Yes (though you should always check the reg.lta with tkregisterfv). Also, why are you calling the output lh.sig.mgh? My question is about "sig"; it is not wrong to call it this, but "sig" is usually reserved for significance files and I wanted to make sure you were not confused by it.External Email - Use Caution
Dear Freesurfer experts,
We are conducting a PETSurfer analysis, and have some questions on the best way to proceed. Briefly, this is what we have done:
After running the standard Freesurfer analysis an all the T1 images, we have generated the segmentation for the GTM.Afterwards, we have registered the PET images with the anatomicals, obtaining the template.reg.lta.To check the preliminary results without any PVC, we have used the template.reg.lta to sample the PET volume onto the surface, with the following command:mri_vol2surf --mov subject_PET.nii \--reg subject_template.reg.lta \--projfrac 0.5 --interp nearest \--hemi lh --o lh.sig.mgh
We therefore obtained the lh.sig.mgh
First question. Is this procedure correct?
Any format (mgh, mgz, nifti) is ok.Second question. Is the format of the of the output (.mgh) correct?
This is probably not right. You will need to run the mri_vol2surf command above for each subject to generate an output (and using --trgsubject fsaverage to put them into the same space), then concatenate all into one file (mri_concat lh.subj1.mgh lh.subj2.mgh ... --o lh.all.mgh), then possibly smooth (mris_fwhm), then feed that output as input to mri_glmfit.
In the wiki it is reported that: “If you are not using PVC, you can use the template.reg.lta to sample the PET volume onto the surface using mri_vol2surf, then apply standard surface-based analysis”.
Third question. At this point should we directly run the mri_glmfit with the previously obtained lh.sig.mgh?
Like in this way:
mri_glmfit \--y lh.sig.mgh \--fsgd fsgd file dods\--C cor.mtx file \--surf fsaverage lh \--cortex \--glmdir glmdir
Many thanks for any information you’ll be able to provide,
Best,
Pilar Maria Ferraro
Il giorno 7 apr 2020, alle ore 6:00 PM, freesurfer-request@nmr.mgh.harvard.edu ha scritto:
Send Freesurfer mailing list submissions to
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When replying, please edit your Subject line so it is more specific
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Today's Topics:
1. vertex number to MNI coordinates (Marina Fern?ndez)
2. Install Freesurfer on Ubuntu (Stephan)
3. Re: vertex number to MNI coordinates (Douglas N. Greve)
4. Re: Install Freesurfer on Ubuntu (Peer Herholz)
5. Re: Install Freesurfer on Ubuntu (fsbuild)
6. Permutation with Non-Orthogonal Matrices (Hua, Jessica)
7. Re: Permutation with Non-Orthogonal Matrices (Douglas N. Greve)
8. Error in Tracula-all -prep (Salah Showiheen)
9. hippocampus subfield segmentation using Siemen and GE scans
(Kate Marvel)
10. Chorid-plexus in Freesurfer reconall (Lijun An)
11. Re: Chorid-plexus in Freesurfer reconall (Bruce Fischl)
12. whether freesurfer version 7 still support GPU (Frank Robert)
13. Re: hippocampus subfield segmentation using Siemen and GE
scans (Iglesias Gonzalez, Juan E.)
14. Re: whether freesurfer version 7 still support GPU
(Hoopes, Andrew)
15. Re: hippocampus subfield segmentation using Siemen and GE
scans (Kate Marvel)
16. Re: whether freesurfer version 7 still support GPU (Frank Robert)
17. Re: whether freesurfer version 7 still support GPU
(Hoopes, Andrew)
----------------------------------------------------------------------
Message: 1
Date: Mon, 6 Apr 2020 22:06:24 +0200
From: Marina Fern?ndez <marina.fdez.alvarez@gmail.com>
Subject: [Freesurfer] vertex number to MNI coordinates
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAALjZmd_9caMAE8uHbn_vu4o_4Lkc8mWyXTatSUr4AAQpznq0w@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Dear Freesurfer experts,
I hope you can help me with the following questions:
1. What is the best way to know the MNI coordinates to which a vertex of a
surface corresponds?
2. I have projected the surfaces of the subjects onto the average subject
from this dataset.
Can I know the MNI coordinates corresponding to a vertex of the average
subject of my dataset?
Or do I need to project it onto the fsaverage to know the correspondence to
de MNI space?
3. I know that the average surface is constructed by computing the MNI305
coordinate at each vertex,
But how can I obtain the MNI152 coordinates (instead of MNI305) to which a
vertex corresponds? (if it is possible).
