Hi Jessica
in general if you specify .nii or .nii.gz as the extension of any output
file we will write it in nifti format. This makes using mri_convert easy:
mri_convert any_volume.mgz any_volume.nii.gz
should work fine
cheers
Bruce
On
Sun, 31 May 2020, Hua, Jessica wrote:
Exte
mri_convert aparc+aseg.mgz aparc+aseg.nii.gz
should do the trick
cheers
Bruce
On Sun, 31 May 2020, Hua, Jessica wrote:
External Email - Use Caution
Hi FreeSurfer experts,
I would like to convert my .mgz parcellation file to a .nii file to be used
in DTI analyses. How would
parcels? (compared to
norm.mgz)
Thanks,
Prad
On Fri, May 29, 2020 at 9:32 AM Bruce Fischl
wrote:
External Email
Hi Prad
for mri_cnr, yes, it samples inwards and outwards 1mm along the
surface
normal. And I think pctsurfcon is the tool I meant, but
hopefully David
it the pctsurfcon tool? (
https://surfer.nmr.mgh.harvard.edu/fswiki/pctsurfcon)
On Thu, May 28, 2020 at 10:12 AM Bruce Fischl
wrote:
External Email
David and Doug: can you point Prad in the right direction
for looking at
gray and white signal changes and ratios
Hi Marina
can you upload this subject? I'm not sure what is going on. Or send us the
recon-all.log?
The vertex error means that the surfaces don't match. This usually means
that you recreated some but not all of the surfaces for one of the hemis
cheers
Bruce
On Thu, 28 May 2020, Marina
to a page with information about this
stream or to a patch?
Thanks,
Prad
On Thu, May 28, 2020 at 9:46 AM Bruce Fischl
wrote:
External Email
I see. I think Doug has a more modern stream for this that David
Salat
has also used a lot
On Thu, 28 May 2020, Pradyumna
differences in
cortical measures were impacted by the CNR in each ROI.
Best,
Prad
On Thu, May 28, 2020 at 9:33 AM Bruce Fischl
wrote:
External Email
Hi Prad
what is your goal? What you describe below should work
cheers
Bruce
On Thu, 28 May 2020,
Pradyumna
mri_cnr to each label.
Best,
Prad
On Thu, May 28, 2020 at 9:14 AM Bruce Fischl
wrote:
External Email
Hi Prad
if you use the cortex.label is will avoid using the non-cortical
regions in
the surface, like the midline, so should be a more accurate
measure
Hi Prad
if you use the cortex.label is will avoid using the non-cortical regions in
the surface, like the midline, so should be a more accurate measure
cheers
Bruce
On Thu, 28 May 2020, Pradyumna Bharadwaj wrote:
External Email - Use Caution
Hi,
I had a question about th
have you also looked at the talairach transform to make sure it is
reasonable? And does the aseg segment the cc properly? That is, does it
label it as wm as it crosses from one hemi to the other?
On Thu, 28 May
2020, Marina Fernández wrote:
External Email - Use Caution
Hi Br
Hi Danny
yes, you can specify up to 100 labels. Make sure that the label name is
exactly as it appears in the parcellation though
cheers
Bruce
On Wed, 27 May 2020, Danny
Kim wrote:
External Email - Use Caution
Hi FreeSurfer experts,
I'm currently working on a brain with
Hi Marina
have you looked at the inputs to mri_fill? Does the aseg.auto_noCCseg.mgz
and the wm.mgz look ok?
Bruce
On Wed, 27 May 2020, Marina
Fernández wrote:
External Email - Use Caution
Dear Freesurfer experts,
When I run "recon-all -autorecon2-wm -subjid post_006" I
Hi Chris
if you specify -w on the command line it will write out a surface
every n iterations of the minimization (-n 1 will write out every step).
You can then write a script to turn those into tiffs with freeview
cheers
Bruce
On Thu,
21 May 2020, Chris Adamson wrote:
External
Sure, send us a .nii volume that fails and we will take a look
Bruce
> On May 19, 2020, at 11:38 PM, Safi Ullah . wrote:
>
>
> External Email - Use Caution
>
> Thank You Sir,
>
> Below is the header info of the volume, I read in Matlab.
> " srcbext: ''
> analyzehd
alle 21.30 Bruce Fischl <
fis...@nmr.mgh.harvard.edu> ha scritto:
Hi Stefano
--replaceonly takes two arguments - the label you want to replace and
the
one you want to replace it with
cheers
Bruce
On Sun, 17 May 2020, std...@virgilio.it wrote:
External Email - Use C
Hi Ken
have you identified why it is missing cortex? Is the wm dark-ish (<<110)
there? Did the skull stripping remove something? Was the wm.mgz/?h.orig
correct?
cheers
Bruce
On Mon, 18 May 2020,
KennethSPrice wrote:
External Email - Use Caution
Hello Freesurfer Experts!
By
visualizing
the output
by
freeview,
I found
that it
was the
same
of ThalamicNuclei.v10.T1.mgz.
Thanks
Il
11
maggio
2020
alle
2.19
Bruce
oh, then check out the bbregister help and see if you can get it working
On
Sun, 17 May 2020, Amar Shukla wrote:
External Email - Use Caution
yes
On Sun, May 17, 2020 at 8:54 PM Bruce Fischl
wrote:
sorry, I'm not sure I understand. bbregister will le
Can I register all the t2 types file with a Structural template,
cross-registration we can do or not?
On Mon, May 11, 2020 at 11:04 PM Douglas N. Greve
wrote:
It is probably more up-to-date to run
bbregister --help
On 5/9/2020 1:10 PM, Bruce Fischl wrote:
because it is a folder we distribute that doesn't change for each study.
You can certainly remove the link and cp -r it in from our distribution
if you prefer.
cheers
Bruce
On Sun, 17 May 2020, ZhangBo wrote:
External Email - Use Caution
Hi teams,
For recon-all in parallel,
Hi Bo
tkmedit and tksurfer have been deprecated for years. Try using freeview
instead.
cheers
Bruce
On Wed, 13 May 2020, ZhangBo wrote:
External Email - Use Caution
Hi teams,
After installing freesurfer-7.0.0 in MacOS 10.15.4, I followed the testing
guid in https://surfer.
Hi Ian
we don't register to an individual subject - we register to a
probabilistic atlas compiled from many subjects. The fsaverage subjects
were also generated from that data so they are in register, but the actual
atlas is a .tif file that you can find as the target of mris_register in
your
Hi Stefano
can you elaborate? Why do you suspect there is an error?
cheers
Bruce
On Mon, 11 May
2020, std...@virgilio.it wrote:
External Email - Use Caution
Please, could you check the command line.
I suspect that an error is there.
Thanks.
Stefano
mri_binarize --i Thalami
no, I wouldn't think so. YOu can try mris_topo_fixer instead if you want,
but really you need to diagnose what the cause of your problem is
On Sun, 10 May 2020, Billah, Tashrif wrote:
Hi Bruce,
Thanks for your prompt reply. I shall look at them as you noted. In the
meantime, putting in some m
what does the aseg look like? Why isn't the cerebllum being removed? Dura
is harder (unless you have a T2 or FLAIR)
On Sun, 10 May 2020, Billah,
Tashrif wrote:
Running the commands separately, I see the following log for some of the
defects. Is the weblink my cue?
