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Hi experts,
I have extracted the area of the significant cluster with the command like the
following:
mri_segstats --i mgh/lh.volume.all.mgh --seg
glmdir_az_vz/lh.volume.all.glmdir/av-group2-vs-group2/cache.th20.neg.sig.ocn.mgh
--id 1 --sumwf
Hi Don, sorry for the delay. It is using the talairach.xfm files in both
subjects to do the mapping.
doug
On 08/24/2018 11:40 AM, Krieger, Donald N. wrote:
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> Dear freesurfers,
>
> I didn’t see a response to this but I might have missed it.
>
> In any
Have you looked at this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
You should be able to generalize the two groups, one covariate, to three
groups
On 08/24/2018 01:06 PM, O'Dell, Ryan wrote:
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> Dear freesurfers,
>
>
> I have what is
You need to specify a surface
mris_convert -c cache.th13.pos.sig.cluster.mgh
$FREESURFER_HOME/subjects/fsaverage/surf/lh.white
cache.th13.pos.sig.cluster.gii
On 08/24/2018 03:18 PM, David.Mackarthy wrote:
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> Hi FS experts,
> I ran surface based analysis
Yes, that is what the cortex flag is for. mris_preproc should
automatically use the cortex flag
On 08/25/2018 05:06 PM, Alon Baram wrote:
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> Hello,
>
> When smoothing with mri_surf2surf, it's possible to use the --cortex
> flag to constrain the
You can just use mri_concat file1.mgh file2.mgh ... fileN.mgh --o stack.mgh
On 08/25/2018 05:03 PM, Alon Baram wrote:
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> Hello,
>
> I have a surface measure calculated for each of my subjects, which I
> have already resampled and smoothed on fsaverage
Yes, you just need to have it in the right format. I've attached an example.
On 08/24/2018 04:48 PM, miracle ozzoude wrote:
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Hello,
Can i specify a lookup table when using mri_gtmpvc? This is because I
have a non-freesurfer segmentation (MALPEM) and i
Yes, you can use mri_binarize with the --surf output option
On 08/26/2018 08:22 PM, Russell Butler wrote:
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>
> hello, i would like to create a mesh, such as the one in surf/lh.pial,
> using an arbitrary binary volume.
>
>
> i'm aware that freesurfer can
Can you send the recon-all.log file?
On 08/29/2018 04:51 PM, Song, Da-Yea wrote:
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>
> There is enough disk space and it works fine with the other subjects. But for
> a few subjects in particular I seem to get the same error message. I checked
> once more
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There is enough disk space and it works fine with the other subjects. But for a
few subjects in particular I seem to get the same error message. I checked once
more and it seems that the rh.white files are being saved in the stats folder
(rather
Check permissions first. Look at the size of the file. Is it much
smaller than other rh.white files in other subjects? Have you run out of
disk space?
On 08/29/2018 04:37 PM, Song, Da-Yea wrote:
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> Hi everyone,
>
> I’m trying to pre-process subjects
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Hi everyone,
I'm trying to pre-process subjects through the pipeline but keep getting a
handful of subjects that error out within seconds of running them. The error
message I get is:
MRISread(/subjects/002_1006/surf/rh.white):could not open file
When
Hi Martin, thanks for your reply.
I tried to re-type the command in the shell but I still have the error.
I don't know what you mean with system install, but we are using the version
5.3 and this is the path, if it can help:
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?Dear Doug:
I am trying to get a table containing pc1 values for each subject in a
longitudinal study and failed to extract this. I use the code below:
long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas thickness --hemi lh
--do-avg
Hi Xiaoyu,
again (see also other email) you should not run left hemispheres on the
right. This could introduce a processing bias, especially when you
force all left to be healthy and right to be diseased (or vice-versa).
Instead run your images normally and then for the univariate , simply
Hi Valeria,
what version of FS are you using (also is it a local install or the
system install)?
Also try to re-type the command in the shell (don't run it from a
script) could be that there are invisible characters , like tab etc
from copy paste that mess things up.
Best, Martin
On Wed,
Hi Xiaoyu,
I don't think it makes sense to model the hemisphere each as a
different group. Do you mean different time point?
The problem is that left hemispheres are probably anatomically slightly
different than right hemispheres (on average in healthy people).
I would run every subject only
Hi Elena,
I've taken a look through the files you shared with us and can only find the
complete subject directories for sub-90188_run-01_T1w and sub-90310. The
subject directory for sub-01262 (and 209 other subjects) is empty. Could you
please send another link with the subject directory for
Hi Maedeh
try mri_aparc2aseg
cheers
Bruce
On Wed, 29 Aug 2018, Maedeh Khalilian wrote:
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Dear Douglas Greve;
Thank you for your great help.I did what you said successfully.Now I have
another question.
I have used "mri_divide_parcellation" to
Dear Freesurfers,
I am trying to re-launch a longitudinal time point after edits by using the
command:
recon-all -long MS069_R01_01_Bay8_3T_03102014.long.MS069_base MS069_base -all
But I am obtaining this type of error:
Unmatched ".
I also tried to launch it on Launchpad but I have an error
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Dear FreeSurfer experts,
How can I save the result of parcellation and segmentation into the original
space?
I would appreciate any help.
Best regards,
Maedeh___
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Dear Douglas Greve;
Thank you for your great help.I did what you said successfully.Now I have
another question.
I have used "mri_divide_parcellation" to have more parcels.this command
gives me a ".annot" file.How can i change this file into a format
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