lRMFC.masked.nii
On Tue, Jul 2, 2019 at 4:14 PM Bruce Fischl wrote:
what are you attempting to open it with? YOu didn't include that command
line
On Tue, 2 Jul 2019, Azeez, Azeezat wrote:
>
> External Email - Use Caution
>
;Talairach View' [#1]
*+ WARNING: Forced switch from 'Talairach View' to 'Original View' [#2]
On Tue, Jul 2, 2019 at 3:26 PM Bruce Fischl wrote:
Hi Azeezat
you need to give us more information than this. Did you try:
mri_convert file.mgh file.nii
Hi Azeezat
you need to give us more information than this. Did you try:
mri_convert file.mgh file.nii
did that give you an error? Where did the process fail? We need full screen
output of what you ran and what failed (in text format please, not as a
snapshot)
cheers
Bruce
On Tue, 2 Jul
2
Hi Kayti
that's pretty hard to say. Even a few ms of TE for example can make a
pretty big differeence in e.g. avoiding dura. In general of course we try
to fix the acquisition parameters and at the very least balance your
populations across different scan types. Can you give us more details or
, Bruce Fischl
wrote:
Hi Ryan
I'm not sure why you would have a surface with 73K vertices on fsaverage. Why
not use one of
the ico representations (40K or 160K vertices)? In any case, mri_surf2surf
should do the
trick, although you will probably need to create a new subject with a set of
Hi Ryan
I'm not sure why you would have a surface with 73K vertices on fsaverage.
Why not use one of the ico representations (40K or 160K vertices)? In any
case, mri_surf2surf should do the trick, although you will probably need to
create a new subject with a set of 73K vertex surfaces
cheer
gh.harvard.edu
on behalf of
Bruce Fischl
Sent: 27 June 2019 15:38
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all multiple subjects 'for' loop?
Hi Benjamin
you can run them all in the same terminal by backgrounding them (adding
the & character at the end of the
Hi Victor
yes, the old names are deprecated - the _exvivo ones are the newest ones to
use
cheers
Bruce
On Thu, 27 Jun 2019, Zeng,Victor (BIDMC - Psychiatry) wrote:
Hi All,
I'm revisiting an old dataset that was previously run using FS 5.1, and now we
upgraded it to FS
6.0. I seem to not
-nan, c_a
=
> >>> -nan
> >>> : x_s = -nan, y_s = -nan, z_s = -nan, c_s
=
> >>> -nan
> >>>
> >>> talairach xfm :
> >>> Orientation : III
> >>> Primary Slice Direction:
Hi Benjamin
you can run them all in the same terminal by backgrounding them (adding
the & character at the end of the command line)
cheers
Bruce
On Thu, 27 Jun 2019,
Benjamin Stott wrote:
External Email - Use Caution
Hello,
I would like to run recon-all on multiple subj
Hi Miguel
depending on the lesions it may not be fixable (since they may change the
topology of the cortex). If you upload the subject we will take a look, or
you can try manually filling in the lesion in the wm.mgz (or marking it as
lesion in the aseg.mgz) and seeing if that helps
cheers
Br
well, we don't run only those steps to generate any volume. Probably your
best bet would be the norm.mgz, although as Doug says it will have a
cerebellum in it, which you can strip with the aseg.mgz
cheers
Bruce
On Sun, 23 Jun 2019, ping cao wrote:
External Email - Use Caution
mri_vol2label should do the trick
cheers
Bruce
On Sat, 22 Jun 2019, Sam W. wrote:
External Email - Use Caution
Hello,
I'm trying to create label files of the aparc+aseg ROIs but cannot find the
aseg annotations. The
?h.aparc.annot does not contain subcortical regions that ex
ld get the
proper output using elastix?
On Fri, Jun 21, 2019 at 1:01 PM Shrabani Ghosh wrote:
Okay Thank You for your all the responses.
On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl
wrote:
Hi Shrabani
you can read about FS on our wiki. We generally require a T1-weighted MRI
:
External Email - Use Caution
So in which case, freesurfer is applicable. Because I got a suggestion for CT
to CT registration, I
can use freesurfer.