CORRECTING DEFECT 0 (vertice
Hi Tashrif
it is most likely not a bug in mris_fix_topology, but rather a defect
that is too large to accurately correct. The topology correction
complexity is quadratic in the side of the largest defects, so small ones
are fast and big ones are super slow. In most cases the really big ones ar
PM Bruce Fischl
wrote:
Hi Amar
no restriction - all of those should be registerable using
Doug's
excellent bbregister tool
cheers
Bruce
On Sat, 9 May 2020, Amar Shukla wrote:
>
> External Email -
e DTI, sMRI, PET and many more or we can go for registration in
any combination in FREE Surfer.
regards
Amar Shukla
On Mon, Apr 13, 2020 at 8:14 PM Amar Shukla wrote:
Thank you so much sir
On Mon, 13 Apr 2020, 19:56 Bruce Fischl,
wrote:
yes, that should be doable if you process i
it looks to me like recon-all finished without a problem. Have you looked
at the outputs? Is there another reason you think there is an issue? There
are lots of internal "error" metrics we use to optimize things that are not
errors in the programatic sense - they are functionals we are
minimiz
can you send us the recon-all.log file (as a text file)?
On Thu, 7 May 2020,
jiahui wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I run the recon-all -all command:
this true error?how to resolve this problem?
ERROR: 245/300: dt: 0.9000, rms radial error=1
On Wed, May 6, 2020 at 10:12 AM Bruce Fischl
wrote:
Hi Qi
it is not obvious from that one image that something is wrong
there. What
does a saggital view look like with the cursor on that region?
Also, can
you send an image of the rh.inflated.nofix in 3D mode? Som
hemicode 0
talairach_flag 0
rescale 0.00
nvertices 163842
nfaces 327680
total_area 65416.984375
group_avg_surf_area 82219.960938
group_avg_vtxarea_loaded 1
avgvtxarea 0.399269
avgvtxdist 0.721953
stdvtxdist 0.195470
vtx0xyz -36.806278 -18.292723 64.461525
On 06/05/2020 15:23, Br
please don't send text files as images! We can't search them, etc...
The final distance error sis not a problem. Does recon-all stop? Please
send the recon-all.log as a text file
cheers
Bruce
On Tue,
5 May 2020, jiahui wrote:
External Email - Use Caution
Hello FreeSurfer
flag 0
rescale 0.00
nvertices 102020
nfaces 204036
total_area 65520.492188
group_avg_vtxarea_loaded 0
avgvtxarea 0.642232
avgvtxdist 0.940503
stdvtxdist 0.417776
vtx0xyz -8.576451 -101.319672 3.333434
On 06/05/2020 15:00, Bruce Fischl wrote:
can you run mris_info on the
Hi Qi
it is not obvious from that one image that something is wrong there. What
does a saggital view look like with the cursor on that region? Also, can
you send an image of the rh.inflated.nofix in 3D mode? Sometime XL
defects are fixable automatically, which may be the case for your
subject
n my commands?
I'll also take a look at mris_apply_reg.
On 05/05/2020 18:01, Douglas N. Greve wrote:
Don't specify a --trg_type. But add --tval-xyz
mris_apply_reg will do the same thing, but the interface might be a
little easier
On 5/5/2020 12:49 PM, Bruce Fischl wrote:
no
l and the lh/rh.white files? I only ask because my
surf2surf command outputs the exact output filename if the end
is ".white", but if it's ".pial" it outputs ".pial.w", which I
find a little curious.
Ian
On 05/05/2020 16:34, Bruce
n, lh.pial, rh.pial, lh.white, and rh.white) rather than values for
something such as thickness - is there an option for mri_surf2surf to allow
this?
On 05/05/2020 14:43, Bruce Fischl wrote:
Hi Ian
you can use mri_surf2surf to map surfaces between subjects, but
our atlas isn&
Hi Ian
you can use mri_surf2surf to map surfaces between subjects, but our atlas
isn't really a surface. You can use the surfaces in the fsaverage dir, but
they are meant for visualization and are much smoother than individuals
cheers
Bruce
On Tue, 5 May
2020, Ian wrote:
Extern
--
Message: 2
Date: Sun, 26 Apr 2020 12:04:36 -0400 (EDT)
From: Bruce Fischl
Subject: Re: [Freesurfer] exporting segmented mgz file
To: Freesurfer support list
Message-ID:
Content-Type: text/plain; charset="utf-8"
white matter. Are there any resources on how you would use control
points to remove intensity inhomogeneity?
