Hi Alan
make sure matlab is in your path. You can check by typing:
which matlab
cheers
Bruce
On Fri, 16 Sep
2016, Alan Francis wrote:
Hi Marie -
I have MATLAB and the Image processing toolbox on my MAC. Unfortunately, I
am unable to get FreeSurfer to recognize this (see below) , so I am
Hi Leila
we are experiencing disk problems at Martinos, which are probably causing
this issue
sorry, not sure when it will be fixed
Bruce
On Fri, 16 Sep 2016, Leila
Reddy wrote:
> Hi,
> I get an error with mri_nu_correct.mni. I've seen on the FS wiki that this
> is because I have a new versi
how would you like them divided? You can also use
mris_make_face_parcellation to make units of approximately equal area
(either in the individual or in the group)
On Fri, 16 Sep 2016, Mamashli,
Fahimeh wrote:
Dear Freesurfer group,
I am going to divide a brain parcellation into divisions usin
Hi Han
the files ?h.curv contain the spatially smoothed mean curvature. You can
compute the mean or Gaussian (or principal) curvatures of any surface
using the mris_curvature command.
cheers
Bruce
On Fri, 16 Sep 2016, Hanbyul Cho wrote:
Dear FreeSurfer Team,
I heard that FreeSurfer co
same but
Gaussian curvature.
cheers
Bruce
On Fri,
16 Sep 2016, Hanbyul Cho wrote:
Dear Bruce Fischl,
Thank you for your explanation.
I think I could not yet fully understand the 'curv' files.
After processed this command,
recon-all -s -i -all
the output files were follo
p.
Best Wishes
Cong Chen
Date: Thu, 8 Sep 2016 10:12:29 -0400 (EDT)
From: Bruce Fischl
Hi Cong
you could try using expert options to modify the
mris_make_surfaces
parameters. It looks like you white surface is too far out. Try
increasing min_border_white and/or increasing max_gray. I
Hi Jason
this is what control points are designed to fix. Why don't they help?
Bruce
On
Tue, 20 Sep 2016, Jason Tourville wrote:
> Hello freesurfers,We've seen some poor surface reconstructions due to local
> inhomogeneities that remain in the brainmask volume. We see omission of
> significant p
Hi Claudia
you need to send us your full command line and the various other
information we ask for when reporting issues (operating system, etc..)
thanks
Bruce
On
Tue, 20 Sep 2016, Claudia Dacquino wrote:
Hi all, after doing GLM analysis I'm trying to run freeview to see results,
but I get
sure, you get each of those for the long runs as well
cheers
Bruce
On Thu, 22 Sep 2016,
Gabor Perlaki wrote:
> Dear all,
>
> Is it possible to get simple ROI data (such as aseg.stats or aparc.stats in
> case of cross-sectional analysis) as the result of the longitudinal
> analysis, which can be
Hi Han
they are computed using the white surface by default but you can easily
use another surface in mris_anatomical_stats.
cheers
Bruce
On Thu, 22 Sep 2016, Hanbyul
Cho wrote:
Dear FreeSurfer Team,
I heard that the
processed subjects/stats/?h.aparc.a2009s.stats
included the integrated
Hi Tamara
it will assume that output type given the .nii extension, so you should
be fine
cheers
Bruce
On Fri, 23 Sep 2016, Tamara Tavares wrote:
Hi All,
I have been using the following command line to convert my dcm/IMA files
into a nii files.
mri_convert -it dicom x.dcm .nii (w
Hi Anna
I'm not exactly sure what you mean, but if you register EEG electrodes to
the white or pial surface, then you can visualize them on the inflated
surface trivially. That is, you can create your ROI on any surface of the
same hemisphere/subject and visualize it on any other
cheers
Bruce
ze
> the anatomical ROI created automatically. How do I create a new ROI?
>
> Thanks,
> Anna
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harva
.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, September 26, 2016 1:16 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> can you explain what the ROI is
1. It is the signed dot product of the movement vector with the outwards
pointing surface normal of the white matter surface during inflation.
