_of_subjects`; do echo $i/gtmpvc.output  >> gtmdirlist

3. Run gtmstats2table with gtmdirlist as the input 

gtmstats2table --f gtmdirlist --o data/gtmstats.csv

Hope that helps.

Best Wishes,
Elijah

Elijah Mak, Research Associate
Department of Psychiatry,  Old Age Psychiatry Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 


On 29 June 2017 at 18:27:13, miracle ozzoude (miracoo...@gmail.com) wrote:

Hello Elijah, 

I want to extract this values like you did. How do I use the script doug 
recommended? 

Thanks
Paul

On Wed, Jun 21, 2017 at 11:47 AM, Elijah Mak  wrote:
Thanks Doug! It works!

Best Wishes,
Elijah 
On 21 June 2017 at 16:09:29, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote:

use this script

https://gate.nmr.mgh.harvard.edu/safelinks/greve/gtmstats2table



On 06/21/2017 10:53 AM, Elijah Mak wrote:
> Hi Freesurfer Team
>
> Apologies for bumping this thread up again. I am wondering if is there
> is a way to extract the ROI stats in gtm.stats.dat after mri_gtmpvc
> (using a similar approach such as asegstats2table)?
>
> Thanks for your help!
>
> Best Wishes,
> Elijah
>
>
>
> On 16 June 2017 at 16:53:33, Elijah Mak (fk...@medschl.cam.ac.uk
> <mailto:fk...@medschl.cam.ac.uk>) wrote:
>
>> Hi Unix experts,
>>
>> I am trying to extract the PVC-ed values from gtm.stats.dat for every
>> subject. Is there a fast way to do this using a similar workflow with
>> asegstats2table? Thanks.
>>
>> Best Wishes,
>> Elijah
>
>
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[Freesurfer] Extracting vertex data from thickness maps after masking by sig.mgh

[Elijah Mak]

Hi Freesurfer Team,

I have previously used mri_binarize to derive the mask.mgh from the sig.mgh 
after a first-level group comparison of cortical thickness. Now, I would like 
to extract the vertex data from from another modality surface within and 
outside the mask in individual subjects. Is there an nice workflow to do that?

Thanks a lot. I hope my question made sense!

Best Wishes,
Elijah 


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Re: [Freesurfer] Extracting vertex data from thickness maps after masking by sig.mgh

[Elijah Mak]

Hi Doug,

Thanks!

mri_segstats —i concat.mgh  --seg mask.mgh --avgwf data

1) concat.mgh is the stack of individual surfaces in fsaverage space
2) mask.mgh is the binarised mask from the sig.mgh 
3) --avgwf to produce the 2 columns of data (inside and outside)

The values from the --avgwf represent the mean value across the vertices in and 
outside the mask, yes? Can I get the vertex-wise data though? 

Appreciate it!

Best Wishes,
Elijah



On 31 July 2017 at 15:17:02, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote:

You can use mri_segstats with either the --sum option (for an input with one 
time point) or --avgwf (for multiple). Pass your mask with --seg. By default it 
will give you both outside the mask (first column) and inside the mask (second 
column).


On 7/28/17 10:44 AM, Elijah Mak wrote:
Hi Freesurfer Team,

I have previously used mri_binarize to derive the mask.mgh from the sig.mgh 
after a first-level group comparison of cortical thickness. Now, I would like 
to extract the vertex data from from another modality surface within and 
outside the mask in individual subjects. Is there an nice workflow to do that?

Thanks a lot. I hope my question made sense!

Best Wishes,
Elijah 




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Re: [Freesurfer] Extracting vertex data from thickness maps after masking by sig.mgh

[Elijah Mak]

Thank you very much! :)

Best Wishes,
Elijah


On 31 July 2017 at 15:37:38, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote:

yes, mean across space. for vertex wise, you'll probably have to go into 
matlab, something like

mask = MRIread('mask.mgh');

imask = find(mask.vol == 1);

cc = MRIread('concat.mgh');

ccmat = fast_vol2mat(cc);

cc_in_mask = ccmat(:,imask);


On 7/31/17 10:25 AM, Elijah Mak wrote:
Hi Doug,

Thanks!

mri_segstats —i concat.mgh  --seg mask.mgh --avgwf data

1) concat.mgh is the stack of individual surfaces in fsaverage space
2) mask.mgh is the binarised mask from the sig.mgh 
3) --avgwf to produce the 2 columns of data (inside and outside)

The values from the --avgwf represent the mean value across the vertices in and 
outside the mask, yes? Can I get the vertex-wise data though? 

Appreciate it!

Best Wishes,
Elijah



On 31 July 2017 at 15:17:02, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote:

You can use mri_segstats with either the --sum option (for an input with one 
time point) or --avgwf (for multiple). Pass your mask with --seg. By default it 
will give you both outside the mask (first column) and inside the mask (second 
column).


On 7/28/17 10:44 AM, Elijah Mak wrote:
Hi Freesurfer Team,

I have previously used mri_binarize to derive the mask.mgh from the sig.mgh 
after a first-level group comparison of cortical thickness. Now, I would like 
to extract the vertex data from from another modality surface within and 
outside the mask in individual subjects. Is there an nice workflow to do that?

Thanks a lot. I hope my question made sense!

Best Wishes,
Elijah 



  
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[Freesurfer] Sampling vertex-wise data across various distances from the core of a mask to a somewhere else on fsaverage

[Elijah Mak]

Hi Doug and Freesurfer Experts,

I am trying to see whether cortical thinning gets progressively less severe as 
we move further away from a seed/voxel (e.g. precuneus). Is it possible to 
perform correlations between the (a) distance between a given vertex to 
specific point on fsaverage, and the (b) measurement (i.e. thickness) of the 
vertex?

Say I have a binary mask of the precuneus seed, as well as a second binary mask 
that surrounds it. How may I go about getting the thickness values at various 
distances, starting from the central core of the precuneus seed to the outer 
boundary of the second mask? 

I was thinking of something analogous to the proj-frac function in mri_vol2surf 
where we could sample PET/fMRI data at different values along the cortical 
ribbon.

Apologies if that was rather confusing. If you like, I could make a drawing of 
what I am trying to do.

Thanks for your time.

Best Wishes,
Elijah

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[Freesurfer] Gcuts erasing voxels within the ventricles

[Elijah Mak]

Hi Freesurfer Team,

I am using gcut to improve the skull stripping on some subjects. I noticed that 
it is also removing some of the voxels in the ventricles of the brainmask.mgz 
(picture attached). Is this normal behaviour? 

Thanks for your time.

Best Wishes,
Elijah 


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[Freesurfer] PetSurfer GTM: gtmstats2table

[Elijah Mak]

Hi Doug,

Would it be possible to use the gtmstats2table command to extract GTM values 
from other parellations?

Thanks!

Best Wishes,
Elijah


Dr. Elijah Mak, Research Associate
Department of Psychiatry
Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities 
Research Group
University of Cambridge,
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24

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Re: [Freesurfer] PetSurfer GTM: gtmstats2table

[Elijah Mak]

Hi Doug,

Thanks for the clarification. According to the PetSurfer guide, it is stated 
that there are “ways to customise this segmentation to use ROI definitions”. 
How may I go about doing that? Appreciate your help.

Best Wishes,
Elijah 

Dr. Elijah Mak, Research Associate
Department of Psychiatry
Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities 
Research Group
University of Cambridge,
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24


On 12 September 2017 at 17:27:10, Douglas N Greve (gr...@nmr.mgh.harvard.edu) 
wrote:

what do you mean? You can only get gtm stats from the parcellations that  
you have used during the process. You can't get new values at the end.  
If you want to use different ROIs, then you need to run gtmseg again  
with a different parcellation, then run mri_gtmpvc with the new gtmseg  


On 09/12/2017 10:42 AM, Elijah Mak wrote:  
> Hi Doug,  
>  
> Would it be possible to use the gtmstats2table command to extract GTM  
> values from other parellations?  
>  
> Thanks!  
>  
> Best Wishes,  
> Elijah  
>  
>  
> *Dr. Elijah Mak, Research Associate  
> *Department of Psychiatry  
> Old Age Psychiatry Group | Cambridge Intellectual & Developmental  
> Disabilities Research Group  
> University of Cambridge,  
> Trinity College, CB21TQ, UK  
> http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24  
>  
>  
>  
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Phone Number: 617-724-2358  
Fax: 617-726-7422  

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Re: [Freesurfer] Adding control points to aparc+aseg

[Elijah Mak]

Hi Nicholas,

In such situations, I have learned that autorecon2-wm after adding WM voxels 
seems to work pretty well. Hope that helps. 