Thank you very much in advance.
Best regards,
Marina
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Message: 2
Date: Mon, 6 Apr 2020 22:50:15 +0200
From: Stephan <stephan.wunderlich22@gmail.com>
Subject: [Freesurfer] Install Freesurfer on Ubuntu
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAJzKAwch6QOUHhd1sSe+exK4EiU-gw-6uos=URxbgO-tm_Kixw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi,
ist there an official guideline how to install Freesurfer on Ubuntu?
Best,
Stephan
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Message: 3
Date: Mon, 6 Apr 2020 16:51:09 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] vertex number to MNI coordinates
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <fb5fba0f-6aa5-a21b-fac9-5e4f54b282d4@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
answers below, but overall, take a look at
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 4/6/2020 4:06 PM, Marina Fern?ndez wrote:
I think freeview will display the mni305 coords
????????External Email - Use Caution
Dear Freesurfer experts,
I hope you can help me with the following questions:
1. What is the best way to know the MNI coordinates to which a vertex
of a surface corresponds?
An average subject is always in mni305
2. I have projected the surfaces of the subjects onto the average
subject from this dataset.
Can I know the MNI coordinates corresponding to a vertex of the
average subject of my dataset?
Or do I need to project it onto the fsaverage to know the
correspondence to de MNI space?
See case 8 in website above
3. I know that the average surface is constructed by computing the
MNI305 coordinate at each vertex,
But how can I obtain the MNI152 coordinates (instead of MNI305) to
which a vertex corresponds? (if it is possible).
Thank you very much in advance.
Best regards,
Marina
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 4
Date: Mon, 6 Apr 2020 17:17:09 -0400
From: Peer Herholz <herholz.peer@gmail.com>
Subject: Re: [Freesurfer] Install Freesurfer on Ubuntu
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <D6B4D694-5DE6-414F-B723-6B8AB66A7C8E@gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi Stephan,
please have a look at the "FreeSurfer Download and Install? page within the FreeSurfer documentation:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall <https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall>
HTH, cheers, Peer
On Apr 6, 2020, at 4:50 PM, Stephan <stephan.wunderlich22@gmail.com> wrote:
External Email - Use Caution
Hi,
ist there an official guideline how to install Freesurfer on Ubuntu?
Best,
Stephan
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 5
Date: Mon, 06 Apr 2020 23:25:11 +0200
From: fsbuild <fsbuild@contbay.com>
Subject: Re: [Freesurfer] Install Freesurfer on Ubuntu
To: freesurfer@nmr.mgh.harvard.edu
Cc: stephan.wunderlich22@gmail.com
Message-ID: <1586208311.5e8b9e3757315@trashmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hello Stephan,
There is some information here about packages to install in order to run freesurfer - see highlighted "apt-get install" commands.
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements
I think you will also need to install these packages,
libjpeg62_6b2-3_amd64.deb
https://drive.google.com/file/d/1Zdd-C3EQEEww180OzxEk1WV0h9obZYkD/view?usp=sharing
libpng12-0_1.2.54-1ubuntu1_amd64.deb
https://drive.google.com/file/d/1OWQSWL8a3Y8f1Weiauj9Lr2d3mtvZOm5/view?usp=sharing
We also have an Ubuntu VM you can download. While you may prefer to run on your own Ubuntu machine, it could also serve as a reference for you to see what we installed on Ubuntu 18.04 (including those extra packages).
https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67
- R.
On Apr 6, 2020, at 16:50, Stephan <stephan.wunderlich22@gmail.com> wrote: External Email - Use Caution Hi,ist there an official guideline how to install Freesurfer on Ubuntu?Best,Stephan_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 6
Date: Mon, 6 Apr 2020 22:45:44 +0000
From: "Hua, Jessica" <jphc55@mail.missouri.edu>
Subject: [Freesurfer] Permutation with Non-Orthogonal Matrices
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BY5PR01MB565249DA0CF1967FD1ACF16E93C20@BY5PR01MB5652.prod.exchangelabs.com>
Content-Type: text/plain; charset="iso-8859-1"
External Email - Use Caution
Hi FreeSurfer Experts,
As recommended I ran the following command:
mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --perm 1000 3.0 abs --perm-resid --cwp 0.05 --2spaces
And I got the following error message:
ERROR: Flag --perm-resid unrecognized.