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: S
Doug is saying that you should replace:
--out lh.pial_lgi
with
--out lh.pial_lgi.mgh
on your command line
cheers
Bruce
On Thu, 30 Apr 2020, 肖伏龙 wrote:
External Email - Use Caution
so how to get the pial_lgi.mgh from the pial_lgi file?
MailScanner has detected a possib
Hi Marina
which surface you use depends on why you are trying to find the vertices
cheers
Bruce
On Wed, 29 Apr 2020, Marina Fernández
wrote:
External Email - Use Caution
Hi Bruce,
Thank you very much for the information. It is very useful. I'm taking a
look at both possib
Hi Marina
what kind of function do you mean? There is c++ code that does this in the
file mrishash.cpp, but it is a bit complicated (you have to build a spatial
lookup table at a user-specified resolution, then use it in the vertex
finding code). Alternatively if you don't have to do this a lo
than remove regions that
aren't white matter. Are there any resources on how you would use control
points to remove intensity inhomogeneity?
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
From: freesurfer-boun...@nmr.mgh.harvard.edu
o
Hi Devavrat
freeview definitely does not modify the values in any volumes you load
for display.
cheers
Bruce
On Sun, 26 Apr 2020, Devavrat Vartak PhD wrote:
External Email - Use Caution
Hi freesurfer developers!,
I am using Freesurfer 6.0 and the latest (freeview -beta) t
Hi Atira
what was your mri_convert command line? Make sure to specify no scaling of
the intensity volume. Can you try adding:
-ns 1
to the mri_convert command line, and if that doesn't work send us the full
command line and full screen output from it? This is always a good thing to
do as it
Hi Victor
the best way to remove intensity inhomogeneities is with control points
usually. The wm.mgz gives us an initial estimate of the surface locations,
but we then deform it based on the intensities in the brain.mgz volume. So
if it looks like wm extends that far out in the brain your wm.
ume as 4000 mm3 after correcting for partial volume
effects. Would it be correct
to just scale the mesh volume to 4000 mm3?
Thanks again,
Jonah
On Fri, Apr 24, 2020 at 10:35 AM Bruce Fischl
wrote:
Hi Jonah
I'm not positive I understand, but I doubt partial volume effects are
s are probably isotropic so a uniform
scaling would leave the
geometry unchanged.
Best,
Jonah
On Thu, Apr 23, 2020 at 9:53 PM Bruce Fischl wrote:
HI Jonah
it depends how you compute volume. mris_volume for example will compute
the
volume of the interior without any partial v
h for the whole brain as well as individual segmentations.
Thanks again for your help,
Jonah
On Thu, Apr 23, 2020 at 5:50 PM Bruce Fischl wrote:
no, they are definitely not negligible. It depends on structure geometry,
but I bet for something like the hippocampus a large fraction of vox
e to get closed meshes for each
segmentation/parcellation.
Is there a way to do this in freesurfer?
On Thu, Apr 23, 2020 at 10:44 AM Bruce Fischl
wrote:
Hi Jonah
when we compute volumes we typically use a partial-volume model, which we
have found improves accuracy and repeatab
Hi Quentin
if you import it as a surface label you should be able to use morphological
operations to smooth it (open, close, dilate, erode)
cheers
Bruce
On Thu, 23 Apr 2020, Funk, Quentin wrote:
External Email - Use Caution
Freesurfer experts,
I have a volumetric ROI (in
you should be fine with the subject metrics we generate. Typically
thickness doesn't need much if any eTIV correction
On Thu, 23 Apr 2020,
Miguel Ángel Rivas Fernández wrote:
External Email - Use Caution
Dear Freesurfer experts,
We are interested in running external analysis
Hi Jonah
when we compute volumes we typically use a partial-volume model, which we
have found improves accuracy and repeatability. That may be the source of
your discrepancy
cheers
Bruce
On Wed, 22 Apr 2020, Peter, Jonah wrote:
Hello,
I'm trying to generate surface meshes for different brai
yes, careg is required. In general you should run things all the way to
the end of recon-all as the surfaces are used to improve the accuracy of
the aseg.