Best Wishes,
Elijah

On 27 September 2017 at 16:46:43, Nicholas Goh (ngo...@gmail.com) wrote:

Bruce,

Thank you for the response. Attempting to use this method has not produced 
results, and I am unsure how to proceed or if I had performed it improperly. I 
have attached an example of the control points being placed, if that helps any.
Thank you,

Nicholas Goh

On Wed, Sep 27, 2017 at 11:04 AM, Bruce Fischl  
wrote:
Hi Nicholas

yes, possibly, depending on why you are missing chunks. If the white matter in 
the regions you are missing has intensity values significantly < 110 then what 
you are doing should help. The control.dat file must be place in the 
subject/tmp dir for us to find it.

cheers
Bruce
On Wed, 27 Sep 2017, Nicholas Goh wrote:

I am attempting to fix the aparc+aseg.mgz file for an image, and wanted to 
check to see if I am
doing it correctly.What I was doing which seemed to be ineffective was 
1)create a new point set of control points labelled control.dat
2)place control points along what should be white matter
3)save point set
4)run recon-all -autorecon2-cp -autorecon3 -subjid 

Is this the correct way to go about fixing aparc+aseg files that are missing 
chunks of the brain? Is
there a better way to go about this?
Thanks for the help,

Nicholas Goh


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[Freesurfer] Constrain smoothing to GM for PET data

[Elijah Mak]

Hi Doug,

I have used PETSURFER to derive MGX GM volumes from PET data.  Now, I would
like to constrain the smoothing to the GM. Is it advisable to use the PVF
in the aux folder for this purpose? If not, what is the best approach do
this?

Thanks!

Best Wishes,
Elijah
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[Freesurfer] PETSURFER: MRTM2 volumes?

[Elijah Mak]

Hi Doug,

Referring to the PETSURFER tutorial for dynamic PET data, I am wondering if it 
is possible to obtain a volume-based equivalent of mrtm2.lh.sm05/bp.nii.gz? As 
I understand, bp.nii.gz is the partial-volumed corrected output that has been 
sampled onto the fsaverage surface. 

Thanks for your time again.

Best Wishes,
Elijah



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Re: [Freesurfer] Overlap between Yeo networks and aparc2009 segments

[Elijah Mak]

Hi Shahin,

You could try binarising the Yeo atlas into individual masks for each of the 
networks. Then, use mri_compute_overlap to quantify the correspondence between 
your labels and the binarised network segments.  

Cheers,
Elijah


> On 11 Oct 2017, at 18:20, sha...@nmr.mgh.harvard.edu wrote:
> 
> Dear Experts,
>   We are looking for a way to measure the amount of overlap between each
> 'aparc 2009 segment' vs. 'Yeo 7 networks segments'. Currently I can do
> that by converting segments to labels and and then measuring the number
> of common vertices between them. But I was wondering if there is a more
> direct way to do it.
> 
> Regards
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Re: [Freesurfer] Constrain smoothing to GM for PET data

[Elijah Mak]

Hi Doug,

Thanks. 

Could I check my workflow to perform the constrained smoothing of PET MGX-GM 
volumes? My objective here is to normalise the PET volumes to the CVS-MNI152 
space to produce group-level PET maps. As such, should I be deriving the GM + 
Subcortical PVFs from the cvs_avg35_inMNI152 subject for the mask in mri_fwhm?

1. mri_cvs_register to bring T1s to CVS MNI152
2. mri_vol2vol to bring the PET MGX-GM volumes (already in anatomical T1 space) 
to CVS MNI152
3. mri_fwhm to smooth the PET volumes, using a binarised mask of GM+Subcortical 
PVFs from the cvs_avg35_inMNI152 subject
4. What is the best way to get the mask from the cvs_avg35_inMNI152 subject? 
5. Obtain group level PET maps in CVS MNI152 space using mri_concat —mean.

Thanks very much.