2. Yes, because moving inwards for gyri the dot product is negative.
3. Yes, I think so, although I'm not sure I understand.
4. mris_anatomical_stats c
ld not open scuba. Is this the correct way to go
> about this, or is there some other means that I should be doing not 'scuba'?
>
> Thank you,
> Anna
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nm
what was different? And can you send us the rawavg.mgz for the two cases?
On Mon, 26 Sep 2016, Tamara Tavares wrote:
Thank you Bruce!
Theoretically, I should get the same results if I pass my nii file through
the recon-all command if I converted my dicom/IMA file into a nii using
Slicer4 or th
inputting it wrong or am I just
> missing information?
>
> Thank you,
> Anna
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sen
r, I found that all values of 'j' are 1. is there something wrongs
with my strategy?
Best Regards,
Aziz.
On Mon, Sep 12, 2016 at 8:40 PM, Bruce Fischl
wrote:
Hi Aziz,
make sure $FREESURFER_HOME/matlab is in your matlab path.
cheers
Bruce
On Mo
Hi Alain
I believe if you specify the transform as identity.nofile that should do
the trick. Most of our tools accept this
cheers
Bruce
On Tue, 27 Sep 2016, Alain Imaging
wrote:
De : Alain Imaging
Envoyé : l
Hi Zhengchen
I don't think there is a general answer to your question as it depends on
how noisy the input image is, what denoising algorithm you use and what
outcome measures you care about. For example, it might improve
putamen/pallidum but worsen thickness measures in low contrast regions
s
; I keep getting an error when I use mri_label2label. Below is my input and
>>>>> output. I have tried various paths all the way down to the label and
>>>>> above the subject level, but still always get the same error. I have also
>>>>> verified it is the pat
Hi Tamara
can you let us know how big the differences are?
thanks
Bruce
On Wed, 28 Sep 2016,
Douglas Greve wrote:
I don't understand what the problem is. Can you elaborate?
On 9/27/16 12:13 PM, Tamara Tavares wrote:
The differences have been found in the outputs from the aseg
t;
>> SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
>> FREESURFER_HOME /tools/freesurfer
>> Loading source label.
>> No such file or directory
>> mri_label2label: could not open label file Testing1.label
>> No such file or directory
>> ERROR rea
eesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, September 28, 2016 4:27 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> what was your freeview command line, an
esurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, September 28, 2016 4:35 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> which lh
appreciate your detailed explanation.
Best Regards,
Han.
On Mon, Sep 26, 2016 at 12:34 PM, Bruce Fischl
wrote:
1. It is the signed dot product of the movement vector with the
outwards pointing surface normal of the white matter surface
during inflation.
2. Yes, beca
Hi Paige
we have stopped development and most support of tksurfer. Can you use
freeview instead or is there still some functionality that you need that
is unique to tksurfer?
cheers
Bruce
On Thu, 29 Sep 2016, Paige Scalf wrote:
> Hello,
>
> I too am having trouble with tksurfer displaying the
Hi Jared
the icosahedra are only used to represent average space surface
(fsaverage[4-7]), not individual subjects.
cheers
Bruce
On Thu, 29 Sep 2016, Jared P
Zimmerman wrote:
I want to project to the native subject surfaces though, not fsaverage. If
I use —trgsubject subjID would that wor
creating the
> label I assume. When I created it, under the ROI tab, I created a new one and
> then drew it in the viewer with a volume (I did both white matter and brain
> mask) also loaded. Was this wrong?
>
> Thank you,
> Anna
> __
label isn't on the surface though.
>>
>> Thank you!
>> Anna
>>
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, September 29, 2016 12:45 PM
>> To: Crawford, Anna; Bruce Fischl
>> Cc: Anna Crawford; freesurfer@nmr.mg
draw it
>> on the surface? As in, everything was done correct, the location of the
>> label isn't on the surface though.
>>
>> Thank you!
>> Anna
>> ____
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>>
@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 29, 2016 1:14 PM
> To: Douglas N Greve
> Cc: freesurfer@nmr.mgh.harvard.edu; Crawford, Anna; Anna Crawford
> Subject: Re: [Freesurfer] I
Hi Anna
I think you are trying to project an overlay on a surface, not create a
surface, right?
Bruce
> On Sep 30, 2016, at 10:44 AM, Crawford, Anna wrote:
>
> I already ran recall-all. I am trying to create a different surface not
> created using recon-all.
>
> Anna
> From: freesurfer-boun..
yes, that's right. You will use mri_vol2surf with the identity matrix
with the parcellation, but some bbregister-generated .dat file with PET
data.
cheers
Bruce
On Fri, 30 Sep 2016, Crawford, Anna wrote:
> No problem. I'm not exactly sure, but I think I just want a surface overlay
> so mri_vol
Hi Seung-Gul
the easiest way to get it to extend further is to play with the intenisty
bounds in mris_make_surfaces. For example, if you reduce
max_gray_at_the_csf_border you will force it to settle further out
cheers
Bruce
On Fri,
30 Sep 2016, Seung Gul Kang wrote:
Hi Freesurfer expert,
that's true, but if the white matter surface is already correct you can
change some of the intensity bounds in mris_make_surfaces. The
automatically calculated ones will be in the recon-all.log and you should
check them before changing them
cheers
Bruce
On Fri, 30 Sep 2016, Trisanna
Sprung
try including --out_type mgh and naming your output something like
lh.wmparc.mgz
cheers
Bruce
On Fri, 30 Sep 2016, Crawford, Anna wrote:
> Thank you! So good news, that worked and created wmparcSlh.w
>
> I'm not sure what the .w means. When I try to load it onto the surface, I
> get an error:
or better yet, use our naming conventions an dcall it lh.wmparcS.mgh (or
.mgz)
On Fri, 30 Sep 2016, Douglas N Greve wrote:
> Anna, try removing --out_type paint and instead specify the output file
> as wmparcSlh.mgh
>
> Trisanna, thanks so much for chipping in!
>
>
>
> On 09/30/2016 01:14 PM, Tr
Hi Duygu
V6 isn't ready yet! We are close (I know I keep saying that) and are in
hopefully final internal testing now, but there is no usable version yet.
We'll announce a beta release when it is ready
cheers
Bruce
On Fri, 30 Sep 2016, Duygu Tosun-Turgut wrote:
>
> Hello FreeSurfer Develop
did you see Doug's earlier response to this question?
On Fri, 30 Sep 2016,
Ali-Reza Mohammadi-Nejad wrote:
Dear Freesurfer experts
Based on the FS wiki, I calculated the cortical thickness difference between
the LH and RH of a subject in subject's native surface.
Now, I want to use FS command
Hi HsinTsung
FreeSurfer V6 isn't out yet, but we are moving towards having a beta.
I'll leave the registration questions for Doug
cheers
Bruce
On Mon, 3 Oct 2016, Hsin-Tsung Lee wrote:
Dear freesurfer community
I have used the freesurfer v5.30 stable on linux, I want to fusion
the C
Hi Han
I'm not sure I understand you question. The sign of the curvature depends
on the arbirary convention you choose for the normal vector field over the
surface. We pick and outwards pointing normal, which means that gyral
regions in general have negative curvature (since they lie 'below' t
yes, I believe so
On Mon, 3 Oct 2016, Hanbyul Cho wrote:
Dear Bruce Fischl
?h.white.H, ?h.curv, and H Mean reflected the vector fields with 'sign(+ or
-)', and MeanCurv reflected the integral of the 'absolute' value of mean
curvature. Am I understanding this correctly
Hi Jeongsik
if you send us the details of each sequence you used and each scanner
platform we can advise you.