Thanks
On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl
wrote:
Hi Shrabani
no, that's not really what I'm
the two volumes so that the model
will warp on to the
patient data perfectly.
regards
Shrabani Ghosh
On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl
wrote:
not unless you also have an image of the whole brain. Even then I'm not
sure it will do what you want, although I'm s
mail - Use Caution
These are skull images of axial representation. Can't I use freesurfer? Because
here interpolation
is important.
On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl
wrote:
Hi Shrabani
I'm not even sure what these are images of. If you are looking for
their size. the smaller one is the moving image and
the bigger one is the
fixed image.
On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl
wrote:
what kinds of volumes are they and why are you registering them?
cheers
Bruce
On Thu, 20
Jun 2019, Shrabani Ghosh
---
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0"
Any idea of what could be wrong in my process?
Thanks
Sincerely,
Loïc
Le jeu. 20 ju
coordinates of CC and its
subregions. I tried using
the command mri_vol2label for cc subregions also. But still I am getting the
error message: found no
voxels matching id 251.
What is the right command to get the coordinates of CC?
Thanks in advance.
Sadia
On Thu, Jun 20, 2019 at 11:08 PM Bruce Fischl
process 0"
Any idea of what could be wrong in my process?
Thanks
Sincerely,
Loïc
Le jeu. 20 juin 2019 à 19:39, Bruce Fischl a écrit
:
Hi Loïc
the .mgz file should having dimensions nvertices x 1 x 1 for freeview to
know it is a surface overlay I believe
che
what kinds of volumes are they and why are you registering them?
cheers
Bruce
On Thu, 20
Jun 2019, Shrabani Ghosh wrote:
External Email - Use Caution
Hi freesurfer,
I want to do registration on two image volumes nifti file. What are the
commands I have to use to do
the regis
if you have multiple cores you can use -openmp which gives a pretty
good speed increase up to about N=4 or 5
cheers
Bruce
On Thu, 20 Jun 2019, Shrabani Ghosh
wrote:
External Email - Use Caution
Thank You. It's working now. But I can see the execution time is really slow.
Hi David
what does the aseg look like in those cases? That is, is it the
hippo/amygdala stuff failing or is the root cause further back in the
stream (something that caused a bad aseg)
cheers
Bruce
On Thu, 20 Jun 2019, David S Lee
wrote:
External Email - Use Caution
Hell
hink it's been this
way
> > for quite a while now. Maybe someone else knows better?
> >
> > The website is at http://www.math.mcgill.ca/keith/surfstat/ and it
says
> > 'Updated 26 September 2008'. I'm not sure whet
Hi Sadia
we subdivide the cc into multiple components:
251 CC_Posterior0 0 64 0
252 CC_Mid_Posterior0 0 112 0
253 CC_Central 0 0 160 0
254 CC_Mid_Anterior 0 0 208 0
255 CC_An
Hi Vale
do you want to tar, gzip and ftp us that entire subject dir so we can
take a look?
cheers
Bruce
On Wed, 19 Jun 2019, Barletta, Valeria wrote:
Dear Freesurfers,
I am having issues with a reconstruction which is giving me giant defects that
I cannot correct (see
screenshots).
I tri
hmmm, that is strange. Can you tar and gzip the entire subject dir then
upload it to our ftp site?
On Mon, 17 Jun 2019, Iglesias Gonzalez, Eugenio
wrote:
External Email - Use Caution
OK yes this is a problem with the main recon-all stream. It’d have been a
miracle for the
qdec processing, what file format should be selected to
load freeview?
best wish
Abby
Bruce Fischl 于2019年6月5日周三 下午9:53写道：
Hi Abby
have you tried using freeview? It is a lot more flexible than qdec and
supports a bunch of different color maps
cheers
Bruce
On
Hi Jiachen
does the fsaverage dir exist? It should be symlinked from you
$SUBJECTS_DIR to $FREESUFER_HOME/subjects/fsaverage.
cheers
Bruce
On Sun, 16 Jun 2019, chen wrote:
External Email - Use Caution
Dear All,
I ran recon-all using single MPRAGE data set, but batching ex
I re-launch "recon-all -all" to fix that problem with lh.curv?