Best,
Jessica
---
Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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Message: 7
Date: Mon, 6 Apr 2020 22:59:09 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Permutation with Non-Orthogonal Matrices
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <9f714ae7-979c-ff50-7514-5f7a7212de59@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
did you download the patch as described here ("If You're Not at an
Organized Course")?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
On 4/6/2020 6:45 PM, Hua, Jessica wrote:
????????External Email - Use Caution
Hi FreeSurfer Experts,
As recommended I ran the following command:
mri_glmfit-sim --glmdir rh.volume.AgeSex.10.glmdir --perm 1000 3.0 abs
--perm-resid --cwp 0.05 --2spaces
And I got the following error message:
ERROR: Flag --perm-resid unrecognized.
Best,
Jessica
---
Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate?Clinical Psychology
University of Missouri
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 8
Date: Tue, 7 Apr 2020 13:49:43 +1000
From: Salah Showiheen <sshowiheen@gmail.com>
Subject: [Freesurfer] Error in Tracula-all -prep
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAFc5Rtf0kovaRpurYSsexxyeCiS8qa=tGdSYX=GMbMxy8s4YxA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi Freesurfer community,
I have an issue that I spent ages trying to figure out and this error has
been asked about back in (17/12/2016) and the title is ([Freesurfer]
Tracula trac -all preprocessing error.
my error is:
ERROR: fio_pushd: /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni
There is an issue that the mini folder is empty.
Attached is the log file and the configuration file (tracula_conf.txt)
Regards,
Salah
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# FreeSurfer SUBJECTS_DIR
# I added this command: export SUBJECTS_DIR=/Volumes/HD/Post_HARDI/PAH_Clinical_110/07
# to allow setting the environment to this: setenv SUBJECTS_DIR /Volumes/../..
# To run the tracula: trac-all -prep -c /Volumes/G_RAID/Backup_Salah/Post_HARDI/PAH_Clinical_110/tracula_conf.txt
# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR /Volumes/HD/Post_HARDI/PAH_Clinical_110/07
# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07
# Subject IDs
#
set subjlist = C07
# In case you want to analyze only Huey and Louie
# Default: Run analysis on all subjects
#
set runlist = (1)
# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then the gradient table and b-value table must be specified (see below)
#
set dcmroot = /Volumes/HD/Post_HARDI/PAH_Clinical_110
set dcmlist = 07/C_64_b3000/0001.dcm
# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified if they cannot be read from the DICOM headers
# The tables must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bveclist = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/DTI/bvecs_C07.txt
# Diffusion gradient table (if using the same one for all scans)
# Must be specified if it cannot be read from the DICOM headers
# The table must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvecfile = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/DTI/bvecs_C07.txt
# Diffusion b-value tables (if there is a different one for each scan)
# Must be specified if they cannot be read from the DICOM headers
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvallist = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/DTI/bvals_C07.txt
# Diffusion b-value table (if using the same one for all scans)
# Must be specified if it cannot be read from the DICOM headers
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvalfile = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/DTI/bvals_C07.txt