As for acccuracy - you need to visually inspect the surfaces and aseg to
decide how accurate they are.
cheers
Bruce
On Tue, 4 Oct 2016, 김정식 wrote:
Dear FreeSurfer team,
First o
Hi Joel
can you include the entire thread when responding? Usually overlay is a
suboption in freeview. So it would probably be something like:
freeview -f lh.inflated:overlay=lh.overlay.mgz
cheers
Bruce
On Tue, 4 Oct
2016, Joel Bruss wrote:
> .mgz format made no difference. I see no optio
Hi Josue
the *.curv won't help you with the volume. If it is a label file you
should be able to give it to mris_anatomical_stats with -l to
compute the volume
cheers
Bruce
On
Wed, 5 Oct 2016, Josue Luiz Dalboni Da Rocha wrote:
> Dear Douglas,
>
> I have a ".curv" file that contains the curv
rf2vol), binarize it (mri_binarize), and then convert to label
> (mri_cor2label).
> Is it a correct way to extract the volumes from a '.curv' file?
>
> Best regards,
> Josue
>
> ____
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on
I believe this is fixed in V6, but if you upload a dataset we can try it
out and confirm
cheers
Bruce
On Wed, 5 Oct 2016, Fire Tech wrote:
Dear freesurfer experts
working with MS patients I have several subjects with pial/white surface
issues due to wm lesions. Following a suggestion I found
Hi Damein
6.0 beta will handle this *much* better if you can wait.
cheers
Bruce
On Thu, 6 Oct 2016,
Damien MARIE wrote:
> Dear experts,
>
> I plan to process some MRI 7T data, 0.6 mm^3 isotropic voxel size. The aim is
> to look a R1 maps.
>
> I was wondering what was your opinion concerning th
#x27;t need rest of the brain. How can I figure out which of these labels
> belong to superior temporal?
> is there any way to do this for a certain parcellation like lh.aparc.annot ?
>
> Thank you,
> Fahimeh
>
>
> From: freesurfer-
yes, that's true
On Thu, 6 Oct 2016, Funk, Quentin wrote:
> I have a few questions regarding the instructions at:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
>
>
> The instructions assume that there is an ROI in the same space as the
> T1.mgz map. Then they do the foll
released?
Thank you and best,
Cheers,
Damien
Bruce Fischl Thu, 06 Oct 2016 07:11:04 -0700
Hi Damein
6.0 beta will handle this *much* better if you can wait.
cheers
Bruce
On 6 Oct 2016, at 15:46, Falk Lüsebrink
wrote:
Hi Damien,
depending on what you want to do you are
Hi Raghav
there are individual steps that can be run, but part of the strength of
FreeSurfer is that the comprehensive nature of our modeling gives us
greater accuracy. For example, the cortical surface models are used to
automatically correct the subcortical segmentation and such. In general
Hi Raghav
We don't resample into MNI (or any other space). Was your input already
resampled? In general you should send us your full command line and screen
output
Cheers
Bruce
> On Oct 9, 2016, at 1:39 PM, Raghav Mehta wrote:
>
> Raghav
___
Fre
ology
International Institute of Information Technology - Hyderabad
researchweb.iiit.ac.in/~raghav.mehta
+91 9712990393
On Sun, Oct 9, 2016 at 11:54 PM, Bruce Fischl
wrote:
Hi Raghav
We don't resample into MNI (or any other space). Was your
input already resampled? In g
No, not yet, although they are high on our list
Bruce
> On Oct 10, 2016, at 2:57 PM, Ankita Sharma wrote:
>
> Hi,
> Does anyone know if subthalamic nuclei and substantial nigra are part of the
> automated sub-cortical segmentation (aseg) in Freesufer?
> Thanks,
> Ankita!
>
> __
what was your vol2surf command line? Make sure that it is using nearest
neighbor interpolation
On Tue, 11 Oct 2016, Crawford, Anna wrote:
> Hi,
>
> I am trying to remap a volume. I am using aparc+aseg.mgz volume. I loaded it
> into Matlab using load_mgh. In Matlab I remap the volume to different
if the surfaces are fine probably not, but you will want to recreate the
stats tables
cheers
Bruce
On Tue, 11 Oct 2016, firet...@web.de wrote:
Dear experts
after editing aseg the Segmentations wiki says one:
" could recreate the final surfaces with the command:
recon-all -autorecon2-noas
Hi Synne
we are (hopefully!) in the final stages of alpha testing and will release
a beta soon
cheers
Bruce
On Wed, 12 Oct 2016, Synne Aanes wrote:
Hello,
I am about to start my project on hippocampal subfield analysis and realise
that this function is highly improved in FS version 6.0.
hbor. What is the proper flag to set it to use nearest neighbor
>> interpolation?
>
> Thanks,
> Anna
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@
Hi Hinke
mri_em_register, mri_ca_label, mri_ca_register and mri_ca_normalize all
take -lh and -rh commands to indicate that only one hemisphere exists. Try
including them and see if it fixes things (you should be able to use expert
options for this). We have only used it for ex vivo analysis i
Hi Falk
you are almost certainly running into a problem with some MAX number of
defects/faces or something. If you upload the subject dir I'll fix it
cheers
Bruce
On
Wed, 12 Oct 2016, Falk Lüsebrink wrote:
Dear all,
using mris_topo_fixer instead of mris_fix_topology also results in a
Hi Sancgeetha
you can use mri_surf2vol to sample the thickness into the volume if you
want. The thickness file itself does not contain any topological
information - that is stored in the surface files (e.g. lh.pial)
cheers
Bruce
On Wed, 12
Oct 2016, Sancgeetha Kulaseharan wrote:
Hello Fre
Hi Brad
it looks like the recon failed as you ran out of disk space:
cvarput: ncid 5: No space left on device
miicv_put: MINC package entry point
nu_evaluate: crashed while running mincmath (termination status=768)
nu_correct: crashed while running nu_evaluate (termination status=768)
as for w
Hi Eelco
it isn't really a question of whether our implementation is senstitive to
this. It's that in general your power will be constrained by the size of
the smaller group (I assume this is Type 2 diabetes by the way).
cheers
Bruce
On Thu, 13 Oct 2016, Eelco van Duinkerken wrote:
> Hi all,
!
So if I understand correctly, the power of say the controls vs. diabetes
(indeed it is type 2 diabetes) comparison is constrained by the sample size
of the obese group?
2016-10-13 11:02 GMT-03:00 Bruce Fischl :
Hi Eelco
it isn't really a question of whether our implementati
you can always look in the recon-all script - the atlas (*.gca) file we
use is listed in there.
cheers
Bruce
On Thu, 13 Oct 2016, GAJENDRA KATUWAL (RIT Student)
wrote:
According to this website
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferVersion3, Freesurfer v
3.0 uses Aseg atlas for
requirements.
What is the nature of this memory error and how do I go about fixing it? I
know that I have 305 Gb of HD.
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Thursday, October
Hi Cong
can you send us your full session history - what exact commands did you
type and what was the screen output?
cheers
Bruce
On Sun, 16 Oct 2016, Cong wrote:
Dear freesurfer experts When I use command "put path/to/my/file”, it’s
always appear an error "229 Entering Extended Passive M
Hi Theo
you can look at the papers referenced by our original Neuron paper for
the definitions (the ones with Caviness, Kennedy and others)
cheers
Bruce
On Sun, 16 Oct
2016, AKUDJEDU, THEOPHILUS wrote:
Dear All,
I want to know the freesurfer anatomical definition for the caudate and th
not at the moment, sorry
Bruce
On Mon, 17 Oct 2016, Rockers, Elijah D. wrote:
> Is it possible for freesurfer to parcellate the substantia nigra from a T1?
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/ma
Cong2Bruce.zip remote:
> /Users/Brainwaver/Desktop/Cong2Bruce.zip
> 227 Entering Passive Mode (132,183,202,158,147,230).
> 553 Could not create file.
> ftp>
>
>> Date: Sun, 16 Oct 2016 16:04:12 -0400 (EDT)
>> From: Bruce Fischl
>>
>> Hi Cong
>>
>
Hi Taha
none that I can think of. The medial wall is pretty substantial region
though - I am more concerned about your subject with only 53 vertices in
it. You can visualize it by loading the ?h.cortex.label onto the inflated
surface. Everything not in the label should be set to 0
cheers
Bru
Hi Erik
if you mean what sequences should you acquire, Andre van der Kouwe has a
website with recommendations for different platforms. Typicall we like a
multi-echo MPRAGE and a T2-SPACE FLAIR scan as well if you have time
cheers
Bruce
On Tue,
18 Oct 2016, Erik Lindberg wrote:
Dear Frees
Hi Marja
can you send us the command you ran and the full screen output and the
recon-all.log file?
thanks
Bruce
On Wed, 19
Oct 2016, Marja Caverlé wrote:
Dear all,
When I want to run a recon-all -all, I keep getting the error saying that the
input file cannot be
found. Any idea what is
Hi Pamela
I'm not sure you need to change the tags at all - as you say they are
just provenance info and not used for any analysis. We could put something
into mri_convert to strip all the tags if it is deidentification you are
concerned about
cheers
Bruce
On Wed, 19 Oct 2016,
LaMontagne, P
PM, Bruce Fischl
wrote:
Hi Marja
can you send us the command you ran and the full screen output and the
recon-all.log file?
thanks
Bruce
On Wed, 19 Oct 2016, Marja Caverlé wrote:
Dear all,
When I want to run a recon-all -all, I keep
Caverle wrote:
I changed it multiple times because I thought it would solve the problem
(applications, desktop, documents). Currently it is in Documents/MRI.
Marja Caverlé
On 19 Oct 2016, at 15:29, Bruce Fischl wrote:
what directory is the file L001.nii.gz in?
cheers
Bruce
On Wed, 19 Oct
du
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, October 19, 2016 8:27 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] MGZ file tag edit
>
> Hi Pamela
>
> I'm not sure you need to change the tags at all - as you say they are
file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On Wed, Oct 19, 2016 at 3:34 PM, Bruce Fischl
wrote:
You need to provide the full path to it with the -i command. Then you can
use -sd
and -s to specify where the output should go.
Make sure that
Hi Sarina
the skull stripping is done by combining a deformable surface with a
watershed algorithm not with a label mask. The volume brainmask.mgz can
be used to specify what is in brain (voxels >5) and what is not in brain
(voxels < 5)
cheers
Bruce
On Wed, 19 Oct 2016, Karmacharya, Sarina w
> Does freesurfer use any binary label map during any processing steps?
>
> Best Regards,
> Sarina
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.m
Hi Sarah
I believe that both load_mgh and MRIread don't load any tags, so if you
use them to load, then MRIwrite or save_mgh to write back to disk all the
tags should be gone.
cheers
Bruce
On Wed, 19 Oct 2016, Keefe, Sarah wrote:
Hi,
I am part of the Freesurfer anonymization project men
Hi Paul
we already do what we can automatically, so if the surfaces are not
accurate you'll need to do visual inspection and manual editing to correct
them (assuming the inaccuracies are somewhere you care about)
cheers
Bruce
On Wed, 19 Oct 2016, miracle ozzoude wrote:
Hello Freesurfer,I
file is 4x larger than the original
file.mgh, which is large enough
that my editor won't open it so I can't check for the tags. Am I using the
commands correctly?
Thanks,
Sarah
h/file_new.mgh')
>>
>> It is successful, but the resulting file is 4x larger than the
>> original file.mgh, which is large enough that my editor won't open it
>> so I can't check for the tags. Am I using the commands correctly?