Thank you,
Vale
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
Bruce Fischl
Sent: Friday, June 14, 2019 12:0
Hi Vale
that typically means that recon-all was rerun and not completed. WHen you
say autorecon2-wm is not working what do you mean?
cheers
BruceOn Fri, 14 Jun 2019,
Barletta, Valeria wrote:
Dear Freesurfers,
I am getting this type of error in the Terminal when I open my images on
Freesur
Hi Ritesh
do you know how those .mgz files were generated? It looks like they were
created using a buggy version. You can try setting:
setenv FS_SKIP_TAGS 1
then rerunning mri_convert and see if that works
cheers
Bruce
On Thu, 13 Jun 2019, Ritesh Mahajan
wrote:
External Email
mer 5 giu 2019 alle ore 18:45 Bruce Fischl
ha scritto:
Hi Francesca
what analysis do you want to run?
cheers
Bruce
On Wed, 5 Jun 2019, Francesca Pentimalli
wrote:
>
> External Email - Use Caution
>
> Dea
some way to achieve this?
RegardsRaunak Swarnkar
Visiting Student Researcher - Summer 2019
Dept. of Mathematics & Statisitcs, uOttawa
MSc Cognitive Science Student, IIT Gandhinagar
On Thu, Jun 6, 2019 at 1:40 PM Bruce Fischl wrote:
Hi Raunak
this page should have the info you
Hi Joerg
can you give us more information than that? Why do you say it is not
possible? It should be
cheers
Bruce
On Mon, 10 Jun 2019, Pfannmoeller, Joerg Peter wrote:
> Hello,
>
> I always used mri_compute_volume_fractions to compute the volume fractions
> in my GE-EPI images (percentage of g
Hi Takashi
what do you mean by " I cannot overlay this mgh file on the lh.inflated"?
Do you get an error message?
Bruce
On Sat, 8 Jun 2019, Yamada, Takashi wrote:
External Email - Use Caution
Hi there,
I try to transform from volume-based ROI mask (nifty file) to suface-base
Hi Jiachen
I think mri_segstats includes the mean (and std) of the intensity within
a structure so you could run it on the orig.mgz and norm.mgz. Doug knows
more about this, but he is off at HBM, which will slow his response time.
cheers
Bruce
On Sat, 8 Jun
2019, chen wrote:
Ex
evelopment
version?
3)Are then any plans to use the FLAIR for multi-modal segmentation in order
to refine the segmentation of the Pallidium and Putamen, and to possibly
segment structures such as the substantia nigra and red nucleus?
Thanks,
Richard
Date: Tue, 4 Jun 2019 12:41:5
Hi Marina
not with our default tools. Koen (ccd) has something that will generate
this, but it is not run by default.
cheers
Bruce
On Thu, 6 Jun 2019, Marina Fernández wrote:
External Email - Use Caution
Dear Freesurfer experts,
Is there any way to obtain a CSF mask in Fr
Hi Raunak
this page should have the info you need:
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
cheers
Bruce
On Thu, 6 Jun
2019, Raunak Swarnkar
wrote:
External Email - Use Caution
Hi
I am using freesurfer to extract just the cortical surface mesh. Next, I
it should be the same I would think
cheers
Bruce
On Thu, 6 Jun 2019, Maedeh Khalilian
wrote:
External Email - Use Caution
Dear Bruce,
Thank u very much for replying. sorry I'm still a little bit doubtful, just as
a confirmation: by
repeatable you mean I can repeat it and ev
Hi Maedeh
I think it divides along the maximum variance eigen-axis, so should be
repeatable.
cheers
Bruce
On Thu, 6 Jun 2019, Maedeh Khalilian wrote:
External Email - Use Caution
Dear experts,
I use the file "lh/rh.aparc.annot" and a splitfile as the inputs of the command
"
Hi Francesca
what analysis do you want to run?
cheers
Bruce
On Wed, 5 Jun 2019, Francesca Pentimalli
wrote:
External Email - Use Caution
Dear Freesurfer experts,
I am trying to create a mask and run the analysis into it considering just the
following anatomical
regions:
anked in a surface,
could I found the index-vector of all the vertices in the circle mask centred
the peak vertex? If
circle is not applicable, how about square?
