Hi everyone,
The Division of Neurotherapeutics at Massachusetts General Hospital (Boston,
MA) has an open postdoctoral position. The posting is below:
NEUROIMAGING POSTDOCTORAL POSITION IN DIVISION OF NEUROTHERAPEUTICS AT HARVARD
MEDICAL SCHOOL/ MASSACHUSETTS GENERAL HOSPITAL
The Division
] Bad Coregistration - Left-Right Reversed
what do you mean "visual inspection shows that they are actually
reversed"? Please give details
On 08/17/2016 01:31 PM, Afzal, Afsana wrote:
> I'm trying to understand why the coregistration for a bunch of subjects are
> bad/
orientation, then you need to switch to
mri_convert. If they are in the right orientation, then I don't
understand what you are trying to do.
doug
On 08/16/2016 05:27 PM, Afzal, Afsana wrote:
> Hi Doug,
>
> After the coregistration failed for the majority of the subjects, I visual
t: Tuesday, August 16, 2016 3:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
How do you know that the structural is left-right reversed? Or that the
fMRI is? How did you create the nifti files?
On 08/16/2016 01:41 PM, Afzal, Afsana w
Hi,
I'm having trouble co-registering a bunch of subjects whose T1 is left-right
reversed. While the orientation of the structural file in the NIfTI header is
LIA and the orientation of the functional volume is LAS, visual inspection
shows that the structural is left-right reversed. I then foll
nday, July 18, 2016 12:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Beta-Zero Correction - No Phase File
You can extract frames from a multi frame file with
mri_convert input.nii.gz --frame 0 output.frame0.nii.gz
On 07/12/2016 02:29 PM, Afzal, Afsana wrote:
> Hi,
>
&g
of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana
[aaf...@mgh.harvard.edu]
Sent: Tuesday
Hi,
I'm working with a dataset that outputs only one file (not two separate mag and
phase files) for the fieldmap. The data was also collected on non-Siemens
scanners: Philips Ingenia and GE SIGNA HDx (not sure if this is the reason the
fieldmaps are unpacking differently). I've attached the .d
Hi,
This question might have already been answered before but is there a way to
take a coordinate in MNI space and create, say, a 5mm sphere in the volume? My
goal is to take the sphere in the volume and convert it to a label using
something like mri_vol2surf.
Thanks for your help,
Afsana
_
Hi everyone,
I'm using mri_convert to reinforce TR information into the Nifti header in the
following manner:
mri_convert $FILE $FILE -tr $TR
Before the conversion, my file size is usually around 550MB but after the
conversion is doubles in size to ~1.1GB. In the Nifto file header I've noticed
01
Input hc001-hRsk_slope hc001000
On 04/11/2016 10:09 AM, Afzal, Afsana wrote:
> Hi Doug,
>
> I've attached the fsgd file and the contrast matrix file. Thanks for your
> help!
>
> - Afsana
>
> __
> Afs
PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group level analysis: Specifying contrasts
I don't know what you mean, can you just send the header of the fsgd
file and the contrast matrix?
On 04/04/2016 11:20 AM, Afzal, Afsana wrote:
> Hi,
>
> I want to perform a linear re
Hi,
I want to perform a linear regression for a task with 3 different risk
conditions (low, medium, high) with the following linear trend: low = 1, medium
= 2, high = 3.
Right now I'm specifying the above weighted under each risk condition in my
contrast matrix. Is this the correct approach? I
dimensions using mri_label2vol
Use mri_label2label specifying the source and target subjects to be the
same, a regmethod as surface, and select the --outmask option
On 04/01/2016 11:37 AM, Afzal, Afsana wrote:
> Hi Doug,
>
> I'm trying to map a cortical label onto the surface (i.e. e
help)
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surf2vol
On 03/28/2016 10:13 AM, Afzal, Afsana wrote:
> Hi, Just wanted to follow up on the issue below regarding the
> dimension of the mri_label2vol output.
>
>
> Hi,
>
> I'm using mri_label2vol with the parameters below
-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana
[aaf...@mgh.harvard.edu]
Sent: Wednesday, March 23, 2016 2:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Mismatch in dimensions using mri_label2vol
Hi,
I'm using mri_label2vol with the parameters
Hi,
I'm using mri_label2vol with the parameters below but the output .nii volume
has the shape 163842x1x1 while the input volume is 27307x1x6. This dimension
mismatch is causing issues in our gPPI pipeline.
How can I generate a .nii output file with the 27307x1x6 dimension?
mri_label2vol
-
-4078
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana
[aaf...@mgh.harvard.edu]
Sent: Monday, February 22, 2016 2:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [FreeSurfer] Repeated Measures
t: Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST
I'm having a hard time deciphering what you are doing. Is this a
functional study? What are the 5 classes? Why are there all 1s
regardless of risk or reward level?
On 02/19/2016 10:52 AM, Afzal, Afsana wrote:
> Hi,
>
&
: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana
[aaf...@mgh.harvard.edu]
Sent: Friday, February 19, 2016 10:52 AM
Hi,
I'm analyzing a decision making task with a 3x3 condition matrix: pairings of
low, medium, high levels of risk with low, medium, high levels of reward.
I've set up the following FSGD file to do a repeated measures/within-subject
ANOVA:
GroupDescriptorFile 1
Class hc001
Class hc002
Class hc
Hi,
How can I convert a surface .label file to a .nii format? I'm using
mri_label2label in the following way but the output is always in .label not
.nii:
mri_label2label
--srclabel dlpfc-lh.label
--outmask dlpfc-lh_mask.nii
--s fsaverage
--trglabel dlpfc-lh_mask.nii
--regmet
(2) variance spanned by that component
(3) cumulative variance spanned up to that component
(4) percent variance spanned by that component
(5) cumulative percent variance spanned up to that component
On 01/13/2016 09:56 AM, Afzal, Afsana wrote:
> Hi,
>
> I have generated whi
Hi,
I have generated white matter regressor files for resting state analysis using
fcseed-config and fcseed-sess. The resulting files include: wm.dat,
wm.dat.pca-stats.dat and wm.dat.log.
How do I interpret the wm.dat.pca-stats.dat file? There are 388 numbered rows
(I'm guessing one per acquis
-726-4078
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana
[aaf...@mgh.harvard.edu]
Sent: Monday, November 16, 2015 2:14 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] FSFAST First
: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
When I look in hc016/msit/001/ I only see:
cfg.txt f.nii mag.dat mag.nii phase.dat phase.nii
Have you deleted the previous analysis?
On 11/16/2015 11:41 AM, Afzal, Afsana wrote:
> Hi Doug,
>
> Command: selxavg3-sess
ubject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
hmmm, not sure. Can you send me your selxavg3-sess command and the folder your
ran it from and the $SUBJECTS_DIR ?
doug
On 11/13/15 4:16 PM, Afzal, Afsana wrote:
Hi,
I'm doing first level analysis in FSFAST and I'm cons
Hi,
I'm doing first level analysis in FSFAST and I'm consistently getting the
following error when running fast_selxavg3():
Saving to
/autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz
SmoothOnly requested, so exiting now
Found 0 voxels with cor
: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Extracing values from ces.nii
It should be interpreted as a 2D structure of size 27307*6= 163842
which are the number of vertices in fsaverage
On 10/29/2015 11:41 AM, Afzal, Afsana wrote:
> Hi,
>
> I'm trying to extract the c
Hi,
I'm trying to extract the contrast values from ces.nii.gz after first-level
analysis. My goal is to average the contrast values for each voxel across
subjects for a given condition and see where an individual from a separate
population falls within the distribution of contrast values.
The
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