# Perform registration-based B0-inhomogeneity compensation?
# Default: 0 (no)
#
# set dob0 = 1
# Input B0 field map magnitude DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
# set b0mlist = 07/C_64_b3000/0001.dcm
# Input B0 field map phase DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
# set b0plist = 07/C_64_b3000/0001.dcm
# Echo spacing for field mapping sequence (from sequence printout)
# Only used if dob0 = 1
# Default: None
#
# set echospacing = 0.7
# Perform registration-based eddy-current compensation?
# Default: 1 (yes)
#
set doeddy = 1
# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1
# Default: 1 (yes)
#
set dorotbvecs = 1
# Fractional intensity threshold for BET mask extraction from low-b images
# This mask is used only if usemaskanat = 0
# Default: 0.3
#
set thrbet = 0.5
# Perform diffusion-to-T1 registration by flirt?
# Default: 0 (no)
#
# set doregflt = 0
# Perform diffusion-to-T1 registration by bbregister?
# Default: 1 (yes)
#
set doregbbr = 1
# Perform registration of T1 to MNI template?
# Default: 1 (yes)
#
set doregmni = 1
# MNI template
# Only used if doregmni = 1
# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
# set mnitemp = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07/mni_template.nii.gz
# Perform registration of T1 to CVS template?
# Default: 0 (no)
#
set doregcvs = 0
# CVS template subject ID
# Only used if doregcvs = 1
# Default: cvs_avg35
#
# set cvstemp = donald
# Parent directory of the CVS template subject
# Only used if doregcvs = 1
# Default: $FREESURFER_HOME/subjects
#
# set cvstempdir = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07
# Use brain mask extracted from T1 image instead of low-b diffusion image?
# Has no effect if there is no T1 data
# Default: 1 (yes)
#
set usemaskanat = 1
# Paths to reconstruct
# Default: All paths in the atlas
#
set pathlist = ( lh.cst_AS rh.cst_AS \
lh.unc_AS rh.unc_AS \
lh.ilf_AS rh.ilf_AS \
fmajor_PP fminor_PP \
lh.atr_PP rh.atr_PP \
lh.ccg_PP rh.ccg_PP \
lh.cab_PP rh.cab_PP \
lh.slfp_PP rh.slfp_PP \
lh.slft_PP rh.slft_PP )
# Number of path control points
# It can be a single number for all paths or a different number for each of the
# paths specified in pathlist
# Default: 7 for the forceps major, 6 for the corticospinal tract,
# 4 for the angular bundle, and 5 for all other paths
#
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)
# List of training subjects
# This text file lists the locations of training subject directories
# Default: $FREESURFER_HOME/trctrain/trainlist.txt
#
# set trainfile = /Volumes/HD/Post_HARDI/PAH_Clinical_110/07
# Number of "sticks" (anisotropic diffusion compartments) in the bedpostx
# ball-and-stick model
# Default: 2
#
set nstick = 2
# Number of MCMC burn-in iterations
# (Path samples drawn initially by MCMC algorithm and discarded)
# Default: 200
#
set nburnin = 200
# Number of MCMC iterations
# (Path samples drawn by MCMC algorithm and used to estimate path distribution)
# Default: 7500
#
set nsample = 7500
# Frequency with which MCMC path samples are retained for path distribution
# Default: 5 (keep every 5th sample)
#
set nkeep = 5
# Reinitialize path reconstruction?
# This is an option of last resort, to be used only if one of the reconstructed
# pathway distributions looks like a single curve. This is a sign that the
# initial guess for the pathway was problematic, perhaps due to poor alignment
# between the individual and the atlas. Setting the reinit parameter to 1 and
# rerunning "trac-all -prior" and "trac-all -path", only for the specific
# subjects and pathways that had this problem, will attempt to reconstruct them
# with a different initial guess.
# Default: 0 (do not reinitialize)
#
set reinit = 0
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Message: 9
Date: Tue, 7 Apr 2020 05:25:32 -0500
From: Kate Marvel <kmarvel54@gmail.com>
Subject: [Freesurfer] hippocampus subfield segmentation using Siemen
and GE scans
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAG9yhu7psfpBdomKPF2Xtu5E+SvGsWKBA20Dy40f7ZrMcawFwA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi Freesurfer Community,
I have run Hippocampus subfield segmentation using scans from GE and
Siemens. The field of view (FOV) for GE and Siemens are different, with FOV
of 8 and 9 respectively. Will this affect the analysis since they have
different FOV?
Thanks,
Kate
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Message: 10
Date: Tue, 7 Apr 2020 19:04:37 +0800
From: Lijun An <lijun.an@hotmail.com>
Subject: [Freesurfer] Chorid-plexus in Freesurfer reconall
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CWLP123MB2180B25276FBC0E5467F0D349AC30@CWLP123MB2180.GBRP123.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Dear Freesurfer experts,
I have a little question about the structure 'chorid-plexus', I am not very
deep in brain anatomy and function. Could anyone have a sense of what is
the normal range of this structure volume from Freesurfer reconall?
I found that mean of 'chorid-plexus' in ADNI is around 1500 mm^3, when I
ran reconall for my local subejcts (a local dataset), I found the mean of
'chorid-plexus' is around 800 mm^3.
Could anyone give an explanation or a paper I could refer to for this
'chorid-plexus' structure?
Thanks so much!
Best Regards,
An Lijun
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Message: 11
Date: Tue, 7 Apr 2020 09:59:49 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Chorid-plexus in Freesurfer reconall
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.21.2004070957190.13248@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi An Lijun
The choroid is a plexus of ependymal cells that produce CSF. it is pretty
tough to segment and mostly we include it to get more accurate segmenations
of the hippocampus where it is adjacent to ventricle and the ventricles
themselves. I'm not sure I've ever seen any normative stats on it though.