Best regards,
Lizhi
On Wed, 5 Jun 2019 at 11:51, Bruce Fischl wrote:
Hi Lizhi
the easiest way to approximate this
Hi Lizhi
the easiest way to approximate this is to generate a label that is just
the peak vertex, then use the label editing tools in the current dev
version of freeview to dilate it 4-5 times.
cheers
Bruce
On Wed, 5 Jun 2019, Zhi Li
wrote:
External Email - Use Caution
Hi Abby
have you tried using freeview? It is a lot more flexible than qdec and
supports a bunch of different color maps
cheers
Bruce
On Wed, 5 Jun 2019, Abby tang wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to get some pictures about my
Hi Aaron
yes, it helps in other situations like blood vessels
cheers
Bruce
On Tue, 4 Jun 2019,
Aaron Tanenbaum wrote:
External Email - Use Caution
I am not too sure if I have asked you this question before. I know the use
of a flair or T2 helps with dealing with the dura. I
Hi Jiachen
the field inhomogeneity can't really be estimated with only one structure
since it is a function of space. You could check the ratio of amygdala in
intensity in the orig.mgz with other gray matter that is far away (e.g.
motor cortex or calcarine), but there may be scaling difference
. Isn't there any
alternative to manually correction for this cases?
Best regards,
Maria
El mié., 29 may. 2019 a las 15:39, Bruce Fischl
() escribió:
Hi Maria
yes, potentially. What acqusitions do you have? Do you have a
highres T2?
You can erase the bright dura th
Hi Maria
yes, potentially. What acqusitions do you have? Do you have a highres T2?
You can erase the bright dura that is causing this effect manually if not
cheers
Bruce
On
Wed, 29 May 2019, María Martínez Rodrigo wrote:
External Email - Use Caution
Dear all,
Some of my i
could use mri_surf2surf to map the
individual fMRI to t
he template? Am I doing the right thing? And when and how should I do the
downsample?
Really sorry for not clearly described my question in last mail! Still looking forward to hear
your reply, thank you!
Best wishes,
Jingyue Zhang
Br
Hi Jingyue
can you explain what your goal is in a bit more detail? My guess is you
can use the existing atlas/template and not create a new one.
As for the gifti conversion, I think mris_convert can handle it
cheers
Bruce
On Tue, 28
May
2019, Jingyue Zhang wrote:
External Email
.
I uninstalled version 5.3.0, and installed 6.0.0, it worked. I finished the
whole recon-all step
without errors.
Thank you so much.
Regards,
Qiannan
On Thu, May 16, 2019 at 9:09 PM Bruce Fischl wrote:
can you give us more details (command line, screen output, recon-all.log
file)?
16:15, Bruce Fischl a écrit :
sure. All the fsaverages are in the same space (they are subsets of
fsaverage)
On Mon, 20 May 2019, Loïc Daumail wrote:
>
> External Email - Use Caution
>
> Hi Bruce,
>
> Thanks f
do you mean of one of the surfaces derived from the image? If so, you can
use mris_euler_numer or mris_info
cheers
Bruce
On Wed, 22 May 2019, Sam W. wrote:
External Email - Use Caution
Hi,
How can I check how many vertices an image of my subject has?
Best regards,
Sam
,
Sincerely,
Loïc
Le lun. 20 mai 2019 à 15:52, Bruce Fischl a écrit :
Hi Loic
if you are on the fsaverage surface you can save the -log10(p) values
using save_mgh.m, then load them in freeview and threshold them or
whatever
cheers
Bruce
On Mon, 20 May
Hi Victor
the lh.white.{KH} are generated from the lh.white file, so I don't think
it can have skipped creating it. Was it deleted? Can you double check?
