Dear All,
I am a newbie to freesurfer and I would like to use our in-house built
probabilistic atlas(each region as a binary mask and available as nifti files).
I would like to create an atlas out of it and use it for our analysis. On
searching the previous mailing list I came across a discussi
Hello,
I've been working on taking the outputs of the fmriprep BOLD preprocessing tool
(https://fmriprep.readthedocs.io/en/latest/index.html) and coercing them into
the fsfast structure so that first levels can be run with mkanalysis-sess and
selxavg3b-sess. It's been a bit trickier than antici
Hi,
I am trying to compare my volume maps (negative_allsocial_proportion.nii)
to someone else's (SN_like_cortical_lh.nii.gz) who have it on a surface
(mni152_subject). So I used the steps for mri_vol2surf command as follows:
Commands:
mri_vol2surf --src negative_allsocial_proportion.nii --reghead
Hello Researchers,
We have received request from lot of researchers to extend the deadline for
abstract submission, We are happy to announce that the deadline for abstract
submission for 1st International Workshop on Predictive Processing (WoPP) has
been extended upto 16th April 2018.
Hope
Hi Anna
from your log file it looks like some other process is using more than 2/3
of the memory on your machine:
total used free sharedbuffers cached
Mem: 24729588 1685252478770644095060 0 10543292
-/+ buffers/cache:6309232
Hi Mageshwar
what kind of an atlas are you talking about? We have multiple atlases for
different purposes.
cheers
Bruce
On Thu, 5 Apr 2018, Mageshwar Selvakumar wrote:
Dear All,
I am a newbie to freesurfer and I would like to use our in-house built
probabilistic atlas(each
region as a bina
Hi Mageshwar
gcs is a surface-based format for cortical segmentation. And it wouldn't be
a conversion as much as it would be a training. If you can sample your
regions onto the surface in .annot format you can use mris_ca_train to
build a new gcs that you can then apply with mris_ca_label
ch
Hi,
I have been trying to edit structural brains and very few times I would get
the following error while running recon-all -s subjID
white matter peak found at 110
cannot allocate memory
Upon looking at the archive, there was only one similar issue and it was
recommend to check mri_info as the
Hi Srishti
are you sure that your machine didn't just run out of memory? The
recon-all.log file includes the amount of free (and total) memory at the
time the process was started.
cheers
Bruce
On Thu, 5 Apr
2018, srishti goel wrote:
Hi,
I have been trying to edit structural brains and v
Hi Bruce,
The machine definitely hasn't run out of memory. Here is the memory usage
from recon-all.log
total usedfree
shared buff/cache available
Mem: 26372696834330048 152102696 1294477294224
191963372
Swap: 2097148
Dear Recipient,
I am a Master student new comer in FS. I am trying toi use the QDEC ti analyse
some longitudinal data. Most probably my issue is related with the file format.
I tried to use several text editors (mac text editor, gedit and text wrangler)
however I end up in 2 different errors w
if you run the command that failed again on the command line directly (that
is, not in recon-all) does it fail again?
On Thu, 5 Apr 2018, srishti goel wrote:
Hi Bruce,
The machine definitely hasn't run out of memory. Here is the memory usage
from recon-all.log
total
I am sorry, I am not sure what do you mean by running the command line
directly?
I use the following command:
sbatch --mem 2200 -t 6-00:00 --mail-type END --mail-user
srish...@email.unc.edu --wrap "export
SUBJECTS_DIR=/proj/hng/sheridanlab/freeSurfer/DukeYAS/Freesurfer_out/;
recon-all -s 13166 -a
Hi Srishti
if you look in the subject's scripts dir there should be a file named
"recon-all.cmd". Try rerunning the last command in it (probably from the
mri dir)
cheers
Bruce
On Thu, 5 Apr 2018, srishti goel wrote:
I am sorry, I am not sure what do you mean by running the command line dire
Should I re-run the recon-all after running the last command from
recon-all.cmd?
Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12
On Thu, Apr 5, 20
let's see if it works. If it does, you should be able to run
recon-all -s SUBJID -make all
cheers
Bruce
On Thu, 5 Apr 2018, srishti goel wrote:
Should I re-run the recon-all after running the last command from recon-all.cmd?
Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Re
So it gave this error:
3d normalization pass 1 of 2
white matter peak found at 110
HISTOalloc(-2147483648): could not allocate histogram
Cannot allocate memory
Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chap
can you email us the input file and the full command line you ran?
On Thu, 5
Apr 2018, srishti goel wrote:
So it gave this error:
3d normalization pass 1 of 2
white matter peak found at 110
HISTOalloc(-2147483648): could not allocate histogram
Cannot allocate memory
Best,
Srishti
Social/
Those commands look ok. My suspicion goes to the use of --regheader. See
whether the registration is ok with
tkregisterfv --mov negative_allsocial_proportion.nii --regheader --s
mni152_subject --surfs --reg reg.deleteme.dat
On 04/05/2018 08:34 AM, srishti goel wrote:
> Hi,
>
> I am trying to c
It looks like there is something wrong with that dicom file/series
because the pixel spacing is "unknown". Where did the dicoms from from?
Have they been anonymized?
On 04/05/2018 12:12 PM, Kan Ding wrote:
> Hello:
>
> I am trying to unpack my DICOM folder and run recon-all. After
> dcmunpack,
Hello,
I have a time series (.hdr/.img) that I want to overlay onto a surface,
specifically the inflated surface from the anatomy. I suspect I have to use
mri_vol2surf, which requires a source registration file. How do I get this
file? Then once I have this file, will I be able to view step by
All,
Just wanted to follow up on this message. Does anyone have recommendations
for the best way to compare this data longitudinally?
Thanks very much,
James
On Thu, Mar 29, 2018 at 1:19 PM, James Gullickson wrote:
> All,
>
> Our lab is working with longitudinal (two time points) data from a
t;of my DICOM folder.
>
>Thank you so much.
>Kan Din, MD
>Assistant Professor- Department of Neurology and Neurotherapeutics
>UT Southwestern Medical Center at Dallas
>Tel: 214-648-9197
>Fax: 214-648-6320
>
>
>
>UT Southwestern
>
>
charset="iso-8859-1"
>>
>> Hello:
>>
>> I am trying to unpack my DICOM folder and run recon-all. After dcmunpack,
>> I selected 301 to run recon-all. But the recon-all didn't go through.
>> Please see the attached scan.log, recon-all.log, error.log,
Use bbregister. Run with --help to get docs (make sure to use --projfrac
0.5). Once you have it on the surface, you can step through each frame
in freeview
On 04/05/2018 01:49 PM, Crawford, Anna wrote:
> Hello,
>
> I have a time series (.hdr/.img) that I want to overlay onto a
> surface, speci
Dear experts,
When it comes to assessing the quality of fMRI integration in Freesurfer, is a
value of > 0.5 considered a good registration? I was led to believe that from
the multimodal tutorial website, and after checking the quality of my output I
was satisfied with the result for each of my
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