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Dear Professor:
In my study ,I want to compare the difference and similarity between the sulci
on the brains of rats and mice. I hope to use Freesurfer to acquire and compare
some specific morphological parameters, such curvature, convexity, geodesic
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Hi Daniel,
Can you please give us some more information? How did you call the script? Did
you get any other output? Did the running case complete without errors?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical
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Hi Eugenia,
I did not get any other output.
I think it was an issue with runtime.
I closed out Matlab and reran the script and had no issues. I think the
problem may have had to do with the fact that I already had a different
version of Matlab up whe
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Hello FreeSurfer,
I would like to know if mri_gtmpvc for PetSurfer is appropriate for Tau
(AV_1451) and FDG pet imaging. Also, is cerebellum a good reference point
for both tracers?
Thanks.
Paul
___
Freesurf
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Dear experts of freesurfer,
I am using freesurfer for the first time, so apologies in advance if I am
asking something it was already answered previously. I looked at previous posts
but I could not find an answer.
This is what I did:
1 run recon-
Hi Chhavi
the automated Talairach transform creation can sometimes fail, particularly
in the presence of very large ventriles or lots of damaged white matter or
both. We have a tutorial on checking and correcting it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview
Try this
mri_glmfit —-table V1_lh_stats.txt —-fsgd glm/gender_age.fsgd dods —-C
lh-Avg-thickness-age-Cor.mtx --glmdir lh.V1_gender_age.glmdir
You would only use --surface if the input is a surface map (not when the input
is a table, even if the table has data derived from the surface)
On 3/23/
The intensity is partially what VBM is picking up, so it is not at all
unreasonable to look at.
On 3/21/19 9:52 PM, Bruce Fischl wrote:
Hi Dorothy
yes, we have looked at intensity effects in the gray matter before (David Salat
for example has done this). It certainly reflects degree of myelinat
About once a year we get an email like this saying that there are inconsistent
results between SPSS and mri_glmfit. I think the problem usually boils down to
having a different design matrix. Can you extract the design matrix from SPSS
and compare it to Xg.dat? Or can you import Xg.dat and use
sorry, it cannot be used for rats and mice
On 3/25/19 4:02 AM, 陈天鸿 wrote:
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Dear Professor:
In my study ,I want to compare the difference and similarity between the sulci
on the brains of rats and mice. I hope to use Freesurfer to acquire and compare
some sp
It is certainly good for FDG. Tau is a little trickier, but I think it has been
used. I think the reference region for tau is still an open question. For FDG,
people often use pons.
On 3/25/19 10:33 AM, miracle ozzoude wrote:
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Hello FreeSurfer,
I would like
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Hello Doug,
Thanks for replying. Anything I should watch out for when using it for Tau
processing?
Thanks.
Best,
Paul
On Mon, Mar 25, 2019 at 11:19 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> It is certainly good for FDG. Tau is a
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HI Bruce,
Thanks for your email.
I actually have 3500 files. So cant do transform on them manually. Any
other way? Like downloading the previous version of freesurfer?
Chhavi
On Mon, Mar 25, 2019 at 10:56 AM Bruce Fischl
wrote:
> Hi Chhavi
>
> the au
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Dear TRACULA expert:
I wonder if it is recommended to turn on performing of registeration-based
B0-inhomogeneity compensation (set dob0 = 1) and utilise the field map
magnitude and phase dicom files? The default is set to not to use these
functions,
did all of them fail? That seems unlikely. Our failure rates are usually
pretty low (less than a couple of percent). If they are all failing
something else is wrong
On Mon, 25 Mar 2019, Chhavi Yadav wrote:
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HI Bruce,Thanks for your email.
I actua
not really. It is more of a question of whether the GTM or MG models are
appropriate (ie, constant signal in an ROI). MG probably better than GTM
because it makes fewer assumptions.
On 3/25/19 12:01 PM, miracle ozzoude wrote:
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Hello Doug,
Thanks for replyin
Hi Chhavi
if you look in the recon-all.log file you will see the volume dimensions
as:
Image information
RunNo 4
SeriesNo 5
ImageNo 56
NImageRows256
NImageCols240
NFrames 1
SliceArr
do you mean the section in the left hemi temporal lobe (the lower right
portion of your image)? That does not look like real white matter to me as
it is adjacent to csf. Did you accidentally put some control points in gray
matter (or csf)?