cheers
Bruce
On Sun, 19 Apr 2020, Ерохин Александр wrote:
External Email - Use Caution
Hello together,
Could you pleas
D
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU
E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628
On 17/04/2020, 15:11, "freesurfer-boun...@nmr.mgh.harvard.edu
Hi Mason
is your filtered_func file already sampled onto the surface or is it a
volume?
cheers
Bruce
On Fri, 17 Apr 2020, Mason Wells wrote:
External Email - Use Caution
Hi all,
I am trying to use an analysis package that works on surface based data
(SamSrf). I have ra
Hi Marina
can you include command line and full screen output (in text!) so we can
understand what you mean by "it doesn't work". Also, note that
.mgh/.nii.gz are volume formats, not surface ones, so you can't convert a
surface to them. You will need to use our surface format
cheers
Bruce
On
olume.
Could you please help me out?
Best Regards,
KC
On Sun, Apr 12, 2020 at 10:46 PM Bruce Fischl
wrote:
Hi Koustav
the current version of FS requires a T1-weighted input but could
also use
a T2 to improve accuracy and automaticity. Future versions will
relax
.
regards
Amar Shukla
On Mon, 13 Apr 2020, 19:09 Bruce Fischl, wrote:
Hi Amar
I'm not quite sure I understand your question, but in FS you
would use
the T1 as input to recon-all, then the outputs of that and the
diffusion
data would let you run tr
Hi Amar
I'm not quite sure I understand your question, but in FS you would use
the T1 as input to recon-all, then the outputs of that and the diffusion
data would let you run tracula
cheers
Bruce
On Mon, 13 Apr 2020, Amar Shukla wrote:
External Email - Use Caution
Hello Fr
Hi Javier
our atlas includes a broad range of ages and is intended to work across
the lifespan except for <=5 or so
cheers
Bruce
On Mon, 13 Apr 2020, javier quilis wrote:
External Email - Use Caution
Dear Freesurfer developers,
I'm interested in trying different possible
Hi Safi
have you tried loading the label file into freeview? You should be able
to type the ras coordinates from the label into the freeview info window
and it will go to that point (not that there are different types of ras
displayed by freeview
cheers
Bruce
On Mon, 13 Apr 2020, Safi
Ullah
On Sun, Apr 12, 2020 at 10:46 PM Bruce Fischl
wrote:
Hi Koustav
the current version of FS requires a T1-weighted input but could
also use
a T2 to improve accuracy and automaticity. Future versions will
relax
this constraint.
As for 2D/3D, you hav
Hi Koustav
the current version of FS requires a T1-weighted input but could also use
a T2 to improve accuracy and automaticity. Future versions will relax
this constraint.
As for 2D/3D, you have to distinguish the acquisition type (which almost
always should be a 3D sequence like an MP-RAGE
Hi David
did you check the skull stripping as suggested? Seems like the input
volume given to the CC finder was empty. Work backwards and find the
earliest volume where something is wrong
cheers
Bruce
On Fri, 10 Apr 2020, David
Schwantner wrote:
External Email - Use Caution
Hi Jason
looks like it is not finding your license file. Did you get one?
cheers
Bruce
On Tue, 7
Apr 2020, Ledesma, Jason wrote:
External Email - Use Caution
Hi,
I am receiving an error when performing recon-all. See attached for recon-all
log. Thanks.
Sincerely,
Ja
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
Hi Kim
are you really sure that you want to use analyze format? I doesn't keep
track of the direction cosines properly so once you go to it it is hard to
know left from right. SPM should be fine with nifti. In any case
conversion should be something like:
mri_convert file.mgz file.nii
or
without error. Thank you for your help!