Bruce
On
Mon, 20 May 2019, Zeng,Victor (BIDMC - Psychiatry) wrote:
Hi all,
I am running 7T scans through FS6, and I have been recomme
at, 17 Mei 2019 21.14.44 WIB, Bruce Fischl
menulis:
Hi Mustafa
1. Your mprage ran through recon-all fine and the results look good. The
saggital field of view is tight, so make sure that they don't crop brain in
that direction.
2. Your recon-all command line is incorrect. You should point t
Hi Loic
if you are on the fsaverage surface you can save the -log10(p) values
using save_mgh.m, then load them in freeview and threshold them or
whatever
cheers
Bruce
On Mon, 20 May 2019, Loïc Daumail wrote:
External Email - Use Caution
Also, one more thing:
My data is on
Hi Amanda
for a surface overlay M is irrelevant (it is a vox2ras or ras2vox matrix,
can't remember what). Just give it eye(4). If you are in fsaverage coords
I believe it is already in MNI space. If you want to convert to a volume
you can use mri_surf2vol
cheers
Bruce
On Sun, 19 May 2019, Wo
ll. Please
have a look. What about the previous dicom that I have sent to you? Please
share some thoughts.Thank
you very much.
Yours faithfully,
Mustafa
Pada Kamis, 16 Mei 2019 20.18.35 WIB, Bruce Fischl
menulis:
Hi Mustafa
can you give us some detials? What didn't work? Can you s
Hi Konrad
sorry, I never really packaged this up nicely. Currently it is embedded in
the mris_thickness binary, and you run it by using:
mris_thickness -variational -w 0
this will write out two files:
?h.normals.init.mgz
?h.normals.mgz
the first is the initial vector field along the pial-
oing it in Indonesia.
>
> Many thanks!
>
>
> Mustafa M. Amin
> Consultant Psychiatrist in Biological Psychiatry
> Department of Psychiatry
> Faculty of Medicine
> Universitas Sumatera Utara
>
>> On 2 Apr 2019, at 20.49, Bruce Fischl wrote:
>>
>>
can you give us more details (command line, screen output, recon-all.log
file)?
On Thu, 16 May 2019, jennifer sorinas wrote:
External Email - Use Caution
Dear Qiannan,
I’m having the same problems, recon-all -all command is not working.
FreeSurfer Developers help please! ?
Hi Jennifer
try
mri_convert -it nifti1 input.img output.nii.gz
you might not need the "-it nifti1"
are you sure it's a nifti and not analyze? You need to be careful you have
the correct direction cosines to make sure you know which is left and which
is right. Definitely bring it up in free
compared to those without the heterotopia.
Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging
On May 15, 2019, at 3:10 PM, Bruce Fischl
wrote:
Hi Ryan
I don't think projection of that kind of ROI is
Hi Ryan
I don't think projection of that kind of ROI is well-posed. Different
parts of it are probably closest to wildly different parts of cortex. What
are you trying to acheive?
cheers
Bruce
On
Wed, 15 May 2019, Nillo, Ryan Michael R wrote:
External Email - Use Caution
temporal). Since our results showed the association between morphometric
measures of MPFC and
behavior (XYZ), therefore, our findings are not due to geometric distortion."
I am not expert in this field, so I would really appreciate any further help.
Thanks.
On Tue, May 14, 2019 at 7:13 AM Bruce
Hi Tim
not sure about area (Doug might have something), but for curvature you
can do:
mris_curvature -w lh.area.midgray
this will create mean (*.H) and Gaussian (*.K) curvature files. You might
add a bit of smoothing with e.g. -a 5, which is what we do by default when
we create the [lr]h.cu
the gradient nonlinearities have almost no effect on thickness. Since they
are spatially smooth they warp both the white and pial surfaces similarly,
so the distance between them doesn't change much.
B0 effects can be large locally depending on your field strength and
bandwidth. These are prett
dates on it.
