[Freesurfer] FSL registration

[Jones, Richard]

I have T1 data that has been run through freesurfer and I want to apply the 
subcortical parcellations from that analysis to some QSM data. The mailing list 
and website refer to using reg-feat2anat but this require an existing feat 
directory. If I make a "pseudo" feat directory with my QSM data so that I can 
use reg-feat2anat does it just need to contain the subfolder reg containing the 
the QSM data as "example_func.nii" and the registration matrix from using FLIRT 
to register the QSM data to MNI space as  "example_func2standard.mat", or is 
there something else that needs to be included?

Thanks,

Richard
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Make average subject from additional data

[Jones, Richard]

I have a group of subjects that I have run through the standard freesurfer 
(version 5.3) pipeline, for the same subjects I also have T2 volumetric data 
and I have created T1/T2 ratio images for each subject. I have registered the 
ratio images into Freesurfer space and used mri_vol2surf to create surface 
overlays at different depths into the cortex for each subject, and these look 
reasonable when displayed with freeview. I now want to create average subjects 
for the ratio images at each depth, but I'm not sure what's the best way of 
doing this? Any suggestions would be appreciated.

Thanks,

Richard

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Freesurfer dev version : recon all error mpr2mni305

[Jones, Richard]

I ran the command shown below to do recon-all on DICOM images from a Philips 
Ingenia scanner using the development version of freesurfer on a Mac running 
high Sierra.

recon-all -i /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
-subject HOPE_SS020 -all

The program crashed with the error "ERROR: mpr2mni305 failed, see 
transforms/talairach_avi.log"

The talairach_avi.log file is shown below, followed by the log file. As a test 
I ran the same command, on the same data, using Freesurfer 6 and that ran 
without problems (except that it didn't handle the diffusion tags in the 
Philips DICOM header correctly so I had to set FS_LOAD_DWI=0, this was not a 
problem in the development version). Any suggestions as to what may be causing 
the problems with the library in the development version?

Thanks,

Richard

/Applications/freesurfer_dev/subjects/HOPE_SS020/mri
/Applications/freesurfer_dev/bin/talairach_avi
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 
22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
Thu Apr 19 08:45:01 EDT 2018
mri_convert.bin orig_nu.mgz talsrcimg.img
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from orig_nu.mgz...
TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
i_ras = (-1, 7.45058e-09, 0)
j_ras = (3.72529e-09, -4.88944e-09, -1)
k_ras = (0, 1, 4.88944e-09)
writing to talsrcimg.img...
Analyze Output Matrix
-1.0   0.0   0.0   128.15305;
0.0  -0.0   1.0  -116.15433;
0.0  -1.0   0.0   128.60870;
0.0   0.0   0.0   1.0;

INFO: set hdr.hist.orient to -1
mpr2mni305 talsrcimg
Thu Apr 19 08:45:02 EDT 2018
/Applications/freesurfer_dev/bin/mpr2mni305 talsrcimg
$Id: mpr2mni305,v 1.5 2015/12/18 23:56:21 zkaufman Exp $
target=711-2C_as_mni_average_305

-
analyzeto4dfp talsrcimg -O0 -y
-

$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $
Thu Apr 19 08:45:02 2018
Writing: talsrcimg.4dfp.hdr
$Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $
Reading: talsrcimg.hdr
header size 348 bytes
hdr.dime.datatype  offset=70value=2
hdr.dime.bitpix offset=72value=8
hdr.hist.orient   offset=252  value=-1
dimensionality 4
dimensions   256   256   256 1
Reading: talsrcimg.img
Writing: talsrcimg.4dfp.img
Writing: talsrcimg.4dfp.ifh
ifh2hdr talsrcimg -r0to255
ori=2

-
gauss_4dfp talsrcimg 1.1
-

dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib
  Referenced from: /Applications/freesurfer_dev/bin/gauss_4dfp
  Reason: image not found
Abort
ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134
ERROR: mpr2mni305 execution aborted


Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
Current Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
INFO: SUBJECTS_DIR is /Applications/freesurfer_dev/subjects
Actual FREESURFER_HOME /Applications/freesurfer_dev
Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 
22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
/Applications/freesurfer_dev/subjects/HOPE_SS020
\n mri_convert /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz \n
mri_convert.bin /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm...
Starting DICOMRead2()
dcmfile = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm
dcmdir = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat
Ref Series No = 301
Found 202 files, checking for dicoms
Found 200 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -0.897217 -0.0611658 0.0354633
Vs: -0.996909 -0.0679621 0.0394038
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 200
ndcmfiles = 200
PE Dir = ROW (dicom read)
Loading pixel data
TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
i_ras = (0.0644896, -0.994415, 0.0835493)
j_ras = (0.0448617, -0.08075, -0.995724)
k_ras = (0.996909, 0.0679621, 0.0394038)
writing to /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz...
#
#@# MotionCor Thu Apr 19 08:44:06 EDT 2018
Found 1 runs
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
Only one run found so motion
correction will not be performed. I'll
copy the 

Re: [Freesurfer] recon all error mpr2mni305

[Jones, Richard]

External Email - Use Caution

Message: 1
Date: Thu, 19 Apr 2018 12:05:03 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] Freesurfer dev version : recon all error
mpr2mni305
To: 
Message-ID: <0b445a3f-8fde-d23e-dab6-442a773c9...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"; format=flowed

How does the input image look, ie, orig.mg>

The images the look the same as the input DICOM images, no scaling or other 
problems. 