Best,
Lily
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
Bruce Fischl
Sent: Monday, March 30, 2020 5:27 PM
To: Freesurfer support list
Subject
Hi Adam
if you are using freeview to display a colormap you can just click the
colorbar button in the top row near the middle to toggle it on/off
cheers
Bruce
On Wed, 1 Apr 2020, Adam Rytina wrote:
External Email - Use Caution
Hello all,
I did the post-processing on brain
ps aux | grep recon-all
To get the pid, then
kill -9 pid
Or
killall recon-all
If it is the only one running on that box
Cheers
Bruce
> On Mar 31, 2020, at 10:10 PM, Octavian Lie wrote:
>
>
> External Email - Use Caution
>
> Dear All,
>
> Is there a way to kill a rec
Hi Xiaojiang
do you have multiple cores? If so, you can use -openmp 4 or something to
reduce the recon time even on your linux box
cheers
Bruce
On Tue, 31 Mar 2020, Xiaojiang
Yang wrote:
External Email - Use Caution
Freesurfer experts:
I know in my powerful Linux machin
Hi Lily
that looks ok I think, although it's hard to tell for sure. The
cerebellum shouldn't be included in the surface. Are you sure you have
enough ram on your machine? It looked like half of it was in use when you
ran recon-all. If you want you can tar and gzip the whole subject dir and
ft
Hi Niels
I don't see why not. vol2surf takes the surface location and the surface
normal and sampled from the volume onto the surface using those two pieces
of local information. Global surface topology shouldn't matter
cheers
Bruce
On Sun,
29 Mar 2020, Niels Janssen . wrote:
Ext
Hi VP
you need to give us more information! What is going wrong? What kind of
system are you installing/running on? Send us the commands you are running
and their output including any error messages.
cheers
Bruce
On Sat, 28 Mar 2020, Parisi Veronica
wrote:
External Email - Use
Hi Devika
the volumes should be in the stats/aseg.stats file for each subject.
cheers
Bruce
On Thu,
26 Mar 2020, Devika K wrote:
External Email - Use Caution
Hi,
I want to extract hippocampal volume from longitudinal samples. I am less
aware of it. I ran recon-all-all with
), Yr Ysgol
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU
E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628
On 25/03/2020, 17:29, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce
Fischl" wrote:
Hi Mason
I can
this is explained? I want to
detail this in my paper and I would like to refer to the source.
Thanks again,
Javier
De: freesurfer-boun...@nmr.mgh.harvard.edu
en nombre de Bruce Fischl
Enviado: miércoles, 25 de mar
"freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce
Fischl" wrote:
something like
freeview -v $SUBJECTS_DIR//mri/norm.mgz \
-f $SUBJECTS_DIR//surf/?h.white
cheers
Bruce
On Wed, 25 Mar 2020, Mason Wells wrote:
>
dd
Heol Maindy
Caerdydd
CF24 4HQ
DU
E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628
On 25/03/2020, 16:11, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce
Fischl" wrote:
Hi Mason
can you confirm that things look ok within FreeSurfer if you look at the
su
Hi Mason
can you confirm that things look ok within FreeSurfer if you look at the
surface over the volume in freeview?
cheers
Bruce
On Wed, 25 Mar 2020, Mason Wells wrote:
External Email - Use Caution
Hello Freesurfer developers,
I am using Freesurfer and SamSrf for prf
Hi Javier
no, that's not correct, depending on which training set you mean. For the
Bayesian segmentation (aseg) we used 40 datasets distributed in age and
pathology (10 each for young, middle age, elderly and AD).
cheers
Bruce
On Wed, 25 Mar
2020, javier quilis wrote:
External E
Hi Harriet
it's tough to diagnose from just this, but that is pretty bad! Can you give
us some details about the editing? Or tar/gzip the whole subject dir and
upload it and we will take a look
cheers
Bruce
On Tue, 24 Mar 2020, Harriet Cornwell
wrote:
External Email - Use Cautio
Hi Renew
please have patience. We are all dealing with a lot. Transitioning to
working at home and trying to figure out how to be productive and such.
cheers
Bruce
On Tue, 17 Mar 2020, Renew Andrade wrote:
External Email - Use Caution
Dear Yendiki Anastasia:
I am replying for seco
Hi Ricky
how did you try to load the defect_labels? The end of the recon-all.log
file lists a defect with 26K vertices, which is probably too big to fix
(it's about 1/5 of a normal surface). You should be able to visualize it
by loading the lh.defect_labels file as an overlay on the
lh.inflat
Hi Bo
looks like you are running out of memory, no?
cheers
Bruce
On Fri, 13 Mar 2020, ZhangBo
wrote:
External Email - Use Caution
Hi team,
I encountered an error when running the test "Candal" dataset.