Thanks
Mona
___
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of
Bruce Fischl
Sent: Friday, May 10, 2019 6:15:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] sp
Hi Alberto
yes, you should be able to. Do you have the individual datasets or some
type of average?
cheers
Bruce
On Mon, 13 May 2019, albertotricker wrote:
>External Email - Use Caution
>
> Hello FreeSurfer technical staff
>
> I hava a data set provided by ADNI initiative, which is fo
hshid
From: Bruce Fischl
To: Mahshid Fouladivanda
Cc: "freesurfer@nmr.mgh.harvard.edu" ,
dgr...@mgh.harvard.edu
Date: Sat, 11 May 2019 14:47:48 -0400 (EDT)
Subject: Re: [Freesurfer] A Question about How to Map Parcels of the Cortex
on the surface of
the Brain Cortex
Hi Mashid
We
surf to map
them (as a "segmentation") onto the surface, then use mris_seg2annot to create
an annotation file.
Run either with --help to get docs and examples
On 5/10/2019 2:26 PM, Bruce Fischl wrote:
Hi Mahsid
matlab is probably the easiest way, but without knowing what format you have
the
Hi Emma
in principle of volume is proportional to ICV you would need to scale the
thickness by (ICV)^(1/3). In practice we find that scaling the thickness
doesn't really change the variance and loses you a DOF so we don't usually
do it.
cheers
Bruce
On Sat, 11 May 2019, Bunting, Emma wrote
Hi Emma
the surfaces are aligned to fsaverage space, which can be extended into the
volume using Lilla's CVS tool. Can you give us more details about what you
mean about the Desikan-Killany atlas not aligning properly? You shouldn't
look at it directly - you should look at the ?h.aparc.annot.
Hi Mahsid,
you can use mri_mc or mri_tessellate to create a mesh for them using the
aseg as input if you want. The cerebellum in particularly will have a
seriously incorrect topology as we can't see the majority of the folia at
in vivo resolutions.
cheers
Bruce
On Sat, 11 May 2019, Mahshid
Hi Chen
sorry, I don't really understand your question. If you have a single
mprage here is no motion correction to be done. If you mean within-scan
motion you could look at the noise in an ROI outside the head, but we don't
typically quantify this. What difference between ROIs are you looking
I don't think it currently works in 3D mode as it is not trivial due to
perspective transforms. Ruopeng is trying some things
On Fri, 10 May 2019,
Greve, Douglas N.,Ph.D. wrote:
here is a pick of it
https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif
On 5/10/2019 3:40 PM, Nasiri
Hi Mahsid
matlab is probably the easiest way, but without knowing what format you
have them in it isn't easy for us to say. In matlab you can use
write_annotation or write_ascii_curv or something to get it into a format
we can handle
cheers
Bruce
cheers
Bruce
On Fri, 10 May 2019, mahshid
On May 8, 2019, at 11:46 AM, Bruce Fischl
wrote:
Hi Dengyu
if you want to upload volumes use our ftp server
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
cheers
Bruce
On Wed, 8 May 2019, Dengyu Wang wrote:
External Email - Use Caution
Hi Bruce,
My
future.
Here are the wm.mgz, lh.orig.nofix and rh.orig.nofix
I tried to open in Freeview but Freeview always collapsed.
Best,
Dengyu
On May 8, 2019, at 10:45 AM, Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Dengyu
I meant images of the brain. In general don't send u
ge without contrast, but in this special case
we only have t1 with contrast. Do you have any ideas about this problem? Thank
you!
Best,
Dengyu
On May 7, 2019, at 4:37 PM, Bruce Fischl wrote:
Hi Dengyu
you need to tell us what went wrong. We have reconned lots of brains with
contrast, although
Hi Dengyu
you need to tell us what went wrong. We have reconned lots of brains with
contrast, although sometimes the skull stripping needs to be played with to
get it to work
cheers
Bruce
On Tue, 7 May 2019,
Dengyu Wang wrote:
External Email - Use Caution
Hello FreeSurfer develo
Hi Marina
it looks like there is something connected to the wm posteriorly, but
impossible to tell from the inflated surface what it is. If you tar and
gzip the entire subject dir and put it on our ftp site someone here will
take a look
cheers
Bruce
On Tue, 7 May 2019, Marina Fernández wrote
can you send us the recon-all.log file?
