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Today's Topics:
1. Re: Questions re slice thickness, aseg and longitudinal
analysis (Martin Reuter)
2. Re: Label created in the symmetric space (Jose Graterol)
3. How to measure the cortical thickness in tumor patients? (???)
4. Re: ECC or non-ECC Memory? (Sotiris Michos)
5. Re: Freesurfer Digest, Vol 188, Issue 13 (Juan Rivas)
6. Re: Brodmann area parcellation (sang ho shin)
7. Re: [FSL] Hippocampus subregions question
(Iglesias Gonzalez, Juan E.)
8. Re: Freesurfer Digest, Vol 188, Issue 13 (Yendiki, Anastasia)
9. Re: How to measure the cortical thickness in tumor patients?
(Bruce Fischl)
10. mri_convert no scaling (Ezequiel Mikulan)
11. Re: mri_convert no scaling (Bruce Fischl)
----------------------------------------------------------------------
Message: 1
Date: Wed, 09 Oct 2019 10:48:48 +0200
From: Martin Reuter <mreuter@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Questions re slice thickness, aseg and
longitudinal analysis
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<7a4d059cb5cb42f390e03f523677a3362d17cb81.camel@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="UTF-8"
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 +0000, 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
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 2
Date: Wed, 9 Oct 2019 11:34:59 +0200
From: Jose Graterol <gpjosealberto13@gmail.com>
Subject: Re: [Freesurfer] Label created in the symmetric space
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAFMm1s5_X3SzSWv=+wUKKH0z3HbVRceBQFG1v7SOA6_jWMbNYg@mail.gmail.com>
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It worked as intended. Thank you very much.
On Tue, Oct 8, 2019 at 6:43 PM Greve, Douglas N.,Ph.D. <
DGREVE@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. <DGREVE@mgh.harvard.edu
> > <mailto:DGREVE@mgh.harvard.edu>> 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.
> > > <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>
> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@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.
> > >> <DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>
> > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@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:
> > >>
> > >> From the linux command line,
> > >> Create the file you want to upload, eg,
> > >> cd $SUBJECTS_DIR
> > >> tar cvfz subject.tar.gz ./subject
> > >> Now log into our anonymous FTP site:
> > >> ftp surfer.nmr.mgh.harvard.edu
> > <http://surfer.nmr.mgh.harvard.edu>
> > >> <http://surfer.nmr.mgh.harvard.edu>
> > >> It will ask you for a user name: use your email address
> > >> It will ask you for a password: use "anonymous" (no
> quotes)
> > >> cd transfer/incoming
> > >> put subject.tar.gz
> > >>
> > >> Send an email that the file has been and the name of
> > the file.
> > >>
> > >> On 10/7/2019 11:53 AM, Jose Graterol wrote:
> > >>>
> > >>> External Email - Use Caution
> > >>>
> > >>> Hi Douglas,
> > >>>
> > >>> thanks for you answer. I have attached the file to the
> > email.
> > >>>
> > >>> On Mon, Oct 7, 2019 at 5:24 PM Greve, Douglas N.,Ph.D.
> > >>> <DGREVE@mgh.harvard.edu
> > <mailto:DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu
> > <mailto:DGREVE@mgh.harvard.edu>>> wrote:
> > >>>
> > >>> Let's backup a moment. Can you send the y.ocn.dat
> file
> > >>> that has problematic values?
> > >>>
> > >>> On 10/4/2019 4:58 AM, Jose Graterol wrote:
> > >>>>
> > >>>> External Email - Use Caution
> > >>>>
> > >>>> Dear Freesurfer Experts,
> > >>>>
> > >>>> I would appreciate your help. I will explain
> > first what
> > >>>> I have done and where my problem is.
> > >>>>
> > >>>> I want to measure the cortical thickness in stroke
> > >>>> patients. Therefore I followed Douglas' instructions
> > >>>> provided in this link
> > >>>>
> > <
> https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+flipping+surface+data%22&o=newest&f=1
> >to
> > >>>> join both affected hemispheres (left or right,
> > >>>> depending on the patient) and to analyze them
> > with xhemi.
