Re: [Freesurfer] Questions re slice thickness, aseg and longitudinal analysis

[Martin Reuter]

Hi David, 

I am not very optimistic:

5mm is too thick for FreeSurfer (recommendation is 1 up to 1.5). You
will certainly get something, but it can be very unreliable and
completely wrong. Especially longitudinally these thick slices will
induce large variance due to different head positioning (and different
slice angulations) in the scanner.

Furthermore, FreeSurfer does not take Gad-Enhanced images. Also it will
not work if tumor lesions are present. 

About your questions:

1. Surfaces update the aseg, but if you are only interested in the
volumes, you can skip this expensive step (potentially at the cost of
slightly higher noise levels in your measurements).

2. I think not (see above). 5mm is too low.

3. Theoretically yes, but I have never tested if the scripts will do
it. You could run up to the aseg in the cross, then create base (up to
aseg) and then run the longs up to aseg. Not even sure you really need
the base aseg. You might be able to just run the initial base
registration step, obtain the transformations and median norm.mgz
image, could be sufficient for the long runs. 

4. No. Gad images won't work. 

Best, Martin


On Mon, 2019-10-07 at 18:12 +, David Kamson wrote:
> External Email - Use Caution
> Freesurfers,
> 
> First of all, I'd like to express my gratitude to the community for
> the support that keeps researchers like myself afloat!
> 
> 
> I have a unique set of oncology patients that I want to evaluate for
> brain atrophy in a retrospective longitudinal analysis.
> I was thinking about using Aseg.auto results to assess longitudinal
> volume changes, but before I invest all the time I wanted to check
> with the community whether this makes any sense at all:
> 
> The dataset that looks like this:
> - 22 patients (no control dataset [yet])
> - 10-25 MRIs per patient acquired over 2-8 years in relatively
> uniform intervals
> - Patients had most of their scans on the same scanner, but
> scanners differed widely between patients
> - All patients have axial T1 post gadolinium scans of 1x1x5mm
> resolution (3D acquisition available in <10%)
> - About 80% of scans have an axial pre-contrast T1 sequence
> - All scans are skullstripped (third party algorithm)
> 
> I'm looking for crude changes, no subtleties; volumes of interest
> are:
> - Whole brain volume
> - White matter volume
> - Ventricular volume (mainly lateral ventricle)
> - Subcortical gray matter volume (whole thalamus most importantly)
> 
> I ran a few test analyses and to my surprise I was able to generate
> pretty acceptable surfaces, however, topology fixing took about 24H
> per scan, and I feel aseg.auto contained all the volumetric data I
> was really interested in.
> 
> My concrete questions are:
> 1) Does the full autorecon pipeline affect Aseg.auto? If there is no
> benefit, I could reduce the per scan analysis time from 28 hours to
> 1-2 h.
> 2) Would this low-resolution dataset be accepted by reviewers if used
> for Aseg? Should I do any quantitative validation beyond a visual
> quality analysis of Aseg?  
> 3) Can I perform a longitudinal analysis only for the Aseg results?
> 4) Is it OK to use T1-gad images for the analysis?
> 
> I'd appreciate any input!
> 
> Best regards,
> David O. Kamson, MD PhD
> Neuro-oncology fellow 
> Johns Hopkins Hospital &
> National Institutes of Health
> 
> 
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Re: [Freesurfer] Label created in the symmetric space

[Jose Graterol]

External Email - Use Caution

It worked as intended. Thank you very much.