You can read more here:
https://en.wikipedia.org/wiki/Choroid_plexus
cheers
Bruce
On Tue, 7 Apr 2020, Lijun An
wrote:
????????External Email - Use Caution????????
Dear Freesurfer experts,?
I have a little question about the structure 'chorid-plexus', I am not very deep in brain
anatomy and function. Could anyone have a sense of what is the normal range of this
structure volume from Freesurfer reconall?
I found that mean of 'chorid-plexus' in ADNI is around 1500 mm^3, when I ran reconall for my
local subejcts (a local dataset), I found the mean of 'chorid-plexus' is around 800 mm^3.
Could anyone give an explanation or a paper I could refer to for this 'chorid-plexus'
structure?
Thanks? so much!? ?
Best Regards,An Lijun
------------------------------
Message: 12
Date: Tue, 7 Apr 2020 09:13:33 -0500
From: Frank Robert <frabob2015@gmail.com>
Subject: [Freesurfer] whether freesurfer version 7 still support GPU
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: frabob2015@gmail.com
Message-ID:
<CANfWN_Y-J8uQ+UaqODBVOHLWpNHGGr0hTUKMSSiv-Cw+7HoQEg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hello Freesurfer team
I checked the freesurfer version 7.0. It says that " but for now you
should know that some features are not present in v7 (QDEC, GPU-capability,
and recon-all -make)."
https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1
But from the hardware setup, it still needs Graphics card: 3D graphics
card with its own graphics memory & accelerated OpenGL drivers.
This makes me confused. Since version 7 does not support GPU anymore,
why does it still need the Graphic card? I found GPU may be helpful for
some abnormal brain such as large ventricles. It may speed the calculation
time. I do not know my observation is correct or not.
Thanks
Frank
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------------------------------
Message: 13
Date: Tue, 7 Apr 2020 14:48:05 +0000
From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
Subject: Re: [Freesurfer] hippocampus subfield segmentation using
Siemen and GE scans
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <EA967479-5618-4412-9A99-4158F261E2F2@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
It should be fine but please make sure you correct by scanner in subsequent analyses.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Kate Marvel <kmarvel54@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, April 7, 2020 at 06:26
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] hippocampus subfield segmentation using Siemen and GE scans
External Email - Use Caution
Hi Freesurfer Community,
I have run Hippocampus subfield segmentation using scans from GE and Siemens. The field of view (FOV) for GE and Siemens are different, with FOV of 8 and 9 respectively. Will this affect the analysis since they have different FOV?
Thanks,
Kate
-------------- next part --------------
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------------------------------
Message: 14
Date: Tue, 7 Apr 2020 15:06:28 +0000
From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: [Freesurfer] whether freesurfer version 7 still support
GPU
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: "frabob2015@gmail.com" <frabob2015@gmail.com>
Message-ID: <737D7BF9-02F7-4498-B9E0-1F37577B7DF6@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Frank,
We still recommend this since freeview benefits from having a fast GPU.
best
Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Frank Robert <frabob2015@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, April 7, 2020 at 10:15 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Cc: "frabob2015@gmail.com" <frabob2015@gmail.com>
Subject: [Freesurfer] whether freesurfer version 7 still support GPU
External Email - Use Caution
Hello Freesurfer team
I checked the freesurfer version 7.0. It says that " but for now you should know that some features are not present in v7 (QDEC, GPU-capability, and recon-all -make)."
https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1
But from the hardware setup, it still needs Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers.
This makes me confused. Since version 7 does not support GPU anymore, why does it still need the Graphic card? I found GPU may be helpful for some abnormal brain such as large ventricles. It may speed the calculation time. I do not know my observation is correct or not.
Thanks
Frank
-------------- next part --------------
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URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200407/fb3366b0/attachment-0001.html
------------------------------
Message: 15
Date: Tue, 7 Apr 2020 10:12:06 -0500
From: Kate Marvel <kmarvel54@gmail.com>
Subject: Re: [Freesurfer] hippocampus subfield segmentation using
Siemen and GE scans
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAG9yhu6g6F_wdBgZ+cGJ=pVUTym9A2iAj=3-RPg=swVfaC859g@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Thank you so much Iglesias.
kate
On Tue, Apr 7, 2020, 9:48 AM Iglesias Gonzalez, Juan E. <
JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
It should be fine but please make sure you correct by scanner in-------------- next part --------------
subsequent analyses.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
*From: *<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Kate Marvel
<kmarvel54@gmail.com>
*Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Date: *Tuesday, April 7, 2020 at 06:26
*To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject: *[Freesurfer] hippocampus subfield segmentation using Siemen
and GE scans
* External Email - Use Caution *
Hi Freesurfer Community,
I have run Hippocampus subfield segmentation using scans from GE and
Siemens. The field of view (FOV) for GE and Siemens are different, with FOV
of 8 and 9 respectively. Will this affect the analysis since they have
different FOV?