>>
>> Thanks,
>>
Hi Dorsa
why do you think it is going out too far? What intensity volume are you
overlaying it on? Many segmentations miss the lateral parts of the
thalamus since they have so much myelin in them
cheers
Bruce
On Wed, 19 Oct 2016, Dorsa
Haji Ghaffari wrote:
> Hi,
> I have done the sub-cortica
er
results?
Thank you
Dorsa
On Wed, Oct 19, 2016 at 5:21 PM, Bruce Fischl
wrote:
Hi Dorsa
why do you think it is going out too far? What intensity volume are you
overlaying it on? Many segmentations miss the lateral parts of the
thalamus since they have so much myel
.nii.gz
ls: /Documents/MRI/L001.nii.gz: No such file or directory
bash-3.2$ ls -l /Desktop/MRI/L001.nii.gz
ls: /Desktop/MRI/L001.nii.gz: No such file or directory
Even though, the niftis are really there.
Best,
Marja
On Wed, Oct 19, 2016 at 3:44 PM, Bruce Fischl
wrote:
what does
Thu, Oct 20, 2016 at 9:51 AM, Bruce Fischl
wrote:
Hi Dorsa
if you upload your subject I'll take a look. What is a 3TC image? I don't
know what contrast the image you sent is
but I would be cautious about only using it to assess the accuracy of the
T1 segmentation
Hi Nicholas
I wouldn't think so. Look at the cortical parcellations and see if they
are accurate. If they are it means that the cross-subject registration
must be pretty good
Bruce
On Thu, 20 Oct 2016, Nicholas Heugel wrote:
I am encountering an odd effect when using the Freesurfer maps in B
S8.nii
bash-3.2$
On Thu, Oct 20, 2016 at 3:52 PM, Bruce Fischl
wrote:
Hi Marja
you need to figure out where the input files are! How do you know they
are there? Can you
run:
ls -l /Desktop/MRI/*.nii*
cheers
Bruce
On Wed, 19 Oct 2016, Marja Cav
uette University
On Thu, Oct 20, 2016 at 4:32 PM, Bruce Fischl
wrote:
Hi Nicholas
I wouldn't think so. Look at the cortical parcellations and see if they
are accurate. If
they are it means that the cross-subject registration must be pretty good
Bruce
On Thu, 2
ch? I would like ultimately import this into MATLAB to do
some statistics and then
view in freeview as a scalar overlay. Please advise.
Thanks for the help,
Taha
On Tue, Oct 18, 2016 at 7:49 PM, Bruce Fischl
wrote:
Hi Taha
none that I can think of. The medial wall is pretty substa
Hi Cleo
can you upload a subject before and after editing so we can replicate what
you are seeing? And what version of FreeSurfer are you using? Does the WM
after editing get signifcantly >110? If so, you may have accidentally
placed a control point in a gray matter voxel
cheers
Bruce
On T
Try using /Users/MarjaCaverle/Desktop/MRI as the path in your -i
> On Oct 20, 2016, at 6:03 PM, Marja Caverlé wrote:
>
> /Users/MarjaCaverle/Desktop/MRI
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mail
Hi Trisanna
not sure about mri_concat, but mri_average -noconform -p ... should do
the trick
cheers
Bruce
On Wed, 19 Oct 2016, Trisanna Sprung-Much wrote:
Something weird is happening with mri_vol2surf - even though the data looks
great, the values are odd
which carries over when I try to a
, 2016 at 4:35 AM, Bruce Fischl
wrote:
Try using /Users/MarjaCaverle/Desktop/MRI as the path in your -i
> On Oct 20, 2016, at 6:03 PM, Marja Caverlé
wrote:
>
> /Users/MarjaCaverle/Desktop/MRI
___
F
Hi Paul
no, I don't think so. If you use our voxel-labeling conventions you
should just be able to copy them in to the mri dir
cheers
Bruce
On Fri, 21 Oct 2016, miracle ozzoude
wrote:
Hello experts, I did my skull stripping and white matter labelling using an
lesion explorer
and I want t
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