On Tue, Oct 8, 2019 at 6:43 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> In that case, run mris_preproc in the same way but don't include the
> paired-diff. Concatenate the two groups together to give you one file.
> Smooth as you did before. Now with that one file run
> mri_segstats --seg csdbase.sig.ocn.mgh --i youronefile.mgh --avgwf
> subject.hemi.cluster.dat --excludeid 0
>
> The output file subject.hemi.cluster.dat will have a row for each
> subject and hemisphere (the order will be subject.lh, subject.rh,
> nextsubject.lh, nextsubject.rh) and a column for each cluster. The
> values will be the thickness.
>
>
>
> On 10/8/19 12:22 PM, Jose Graterol wrote:
> >
> > External Email - Use Caution
> >
> > Aha, yes. That is what I want. The original thickness values.
> >
> > Greve, Douglas N.,Ph.D.  > > schrieb am Di., 8. Okt. 2019, 17:36:
> >
> > That all looks fine, I'm just not sure what problem you want me to
> > solve. You said that the values in the y.ocn.dat file were all
> > negative,
> > it has to be this way because you specified only negative values when
> > you ran glmfit-sim (and negative values are possible because you have
> > computed left-right and negated half of your subjects). Do you
> > want the
> > original thickness values?
> >
> > On 10/8/19 11:14 AM, Jose Graterol wrote:
> > >
> > > External Email - Use Caution
> > >
> > > I will try to go back a bit, just to be sure I did not make a
> > mistake.
> > > I registered both hemispheres of every subject (affected and
> > > non-affected) with xhemi.
> > >
> > > Then for the left-affected subjects I ran:
> > > mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff
> > > --srcsurfreg fsaverage_sym.sphere.reg --meas thickness --out
> > > leftlesionsubjects.lh.lh-rh.thickness.sm00.mgh --s sub-xxx
> > >
> > > For the right-affected:
> > > mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff
> > > --srcsurfreg fsaverage_sym.sphere.reg --meas thickness --out
> > > rightlesionsubjects.lh.lh-rh.thickness.sm00.mgh --s sub-xxx
> > >
> > > Then I changed the sign of the right-affected subjects:
> > > fscalc rightlesionsubjects.lh.lh-rh.thickness.sm00.mgh mul -1 -o
> > > rightlesionsubjects.lh.rh-lh.thickness.sm00.mgh
> > >
> > > Then I concatenated them:
> > >
> > > mri_concat leftlesionsubjects.lh.lh-rh.thickness.sm00.mgh
> > > rightlesionsubjects.lh.rh-lh.thickness.sm00.mgh --o
> > > allsubjects.lh.lesion-healthy.thickness.sm00.mgh
> > >
> > > Then I smoothed the file:
> > > mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only
> > --fwhm 10
> > > --i allsubjects.lh.lesion-healthy.thickness.sm00.mgh --o
> > > allsubjects.lh.lesion-healthy.thickness.sm10.mgh
> > >
> > > Then glmfit:
> > > mri_glmfit --y allsubjects.lh.lesion-healthy.thickness.sm10.mgh
> > > --glmdir glmdir.allsubjects.lh.lesion-healthy.thickness.sm10 --osgm
> > > --surf fsaverage_sym lh
> > >
> > > and finally the correction for multiple comparisons:
> > >
> > > mri_glmfit-sim --y allsubjects.lh.lesion-healthy.thickness.sm10.mgh
> > >  --glmdir glmdir.allsubjects.lh.lesion-healthy.thickness.sm10
> > > --cwpvalthresh 0.05 --cache 4 neg
> > >
> > >
> > > Hopefully this helps.
> > >
> > >
> > >
> > >
> > > On Tue, Oct 8, 2019 at 4:45 PM Greve, Douglas N.,Ph.D.
> > > mailto:dgr...@mgh.harvard.edu>
> > >>
> > wrote:
> > >
> > > The input has both positives and negatives, so is is not
> > > surprising that the y.ocn.dat also has positive and
> > negative. Not
> > > sure what is going wrong here ...
> > >
> > > On 10/7/2019 5:48 PM, Jose Graterol wrote:
> > >>
> > >> External Email - Use Caution
> > >>
> > >> Ok, I uploaded it with the name
> > "glmdir.jg.allsubjects.tar.gz". I
> > >> had to log in as anonymous and not with my email, otherwise it
> > >> would throw an error (503 Login with USER first. Login
> > failed.).
> > >> The mgh file is inside the gz file too. Thanks again for your
> > >> time and help.
> > >>
> > >> On Mon, Oct 7, 2019 at 7:06 PM Greve, Douglas N.,Ph.D.
> > >> mailto:dgr...@mgh.harvard.edu>
> > >>
> > wrote:
> > >>
> > >> ok, I still don't know what is going on. Can you upload
> the
> > >> glmdir and the input to mri_glmfit (ie, the argument of
> the
> > >> --y flag). You can upload it using these instructions:
> > >>
> 

[Freesurfer] How to measure the cortical thickness in tumor patients?

[王子谦]

External Email - Use Caution

Dear developers,

right now I'm trying to measure the cortical thickness of the right
hemisphere in the left side tumor patients. Here I met some problem. Since
the complex intensities in the tumor, it makes the 'recon-all -all' command
to be very time consuming(3 days per subject). Do you have any experience
dealing with the tumor patients?
I also tried the '-lh' flag, but there is only one file named
'rh.curv.stats' in stats folder.  The command is:recon-all -s 130 -i
130.nii -qcache -3T -hemi rh -all

Do you have any idea about where the problem is?

Best wishes,
James
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Re: [Freesurfer] ECC or non-ECC Memory?