Best Wishes,
Elijah

> On 4 Oct 2017, at 14:51, Douglas Greve  wrote:
> 
> You mean for volume-based analysis? Yes, use the pvf. 
> 
> On 10/4/17 9:42 AM, Elijah Mak wrote:
>> Hi Doug,
>> 
>> I have used PETSURFER to derive MGX GM volumes from PET data.  Now, I would 
>> like to constrain the smoothing to the GM. Is it advisable to use the PVF in 
>> the aux folder for this purpose? If not, what is the best approach do this?
>> 
>> Thanks!
>> 
>> Best Wishes,
>> Elijah
>> 
>> 
>> 
>> ___
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>> <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 
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Re: [Freesurfer] Normalize to mni

[Elijah Mak]

Hi Jan,

Is the functional image already coregistered to the T1? If you have a 
registration file, you could try:

mri_vol2vol --mov fstcmc.nii.gz --reg registrationfile --tal --talres 2 --o 
fstcmc.mni305.2mm.nii.gz

.. to bring the functional image to MNI305. Are you planning to your restrict 
your analysis (assuming it is a voxelwise analysis?) to the subcortical 
regions? You could use the subcort.mask.mgz in fsaverage/mri.2mm as as mask in 
your mri_glmfit.

I will leave it to Doug to confirm if those steps are suitable for your 
objectives.

Best Wishes,
Elijah 


Dr. Elijah Mak, Research Associate
Department of Psychiatry
Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities 
Research Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24


> On 12 Oct 2017, at 16:14, Jan Willem Koten  wrote:
> 
> Normalize to mni
>  
> Dear Doug,
>  
> We have a very simple question. In a first step we segmented brains using the 
> recon all command. Our functional pipeline created a „fstcmc.nii.gz“ file. We 
> would like to do some subcortical analysis and need to perfrorm this in MNI 
> 305 space. We also need the subcortical labels for the actual analysis 
> itself. Does someone know the trick? In short how do we get from 
> fstcmc.nii.gz“ to subcortical functional ROI's?
>  
> Greetings Jan
> Jan Willem Koten (van Grevenbicht)
> 
> Zollernstrasse 57, 52070 Aachen, Germany
> Telephone: (0049) (0)241 212 44
>  
> ___
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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 
> <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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Re: [Freesurfer] Constrain smoothing to GM for PET data

[Elijah Mak]

Hi Doug,  

Yes, but I am using the GM rather than the subcortical volume. How can we get a 
similar GM mask on CVS 2mm space?  

Thanks for your help.  

Best Wishes,  
Elijah  

Dr. Elijah Mak, Research Associate
Department of Psychiatry,  
Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities 
Research Group
University of Cambridge,
Trinity College, CB21TQ, UK  
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24





From: Douglas Greve 
(mailto:gr...@nmr.mgh.harvard.edu)
Reply: list Freesurfer support 
(mailto:freesurfer@nmr.mgh.harvard.edu)
Date: 13 October 2017 at 16:14:34
To: Elijah Mak (mailto:fk...@medschl.cam.ac.uk), list 
Freesurfer support 
(mailto:freesurfer@nmr.mgh.harvard.edu)
Subject: Re: [Freesurfer] Constrain smoothing to GM for PET data

>  
> Are you using mri_vol2vol to go into the cvs 2mm space? If so, then use 
> $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/subcort.mask.mgz
>  
>  
>  
> On 10/11/17 3:15 PM, Elijah Mak wrote:
> > Hi Doug,  
> >  
> > Thanks.  
> >  
> > Could I check my workflow to perform the constrained smoothing of PET 
> > MGX-GM volumes? My objective here is to normalise the PET volumes to the 
> > CVS-MNI152 space to produce group-level PET maps. As such, should I be 
> > deriving the GM + Subcortical PVFs from the cvs_avg35_inMNI152 subject for 
> > the mask in mri_fwhm?  
> >  
> > 1. mri_cvs_register to bring T1s to CVS MNI152  
> > 2. mri_vol2vol to bring the PET MGX-GM volumes (already in anatomical T1 
> > space) to CVS MNI152
> > 3. mri_fwhm to smooth the PET volumes, using a binarised mask of 
> > GM+Subcortical PVFs from the cvs_avg35_inMNI152 subject
> > 4. What is the best way to get the mask from the cvs_avg35_inMNI152 
> > subject?  
> > 5. Obtain group level PET maps in CVS MNI152 space using mri_concat —mean.
> >  
> > Thanks very much.  
> >  
> > Best Wishes,  
> > Elijah
> >  
> > > On 4 Oct 2017, at 14:51, Douglas Greve 
> > > mailto:gr...@nmr.mgh.harvard.edu)> wrote:  
> > >  
> > > You mean for volume-based analysis? Yes, use the pvf.
> > >  
> > >  
> > >  
> > > On 10/4/17 9:42 AM, Elijah Mak wrote:
> > > > Hi Doug,
> > > >  
> > > > I have used PETSURFER to derive MGX GM volumes from PET data. Now, I 
> > > > would like to constrain the smoothing to the GM. Is it advisable to use 
> > > > the PVF in the aux folder for this purpose? If not, what is the best 
> > > > approach do this?
> > > >  
> > > > Thanks!
> > > >  
> > > > Best Wishes,
> > > > Elijah
> > > >  
> > > >  
> > > >  
> > > > ___ 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.
> >  
>  
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>  
> The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Constrain smoothing to GM for PET data

