Can you say more about your approach? Are you subtracting the two time
points explicitly and computing a paired t? Or are you using the
repeated measures anova approach. Send the FSGD file
On 11/30/2021 11:04 AM, PDMD SRALab wrote:
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We are using a paired
You can merge them yourself or you could run mri_annotation2label with
one of the --lobes options to generate a new annotation of lobes, run
use that to generate a new wmparc.mgz file (look in the recon-all.log
file to get the command, specify your new annotation and change the
output file
Hard to say what is going wrong from that. Can you try removing the
trailing "/" from the subject name? Also, do you need --conform? Often
the recon-all output is already conformed, so --conformed is not usually
needed. It would be interesting to know if this is making it fail.
On 12/6/2021
Is the problem that there is an overlap? The exvivo labels and aparc
labels are not going to be mutually exclusive.
On 12/6/2021 5:34 PM, Tsolaki, Evangelia C. wrote:
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Hello Freesurfer Team,
I am interested in using premotor, precentral gyrus and
How did you create the new MNI chimp average surface?
On 12/5/2021 11:08 AM, Trisanna Sprung-Much wrote:
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Hi Bruce
So I have 77 chimp scans reconstructed in FS (NOT registered to MNI
space, but rather a chimp volume template, to avoid scaling). After a
If you run it with --eres-save, it will save the residuals in eres.mgh
On 12/4/2021 11:17 AM, Laura Willers de Souza wrote:
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Hello FreeSurfer Developers,
I would like to assess whether my regression model meets the GLM
assumptions, especially if there is
Don, can you send your command line? If you are using surface-based
registration, then the origin should not matter. You are right that
there is not a one-to-one correspondence. The way it works is that it
starts on the target surface, goes through all the vertices and finds
the closest
The data look pretty noisy in those images. My guess is that the WM is
not getting segmented properly in that temporal area or there is an
incorrectly fixed topology error. Try looking at the wm.mgz (or the
filled.mgz instead if you have 7.2). YOu can load surface.defects.mgz to
see where the
are you just running gcut or all of recon-all? If all of recon-all,
please send the recon-all.log file
On 12/2/2021 2:43 PM, Vishal Mohanty wrote:
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Hi
This is Vishal Mohanty, a Research Assistant at the CNS Lab
We are not supporting qdec anymore. Try using the "command line stream",
ie, mris_preproc, FSGD, etc
On 12/1/2021 6:47 PM, Arian Klows wrote:
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Dear FS experts,
I have freesurfer-linux-centos7_x86_64-7.1.1 on my computer and when I
run qdec, I get the
There is no way to model a missing cell in the FSGD. You'd have to
figure out a value (eg, using imputation) or exclude those subjects
On 11/30/2021 2:59 PM, Laura Willers de Souza wrote:
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Hello FreeSurfer Developers,
I would like to know what I put in
sorry, I don't know what you mean by perimeter
On 11/29/2021 8:09 PM, Fernanda Hansen P. de Moraes wrote:
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Dear FreeSurfer experts,
Is there a way to estimate the perimeter from a surface (e.g. ?h.pial)
for each slice in an automated manner at any
you need to run it as a DOSS, ie, --fsgd Repeted_measure.fsgd doss
On 11/29/2021 6:50 PM, std...@virgilio.it wrote:
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Hi list,
I have two groups undergoing two different treatments: one's placebo
(n=12), one's drug (n=12). Two timepoints, at baseline (T1,
Try removing the mask and funcstem flags
On 11/29/2021 12:49 PM, Hiersche, Kelly J. wrote:
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Hello,
I was adapting existing code in my lab that was used for doing a
volume-based analysis, so I tried to keep the inputs the same.
Do you think removing the
On 11/29/2021 11:55 AM, Alexopoulos, Dimitrios wrote:
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A quick question.
Is it feasible or even possible to edit the aseg.mgz using another
program (i.e. ITK-snap after converting to nifti), and rerunning the
pipeline using the revised aseg as input
It could be that your memory allocation is right on the edge of the
requirements, and some subjects go over the bounds while others do not. Is it a
possibility to allocate more RAM for your jobs?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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Hi Juan,
Thank you.
I don't believe so. I reran freesurfer on this participant with another
participant on the same day on our HPC. This participant did not populate the
data while the other did populate the data, so I am not sure if there is
Dear Lisa,
Is it possible that you’re running out of RAM memory? How much RAM do you have
available?
Cheers,
Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
On Dec 10, 2021, at 14:19, Taylor, Lisa
mailto:ltayl...@hs.uci.edu>>
Hi Elizabeth - From your log file, I see that you're using FreeSurfer 6. Please
use the latest version (7.2), as TRACULA has undergone a drastic overhaul in
this version. The TRACULA tutorials and documentation on the wiki apply to this
new version.
To use field maps, you need one more
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At the Center for Lifespan Changes in Brain and Cognition, University of
Oslo, Norway, we have an available PhD fellowship for a candidate highly
interested in applying longitudinal, multimodal models on neuroimaging data
and its relation to genetics
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