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Dear FreeSurfer Developers
If we want to rerun FreeSurfer dev 6.1 on an old dataset, is it better to rerun
with the original DICOMS or to rerun over the 5.3 output? Would that even work?
Thanks very much.
Kind regards,
FREDA SCHEFFLER
Research Ass
Hi all,
I am currently developing a pipeline to remove physiological noise (respiratory
and cardiac) from rsMRI images. I am at the point where I have created the
regressors using fast_retroicor.m from the physiological data logs. When I add
the columns of the regressors up and plot the result
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Dear Free Surfer team,
Surely this is a basic question but I am having a trouble setting the
subjects_dir in my terminal and, as a result, any of the commands work.
This is how I have my Free Surfer configurated in my computer:
freesurfer-Li
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Thank you for the response.
Which smoothing option would you recommend, there is one in mris_preproc,
but there is also mris_smooth.
Thanks You
On Wed, Oct 17, 2018 at 1:56 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> You cannot use Q
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Hi,
I am referring to a paper of Vuoksimaa et al. 2016. The authors used relative
instead of absolute cortical measures (cortical thickness and surface area) to
compute individual vertex-cognitive ability correlations throughout the cortex.
To
Hi Rosalia
you either need to give recon-all an input file (or more than one) with the
-i switch, or create the subject directory tree under SUBJECTS_DIR for that
subject, and put a file named 001.mgz in the mri/orig subdir. Note you can
also specify SUBJECTS_DIR explicitly on the recon-all co
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Hi Bruce,
Thank you very much for answering my questions.
This is how I have organized my subject_dir for one subject so you can see
better. It is still not working.
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ ls
FOLDERS S_01
Hi Rosalia
can you send us the full command line, screen output and recon-all.log?
In the arrangement you show below it would be:
recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i -all
cheers
Bruce
On Thu, 18 Oct 2018, Rosalia
Dacosta Aguayo wrote:
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Hi Bruce,
There is not recon-all.log.
The full command line is:
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects $ *recon-all
-sd ~/Desktop/MS_STUDY/subjects -s 001 -i
/home/rosalia/Desktop/MS_STUDY/subjects/MS001/mri -autorecon1*
*ERROR
Hi Rosalia
-i must point to a file that you want to import, usually a single dicom
file in the correct (e.g. mprage) series.
cheers
Bruce
On Thu, 18 Oct 2018, Rosalia
Dacosta Aguayo wrote:
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Hi Bruce,
There is not recon-all.log.
The full comman
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Yes, you are right. I saw the error.
I have been running one of the participants and here it is the report.log.
Also, because these kind of participants are special, I used some bet
parameters to run the skull-stripping. This is the main reason why I di
yes, you can do that. If you run recon-all through the skill stripping,
then replace the brainmask.mgz with yours generated by bet, we should
detect that and retain it for further processing
cheers
Bruce
On Thu, 18 Oct 2018,
Rosalia Dacosta Aguayo wrote:
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Hello I keep getting the same error and am not sure how to address the
issue.
I have attached the design matrix and the FSGD file and contrast file of
interest
Thanks for the help
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
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Thank you a lot Bruce.
Just one more question. If I would like to run all the participants. where
should I include the subject.list?
Regards,
Rosalia
On Thu, Oct 18, 2018 at 7:56 PM Bruce Fischl
wrote:
> yes, you can do that. If you run recon-all thr
Hi Rosalia
that you would do outside of FreeSurfer, probably with a shell script. I
typically make a scripts dir under SUBJECTS_DIR and put a file names
subjects.csh that creates an env variable listing the subjects and setting
the SUBJECTS_DIR, then write scripts that source it and run things
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Dear FreeSurfer experts,
I have created a custom measure on the pial surface of a number of subjects,
and I would like to map the data to the fsaverage subject. (By custom measure I
mean something like 'area' or 'curv', i.e., one scalar value per sur
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Dear FreeSurfer Team :
I used the freeSurfer brainstem structure to segment the brainstem from the
MRI successfully. But I have several questions as followed:
1. I want to export this data in dcm file with all the ROI information,
what should I do?
2.
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