[Elijah Mak]

Got it. Thanks, Doug! :)

Best Wishes,
Elijah

> On 13 Oct 2017, at 17:06, Douglas Greve  wrote:
> 
> That subcort mask is only GM (sorry, should have indicated that when I named 
> it).
> 
> On 10/13/17 11:15 AM, Elijah Mak wrote:
>> Hi Doug,
>> 
>> Yes, but I am using the GM rather than the subcortical volume. How can we 
>> get a similar GM mask on CVS 2mm space?
>> 
>> Thanks for your help.
>> 
>> Best Wishes,
>> Elijah 
>> 
>> Dr. Elijah Mak, Research Associate
>> Department of Psychiatry,  
>> Old Age Psychiatry Group | Cambridge Intellectual & Developmental 
>> Disabilities Research Group
>> University of Cambridge,
>> Trinity College, CB21TQ, UK
>> http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 
>> <http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24>
>> 
>> 
>> From: Douglas Greve  
>> <mailto:gr...@nmr.mgh.harvard.edu>
>> Reply: list Freesurfer support  
>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>> Date: 13 October 2017 at 16:14:34
>> To: Elijah Mak  <mailto:fk...@medschl.cam.ac.uk>, 
>> list Freesurfer support  
>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>> Subject:  Re: [Freesurfer] Constrain smoothing to GM for PET data 
>> 
>>> Are you using mri_vol2vol to go into the cvs 2mm space? If so, then use 
>>> $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/subcort.mask.mgz
>>> 
>>> On 10/11/17 3:15 PM, Elijah Mak wrote:
>>>> Hi Doug,
>>>> 
>>>> Thanks. 
>>>> 
>>>> Could I check my workflow to perform the constrained smoothing of PET 
>>>> MGX-GM volumes? My objective here is to normalise the PET volumes to the 
>>>> CVS-MNI152 space to produce group-level PET maps. As such, should I be 
>>>> deriving the GM + Subcortical PVFs from the cvs_avg35_inMNI152 subject for 
>>>> the mask in mri_fwhm?
>>>> 
>>>> 1. mri_cvs_register to bring T1s to CVS MNI152
>>>> 2. mri_vol2vol to bring the PET MGX-GM volumes (already in anatomical T1 
>>>> space) to CVS MNI152
>>>> 3. mri_fwhm to smooth the PET volumes, using a binarised mask of 
>>>> GM+Subcortical PVFs from the cvs_avg35_inMNI152 subject
>>>> 4. What is the best way to get the mask from the cvs_avg35_inMNI152 
>>>> subject? 
>>>> 5. Obtain group level PET maps in CVS MNI152 space using mri_concat —mean.
>>>> 
>>>> Thanks very much.
>>>> 
>>>> Best Wishes,
>>>> Elijah
>>>> 
>>>>> On 4 Oct 2017, at 14:51, Douglas Greve >>>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>>>> 
>>>>> You mean for volume-based analysis? Yes, use the pvf.
>>>>> 
>>>>> On 10/4/17 9:42 AM, Elijah Mak wrote:
>>>>>> Hi Doug,
>>>>>> 
>>>>>> I have used PETSURFER to derive MGX GM volumes from PET data.  Now, I 
>>>>>> would like to constrain the smoothing to the GM. Is it advisable to use 
>>>>>> the PVF in the aux folder for this purpose? If not, what is the best 
>>>>>> approach do this?
>>>>>> 
>>>>>> Thanks!
>>>>>> 
>>>>>> Best Wishes,
>>>>>> Elijah
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> ___
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>>>>>> <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 
>>>>> <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 
>>>>> H

Re: [Freesurfer] PETSURFER: MRTM2 volumes?