For some patients' files, I found the error information in the log file.
Hi Fraser
if you look at the mris_register help there is an option to specify a
manual label that corresponds to an atlas parcel:
-L
Specify a manual label to align with atlas label
in the past I have used this to draw a central sulcus and force it to align
using the
Hi Frank
sorry, I've been busy with local deadlines that are over now. Can you send
us the recon-all.log file? Or tar and gzip the entire subject dir and
upload it to our ftp site? Apologies if any of this has been done.
cheers
Bruce
On Thu, 12 Mar 2020, Frank Chau wrote:
External
I don't think our memory requirements change dramatically on a
per-subject basis. The one exception might be topology fixing, but if it
requires that much ram there are probably to many (or too large) defects to
succeed in any case.
cheers
Bruce
On Thu, 5 Mar 2020, Ian wrote:
Exte
sure, as long as you have more than one core. You can run them in the same
terminal as long as you put & at the end of the line
On Thu, 5 Mar 2020, ZhangBo wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
My computer doesn't support cuda. To speed up data proc
Hi Doro
it's hard to tell from your image, but it looks like at least one of your
cps is not in wm but in the gm. This will mess everything up. Make sure
that they are in unpartial-volumed wm
cheers
Bruce
On Tue, 3 Mar 2020, Meike Hettwer
wrote:
>External Email - Use Caution
>
> Dear
no cerebellum) but also mesial temporal structures
> hippocampus/amygdala etc; is there such a mask in the recon pipeline,
> or it has to be constructed?
> Thank you,
> OL
>
> On Sun, Feb 23, 2020 at 8:51 PM Bruce Fischl
> wrote:
>>
>> Hi Octavian
>>
>>
Hi Dylan
I think you could probably do a recon without topology fixing although of
course the spherical mapping will then be multi-valued. It will take a bit
of hacking at recon-all to get it to work though as it is not a use-case
that we explicitly support.
cheers
Bruce
On Thu, 27 Feb 2020
Where should I look to get all these files?
The idea to check them is to confirm that the MRI went wrong at some point,
right?
Thanks,
Gabriel Tapia
www.Partage3D.fr
+33 6 62 90 11 67
Le mar. 25 févr. 2020 à 04:09, Bruce Fischl a
écrit :
Hi Gabriel,
that is a huge defect and generally
Hi Gabriel,
that is a huge defect and generally means something major has gone wrong.
Look at the lh or rh.orig.nofix and the corresponding ?h.inflated.nofix
over the wm.mgz file to see what is wrong (usually something like a big
chunk of skull is left over and connected to the surface, someti
Hi Kate
the .lta format is for a linear registration (in ascii). YOu can just cat
it to see the contents - it is not a PET image (which will be stored in
.mgz or .nii). mri_convert or mri_vol2vol can be used to apply the
registration and/or change the output format (if you specify file.nii or
Hi Octavian
1. Not sure - you should try them. If you have reasonable surfaces I
think bbreg lets you specify masks to ignore, which should be giant help
in this scenario. On the other hand, mri_robust_register does this
automatically. They are both relatively fast so why not try and see?
2. S
Hi Emalie
tksurfer and tkmedit have been deprecated for a long time. Can you try
using freeview instead?
cheers
Bruce
On Fri, 21 Feb 2020, Emalie McMahon wrote:
External Email - Use Caution
Hello,
I get an error (see below) when opening tksurfer and tkmedit. Is there
anywa
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