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] T2/Flair benefits in freesurfer 6.0

[Jones, Richard]

External Email - Use Caution

A few more questions regarding the use of a FLAIR image.

1)  If one is using the hires option on T1 images acquired with 
sub-millimeter spatial resolution then, to get the best results with the FLAIR 
option, is matching spatial resolution required for the FLAIR sequence?

2)  In a post some time ago 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51413.html) you 
said "V6 was not meant for T2/FLAIR and we didn't test it extensively. We  have 
been optimizing things in the past week for T2/FLAIR and I expect 6.1 will be 
better for them". Are the changes you were referring to incorporated in the 
current development version?

3)  Are then any plans to use the FLAIR for multi-modal segmentation in 
order to refine the segmentation of the Pallidium and Putamen, and to possibly 
segment structures such as the substantia nigra and red nucleus?

Thanks,

Richard

Date: Tue, 4 Jun 2019 12:41:51 -0400 (EDT)
From: Bruce Fischl 
Subject: Re: [Freesurfer] T2/Flair benefits in freesurfer 6.0
To: Freesurfer support list 
Message-ID:

Content-Type: text/plain; charset="utf-8"

Hi Aaron

yes, it helps in other situations like blood vessels

cheers
Bruce
On Tue, 4 Jun 2019,
Aaron Tanenbaum wrote:

>
> External Email - Use Caution
>
> I am not too sure if I have asked you this question before. I know the use
> of a flair or T2 helps with dealing with the dura. I was wondering if there
> are other benefits??
>
>




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Which pial surface to trust

[Jones, Richard]

External Email - Use Caution

A couple of questions:-
1) Do you experience similar variability with the T2 and FLAIR options or is 
FLAIR more variable due to it's generally lower SNR?
2) Should the spatial resolution of the T2/FLAIR scan match that of the T1 scan?

Richard

Message: 8
Date: Wed, 17 Mar 2021 17:51:51 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] Which pial surface to trust, with or without
-FLAIR option
To: 
Message-ID: <3c789103-dad7-974a-0d76-58a02cba2...@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

We get a lot of variable results with FLAIR. Sometimes it helps,
sometimes it hurts. FLAIR scans themselves can be very variable across
sites. If it is looking like it is hurting your results, then just run
without it.

On 3/12/2021 11:07 AM, Xiaojiang Yang wrote:
>
> External Email - Use Caution
>
> Dear FS developers,
>
> I have run FS?s recon-all on many cases, with and without -FLAIR
> options. I found the pial? surface results (?h.pial) I obtained
> without -FLAIR option fit to the original image
> (subjected/mri/orig.mgz) much better than those with -FLAIR option, at
> least from my visual judgment. See *MailScanner has detected a
> possible fraud attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1kdfPWDTAquCY3qAKfDNtc8TRiBI5hNHL96VYA9_mTvUn4qpO75SL3h5c4SdXB7ViTEwQr3qvBdcNSLFjdejtW60w8ivtHhUzNRG8q3lZ1xbTIeqmxzu5UakhOAKktPA6QRnwdwkJndw3FM8BTgEY5zvq8wxfJDDr0yrIvj-8mnF4PHlJi1y3SfCiVWPakRs0mSeQjRO-dRiFpl7IoDxugFH1C4OHRgZGkARvy-KxV4pKw_0ubMRqVmKUV5rqXP3m0SDssF44schYVSa5wqU_Bg/https%3A%2F%2Fimgur.com%2Fa%2FwrY0HTY
> ?for
> one example.
>
> I know -FLAIR option was introduced to improve the quality of pial
> surface segmentation. Now for many cases, my intuition is that -FLAIR
> option decreases the pial quality. My questions are:
>
>   * Is this intuition correct?
>   * Should I trust the pial surface that?s obtained with or without
> -FLAIR option in general?
>
> In addition, when I use the -FLAIR option, I sometimes get failed when
> running recon-all. After I did some manual edits to the brainmask
> image, and re-run the recon-all:
>
> recon-all -autorecon-pial -subjid 
>
> I can get recon-all successful. But if I run recon-all without -FLAIR
> option, I can get successful results without needing to manually edit
> the brainmask image.
>
> So my last question is:
>
>   * Should I just run recon-all without -FLAIR option, or, with -FLAIR
> option + manual edit + re-run with -autorecon-pial? Which is better?
>
> Thank you very much!
>
> John
>


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer