Postdoctoral Researcher:
The Dynamic Memory Lab (C. Ranganath, PI) at the University of California,
Davis, now has an open position for a funded postdoctoral researcher. We
currently are running studies that involve multimodal imaging (EEG, fMRI,
ECoG, Diffusion Imaging, MR Spectroscopy) as well a
Dear experts,
I am potentially also interested in correct using of -T2pial feature with
longitudinal stream.
The first (standard cross-sectional) and third step (-long ) was already
elaborated here, but I am, however, not sure how to process by T2pial in the
second step ( -base), which crea
Hi Bruce,
that command also says there is no file or directory:
bash-3.2$ ls -l /Documents/MRI/L001.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
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
Hi,
I have done the sub-cortical segmentation in Freesurfer and have extracted
the left thalamus, when I put it on top of the original MRI, it seems like
it is getting out of the border of thalamus, also it is not smooth. I
wanted to ask if anyone knows how to limit the computation only to
thalamu
Dear experts,
I ran surface based analysis using PET maps. As the following:
spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh
mri_surf2sur
even better!
Bruce
On Wed, 19 Oct 2016, Douglas N Greve wrote:
> It is saving the output as a float instead of uchar. Try
> MRIwrite(result,filename,'uchar');
>
>
> On 10/19/2016 04:38 PM, Keefe, Sarah wrote:
>>
>> Hi Bruce,
>>
>> Thanks for your response. When I try to use load_mgh on an mgh fil
that's because it is saving as float I expect. For load_mgh you need to put
a semicolon (;) at the end of the line to suprrss output. If you waant to
change back to the original type you could do something like:
[vol,M,mr] = load_mgh('orig.mgz');
save_mgh(vol, 'orig.stripped.mgz', M,mr);
quit
It is saving the output as a float instead of uchar. Try
MRIwrite(result,filename,'uchar');
On 10/19/2016 04:38 PM, Keefe, Sarah wrote:
>
> Hi Bruce,
>
> Thanks for your response. When I try to use load_mgh on an mgh file I
> get an endless output of zeroes that I need to cancel, and when I try
Hi Bruce,
Thanks for your response. When I try to use load_mgh on an mgh file I get an
endless output of zeroes that I need to cancel, and when I try to use MRIread
like this:
result = MRIread('filepath/file.mgh')
err = MRIwrite(result, 'filepath/file_new.mgh')
It is successful, but the resu
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
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
Hello Freesurfer,
I have 100 participants for my study and I would like to add control points
and edit the pial for all of them. Is there a command that can
automatically do both or do I have to manually inspect all 100 participants
and add control point/ pial edit where necessary. thanks.
Best,
Pa
Hi,
I am part of the Freesurfer anonymization project mentioned in an earlier
thread- sorry to start a new thread but I was unable to reply to the previous
one. We are trying to find out how to remove all provenance information from
.mgh files.
I am having trouble reading .mgh files into Mat
Hello,
I am interested in looking at ventricular changes over time and thus, have
ran the longitudinal stream on my participants scans. As suggested online,
I am checking the ventricular segmentation in the longitudinal outputs and
am planning on making any edits to the longitudinal stream if the
Dear Bruce,
I needed the label maps for other registration purposes to run other software.
So I was thinking if freesurfers outputs one I can use the same one instead of
creating new ones.
Thanks for the suggestion and time, I will try to binarize the brainmask.
Thanks again
Best Regards,
Thank you Bruce.
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.mgh.harvard.edu]
Sen
sure, internally at times but most of the volumes we save have a bit more
info than that. Is there some reason you need something to actually be
binary? You could binarize the brainmask if you wanted
cheers
Bruce
On Wed, 19 Oct 2016, Karmacharya, Sarina wrote:
> Thank you Bruce.
>
> Does free
Something weird is happening with mri_vol2surf - even though the data looks
great, the values are odd which carries over when I try to average with
mri_concat. I would just like to get percentage values with mri_concat.
thanks!
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in
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
Hi Dear Bruce
Thanks for your reply. Do you mean change to source directory in my
computer? but I can’t, It appears 550 Failed to change directory. I find I can
only change to / directory. I did some try but all failed.
Name (surfer.nmr.mgh.harvard.edu:Brainwaver): anonymous
331 Please
Ok this is a known issue with the
freesurfer-Darwin-lion-stable-pub-v5.3.0 release. Please download a copy
of mris_resample from the following link and copy it into your
FREESURFER_HOME/bin directory. Also, make sure it is executable (chmod
+a mris_resample)
ftp://surfer.nmr.mgh.harvard.edu/
Dear Freesurfer team,
I have a questions for you regarding the binary masks (labels maps) that
freesufer uses to skull strip the brain in the first part of recon-all.
I was wondering if freesurfer stores/saves this label mask that it uses to
skullstrip? If so what would be the naming convention
what does:
ls -l /Documents/MRI/L001.nii.gz
show?
On Wed, 19 Oct 2016, Marja Caverlé wrote:
Dear Bruce,
Thanks for your reply. I tried that, but it does not change anything (at least
if I did correctly what
you suggested):
bash-3.2$ recon-all -i /Documents/MRI/L001.nii.gz -sd MRI -subjid
the easiest thing to do is to read it and write it from matlab. The
should remove pretty much everything. We can add something to mri_convert
for the future
cheers
Bruce
On Wed, 19 Oct 2016, LaMontagne, Pamela
wrote:
> Yes we are interested in removing all provenance. I am not an end user so I
Dear Bruce,
Thanks for your reply. I tried that, but it does not change anything (at
least if I did correctly what you suggested):
bash-3.2$ recon-all -i /Documents/MRI/L001.nii.gz -sd MRI -subjid L1 -all
ERROR: cannot find /Documents/MRI/L001.nii.gz
Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin
Yes we are interested in removing all provenance. I am not an end user so I
wasn't sure if the Subjects_Dir is contained within the file and necessary for
other freesurfer functions. Anything that can help would be appreciated.
Thanks
Pamela
-Original Message-
From: freesurfer-boun...@nm
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 the directory exists and is
writeable by you, as recon-all will create a subtree called
under it
cheers
Bruce
On Wed, 19 Oct 2016, Marja Cav
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 2
what directory is the file L001.nii.gz in?
cheers
Bruce
On Wed, 19 Oct 2016, Marja
Caverlé wrote:
Hi Bruce,
I tried a lot of different commands, trying to figure it out, with .nii and
.nii.gz, and changing the
SUBJECTS_DIR to different folders, but it did not really matter, it keeps on
sa
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
Hi Bruce,
I tried a lot of different commands, trying to figure it out, with .nii and
.nii.gz, and changing the SUBJECTS_DIR to different folders, but it did not
really matter, it keeps on saying that the inputfile does not exist, or
that the subject folder does not exist.
---
*bash-3.2$ recon-all
We have several data sharing efforts going on in which we would like to assign
new Subject IDs and paths. We have identified the following mgz files that have
provenance info including timestamps, dcm file name, subject ID
(subject_name/assessors/session_name/DATA/subject_name/mri).
aparc.a2009
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
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 going wrong?
Best,
Marja
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