[Elijah Mak]

Hi Doug,

I wonder what is the difference between this approach (mri_surf2vol) as opposed 
to doing the MRTM2 modelling on the MGX GM output (58 frames), which will give 
us the bp.nii.gz in volume space?

Thanks.

Best Wishes,
Elijah



> On 13 Oct 2017, at 16:19, Douglas Greve  wrote:
> 
> do you mean you want to map the surface-based data into the volume? If 
> so, you can use mri_surf2vol. If you want to analyze your pet data in 
> the volume you can just do that with mri_glmfit
> 
> 
> On 10/5/17 4:59 PM, Elijah Mak wrote:
>> Hi Doug,
>> 
>> Referring to the PETSURFER tutorial for dynamic PET data, I am wondering if 
>> it is possible to obtain a volume-based equivalent of 
>> mrtm2.lh.sm05/bp.nii.gz? As I understand, bp.nii.gz is the partial-volumed 
>> corrected output that has been sampled onto the fsaverage surface.
>> 
>> Thanks for your time again.
>> 
>> Best Wishes,
>> Elijah
>> 
>> 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
> 
> ___
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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
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Re: [Freesurfer] Constrain smoothing to GM for PET data

[Elijah Mak]

Hi Doug,
> That subcort mask is only GM (sorry, should have indicated that when I named 
> it).
> 

I just looked at the subcort mask in the cvs 2mm folder and it looks like it is 
only subcortical? I am looking for a similar mask that also  includes the GM 
regions.  Any idea?



Best Wishes,
Elijah



> On 13 Oct 2017, at 17:06, Douglas Greve  wrote:
> 
> That subcort mask is only GM (sorry, should have indicated that when I named 
> it).
> 
> On 10/13/17 11:15 AM, Elijah Mak wrote:
>> Hi Doug,
>> 
>> Yes, but I am using the GM rather than the subcortical volume. How can we 
>> get a similar GM mask on CVS 2mm space?
>> 
>> Thanks for your help.
>> 
>> Best Wishes,
>> Elijah 
>> 
>> Dr. Elijah Mak, Research Associate
>> Department of Psychiatry,  
>> Old Age Psychiatry Group | Cambridge Intellectual & Developmental 
>> Disabilities Research Group
>> University of Cambridge,
>> Trinity College, CB21TQ, UK
>> http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 
>> <http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24>
>> 
>> 
>> From: Douglas Greve  
>> <mailto:gr...@nmr.mgh.harvard.edu>
>> Reply: list Freesurfer support  
>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>> Date: 13 October 2017 at 16:14:34
>> To: Elijah Mak  <mailto:fk...@medschl.cam.ac.uk>, 
>> list Freesurfer support  
>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>> Subject:  Re: [Freesurfer] Constrain smoothing to GM for PET data 
>> 
>>> Are you using mri_vol2vol to go into the cvs 2mm space? If so, then use 
>>> $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/subcort.mask.mgz
>>> 
>>> On 10/11/17 3:15 PM, Elijah Mak wrote:
>>>> Hi Doug,
>>>> 
>>>> Thanks. 
>>>> 
>>>> Could I check my workflow to perform the constrained smoothing of PET 
>>>> MGX-GM volumes? My objective here is to normalise the PET volumes to the 
>>>> CVS-MNI152 space to produce group-level PET maps. As such, should I be 
>>>> deriving the GM + Subcortical PVFs from the cvs_avg35_inMNI152 subject for 
>>>> the mask in mri_fwhm?
>>>> 
>>>> 1. mri_cvs_register to bring T1s to CVS MNI152
>>>> 2. mri_vol2vol to bring the PET MGX-GM volumes (already in anatomical T1 
>>>> space) to CVS MNI152
>>>> 3. mri_fwhm to smooth the PET volumes, using a binarised mask of 
>>>> GM+Subcortical PVFs from the cvs_avg35_inMNI152 subject
>>>> 4. What is the best way to get the mask from the cvs_avg35_inMNI152 
>>>> subject? 
>>>> 5. Obtain group level PET maps in CVS MNI152 space using mri_concat —mean.
>>>> 
>>>> Thanks very much.
>>>> 
>>>> Best Wishes,
>>>> Elijah
>>>> 
>>>>> On 4 Oct 2017, at 14:51, Douglas Greve >>>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>>>> 
>>>>> You mean for volume-based analysis? Yes, use the pvf.
>>>>> 
>>>>> On 10/4/17 9:42 AM, Elijah Mak wrote:
>>>>>> Hi Doug,
>>>>>> 
>>>>>> I have used PETSURFER to derive MGX GM volumes from PET data.  Now, I 
>>>>>> would like to constrain the smoothing to the GM. Is it advisable to use 
>>>>>> the PVF in the aux folder for this purpose? If not, what is the best 
>>>>>> approach do this?
>>>>>> 
>>>>>> Thanks!
>>>>>> 
>>>>>> Best Wishes,
>>>>>> Elijah
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> ___
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>>>>>> <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 
>>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>>>> 
>>>>> 
>>>>> The information in this e-mail is intended only for the person to whom

