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Hello,
I am having problems generating the aparc stats files for all my scans. I have
checked the surfaces for all scans and they were all generated correctly.
However, when I go to generate the stats files, I am able to get all the aseg
stats
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Hi Freesurfer experts,
We ran a functional language localizer analysis in FSL and we want to apply
the mask from this analysis to our SMRI analyses using the mri_glmfit
command with the --mask option. Basically, we want to examine whether GMV
within
Thank you so very much.
Yes, the values look normal now.
Mona
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: Thursday, April 11, 2019 4:33:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer]
You probably need to remove the mean. Add --avgwf-remove-mean to the
command line
On 4/11/19 4:29 PM, Nasiriavanaki, Zahra wrote:
>
> Thank you for your reply.
>
> The values of mri_segstatsoutput text file (lateral.txt) are high. I
> attached it to this email.
>
>
> mri_segstats --i
>
Thank you for your reply.
The values of mri_segstats output text file (lateral.txt) are high. I attached
it to this email.
mri_segstats --i $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz
--seg $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt
The value of what is too high?
On 4/11/19 4:07 PM, Nasiriavanaki, Zahra wrote:
>
> Hi
>
>
> I have not got the answer to my question yet, and I appreciate if you
> could please let me know what you think about it.
>
>
> Thanks
>
> Mona
>
>
Hi
I have not got the answer to my question yet, and I appreciate if you could
please let me know what you think about it.
Thanks
Mona
From: Nasiriavanaki, Zahra
Sent: Tuesday, April 9, 2019 5:55:58 PM
To: Freesurfer support list
Subject: mri_segstats
Dear
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I thought it might be a stretch. Thanks, though!
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Greve, Douglas N.,Ph.D.
Sent: Thursday, April 11, 2019 2:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re:
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mri_glmfit --y lh.t1t2ratio_12CMT_fmed_3sm_decurv.fsavg.mgh --fsgd
age_dexterity.fsgd --surf fsaverage lh --C contrast.mtx --o
lh_NHPT_T1T2_12CMT_allbrain
Il giorno gio 11 apr 2019 alle ore 21:58 Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> ha
what is your command line?
On 4/11/19 3:53 PM, TMS lab wrote:
>
> External Email - Use Caution
>
> Unfortunately I get such error message with the matrix 0 0 0 1
> ERROR: dimension mismatch between X and contrast contrast.mtx X has
> 3 cols, C has 4 cols
>
> Instead if I use 0 0 1, it
Well, you could go through and correct them, then count the number of
corrections:). But I don't think there is an automated procedure. You
could count the number of topological defects (but these are fixed
anyway). The values are in the aseg.stats file
On 4/11/19 3:38 PM, Weber, Wade A wrote:
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Unfortunately I get such error message with the matrix 0 0 0 1
ERROR: dimension mismatch between X and contrast contrast.mtx X has 3
cols, C has 4 cols
Instead if I use 0 0 1, it works
Best,
RAFAEL
That should have failed because it only has 3
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Hi all you Freesurfer users!
I have scans on a person that are slightly different protocols (like 1mm voxels
vs. 0.8mm voxels amongst other setting differences), and I ran them through
recon-all. Is there a way to quantify which one came through
In that case, you will have to create your own design matrix. The
easiest way to do that is to start with the DODS Xg.dat matrix that you
sent. There will be two columns for the NSI_1 variable (one for males,
one for females). You need to reduce it down to one column. In the
Xg.dat that you
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Hi Dr Greve,
I can’t do the Fsgd in the DOSS format since it won’t be ok for my other 6
variables. I would appreciate it if you could guide me through it.
Best
Amrita
On Thursday, April 11, 2019, Greve, Douglas N.,Ph.D.
wrote:
> Hi Amrita, first
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Douglas,
I've run the recon-all script with images from patients that were previously
run using FreeSurfer 5.3.0 and I received the same error.
I haven't run it outside of the HCP pipeline. I can attempt that to see if it
gives a different
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Hi Emily,
I suspect that you’re mixing versions. Please make sure that you source the dev
version.
Cheers,
/E
--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Emily
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Hi Eugenio,
Thank you so much. I downloaded the development version, but when I run
"segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR],"
it says command not found.
After I download the runtime2014 version, I get the MCRv84
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Hi:
Do you know any library that allows to show freesurfer generated
data (mesh and axial, coronal, sagittal slices) embedded in a web
page? We were working using "BrainBrowser Volume Viewer"
(brainbrowser.cbrain.mcgill.ca) and "AMI Medical Imaging
Hi Amrita, first of all, thanks for following the instructions on
submitting the bug report! It helps us a lot to get all the information
the first time. As for your issue, there is a confound between the
Female class and the NSI_1 variable. All the Females have a NSI_1 value
of 0, meaning
That should have failed because it only has 3 values (should have 4). I
think it should be 0 0 0 1
On 4/11/19 3:20 AM, TMS lab wrote:
>
> External Email - Use Caution
>
> You are right. I want simply to correlate myelin and nhpt regressing
> out age.
> I did it with the following
You are almost there. You need to swap mov and targ in your tkregister2
command. I also found these instructions on how to do this, but you
seemed to have figured it out already
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 4/10/19 6:38 PM, Larson, Kathleen E wrote:
>
check out
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
On 4/11/19 10:58 AM, Abby tang wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer Developers, I'm attempting to recon-all subjects but
> for some of my subjects I get the following error
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Hello FreeSurfer Developers,
I'm attempting to recon-all subjects but for some of my subjects I get
the following error when I run recon-all command:
CORRECTING DEFECT 0 (vertices=18460, convex hull=3400, v0=4)
XL defect detected...
Killed
Linux
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Hi Lilla,
Good to know. Thank you for the reply!
Anna
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Lilla Zollei
Sent: Thursday, April 11, 2019 10:46 AM
To: Freesurfer support list
Subject: [EXT]
Hi Anna,
We have not tried the pipeline on 1.5T data, but you are welcome to
download the beta version and see how well it is doing.
https://surfer.nmr.mgh.harvard.edu/fswiki/infantFS
Lilla
On Thu, 11 Apr 2019, Crawford, Anna wrote:
>
> Hello,
>
>
> I was looking to use the Freesurfer
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Hello,
I was looking to use the Freesurfer infant brains pipeline. I have found it
used with 3T data, but I was wondering if it can be used with 1.5T data as well.
Thanks,
Anna
Please consider the environment before printing this e-mail
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-- Forwarded message --
From: *abedi...@citymail.cuny.edu * <
abedi...@citymail.cuny.edu>
Date: Thursday, April 11, 2019
Subject: Fw: mriglmfit error
To: Amrita Bedi
Amrita Bedi
*Biomedical Engineering - Class of 2018*
*The City
Hi Maxime,
please keep previous conversation in the email (so that it is easier to check
the original question). Also let’s keep this on the list.
I do not understand what you mean with “there is not strict alignment”. If you
open the norm.mgz from base, tp1.long.base and tp2.long.base they
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You are right. I want simply to correlate myelin and nhpt regressing out
age.
I did it with the following matrix:
0 0 1
And it seems to work. Is it ok this matrix?
Thanks a lot
Rafael
Il giorno gio 11 apr 2019 alle 00:22 Greve, Douglas N.,Ph.D. <
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