> > >>>>
> > >>>> After mri_glmfit and mri_glmfit-sim (--cwpvalthresh
> > >>>> 0,05 --cache 4 abs/neg) have run I obtained 2
> > >>>> significant clusters. One in the precentral area,
> > which
> > >>>> I am interested in. When I check the
> > *abs/neg.y.ocn.dat
> > >>>> file the values are all -0.XXXX. If I understood it
> > >>>> correctly, those should be cortical thickness
> > values in
> > >>>> mm, making those values implausible. For that
> > reason I
> > >>>> made a label of that cluster using the autofill
> > option
> > >>>> from tksurfer. The idea was to obtain the mean
> > cortical
> > >>>> thickness using mris_anatomical_stats after
> > mapping the
> > >>>> label to the subjects.
> > >>>>
> > >>>> Now my questions, what would be the best method
> > to map
> > >>>> the label created from the fsaverage_sym space to
> the
> > >>>> subject space? Or just simply, is this the right
> > way to
> > >>>> do this? or should I check why I am obtaining those
> > >>>> values in the *y.ocn.dat file?
> > >>>>
> > >>>> Thanks in advance.
> > >>>>
> > >>>> Kind Regards
> > >>>>
> > >>>> Jos? Graterol
> > >>>>
> > >>>> _______________________________________________
> > >>>> Freesurfer mailing list
> > >>>> Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto: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>
> > >>> <mailto: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>
> > <mailto: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>
> > >> <mailto: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>
> > <mailto: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>
> > <mailto: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>
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> >
> >
> > _______________________________________________
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> Freesurfer@nmr.mgh.harvard.edu>
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> >
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------------------------------
Message: 3
Date: Wed, 9 Oct 2019 12:08:13 +0200
From: ??? <ziqianwang9@gmail.com>
Subject: [Freesurfer] How to measure the cortical thickness in tumor
patients?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAJN_0bRrt-CG_9Lo_bf4X7wQGrcDzyfAXoE=vaYNO=rov7Vh4Q@mail.gmail.com>
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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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Message: 4
Date: Wed, 9 Oct 2019 13:54:47 +0300
From: Sotiris Michos <sotmihos@gmail.com>
Subject: Re: [Freesurfer] ECC or non-ECC Memory?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <C970FF58-3A39-4DED-925C-88B414B2ADAE@gmail.com>
Content-Type: text/plain; charset="utf-8"
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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
------------------------------
Message: 5
Date: Wed, 9 Oct 2019 08:36:48 -0400
From: Juan Rivas <jcrn12@gmail.com>
Subject: Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 13
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CACYE61ArY4i1L4RkCj4bhdwBkaSHKTvebq+6wjNKKu8QGfvK-g@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
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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 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<
BL0PR04MB4833DA61A1A5E068536924AF8A9A0@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 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
And I gave this command: [shiraz:processing] (nmr-stable6-env) trac-all
-prep -c dmrirc-esq-15-hc
But there is an error:
INFO: SUBJECTS_DIR is
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing
INFO: Diffusion root is
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/stable6
trac-preproc -c
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/scripts/dmrirc.local
-log
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/scripts/trac-all.log
-cmd
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/scripts/trac-all.cmd
#-------------------------------------
/usr/local/freesurfer/stable6/bin/trac-preproc
#-------------------------------------
#@# Image corrections Tue Oct 8 17:53:12 EDT 2019
mri_convert --bvec-voxel
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.nii.gz
niiRead(): error opening file
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz...
Linux shiraz.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov
29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Tue Oct 8 17:53:12 EDT 2019
>
> ------------------------------
>
>
>
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------------------------------
Message: 6
Date: Wed, 9 Oct 2019 13:36:34 +0100
From: sang ho shin <happysaram20@gmail.com>
Subject: Re: [Freesurfer] Brodmann area parcellation
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CANnEPJK0pt22h=8O6RmfSgAtZjJ2icOs9HjoZ53n93beYPRLqw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Dear Douglas,
Thank your for your reply.
I already knew the label files, but when I saw the images on through
freeview and load ROI, I could just see border of motor cortex.