Re: [Freesurfer] Constrain smoothing to GM for PET data

[Elijah Mak]

Hi Doug,

I am looking for a total GM mask that includes cortical and subcortical regions.

Best Wishes,
Elijah

Dr. Elijah Mak, Research Associate
Department of Psychiatry
Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities 
Research Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24


> On 16 Oct 2017, at 16:09, Douglas Greve  wrote:
> 
> that includes GM regions. not sure what you want
> 
> On 10/13/17 8:58 PM, Elijah Mak wrote:
>> Hi Doug,
>>> That subcort mask is only GM (sorry, should have indicated that when I 
>>> named it).
>>> 
>> 
>> I just looked at the subcort mask in the cvs 2mm folder and it looks like it 
>> is only subcortical? I am looking for a similar mask that also  includes the 
>> GM regions.  Any idea?
>> 
>> 
>> 
>> Best Wishes,
>> Elijah
>> 
>> 
>> 
>>> On 13 Oct 2017, at 17:06, Douglas Greve >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>> 
>>> That subcort mask is only GM (sorry, should have indicated that when I 
>>> named it).
>>> 
>>> On 10/13/17 11:15 AM, Elijah Mak wrote:
>>>> Hi Doug,
>>>> 
>>>> Yes, but I am using the GM rather than the subcortical volume. How can we 
>>>> get a similar GM mask on CVS 2mm space?
>>>> 
>>>> Thanks for your help.
>>>> 
>>>> Best Wishes,
>>>> Elijah 
>>>> 
>>>> Dr. Elijah Mak, Research Associate
>>>> Department of Psychiatry,  
>>>> Old Age Psychiatry Group | Cambridge Intellectual & Developmental 
>>>> Disabilities Research Group
>>>> University of Cambridge,
>>>> Trinity College, CB21TQ, UK
>>>> http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 
>>>> <http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24>
>>>> 
>>>> 
>>>> From: Douglas Greve  
>>>> <mailto:gr...@nmr.mgh.harvard.edu>
>>>> Reply: list Freesurfer support  
>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>> Date: 13 October 2017 at 16:14:34
>>>> To: Elijah Mak  <mailto:fk...@medschl.cam.ac.uk>, 
>>>> list Freesurfer support 
>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>>>> Subject:  Re: [Freesurfer] Constrain smoothing to GM for PET data 
>>>> 
>>>>> Are you using mri_vol2vol to go into the cvs 2mm space? If so, then use 
>>>>> $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/subcort.mask.mgz
>>>>> 
>>>>> On 10/11/17 3:15 PM, Elijah Mak wrote:
>>>>>> Hi Doug,
>>>>>> 
>>>>>> Thanks. 
>>>>>> 
>>>>>> Could I check my workflow to perform the constrained smoothing of PET 
>>>>>> MGX-GM volumes? My objective here is to normalise the PET volumes to the 
>>>>>> CVS-MNI152 space to produce group-level PET maps. As such, should I be 
>>>>>> deriving the GM + Subcortical PVFs from the cvs_avg35_inMNI152 subject 
>>>>>> for the mask in mri_fwhm?
>>>>>> 
>>>>>> 1. mri_cvs_register to bring T1s to CVS MNI152
>>>>>> 2. mri_vol2vol to bring the PET MGX-GM volumes (already in anatomical T1 
>>>>>> space) to CVS MNI152
>>>>>> 3. mri_fwhm to smooth the PET volumes, using a binarised mask of 
>>>>>> GM+Subcortical PVFs from the cvs_avg35_inMNI152 subject
>>>>>> 4. What is the best way to get the mask from the cvs_avg35_inMNI152 
>>>>>> subject? 
>>>>>> 5. Obtain group level PET maps in CVS MNI152 space using mri_concat 
>>>>>> —mean.
>>>>>> 
>>>>>> Thanks very much.
>>>>>> 
>>>>>> Best Wishes,
>>>>>> Elijah
>>>>>> 
>>>>>>> On 4 Oct 2017, at 14:51, Douglas Greve >>>>>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>>>>>> 
>>>>>>> You mean for volume-based analysis? Yes, use the pvf.
>>>>>>> 
>>>>>>> On 10/4/17 9:42 AM, Elijah Mak wrote:
>>>>>>>> Hi Doug,
>>>>>>>> 
>>>>>>>> I have used PETSURFER to derive MGX GM volumes from PET data.  Now, I 
>>>>>>>> would like to cons