[Sotiris Michos]

External Email - Use Caution

Dear Matt,

Memtest 86+ and similar tools can test the DRAM module only for hard errors 
(hardware defects). Are you suggesting that the soft errors (the common 
spontaneous flipping of a bit state) that happen in all memories do not have a 
considerable effect in Freesurfer’s results?

Best Regards,
Sotiris

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Re: [Freesurfer] [FSL] Hippocampus subregions question

[Iglesias Gonzalez, Juan E.]

Dear Frederic,

I’ll defer to Jean Augustinack (CCed) for a more granular answer (pun 
intended), but here are my initial thoughts.

  1.  You can find the definition in Table 2 of the paper, which is open 
access: https://www.sciencedirect.com/science/article/pii/S1053811915003420
  2.  Yes.
  3.  Both. We initially subdivided but it was too hard to do it consistently, 
so we merged them.

Kind regards,

/Eugenio

PS: FSL is not FreeSurfer (FS) :-P

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From:  on behalf of "briend, Frederic" 

Reply-To: Freesurfer support list 
Date: Tuesday, 8 October 2019 at 18:23
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] [FSL] Hippocampus subregions question


External Email - Use Caution
Dear FSL members,
First, thanks for your great work about the hippocampus subfield. Second, I 
have some question about your subfield/subregions definitions:

  1.  Can you give me your actual definition of the GC-ML-DG in your last 
release (FSL6.0) of the hippocampus segmentation? Is-it possible to speak about 
granular cell layer, like used in the Ho, 2017 (Molecular psychiatry) article?
  2.  Moreover, is-it possible to say for the the hippocampal tail that it is 
comprised of portions of CA and dentate gyrus?
  3.  For molecular layer (ML), is it the ML of the CA subiculum sub volumes or 
the ML of the DG or both?

Thank you in advance,

--

Frederic Briend, PhD
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Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 13

[Yendiki, Anastasia]

When you run mri_info on that file, what do you see?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Juan Rivas 

Sent: Wednesday, October 9, 2019 8:36:48 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 13


External Email - Use Caution

Hi, thank you for your answer. This file does exist, it contains 59.3 MB.
JC.

 Message: 10
Date: Tue, 8 Oct 2019 22:23:11 +
From: "Yendiki, Anastasia" 
mailto:ayend...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:

mailto:bl0pr04mb4833da61a1a5e068536924af8a...@bl0pr04mb4833.namprd04.prod.outlook.com>>

Content-Type: text/plain; charset="us-ascii"

Does this file exist?
niiRead(): error opening file 
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz
Hi, I have been trying to process my diffusion images, but I have a new
problem:
I wrote this dmrirc:
# FreeSurfer SUBJECTS_DIR

# T1 images and FreeSurfer segmentations are expected to be found here
#


setenv SUBJECTS_DIR /autofs/cluster/neuromod/rivas/imagenes/DICOM

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc

# Subject IDs
#
set subjlist = (esq-15-hc)

# 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 bvecfile and bvalfile must be specified (see below)
#
set dcmroot = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc

set dcmlist = (dwi.nii.gz)


# Diffusion gradient table
# Must be specified if inputs are not MGH DICOMs
# Three-column format, one row for each volume in the diffusion data set
# Default: Read from DICOM header
#

set bvecfile =
/autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc/processing/31190669_bvecs.dat

# Diffusion b-value table
# Must be specified if inputs are not MGH DICOMs
# Single-column format, one value for each volume in the diffusion data set
# Default: Read from DICOM header
#
set bvalfile =
/autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc/processing/31190669_bvals.dat


# 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 = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm
louie/fmag/XXX-1.dcm)

# Input B0 field map phase DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
# set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm
louie/fphas/XXX-1.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 = $FSLDIR/data/standard/MNI152_T1_1mm_brain.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:
#
set cvstempdir = $FREESURFER_HOME/subjects

# 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 

Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 13

[Juan Rivas]

External Email - Use Caution

Hi, thank you for your answer. This file does exist, it contains 59.3 MB.
JC.