I don't think that they were the masks.
So, could you help me how to get the masks from the labels?
I have had tough time because of that and couldn't process my analysis.
I think that it is better to get the masks from freesurfer pacellation, but
while I have waited for your reply, I found out two method to get the masks.
My steps are as follows,
I am getting tractography between sensorimotor striatum and premotor &
motor cortex.
At first, I completed 'recon-all -all' through freesurfer for brain
parcellation and mask.
(*SHINui-iMac:~ shinsangho$ recon-all -s
NOR82_PJI -i ~/sangho/NOR82_PJI/NOR82_PJI_T1/coT1.nii ?all)*
I got the results(label, mri, scripts, stats, surf, tmp, touch, trash
folders).
But though I tried to get the mask of premotor & motor cortex, I couldn't
get the masks.
*FreeSurferColorLUT*
<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT?action=fullsearch&context=180&value=linkto%3A%22FsTutorial/AnatomicalROI/FreeSurferColorLUT%22>
*Premotor - 9002 ctx_lh_premotor, 9502 ctx_rh_premotor*
*Primary motor - 9001 ctx_lh_primary motor, 9501 ctx_rh_primary motor*
*or,*
*Bordmann area : Premotor 406 BA6, primary motor 404 BA4a, 405 **BA4p*
The command lines are follows.
*SHINui-iMac:dti_analysis_kings shinsangho$ mri_binarize --i
nor82_pji/nor82_pji_fs/mri/aparc.a2009s+aseg.mgz --match 404** --o
nor82_pji/nor82_pji_dlpfc/**NOR82_PJI_LH_PREMOTOR.nii.gz*
Even though I replaced aparc.a2009s+aseg.mgzn with any other atlases(
*aparc.DKTatlas+aseg.mgz, **aparc+aseg.mgz...) & matching number(9001,
9002, and ..)*, I couldn't get the masks. The results are as follows.
--------------------------------------------
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /Users/shinsangho/sangho/DTI_analysis_kings
cmdline mri_binarize.bin --i nor82_pji/nor82_pji_fs/mri/
*aparc.a2009s+aseg.mgz* --match *404* --o nor82_pji/nor82_pji_dlpfc/
NOR82_PJI_PREMOTOR.nii.gz
sysname Darwin
hostname SHINui-iMac.local
machine x86_64
user shinsangho
input nor82_pji/nor82_pji_fs/mri/aparc.a2009s+aseg.mgz
frame 0
nErode3d 0
nErode2d 0
output nor82_pji/nor82_pji_dlpfc/NOR82_PJI_PREMOTOR.nii.gz
Binarizing based on matching values
nMatch 1
0 404
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 0 values in range
Counting number of voxels in first frame
*Found 0 voxels in final mask*
Count: 0 0.000000 16777216 0.000000
mri_binarize done
----------------------------------------
So,
I used two different methods to get masks of the premotor & motor cortex
*Firstly,*
I got masks of 'the GM Primary motor cortex BA4a L, GM Primary motor cortex
BA4a R, GM Primary motor cortex BA4b L, GM Primary motor cortex BA4b R, GM
Premotor cortex BA6 L, and GM Premotor cortex BA6 R' in Juelich
Histological Atlas on atlas panel(on standard space of
avg152T_bain.nii.gz)FSLeyes.
To transform masks from on *standard space of avg152T_bain.nii.gz* to *the
individual image*, I tried to get the mat file.
*flirt -in /usr/local/fsl/data/standard/avg152T1_brain.nii.gz -ref
/Users/shinsangho/sangho/DTI_analysis_kings/NOR82_PJI/NOR82_PJI_FS/mri/brain.nii.gz
-out
/Users/shinsangho/sangho/DTI_analysis_kings/NOR82_PJI/st2ind -omat
/Users/shinsangho/sangho/DTI_analysis_kings/NOR82_PJI/st2ind.mat -bins 256
-cost mutualinfo -searchrx -180.0 180 -searchry -180 180 -searchrz -180 180
-dof 12 -interp trilinear*
(question: I used brain.nii.gz on 'mri' folder as a reference image, but
the brain.nii.gz is from the results of recon-all on freesurfer space
automatically(including skull ripening). Can I use the image as a
reference? Otherwise, should I use original T1 image(after skull ripening
*'BET'* or before skull ripening using as a reference image?)