Re: [Freesurfer] PETSURFER: MRTM2 volumes?

[Elijah Mak]

Got it, thanks! I have already performed smoothing on the MGX surfaces so I’d 
like to proceed with mri_surf2vol.

According to the “hidden secrets of success” for mri_surf2vol, there are 2 
methods.  Is the command below correct?

mri_surf2vol --so lh.bp.nii.gz (the PET surface BPNDs) --so rh.bp.nii.gz 
--subject fsaverage --o smoothed.bpnd.in.volume.nii.gz 

The next step is to bring the volumes into CVS-MNI152 space. Mri_cvs_register 
has been done on the T1.

Thanks Doug.

Best Wishes,
Elijah


Dr. Elijah Mak, Research Associate
Department of Psychiatry
Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities 
Research Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24


> On 16 Oct 2017, at 16:08, Douglas Greve  wrote:
> 
> it comes down to have you smooth it. If you do it in the volume, then 
> you need to smooth it in the volume, and that is an invalid analysis 
> with MG.
> 
> 
> On 10/13/17 8:42 PM, Elijah Mak wrote:
>> Hi Doug,
>> 
>> I wonder what is the difference between this approach (mri_surf2vol) as 
>> opposed to doing the MRTM2 modelling on the MGX GM output (58 frames), which 
>> will give us the bp.nii.gz in volume space?
>> 
>> Thanks.
>> 
>> Best Wishes,
>> Elijah
>> 
>> 
>> 
>>> On 13 Oct 2017, at 16:19, Douglas Greve  wrote:
>>> 
>>> do you mean you want to map the surface-based data into the volume? If
>>> so, you can use mri_surf2vol. If you want to analyze your pet data in
>>> the volume you can just do that with mri_glmfit
>>> 
>>> 
>>> On 10/5/17 4:59 PM, Elijah Mak wrote:
>>>> Hi Doug,
>>>> 
>>>> Referring to the PETSURFER tutorial for dynamic PET data, I am wondering 
>>>> if it is possible to obtain a volume-based equivalent of 
>>>> mrtm2.lh.sm05/bp.nii.gz? As I understand, bp.nii.gz is the partial-volumed 
>>>> corrected output that has been sampled onto the fsaverage surface.
>>>> 
>>>> Thanks for your time again.
>>>> 
>>>> Best Wishes,
>>>> Elijah
>>>> 
>>>> 
>>>> 
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Re: [Freesurfer] (no subject)

[Elijah Mak]

Hi Vidhu,

After your standard recon-all, do:

mri_binarize --i yoursubjectname/mri/aseg.mgz --match 17 --o left_hip.nii
mri_binarize --i yoursubjectname/mri/aseg.mgz--match 53 --o right_hip.nii

Hope that helps.

Best Wishes,
Elijah


On Wed, Nov 1, 2017 at 5:57 AM, Vidhu Agrawal 
wrote:

> Respected Sir,
>
> How can i scoop out or separate  only hippocampus from a 3D MRI of whole
> brain?
>
> With regards
> vidhu agarwal
>
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-- 

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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[Freesurfer] Accounting for WMHs in PETSURFER PVC?

[Elijah Mak]

Hi Doug,

Could we tweak the PETSURFER pipeline in order to account for inhomogeneous PET 
activity in WM due to WMHs?

Will running gtmseg with the command --keep-hypo be useful in this context?

Thanks for any inputs.

Best Wishes,
Elijah


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