 Message: 10
Date: Tue, 8 Oct 2019 22:23:11 +
From: "Yendiki, Anastasia" 
Subject: Re: [Freesurfer] Tracula
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID:
<
bl0pr04mb4833da61a1a5e068536924af8a...@bl0pr04mb4833.namprd04.prod.outlook.com
>

Content-Type: text/plain; charset="us-ascii"

Does this file exist?
niiRead(): error opening file
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz
Hi, I have been trying to process my diffusion images, but I have a new
problem:
I wrote this dmrirc:
# FreeSurfer SUBJECTS_DIR

# T1 images and FreeSurfer segmentations are expected to be found here
#


setenv SUBJECTS_DIR /autofs/cluster/neuromod/rivas/imagenes/DICOM

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc

# Subject IDs
#
set subjlist = (esq-15-hc)

# 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 bvecfile and bvalfile must be specified (see below)
#
set dcmroot = /autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc

set dcmlist = (dwi.nii.gz)


# Diffusion gradient table
# Must be specified if inputs are not MGH DICOMs
# Three-column format, one row for each volume in the diffusion data set
# Default: Read from DICOM header
#

set bvecfile =
/autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc/processing/31190669_bvecs.dat

# Diffusion b-value table
# Must be specified if inputs are not MGH DICOMs
# Single-column format, one value for each volume in the diffusion data set
# Default: Read from DICOM header
#
set bvalfile =
/autofs/cluster/neuromod/rivas/imagenes/DICOM/esq-15-hc/processing/31190669_bvals.dat


# 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 = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm
louie/fmag/XXX-1.dcm)

# Input B0 field map phase DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
# set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm
louie/fphas/XXX-1.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 = $FSLDIR/data/standard/MNI152_T1_1mm_brain.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:
#
set cvstempdir = $FREESURFER_HOME/subjects

# 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 = $FREESURFER_HOME/trctrain/trainlist.txt

# 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 

Re: [Freesurfer] How to measure the cortical thickness in tumor patients?

[Bruce Fischl]

Hi James

I think the -lh/-rh flags are for processing single (ex vivo) hemis, not 
for only processing one hemi in a whole-brain image. If you want to erase 
the hemi with the tumor it will probably work


cheers
Bruce
On Wed, 9 Oct 2019, 王子谦 
wrote:




External Email - Use Caution

Dear developers,
right now I'm trying to measure the cortical thickness of the right
hemisphere in the left side tumor patients. Here I met some problem. Since
the complex intensities in the tumor, it makes the 'recon-all -all' command
to be very time consuming(3 days per subject). Do you have any experience
dealing with the tumor patients? 
I also tried the '-lh' flag, but there is only one file named
'rh.curv.stats' in stats folder.  The command is:recon-all -s 130 -i 130.nii
-qcache -3T -hemi rh -all

Do you have any idea about where the problem is?

Best wishes,
James

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[Freesurfer] mri_convert no scaling

[Ezequiel Mikulan]

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Dear All, 
I have a similar problem to the one posted here ( Re: [Freesurfer] mri_convert 
scaling ). In my case I'm trying to convert from ANALYZE (.img, .hdr and .mat) 
to NIFTI and I need to keep the scale as in the original file. I've tried the 
-ns 1 flag but it doesn't work (which is not surprising as I've seen on the 
help page that it is for COR). 
The file was originally in NIFTI format and was converted to ANALYZE 
(mri_convert), as I had to use a tool that only accepts this format, and now 
I'm trying to go back to NIFTI. I would like to know if there is a way of doing 
it without rescaling the output. 
These are the contents of the folder:.
├── CC0061_philips_3_55_F_full_normfilter.hdr
├── CC0061_philips_3_55_F_full_normfilter.img
├── CC0061_philips_3_55_F_full_normfilter.mat

And this is the output of the command call:
$ mri_convert -ns 1 CC0061_philips_3_55_F_full_normfilter.img test.nii
mri_convert.bin -ns 1 CC0061_philips_3_55_F_full_normfilter.img test.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from CC0061_philips_3_55_F_full_normfilter.img...
  analyzeRead() roi_scale   0.003921570
  analyzeRead() scaling by   0.003921570
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.984889, -0.156173, 0.0748529)
j_ras = (0.154421, 0.987589, 0.0286842)
k_ras = (-0.0784036, -0.0166919, 0.996782)
writing to test.nii...

Thanks in advance for your time,
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Re: [Freesurfer] [FSL] Hippocampus subregions question

[briend, Frederic]

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Shame on me; this list is for Freesurfer indeed. Sorry.

However, thanks for your reply Eugenio! I am looking forward to getting 
the more granular answer (;)) from Jean Augustinack.

-- 
Frederic Briend, PhD


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Re: [Freesurfer] mri_convert no scaling

[Bruce Fischl]

Hi Ezequiel

-noscale 1 works in most cases, but here the analyze file itself specifies 
a scalling that is done as part of the reading process. If you want to 
disable it try (in tcsh):


setenv FS_ANALYZE_NO_RESCALE 1

then run mri_convert as before. You should see an addition printout in the 
output saying it is not rescaling


cheers
Bruce




On Wed, 9 Oct 2019, Ezequiel Mikulan wrote:



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Dear All, 
I have a similar problem to the one posted here ( Re: [Freesurfer]
mri_convert scaling ). In my case I'm trying to convert from ANALYZE (.img,
.hdr and .mat) to NIFTI and I need to keep the scale as in the original
file. I've tried the -ns 1 flag but it doesn't work (which is not surprising
as I've seen on the help page that it is for COR). 