Thanks,
Kate
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------
Message: 16
Date: Tue, 7 Apr 2020 10:23:42 -0500
From: Frank Robert <frabob2015@gmail.com>
Subject: Re: [Freesurfer] whether freesurfer version 7 still support
GPU
To: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CANfWN_YPoEBKDNK6evpr9HWvMj5b_xagWDDEbn1dO_HLEiJT0w@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hello Dr. Hoopes
Does it mean that in Beta version 7, there is no GPU capability. But
stable version 7 still support the existing GPU capacity.. Is it correct?
BR
Frank
On Tue, Apr 7, 2020 at 10:06 AM Hoopes, Andrew <AHOOPES@mgh.harvard.edu>
wrote:
Hi Frank,-------------- next part --------------
We still recommend this since freeview benefits from having a fast GPU.
best
Andrew
*From: *<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Frank
Robert <frabob2015@gmail.com>
*Reply-To: *FS Help <freesurfer@nmr.mgh.harvard.edu>
*Date: *Tuesday, April 7, 2020 at 10:15 AM
*To: *FS Help <freesurfer@nmr.mgh.harvard.edu>
*Cc: *"frabob2015@gmail.com" <frabob2015@gmail.com>
*Subject: *[Freesurfer] whether freesurfer version 7 still support GPU
* External Email - Use Caution *
Hello Freesurfer team
I checked the freesurfer version 7.0. It says that " but for now you
should know that some features are not present in v7 (QDEC, GPU-capability,
and recon-all -make)."
https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1
But from the hardware setup, it still needs Graphics card: 3D graphics
card with its own graphics memory & accelerated OpenGL drivers.
This makes me confused. Since version 7 does not support GPU anymore,
why does it still need the Graphic card? I found GPU may be helpful for
some abnormal brain such as large ventricles. It may speed the calculation
time. I do not know my observation is correct or not.
Thanks
Frank
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
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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------------------------------
Message: 17
Date: Tue, 7 Apr 2020 15:27:40 +0000
From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Subject: Re: [Freesurfer] whether freesurfer version 7 still support
GPU
To: Frank Robert <frabob2015@gmail.com>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <FBF997D9-29E3-4698-AD28-FA72846B81D0@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
It means CUDA-accelerated binaries/recons on the GPU are no longer supported after freesurfer 6.0. I will make that clarification in the wiki page. Sorry for the confusion.
Andrew
From: Frank Robert <frabob2015@gmail.com>
Date: Tuesday, April 7, 2020 at 11:24 AM
To: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Cc: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] whether freesurfer version 7 still support GPU
External Email - Use Caution
Hello Dr. Hoopes
Does it mean that in Beta version 7, there is no GPU capability. But stable version 7 still support the existing GPU capacity.. Is it correct?
BR
Frank
On Tue, Apr 7, 2020 at 10:06 AM Hoopes, Andrew <AHOOPES@mgh.harvard.edu<mailto:AHOOPES@mgh.harvard.edu>> wrote:
Hi Frank,
We still recommend this since freeview benefits from having a fast GPU.
best
Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Frank Robert <frabob2015@gmail.com<mailto:frabob2015@gmail.com>>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, April 7, 2020 at 10:15 AM
To: FS Help <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: "frabob2015@gmail.com<mailto:frabob2015@gmail.com>" <frabob2015@gmail.com<mailto:frabob2015@gmail.com>>
Subject: [Freesurfer] whether freesurfer version 7 still support GPU
External Email - Use Caution
Hello Freesurfer team
I checked the freesurfer version 7.0. It says that " but for now you should know that some features are not present in v7 (QDEC, GPU-capability, and recon-all -make)."
https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1
But from the hardware setup, it still needs Graphics card: 3D graphics card with its own graphics memory & accelerated OpenGL drivers.
This makes me confused. Since version 7 does not support GPU anymore, why does it still need the Graphic card? I found GPU may be helpful for some abnormal brain such as large ventricles. It may speed the calculation time. I do not know my observation is correct or not.
Thanks
Frank
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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End of Freesurfer Digest, Vol 194, Issue 8
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