And then,
*flirt -ref nor82_pji/nor82_pji_fs/mri/brain.nii.gz -in
motor_crotex/premotor_l.nii -applyxfm -init nor82_pji/st2ind.mat -out
nor82_pji/nor82_pji_premotor_l.nii.gz*
I got the mask of premotor on individual image space.
*Secondary,*
After I got the masks the same way above.
(I got the GM Primary motor cortex BA4a L, GM Primary motor cortex BA4a R, GM
Primary motor cortex BA4b L, GM Primary motor cortex BA4b R, GM Premotor
cortex BA6 L, and GM Premotor cortex BA6 R in Juelich Histological Atlas on
atlas panel(on standard space of avg152T_bain.nii.gz)FSLeyes)
To transform masks from on standard space of avg152T_bain.nii.gz to the
individual image,
*mri_convert* motor_crotex/premotor_l.nii *--apply_inverse_transform*
./NOR82_PJI_FS/mri/transforms/*talairach.m3z* nor82_pji_premotor_l.nii.gz
I got the masks on individual image space.
Because I couldn't get the masks of premotor & motor cortex through
freesurfer parcellation(recon-all -all),
I tried to get the masks through two methods. But the masks on individual
image from two methods are not same, slightly different .
I am wondering if two methods to get premotror & motor cortex are right or
not and if right, I can use the masks of premotor & motor cortex as target
masks in analysis of tractography.
While I have found how to get the masks of premotor & motor cortex all the
week searching and reading articles and command lines online , I couldn't
get them at all.
I appreciate so much if you can help me. Have a nice day!?
Best regards,
Sangho
?
2019? 10? 7? (?) ?? 6:01, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>??
??:
> when you look in the label file, do you see
> lh.BA1_exvivo.label
> lh.BA2_exvivo.label
> lh.BA3a_exvivo.label
> lh.BA3b_exvivo.label
> lh.BA44_exvivo.label
> lh.BA45_exvivo.label
> lh.BA4a_exvivo.label
> lh.BA4p_exvivo.label
> lh.BA6_exvivo.label
>
>
> On 10/7/2019 11:50 AM, sang ho shin wrote:
>
> External Email - Use Caution
> Dear Douglas,
>
> Thank you for your reply.?
> I already ran the full recon-all and I got the results(label, mri,
> scripts, stats, surf, tmp, touch, trash).
> But though I tried to get the mask of both brodmann area 4 and 6, I
> couldn't get the masks.
> (404BA4a, 405BA4p, 406BA6)
>
> The command lines are follows.
>
> SHINui-iMac:dti_analysis_kings shinsangho$ mri_binarize --i
> nor82_pji/nor82_pji_fs/mri/*aparc.a2009s+aseg.mgz* --match *404* --o
> nor82_pji/nor82_pji_dlpfc/NOR82_PJI_LH_PREMOTOR.nii.gz
>
> Even though I replaced aparc.a2009s+aseg.mgzn with any other atlases(
> *aparc.DKTatlas+aseg.mgz, **aparc+aseg.mgz...)*, I couldn't get the mask.
> Could you help me how to get the Brodmann area 4 & 6?
>
> Best regards,
> Sangho
>
> =============
> $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
>
> cwd /Users/shinsangho/sangho/DTI_analysis_kings
>
> cmdline mri_binarize.bin --i
> nor82_pji/nor82_pji_fs/mri/aparc.a2009s+aseg.mgz --match 404 --o
> nor82_pji/nor82_pji_dlpfc/NOR82_PJI_PREMOTOR.nii.gz
>
> sysname Darwin
>
> hostname SHINui-iMac.local
>
> machine x86_64
>
> user shinsangho
>
>
> input nor82_pji/nor82_pji_fs/mri/aparc.a2009s+aseg.mgz
>
> frame 0
>
> nErode3d 0
>
> nErode2d 0
>
> output nor82_pji/nor82_pji_dlpfc/NOR82_PJI_PREMOTOR.nii.gz
>
> Binarizing based on matching values
>
> nMatch 1
>
> 0 404
>
> binval 1
>
> binvalnot 0
>
> fstart = 0, fend = 0, nframes = 1
>
> Found 0 values in range
>
> Counting number of voxels in first frame
>
> *Found 0 voxels in final mask*
>
> Count: 0 0.000000 16777216 0.000000
>
> mri_binarize done
>
> ========================
>
> ?