The file was originally in NIFTI format and was converted to ANALYZE
(mri_convert), as I had to use a tool that only accepts this format, and now
I'm trying to go back to NIFTI. I would like to know if there is a way of
doing it without rescaling the output. 

These are the contents of the folder:
.
├── CC0061_philips_3_55_F_full_normfilter.hdr
├── CC0061_philips_3_55_F_full_normfilter.img
├── CC0061_philips_3_55_F_full_normfilter.mat

And this is the output of the command call:

$ mri_convert -ns 1 CC0061_philips_3_55_F_full_normfilter.img test.nii
mri_convert.bin -ns 1 CC0061_philips_3_55_F_full_normfilter.img test.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from CC0061_philips_3_55_F_full_normfilter.img...
  analyzeRead() roi_scale   0.003921570
  analyzeRead() scaling by   0.003921570
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.984889, -0.156173, 0.0748529)
j_ras = (0.154421, 0.987589, 0.0286842)
k_ras = (-0.0784036, -0.0166919, 0.996782)
writing to test.nii...

Thanks in advance for your time,

Best

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Re: [Freesurfer] Notice about macOS Catalina Notarization and FreeSurfer

[Aditya Kulkarni]

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You are absolutely right—once each binary is approved once then it is saved in 
that state much like previous versions of macOS. I’m sure the next few updates 
for Catalina will tackle this issue to allow nested permissions extensions.

Cheers,

Aditya

From: fsbuild 
Sent: Tuesday, October 8, 2019 11:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Aditya Kulkarni 
Subject: Re: [Freesurfer] Notice about macOS Catalina Notarization and 
FreeSurfer

Hello Aditya,

We are aware of the security changes in Mac OS 10.15 such as notarization 
whereby Apple has decided to extend security rules for applications (*.app 
bundles) to command line tool/binaries.   From my reading of developer postings 
it is not clear that the notarization process in the current release of 
Catalina can actually detect the linkages in and authorize all the Mac software 
that has been built on and distributed for older versions of Mac OS.  I suspect 
this is why in the past weeks I have started to receive at least 1 email a day 
from commercial vendors of Mac software saying not to upgrade to Catalina if 
you want to use their existing software releases.   So perhaps the the first 
(10.15.0) release of Catalina cannot support or be backwards compatible with 
all previous releases of Mac software.   My understanding is that each binary 
only needs to be authorized once and subsequently the approved state is saved, 
and the binary will run.  I can imagine writing something to try and authorize 
each individual command under ./freesurfer/bin starting with the lowest level 
commands, but I would not start with using the recon-all command.

- R.


Aditya Kulkarni
October 8, 2019 at 22:26
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Hello FreeSurfer team,

With Apple’s recent release of macOS Catalina, I wanted to test its 
compatibility with FreeSurfer. Indeed the executables in the freesurfer/bin 
folder are subject to the “notarization” problem in the OS, such that every 
dependent executable that is used in a recon-all stream requires the user to 
allow it manually through security (a process which becomes cumbersome and 
interrupts recon-all runs with the many libraries it requires). I know you are 
all working very hard on the software’s development and just wanted to update 
with this information in case other users are updating to Catalina and going to 
run a FreeSurfer stream soon.

Best,

Aditya Kulkarni

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Re: [Freesurfer] ERROR gtmseg

[Marina Fernández]

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Dear Douglas,

Thank you very much for the help. We could solve the problem with that
subject but now we have a similar problem with another subject. In the
previous case, we have only one problematic voxel in the skull, but now the
label 75 (it shouldn't exist either) is taking a lot of voxels in the
ventricles and the caudate. So, I think that we should use other solution
to fix it.

I know that this issue is weird. We use gtmseg command with more or less
500 subjects and we only have this type of problem with two subjects.

Best regards,
Marina.

 > Probably the easiest thing is just to edit that voxel  to be one of the
neighboring
 > segments. First, load the aseg and find that voxel. See which segment(s)
are around
 > that voxel and get the segmentation id. Then run
 > mri_binarize --replaceonly 229 YourNewSegID --i aparc+aseg.mgz --o
 > aparc+aseg.mgz
 >  then re-run gtmseg
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