On Mon, 25 Mar 2019, Erika Portera wrote:
E
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Unfortunately I tried this before emailing and no luck. Any other advice?
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: Monday, March 25, 2019 11:06:53 AM
To: freesurfer@nmr
can you give more information? send the command line and terminal output
and a fuller description of the actual problem
On 3/25/19 1:05 PM, Olamide Abiose wrote:
>
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>
> Unfortunately I tried this before emailing and no luck. Any other advice?
>
>
Hi Valeria
Jon Polimeni and Andre van der Kouwe put together a specific acquisition
and set of preprocessing steps for 7T (mp2rage I believe). You need to
account for the transmit inhomogeneities, which are what is causing you to
lose the temporal lobes.
cheers
Bruce
On Mon, 25 Mar 2019, B
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Hi Doug,
I just want to verify that I'm using the patch for high resolution scans
properly. We noticed that the output of "recon-all.v6.hires -conf2hires" has
many volumes with 1 mm isotropic voxels. The only volumes with the original
resolution (
Hi Chhavi
can you post this type of question to the FS list (which I'll cc on my
response)? You only need to give recon-all a single dicom slice that is
from the correct series. If the rest of the dicoms are in the same dir we
will find them and properly assemble the volume from them.
cheers
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I meant I want to run autorecon1 over all the slices. I am trying to
preprocess all the slices.
" If the rest of the dicoms are in the same dir we
will find them and properly assemble the volume from them." means I dont
have to preprocess all the slices
yes, you don't need to process them separately. We don't in general
process slices - we process entire volumes
cheers
Bruce
On Mon, 25 Mar 2019, Chhavi Yadav
wrote:
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I meant I want to run autorecon1 over all the slices. I am trying to preprocess
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Okay but then how do I access the mgzs of the rest of the slices? since
only one folder was formed which I suppose has the output for a single
slice which was mentioned in the recon-all command with -i flag.
On Mon, Mar 25, 2019 at 7:15 PM Bruce Fischl
there are no outputs for single slices, only for volumes. After we
convert the dicom series everything is a volume from then on, no more
single slices
On Mon, 25 Mar 2019, Chhavi Yadav wrote:
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Okay but then how do I access the mgzs of the rest of t
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ok so after the recon-all command runs, in the output directory's mri
folder, a file called brainmask.mgz is formed. I have been doing a freeview
-v of this file which corresponds to the final skull stripped output for my
input slice that I wanted.
Now
I'm not sure what you mean by "what my system will further deal with". You
could extract slices I suppose, but typical MRI acquisitions that are
highres are volumes. The brainmask.mgz will be volume as will everthing
else in the mri dir
On
Mon, 25 Mar 2019, Chhavi Yadav wrote:
Ex
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He¹s probably got some clinical software that only accepts DICOMs. While
converting volume files back to DICOMs is possible, I don¹t know if that
is something FreeSurfer supports. You might need to find another tool to
do that conversion.
Matt.
On 3
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Hi Bruce,
The MRI machine is from Phillips with 1.5 Tesla. How about the slice? Do I need
to prepare sagittal, coronal or else? Thank you in advance.
Yours faithfully,
Mustafa M. Amin
Consultant Psychiatrist in Biological Psychiatry
Department of Ps
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Greve, Thank you very much for your answer.
I used QDEC for analysis in FS. The FS results were analyzed on a whole brain
level by ANOVA (2*2, with one covariate ); the group comparison in SPSS was
conducted in a ROI manner (the ROI is the cluster wit
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Hi Stefano,
Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001,
1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
If so, you will just need the right colortable to view the Yeo_17Net.mgz.
We are currently g
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Dear Douglas,
I mentioned your suggestion i.e., multiecho mprage at about 1 mm, however the
radiologist and operator of the MRI did not understand with the term. Can you
explain it further please? We never done it before, here in Medan Indonesia.
Th
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