>
> 2019? 10? 7? (?) ?? 4:20, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>??
> ??:
>
>> You can to run the full recon-all on a given subject's data, and it will
>> create the broadmann areas
>>
>> On 10/5/2019 1:31 AM, sang ho shin wrote:
>>
>> External Email - Use Caution
>>
>> Dear Freesurfer Developers,
>>
>> I am trying to get the seed mask of premotor and motor cortex. Because I
>> can't get it through 'recon-all -all', I tried to find brodmann area ('recon-all
>> -s subjid -ba-labels')
>>
>> But I received ERROR message. Can you tell me how to get Brodmann area
>> through recon-all or freesurfer parcellation? And I appreciate if you can
>> help me to solve this error message as follows,
>>
>> =================================================================
>>
>> sinsanghoui-MBP:~ shinsangho$ export SUBJECTS_DIR=~/freesurfer_subjects
>>
>> sinsanghoui-MBP:~ shinsangho$ echo $SUBJECTS_DIR
>>
>> *sinsanghoui-MBP:~ shinsangho$ recon-all -s NOR82_PJI -i
>> ~/DTI_analysis/nor82_pji_t1/coT1.nii -ba-labels*
>>
>> Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>>
>> Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>>
>> INFO: SUBJECTS_DIR is /Users/shinsangho/freesurfer_subjects
>>
>> Actual FREESURFER_HOME /Applications/freesurfer
>>
>> Darwin sinsanghoui-MBP 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23
>> 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64
>>
>> /Users/shinsangho/freesurfer_subjects/NOR82_PJI
>>
>> \n mri_convert /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii
>> /Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz \n
>>
>> mri_convert.bin /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii
>> /Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz
>>
>> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>>
>> reading from /Users/shinsangho/DTI_analysis/nor82_pji_t1/coT1.nii...
>>
>> TR=1670.00, TE=0.00, TI=0.00, flip angle=0.00
>>
>> i_ras = (0.000121244, -1, 0)
>>
>> j_ras = (-0.0235518, -2.85817e-06, 0.999723)
>>
>> k_ras = (0.999723, 0.000121211, 0.0235518)
>>
>> writing to
>> /Users/shinsangho/freesurfer_subjects/NOR82_PJI/mri/orig/001.mgz...
>>
>> /Users/shinsangho/freesurfer_subjects/NOR82_PJI/label
>>
>> #--------------------------------------------
>>
>> #@# BA_exvivo Labels lh Fri Oct 4 17:43:23 BST 2019
>>
>> \n mri_label2label --srcsubject fsaverage --srclabel
>> /Users/shinsangho/freesurfer_subjects/fsaverage/label/lh.BA1_exvivo.label
>> --trgsubject NOR82_PJI --trglabel ./lh.BA1_exvivo.label --hemi lh
>> --regmethod surface \n
>>
>>
>>
>> srclabel =
>> /Users/shinsangho/freesurfer_subjects/fsaverage/label/lh.BA1_exvivo.label
>>
>> srcsubject = fsaverage
>>
>> trgsubject = NOR82_PJI
>>
>> trglabel = ./lh.BA1_exvivo.label
>>
>> regmethod = surface
>>
>>
>>
>> srchemi = lh
>>
>> trghemi = lh
>>
>> trgsurface = white
>>
>> srcsurfreg = sphere.reg
>>
>> trgsurfreg = sphere.reg
>>
>> usehash = 1
>>
>> Use ProjAbs = 0, 0
>>
>> Use ProjFrac = 0, 0
>>
>> DoPaint 0
>>
>>
>>
>> SUBJECTS_DIR /Users/shinsangho/freesurfer_subjects
>>
>> FREESURFER_HOME /Applications/freesurfer
>>
>> Loading source label.