On Fri, 3 May 2019, 王梦星 wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attampting to do a structural MRI analysis with the command "recon-all
-i sub102.nii.gz -s bert -all", as described in the FreeSurfer Download
Hi Darinka
what is fieldtrip? I don't think it is anything of ours. What happens if
you call read_surf directly?
cheers
Bruce
On Wed, 1 May 2019, Darinka Trübutschek wrote:
External Email - Use Caution
Dear freesurfer community,
I am currently trying to import cortical su
Hi Anna
can you send us some images of upload a subject so we can see what you
mean?
cheers
Bruce
On Thu, 2 May 2019, Mun, Anna wrote:
Hi Freesurfer team,
I have a question about segmentation. I am working with scans of patients with
Down syndrome and the
segmentation (aseg.presurf.mgz a
Hi Ebru
are you sure yo uare loading a label and not a color lut? What is the name
of the file you are trying to load?
cheers
Bruce
On Thu, 2 May 2019, Ebru Ayyürek wrote:
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Hi FreeSurfer Developers,
I'm attempting to perform a freeview visual
Hi Reetta-Liina
we only compute the Euler number for surface meshes, which in this
case means only for cortex.
cheers
Bruce
On Fri, 26 Apr 2019, Reetta-Liina Armio wrote:
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> Dear Freesurfer experts!
>
> I have run the hippocampus segmentation with FS 6 (st
Hi Marina
there is a tutorial on fixing defects you can look at here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview?highlight=%28tutorial%29%7C%28topology%29
I find the best way to do this is to load the lh.orig.nofix and
lh.inflated.nofix (or the rh), then lo
Hi René
our volume calculation corrects for partial volume effects, so it does
more than just counting voxels.
cheers
Bruce
On Thu, 25 Apr
2019, Schranzer René wrote:
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Hello FreeSurfer Developers,
I was wondering about the volume calculation
hmmm, how long did you let it run? I've never seen this before. Can you
upload your subject to our ftp site?
cheers
Bruce
On Wed, 24 Apr 2019, 1013364183 wrote:
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Dear freesurfer
We run the recon-all command of freesurfer, but when it runs to the
Hi Ani
can you send us the recon-all.log file and your full command line?
thanks
Bruce
On Tue,
23 Apr 2019, Anik Dar wrote:
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Hello All,
I am running recon-all highres on 10 7T MP2RAGE datasets that has been skull
striped and in two
subjects, I
ll me how to get rid of this?
I have attached a picture FYI.
Best regards,
Ruwan
On Mon, Apr 22, 2019 at 11:10 AM Bruce Fischl
wrote:
sorry, I've been traveling
On Mon, 22 Apr 2019, Abby tang wrote:
>
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五 上午8:32写道：
Hello，BruceI attached my subjects. Please help me.
Thank you.
Abby
[icon_10_generic_list.png] 2851A_T1_w4.nii[IMAGE]
Bruce Fischl 于2019年4月18日周四 下午10:53写道：
Hi Abby
it's hard to tell from the image, but it looks like there is a big I/S
bias field as well as l
What command did you use to apply the transform? If mri_convert add -rt nearest
to your command line.
The issue is that you are using trilinear interpolation our a label map instead
of nearest neighbor
> On Apr 20, 2019, at 5:22 AM, Sadia Sheikh wrote:
>
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Hi Abby
it's hard to tell from the image, but it looks like there is a big I/S
bias field as well as large amounts of pathology.
If you upload the subject to our ftp site we will take a look
cheers
Bruce
On Thu, 18 Apr
2019, Abby
tang wrote:
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Hi Ileana
you use "anonymous" for the user name and your email for the password I
believe.
cheers
Bruce
On Wed, 17 Apr 2019, Camerino, .I.L. (Ileana) wrote:
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Hi Greve,
Thank you very much for your reply.
How do I add data to the link you sent me? When I
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