>>
>> Found 4129 points in source label.
>>
>> MRISread(/Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white):
>> could not open file
>>
>> Starting surface-based mapping
>>
>> Reading source registration
>>
>> /Users/shinsangho/freesurfer_subjects/fsaverage/surf/lh.sphere.reg
>>
>> Rescaling ... original radius = 100
>>
>> Reading target surface
>>
>> * /Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white*
>>
>> *No such file or directory*
>>
>> *ERROR: could not read
>> /Users/shinsangho/freesurfer_subjects/NOR82_PJI/surf/lh.white*
>>
>> Darwin sinsanghoui-MBP 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23
>> 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64
>>
>>
>>
>> recon-all -s NOR82_PJI exited with ERRORS at Fri Oct 4 17:43:25 BST 2019
>>
>>
>>
>> For more details, see the log file
>> /Users/shinsangho/freesurfer_subjects/NOR82_PJI/scripts/recon-all.log
>>
>> To report a problem, see
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>> ==================================================
>>
>>
>>
>> Best wishes,
>>
>> Sangho
>>
>>
>> ?
>>
>> _______________________________________________
>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------
Message: 7
Date: Wed, 9 Oct 2019 13:14:56 +0000
From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
Subject: Re: [Freesurfer] [FSL] Hippocampus subregions question
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Jean Augustinack <jean@nmr.mgh.harvard.edu>
Message-ID: <0313ABA9-15E2-4A20-A187-0ADD2AEB77B8@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
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: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "briend, Frederic" <briend@cyceron.fr>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 8 October 2019 at 18:23
To: "freesurfer@nmr.mgh.harvard.edu" <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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Message: 8
Date: Wed, 9 Oct 2019 13:25:18 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer Digest, Vol 188, Issue 13
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BL0PR04MB4833AD296196C203424489498A950@BL0PR04MB4833.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
When you run mri_info on that file, what do you see?
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Juan Rivas <jcrn12@gmail.com>
Sent: Wednesday, October 9, 2019 8:36:48 AM
To: freesurfer@nmr.mgh.harvard.edu <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 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu<mailto:AYENDIKI@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
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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 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
And I gave this command: [shiraz:processing] (nmr-stable6-env) trac-all
-prep -c dmrirc-esq-15-hc
But there is an error:
INFO: SUBJECTS_DIR is
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing
INFO: Diffusion root is
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/stable6
trac-preproc -c
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/scripts/dmrirc.local
-log
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/scripts/trac-all.log
-cmd
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/scripts/trac-all.cmd
#-------------------------------------
/usr/local/freesurfer/stable6/bin/trac-preproc
#-------------------------------------
#@# Image corrections Tue Oct 8 17:53:12 EDT 2019
mri_convert --bvec-voxel
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/esq-15-hc/dmri/dwi_orig.nii.gz
niiRead(): error opening file
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from
/autofs/cluster/neuromod/rivas/imagenes/Diffusion_Processing/esq-15-hc/dwi.nii.gz...
Linux shiraz.nmr.mgh.harvard.edu<http://shiraz.nmr.mgh.harvard.edu/> 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov
29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Tue Oct 8 17:53:12 EDT 2019
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Message: 9
Date: Wed, 9 Oct 2019 09:38:33 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to measure the cortical thickness in
tumor patients?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.21.1910090937520.17053@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
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, ???
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
>
>
------------------------------
Message: 10
Date: Wed, 9 Oct 2019 15:05:15 +0000 (UTC)
From: Ezequiel Mikulan <emikulan@yahoo.com>
Subject: [Freesurfer] mri_convert no scaling
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <591132197.6144282.1570633515387@mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
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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Message: 11
Date: Wed, 9 Oct 2019 11:15:17 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_convert no scaling
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.21.1910091113320.17053@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="koi8-r"
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:
>
> ????????External Email - Use Caution????????
>
> 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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